%0 Journal Article %A Zhou, F. %A Badillo-Corona, J. A. %A Karcher, D. %A Gonzalez-Rabade, N. %A Piepenburg, K. %A Borchers, A. M. I. %A Maloney, A. P. %A Kavanagh, T. A. %A Gray, J. C. %A Bock, R. %D 2008 %T High-level expression of human immunodeficiency virus antigens from the tobacco and tomato plastid genomes %J Plant Biotechnology Journal %V 6 %N 9 %P 897-913 %8 Dec %! High-level expression of human immunodeficiency virus antigens from the tobacco and tomato plastid genomes %@ 1467-7644 %1 Bock~Organelle Biology, Biotechnology and Molecular Ecophysiology~ %3 1 %M ISI:000261079600004 %K antigen hiv molecular farming nef nicotiana tabacum plastid transformation p24 solanum lycopersicum green fluorescent protein transgenic tobacco genetic-transformation protective antigen chloroplasts leads messenger-rnas higher-plants bacterial vaccine mice %X Transgene expression from the plant's plastid genome represents a promising strategy in molecular farming because of the plastid's potential to accumulate foreign proteins to high levels and the increased biosafety provided by the maternal mode of organelle inheritance. In this article, we explore the potential of transplastomic plants to produce human immunodeficiency virus (HIV) antigens as potential components of an acquired immunodeficiency syndrome (AIDS) vaccine. It is shown that the HIV antigens p24 (the major target of T-cell-mediated immune responses in HIV-positive individuals) and Nef can be expressed to high levels in plastids of tobacco, a non-food crop, and tomato, a food crop with an edible fruit. Optimized p24-Nef fusion gene cassettes trigger antigen protein accumulation to up to approximately 40% of the plant's total protein, demonstrating the great potential of transgenic plastids to produce AIDS vaccine components at low cost and high yield. %Z 374YM Times Cited:1 Cited References Count:44 %U ://000261079600004 %+ Bock, R Max Planck Inst Mol Pflanzenphysiol, Muhlenberg 1, D-14476 Potsdam, Germany Max Planck Inst Mol Pflanzenphysiol, D-14476 Potsdam, Germany Univ Cambridge, Dept Plant Sci, Cambridge CB2 3EA, England Trinity Coll Dublin, Smurfit Inst Genet, Dublin 2, Ireland %G English %0 Journal Article %A Willmund, F. %A Dorn, K. V. %A Schulz-Raffelt, M. %A Schroda, M. %D 2008 %T The Chloroplast DnaJ Homolog CDJ1 of Chlamydomonas reinhardtii Is Part of a Multichaperone Complex Containing HSP70B, CGE1, and HSP90C %J Plant Physiology %V 148 %N 4 %P 2070-2082 %8 Dec %! The Chloroplast DnaJ Homolog CDJ1 of Chlamydomonas reinhardtii Is Part of a Multichaperone Complex Containing HSP70B, CGE1, and HSP90C %@ 0032-0889 %1 Schroda~GoFORSYS III - Schroda~ %3 1 %M ISI:000261501500026 %K escherichia-coli dnaj blue native electrophoresis membrane-protein complexes heat-shock proteins molecular chaperones chlorate-resistant crystal-structure j-domain in-vivo plastidic hsp70b %X We report on the molecular and biochemical characterization of CDJ1, one of three zinc-finger-containing J-domain proteins encoded by the Chlamydomonas reinhardtii genome. Fractionation experiments indicate that CDJ1 is a plastidic protein. In the chloroplast, CDJ1 was localized to the soluble stroma fraction, but also to thylakoids and to low density membranes. Although the CDJ1 gene was strongly heat shock inducible, CDJ1 protein levels increased only slightly during heat shock. Cellular CDJ1 concentrations were close to those of heat shock protein 70B (HSP70B), the major HSP70 in the Chlamydomonas chloroplast. CDJ1 complemented the temperature-sensitive phenotype of an Escherichia coli mutant lacking its dnaJ gene and interacted with E. coli DnaK, hence classifying it as a bona fide DnaJ protein. In soluble cell extracts, CDJ1 was found to organize into stable dimers and into complexes of high molecular mass. Immunoprecipitation experiments revealed that CDJ1 forms common complexes with plastidic HSP90C, HSP70B, and CGE1. In blue native-polyacrylamide gel electrophoresis, all four (co) chaperones migrated at 40% to 90% higher apparent than calculated molecular masses, indicating that greatest care must be taken when molecular masses of protein complexes are estimated from their migration relative to standard native marker proteins. Immunoprecipitation experiments fromsize-fractioned soluble cell extracts suggested that HSP90C and HSP70B exist as preformed complex that is joined by CDJ1. In summary, CDJ1 and CGE1 are novel cohort proteins of the chloroplast HSP90-HSP70 multichaperone complex. As HSP70B, CDJ1, and CGE1 are derived from the endosymbiont, whereas HSP90C is of eukaryotic origin, we observe in the chloroplast the interaction of two chaperone systems of distinct evolutionary origin. %Z 380YH Times Cited:0 Cited References Count:70 %U ://000261501500026 %+ Schroda, M Univ Freiburg, Inst Biol 2, D-79104 Freiburg, Germany Univ Freiburg, Inst Biol 2, D-79104 Freiburg, Germany Max Planck Inst Mol Plant Physiol, D-14476 Potsdam, Germany %G English %0 Journal Article %A Wienkoop, S. %A Morgenthal, K. %A Wolschin, F. %A Scholz, M. %A Selbig, J. %A Weckwerth, W. %D 2008 %T Integration of metabolomic and proteomic phenotypes %J Molecular & Cellular Proteomics %V 7 %N 9 %P 1725-1736 %8 Sep %! Integration of metabolomic and proteomic phenotypes %@ 1535-9476 %1 Selbig~Bioinformatics crg~Weckwerth~Integrative Proteomics and Metabolomics~ %3 1 %M ISI:000259154800010 %K rna-binding protein independent component analysis quantitative shotgun proteomics cold response pathway pre-messenger-rna arabidopsis-thaliana low-temperature freezing tolerance pattern-recognition escherichia-coli %X Statistical mining and integration of complex molecular data including metabolites, proteins, and transcripts is one of the critical goals of systems biology (Ideker, T., Galitski, T., and Hood, L. (2001) A new approach to decoding life: systems biology. Annu. Rev. Genomics Hum. Genet. 2, 343-372). A number of studies have demonstrated the parallel analysis of metabolites and large scale transcript expression. Protein analysis has been ignored in these studies, although a clear correlation between transcript and protein levels is shown only in rare cases, necessitating that actual protein levels have to be determined for protein function analysis. Here, we present an approach to investigate the combined covariance structure of metabolite and protein dynamics in a systemic response to abiotic temperature stress in Arabidopsis thaliana wild-type and a corresponding starch-deficient mutant (phosphoglucomutase-deficient). Independent component analysis revealed phenotype classification resolving genotype-dependent response effects to temperature treatment and genotype-independent general temperature compensation mechanisms. An observation is the stress-induced increase of raffinose-family-oligosaccharide levels in the absence of transitory starch storage/mobilization in temperature-treated phosphoglucomutase plants indicating that sucrose synthesis and storage in these mutant plants is sufficient to bypass the typical starch storage/mobilization pathways under abiotic stress. Eventually, sample pattern recognition and correlation network topology analysis allowed for the detection of specific metabolite-protein co- regulation and assignment of a circadian output regulated RNA-binding protein to these processes. The whole concept of high-dimensional profiling data integration from many replicates, subsequent multivariate statistics for dimensionality reduction, and covariance structure analysis is proposed to be a major strategy for revealing central responses of the biological system under study. %Z 347PZ Times Cited:0 Cited References Count:85 %U ://000259154800010 %+ Weckwerth, W Max Planck Inst Mol Plant Physiol, D-14424 Potsdam, Germany Max Planck Inst Mol Plant Physiol, D-14424 Potsdam, Germany Univ Potsdam, GoFORSYS, Inst Biochem & Biol, D-14424 Potsdam, Germany Arizona State Univ, Sch Life Sci, Tempe, AZ 85287 USA Ernst Moritz Arndt Univ Greifswald, CC FG, D-17487 Greifswald, Germany Univ Potsdam, Inst Biochem & Biol, Potsdam, Germany Univ Vienna, Dept Mol Plant Physiol & Syst Biol, A-1010 Vienna, Austria %G English %0 Journal Article %A Wen, F. S. %A Celoy, R. M. %A Nguyen, T. %A Zeng, W. Q. %A Keegstra, K. %A Immerzeel, P. %A Pauly, M. %A Hawes, M. C. %D 2008 %T Inducible expression of Pisum sativum xyloglucan fucosyltransferase in the pea root cap meristem, and effects of antisense mRNA expression on root cap cell wall structural integrity %J Plant Cell Reports %V 27 %N 7 %P 1125-1135 %8 Jul %! Inducible expression of Pisum sativum xyloglucan fucosyltransferase in the pea root cap meristem, and effects of antisense mRNA expression on root cap cell wall structural integrity %@ 0721-7714 %1 Plant Cell Walls~ %3 1 %M ISI:000256477200001 %K fucose cell walls hairy roots root cap meristem arabidopsis-thaliana hairy root proteins polysaccharides plants genes elongation oligosaccharides growth endotransglucosylase/hydrolase %X Mitosis and cell wall synthesis in the legume root cap meristem can be induced and synchronized by the nondestructive removal of border cells from the cap periphery. Newly synthesized cells can be examined microscopically as they differentiate progressively during cap development, and ultimately detach as a new population of border cells. This system was used to demonstrate that Pisum sativum L. fucosyl transferase (PsFut1) mRNA expression is strongly expressed in root meristematic tissues, and is induced > 2-fold during a 5-h period when mitosis in the root cap meristem is increased. Expression of PsFut1 antisense mRNA in pea hairy roots under the control of the CaMV35S promoter, which exhibits meristem localized expression in pea root caps, resulted in a 50-60% reduction in meristem localized endogenous PsFut1 mRNA expression measured using whole mount in situ hybridization. Changes in gross levels of cell wall fucosylated xyloglucan were not detected, but altered surface localization patterns were detected using whole mount immunolocalization with CCRC-M1, an antibody that recognizes fucosylated xyloglucan. Emerging hairy roots expressing antisense PsFut1 mRNA appeared normal macroscopically but scanning electron microscopy of tissues with altered CCRC-M1 localization patterns revealed wrinkled, collapsed cell surfaces. As individual border cells separated from the cap periphery, cell death occurred in correlation with extrusion of cellular contents through breaks in the wall. %Z 309RF Times Cited:0 Cited References Count:76 %U ://000256477200001 %+ Hawes, MC Univ Arizona, Dept Plant Sci, Div Plant Pathol & Microbiol, Forbes Hall, Tucson, AZ 85721 USA Univ Arizona, Dept Plant Sci, Div Plant Pathol & Microbiol, Tucson, AZ 85721 USA Michigan State Univ, Dept Plant Biol, E Lansing, MI 48824 USA Michigan State Univ, Dept Energy, Plant Res Lab, E Lansing, MI 48824 USA Max Planck Inst Mol Plant Physiol, Plant Cell Wall Grp, D-14476 Golm, Germany %G English %0 Journal Article %A Weigelt, K. %A Kuster, H. %A Radchuk, R. %A Muller, M. %A Weichert, H. %A Fait, A. %A Fernie, A. R. %A Saalbach, I. %A Weber, H. %D 2008 %T Increasing amino acid supply in pea embryos reveals specific interactions of N and C metabolism, and highlights the importance of mitochondrial metabolism %J Plant Journal %V 55 %N 6 %P 909-926 %8 Sep %! Increasing amino acid supply in pea embryos reveals specific interactions of N and C metabolism, and highlights the importance of mitochondrial metabolism %@ 0960-7412 %1 Fernie~Central Metabolism~ %3 1 %M ISI:000259221900002 %K legume seed maturation amino acid metabolism c/n interaction nitrogen metabolic regulation mitochondria vicia-faba l seed-specific expression abscisic-acid medicago-truncatula ectopic expression mass-spectrometry sugar-starvation sucrose-synthase gene-expression phosphoenolpyruvate carboxylase %X The application of nitrogen to legumes regulates seed metabolism and composition. We recently showed that the seed-specific overexpression of amino acid permease VfAAP1 increases amino acid supply, and the levels of N and protein in the seeds. Two consecutive field trials using Pisum sativum AAP1 lines confirmed increases in the levels of N and globulin in seed; however, compensatory changes of sucrose/starch and individual seed weight were also observed. We present a comprehensive analysis of AAP1 seeds using combinatorial transcript and metabolite profiling to monitor the effects of nitrogen supply on seed metabolism. AAP1 seeds have increased amino acids and stimulated gene expression associated with storage protein synthesis, maturation, deposition and vesicle trafficking. Transcript/metabolite changes reveal the channelling of surplus N into the transient storage pools asparagine and arginine, indicating that asparagine synthase is transcriptionally activated by high N levels and/or C limitation. Increased C-acceptor demand for amino acid synthesis, resulting from elevated levels of N in seeds, initiates sucrose mobilization and sucrose-dependent pathways via sucrose synthase, glycolysis and the TCA cycle. The AAP1 seeds display a limitation in C, which leads to the catabolism of arginine, glutamic acid and methionine to putrescine, beta-alanine and succinate. Mitochondria are involved in the coordination of C/N metabolism, with branched-chain amino acid catabolism and a gamma-amino-butyric acid shunt. AAP1 seeds contain higher levels of ABA, which is possibly involved in storage-associated gene expression and the N-dependent stimulation of sucrose mobilization, indicating that a signalling network of C, N and ABA is operating during seed maturation. These results demonstrate that legume seeds have a high capacity to regulate N:C ratios, and highlight the importance of mitochondria in the control of N-C balance and amino acid homeostasis. %Z 348PH Times Cited:0 Cited References Count:80 %U ://000259221900002 %+ Weber, H Leibniz Inst Pflanzengenet & Kulturpflanzenfors, D-06466 Gatersleben, Germany Leibniz Inst Pflanzengenet & Kulturpflanzenfors, D-06466 Gatersleben, Germany Univ Bielefeld, Ctr Biotechnol, Inst Genome Res & Syst Biol, D-33615 Bielefeld, Germany Max Planck Inst Mol Pflanzenphysiol, D-14476 Potsdam, Germany %G English %0 Journal Article %A Weckwerth, W. %D 2008 %T Integration of metabolomics and proteomics in molecular plant physiology - coping with the complexity by data-dimensionality reduction %J Physiologia Plantarum %V 132 %N 2 %P 176-189 %8 Feb %! Integration of metabolomics and proteomics in molecular plant physiology - coping with the complexity by data-dimensionality reduction %@ 0031-9317 %1 Weckwerth~Integrative Proteomics and Metabolomics~ %3 1 %M ISI:000252261900006 %K flight mass-spectrometry hydrophilic interaction chromatography protein identification technology 2-dimensional gas-chromatography quantitative shotgun proteomics liquid-chromatography pattern-recognition systems biology arabidopsis-thaliana capillary columns %X In recent years, genomics has been extended to functional genomics. Toward the characterization of organisms or species on the genome level, changes on the metabolite and protein level have been shown to be essential to assign functions to genes and to describe the dynamic molecular phenotype. Gas chromatography (GC) and liquid chromatography coupled to mass spectrometry (GC- and LC-MS) are well suited for the fast and comprehensive analysis of ultracomplex metabolite samples. For the integration of metabolite profiles with quantitative protein profiles, a high throughput (HTP) shotgun proteomics approach using LC-MS and label-free quantification of unique proteins in a complex protein digest is described. Multivariate statistics are applied to examine sample pattern recognition based on data-dimensionality reduction and biomarker identification in plant systems biology. The integration of the data reveal multiple correlative biomarkers providing evidence for an increase of information in such holistic approaches. With computational simulation of metabolic networks and experimental measurements, it can be shown that biochemical regulation is reflected by metabolite network dynamics measured in a metabolomics approach. Examples in molecular plant physiology are presented to substantiate the integrative approach. %Z 249WV Times Cited:0 Cited References Count:79 %U ://000252261900006 %+ Weckwerth, W Max Planck Inst Mol Planzenphysiol, Dept Metab Network, Am Muhlenberg 1, D-14476 Potsdam, Germany Max Planck Inst Mol Planzenphysiol, Dept Metab Network, D-14476 Potsdam, Germany Univ Potsdam, Dept Biochem & Biol, GoFORSYS, D-14469 Potsdam, Germany %G English %0 Journal Article %A Waadt, R. %A Schmidt, L. K. %A Lohse, M. %A Hashimoto, K. %A Bock, R. %A Kudla, J. %D 2008 %T Multicolor bimolecular fluorescence complementation reveals simultaneous formation of alternative CBL/CIPK complexes in planta %J Plant Journal %V 56 %N 3 %P 505-516 %8 Nov %! Multicolor bimolecular fluorescence complementation reveals simultaneous formation of alternative CBL/CIPK complexes in planta %@ 0960-7412 %1 Bock~Organelle Biology, Biotechnology and Molecular Ecophysiology~Integrative Carbon Biology~ %3 1 %M ISI:000260308800014 %K protein-protein interaction bimolecular fluorescence complementation multicolor bimolecular fluorescence complementation calcium signaling cbl cipk protein-protein interactions living cells fragment complementation visualization arabidopsis system family identification localization ubiquitin %X The specificity of intracellular signaling and developmental patterning in biological systems relies on selective interactions between different proteins in specific cellular compartments. The identification of such protein-protein interactions is essential for unraveling complex signaling and regulatory networks. Recently, bimolecular fluorescence complementation (BiFC) has emerged as a powerful technique for the efficient detection of protein interactions in their native subcellular localization. Here we report significant technical advances in the methodology of plant BiFC. We describe a series of versatile BiFC vector sets that are fully compatible with previously generated vectors. The new vectors enable the generation of both C-terminal and N-terminal fusion proteins and carry optimized fluorescent protein genes that considerably improve the sensitivity of BiFC. Using these vectors, we describe a multicolor BiFC (mcBiFC) approach for the simultaneous visualization of multiple protein interactions in the same cell. Application to a protein interaction network acting in calcium-mediated signal transduction revealed the concurrent interaction of the protein kinase CIPK24 with the calcium sensors CBL1 and CBL10 at the plasma membrane and tonoplast, respectively. We have also visualized by mcBiFC the simultaneous formation of CBL1/CIPK1 and CBL9/CIPK1 protein complexes at the plasma membrane. Thus, mcBiFC provides a useful new tool for exploring complex regulatory networks in plants. %Z 364AO Times Cited:0 Cited References Count:40 %U ://000260308800014 %+ Kudla, J Univ Munster, Inst Bot & Bot Garten, Schlosspl 4, D-48149 Munster, Germany Univ Munster, Inst Bot & Bot Garten, D-48149 Munster, Germany Max Planck Inst Mol Pflanzenphysiol, D-14476 Potsdam, Germany %G English %0 Journal Article %A Vigeolas, H. %A Chinoy, C. %A Zuther, E. %A Blessington, B. %A Geigenberger, P. %A Domoney, C. %D 2008 %T Combined metabolomic and genetic approaches reveal a link between the polyamine pathway and albumin 2 in developing pea seeds %J Plant Physiol %V 146 %N 1 %P 74-82 %8 Jan %! Combined metabolomic and genetic approaches reveal a link between the polyamine pathway and albumin 2 in developing pea seeds %O Plant physiology %@ 0032-0889 (Print) %1 Geigenberger~Storage Carbohydrate Metabolism~ %3 1 %M 18024559 %X Several legume seed proteins that are potentially allergenic, poorly digested by farm animals, and/or have undesirable functional properties, have been described. One of these is the albumin protein in pea (Pisum sativum) called PA2. A naturally occurring mutant line that lacks PA2 has been exploited in studies to determine the biological function of this nonstorage protein in seed development. The mutant, which has a small seed, a tall plant phenotype, and lacks most of the PA2-encoding genes, has been crossed with a standard cultivar, 'Birte,' which contains PA2 to give rise to a recombinant inbred (RI) population. An F(3) line carrying the mutation and having a short plant phenotype has been used to generate backcross (BC) lines with 'Birte.' Despite having a lower albumin content, seeds from the mutant parent and RI lines lacking PA2 have an equivalent or higher seed nitrogen content. Metabolite profiling of seeds revealed major differences in amino acid composition and polyamine content in the two parent lines. This was investigated further in BC lines, where the effects of differences in seed size and plant height between the two parents were eliminated. Here, differences in polyamine synthesis were maintained as was a difference in total seed protein between the BC line lacking PA2 and 'Birte.' Analysis of enzyme activities in the pathways of polyamine synthesis revealed that the differences in spermidine content were attributable to changes in the overall activities of spermidine synthase and arginine decarboxylase. Although the genes encoding spermidine synthase and PA2 both localized to the pea linkage group I, the two loci were shown not to be closely linked and to have recombined in the BC lines. A distinct locus on linkage group III contains a gene that is related to PA2 but expressed predominantly in flowers. The results provide evidence for a role of PA2 in regulating polyamine metabolism, which has important functions in development, metabolism, and stress responses in plants. %Z Journal Article Research Support, Non-U.S. Gov't United States %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18024559 %+ Max-Planck Institute of Molecular Plant Physiology, 14476, Golm, Germany. %G eng %0 Journal Article %A Verdier, J. %A Kakar, K. %A Gallardo, K. %A Le Signor, C. %A Aubert, G. %A Schlereth, A. %A Town, C. D. %A Udvardi, M. K. %A Thompson, R. D. %D 2008 %T Gene expression profiling of M-truncatula transcription factors identifies putative regulators of grain legume seed filling %J Plant Molecular Biology %V 67 %N 6 %P 567-580 %8 Aug %! Gene expression profiling of M-truncatula transcription factors identifies putative regulators of grain legume seed filling %@ 0167-4412 %1 System Regulation~ %3 1 %M ISI:000257124600001 %K legume seed development transcription factors storage protein embryo endosperm seed coat storage-protein genes arabidopsis-thaliana embryo development abscisic-acid leafy cotyledon1 domain protein messenger-rnas maturation encodes bzip %X Legume seeds represent a major source of proteins for human and livestock diets. The model legume Medicago truncatula is characterized by a process of seed development very similar to that of other legumes, involving the interplay of sets of transcription factors (TFs). Here, we report the first expression profiling of over 700 M. truncatula genes encoding putative TFs throughout seven stages of seed development, obtained using real-time quantitative RT-PCR. A total of 169 TFs were selected which were expressed at late embryogenesis, seed filling or desiccation. The site of expression within the seed was examined for 41 highly expressed transcription factors out of the 169. To identify possible target genes for these TFs, the data were combined with a microarray-derived transcriptome dataset. This study identified 17 TFs preferentially expressed in individual seed tissues and 135 corresponding co-expressed genes, including possible targets. Certain of the TFs co-expressed with storage protein mRNAs correspond to those already known to regulate seed storage protein synthesis in Arabidopsis, whereas the timing of expression of others may be more specifically related to the delayed expression of the legumin-class storage proteins observed in legumes. %Z 318WX Times Cited:2 Cited References Count:64 %U ://000257124600001 %+ Thompson, RD INRA, Unite Mixte Rech Genet & Ecophysiol Legumineuses, F-21110 Domaine Depoisses, Bretenieres, France Inst Mol Plant Physiol, D-14476 Golm, Germany INRA, Unite Mixte Rech Genet & Ecophysiol Legumineuses, F-21110 Domaine Depoisses, Bretenieres, France TIGR, Rockville, MD 20850 USA Samuel Roberts Noble Fdn Inc, Ardmore, OK 73401 USA %G English %0 Journal Article %A Usadel, B. %A Blaesing, O. E. %A Gibon, Y. %A Retzlaff, K. %A Hoehne, M. %A Guenther, M. %A Stitt, M. %D 2008 %T Global transcript levels respond to small changes of the carbon status during progressive exhaustion of carbohydrates in Arabidopsis rosettes %J Plant Physiology %V 146 %N 4 %P 1834-1861 %8 Apr %! Global transcript levels respond to small changes of the carbon status during progressive exhaustion of carbohydrates in Arabidopsis rosettes %@ 0032-0889 %1 Stitt~System Regulation~Usadel~Integrative Carbon Biology~ %3 1 %M ISI:000256417900030 %K adp-glucose pyrophosphorylase photosynthetic period duration posttranslational redox-modification trehalose 6-phosphate enzyme-activities starch synthesis circadian clock gene-expression diurnal changes adpglucose pyrophosphorylase %X The balance between the supply and utilization of carbon (C) changes continually. It has been proposed that plants respond in an acclimatory manner, modifying C utilization to minimize harmful periods of C depletion. This hypothesis predicts that signaling events are initiated by small changes in C status. We analyzed the global transcriptional response to a gradual depletion of C during the night and an extension of the night, where C becomes severely limiting from 4 h onward. The response was interpreted using published datasets for sugar, light, and circadian responses. Hundreds of C-responsive genes respond during the night and others very early in the extended night. Pathway analysis reveals that biosynthesis and cellular growth genes are repressed during the night and genes involved in catabolism are induced during the first hours of the extended night. The C response is amplified by an antagonistic interaction with the clock. Light signaling is attenuated during the 24-h light/dark cycle. A model was developed that uses the response of 22K genes during a circadian cycle and their responses to C and light to predict global transcriptional responses during diurnal cycles of wild-type and starchless pgm mutant plants and an extended night in wild-type plants. By identifying sets of genes that respond at different speeds and times during C depletion, our extended dataset and model aid the analysis of candidates for C signaling. This is illustrated for AKIN10 and four bZIP transcription factors, and sets of genes involved in trehalose signaling, protein turnover, and starch breakdown. %Z 308VJ Times Cited:3 Cited References Count:85 %U ://000256417900030 %G English %0 Journal Article %A Usadel, B. %A Blaesing, O. E. %A Gibon, Y. %A Poree, F. %A Hoehne, M. %A Guenter, M. %A Trethewey, R. %A Kamlage, B. %A Poorter, H. %A Stitt, M. %D 2008 %T Multilevel genomic analysis of the response of transcripts, enzyme activities and metabolites in Arabidopsis rosettes to a progressive decrease of temperature in the non-freezing range %J Plant Cell and Environment %V 31 %N 4 %P 518-547 %8 Apr %! Multilevel genomic analysis of the response of transcripts, enzyme activities and metabolites in Arabidopsis rosettes to a progressive decrease of temperature in the non-freezing range %@ 0140-7791 %1 Stitt~System Regulation~Usadel~Integrative Carbon Biology~ %3 1 %M ISI:000253981000010 %K arabidopsis chilling expression arrays metabolite profile plant cold-acclimation synthase gene family mays l. seedlings chilling tolerance abscisic-acid lycopersicon-esculentum hydraulic conductance secondary metabolism environmental-stress circadian regulation %X This paper characterizes the transcriptional and metabolic response of a chilling-tolerant species to an increasingly large decrease of the temperature. Arabidopsis Col-0 was grown at 20 degrees C and transferred to 17, 14, 12, 10 or 8 degrees C for 6 and 78 h, before harvesting the rosette and profiling > 22 000 transcripts, > 20 enzyme activities and > 80 metabolites. Most parameters showed a qualitatively similar response across the entire temperature range, with the amplitude increasing as the temperature decreased. Transcripts typically showed large changes after 6 h, which were often damped by 78 h. Genes were induced for sucrose, proline, raffinose, tocopherol and polyamine synthesis, phenylpropanoid and flavonoid metabolism, fermentation, non-phosphorylating mitochondrial electron transport, RNA processing, and protein synthesis, targeting and folding. Genes were repressed for carbonic anhydrases, vacuolar invertase, and ethylene and jasmonic acid signalling. While some enzyme activities and metabolites changed rapidly, most changed slowly. After 6 h, there was an accumulation of phosphorylated intermediates, a shift of partitioning towards sucrose, and a perturbation of glycine decarboxylation and nitrogen metabolism. By 78 h, there was an increase of the overall protein content and many enzyme activities, a general increase of carbohydrates, organic and amino acids, and an increase of many stress-responsive metabolites including raffinose, proline, tocopherol and polyamines. When the responses of transcripts and metabolism were compared, there was little agreement after 6 h, but considerable agreement after 78 h. Comparison with the published studies indicated that much, but not all, of the response was orchestrated by the CBF programme. Overall, our results showed that transcription and metabolism responded in a continuous manner across a wide range of temperatures. The general increase of enzyme activities and metabolites emphasized the positive and compensatory nature of this response. %Z 274DC Times Cited:2 Cited References Count:114 %U ://000253981000010 %+ Stitt, M Max Planck Inst Mol Plant Physiol, Muhlenberg 1, D-14476 Golm, Germany Max Planck Inst Mol Plant Physiol, D-14476 Golm, Germany Univ Utrecht, NL-3584 CA Utrecht, Netherlands Metanom GmbH, D-10589 Berlin, Germany %G English %0 Journal Article %A Udvardi, M. K. %A Czechowski, T. %A Scheible, W. R. %D 2008 %T Eleven golden rules of quantitative RT-PCR %J Plant Cell %V 20 %N 7 %P 1736-1737 %8 Jul %! Eleven golden rules of quantitative RT-PCR %@ 1040-4651 %1 Scheible~Molecular Genomics~ %3 1 %M ISI:000258725600006 %K genes arabidopsis %Z 341PE Times Cited:0 Cited References Count:6 %U ://000258725600006 %+ Udvardi, MK Samuel Roberts Noble Fdn Inc, Ardmore, OK 73401 USA Samuel Roberts Noble Fdn Inc, Ardmore, OK 73401 USA Univ York, CNAP Res Labs, Dept Biol Area 7, York YO10 5YW, N Yorkshire, England Max Planck Inst Mol Plant Physiol, D-14476 Potsdam, Germany %G English %0 Journal Article %A Toerjek, O. %A Meyer, R. C. %A Zehnsdorf, M. %A Teltow, M. %A Strompen, G. %A Witucka-Wall, H. %A Blacha, A. %A Altmann, T. %D 2008 %T Construction and analysis of 2 reciprocal Arabidopsis introgression line populations %J Journal of Heredity %V 99 %N 4 %P 396-406 %8 Jul-Aug %! Construction and analysis of 2 reciprocal Arabidopsis introgression line populations %@ 0022-1503 %1 Altmann~Developmental Physiology and Genomics~ %3 1 %M ISI:000256761200008 %K quantitative trait locus flowering time genes epistatic interaction cultivated tomato natural variation plant physiology thaliana genome qtl identification %X Two new large reciprocal sets of introgression lines (ILs) were created between the Arabidopsis accessions Col-0 and C24. In both sets (78 ILs with Col-0 background and 62 ILs with C24 background), the donor segments cover almost the entire genome with an average substitution size of 18.3 cM. In addition to the basic sets of ILs, further subILs were developed for 2 genomic regions allowing better mapping resolution. SubILs carrying donor segments with candidate genes for flowering time and reduced fertility were used to demonstrate the usefulness of the reciprocal ILs for quantitative trait loci detection and fine mapping. For subIL development at high resolution around the reduced fertility locus, we used modified CelI-based assays in one-well format for both marker development and genotyping. This serves as a very flexible and cost-effective approach. %Z 313SV Times Cited:0 Cited References Count:46 %U ://000256761200008 %+ Meyer, RC Univ Potsdam, Inst Biochem & Biol, Dept Genet, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany Univ Potsdam, Inst Biochem & Biol, Dept Genet, D-14476 Potsdam, Germany Max Planck Inst Mol Plant Physiol, D-14476 Golm, Germany %G English %0 Journal Article %A Timm, S. %A Nunes-Nesi, A. %A Pamik, T. %A Morgenthal, K. %A Wienkoop, S. %A Keerberg, O. %A Weckwerth, W. %A Kleczkowski, L. A. %A Fernie, A. R. %A Bauwe, H. %D 2008 %T A Cytosolic Pathway for the Conversion of Hydroxypyruvate to Glycerate during Photorespiration in Arabidopsis %J Plant Cell %V 20 %N 10 %P 2848-2859 %8 Oct %! A Cytosolic Pathway for the Conversion of Hydroxypyruvate to Glycerate during Photorespiration in Arabidopsis %@ 1040-4651 %1 Fernie~Central Metabolism~Weckwerth~Integrative Proteomics and Metabolomics~ %3 1 %M ISI:000261378600027 %K spinach leaf peroxisomes glyoxylate reductase immunological-properties malate-dehydrogenase plant peroxisomes redox homeostasis photosynthesis purification thaliana enzyme %X Deletion of any of the core enzymes of the photorespiratory cycle, one of the major pathways of plant primary metabolism, results in severe air-sensitivity of the respective mutants. The peroxisomal enzyme hydroxypyruvate reductase ( HPR1) represents the only exception to this rule. This indicates the presence of extraperoxisomal reactions of photorespiratory hydroxypyruvate metabolism. We have identified a second hydroxypyruvate reductase, HPR2, and present genetic and biochemical evidence that the enzyme provides a cytosolic bypass to the photorespiratory core cycle in Arabidopsis thaliana. Deletion of HPR2 results in elevated levels of hydroxypyruvate and other metabolites in leaves. Photosynthetic gas exchange is slightly altered, especially under long-day conditions. Otherwise, the mutant closely resembles wild-type plants. The combined deletion of both HPR1 and HPR2, however, results in distinct air-sensitivity and a dramatic reduction in photosynthetic performance. These results suggest that photorespiratory metabolism is not confined to chloroplasts, peroxisomes, and mitochondria but also extends to the cytosol. The extent to which cytosolic reactions contribute to the operation of the photorespiratory cycle in varying natural environments is not yet known, but it might be dynamically regulated by the availability of NADH in the context of peroxisomal redox homeostasis. %Z 379ED Times Cited:1 Cited References Count:50 %U ://000261378600027 %+ Bauwe, H Univ Rostock, BioSci Inst, Dept Plant Physiol, D-18051 Rostock, Germany Univ Rostock, BioSci Inst, Dept Plant Physiol, D-18051 Rostock, Germany Max Planck Inst Mol Plant Physiol, D-14476 Potsdam, Germany Estonian Univ Life Sci, Inst Agr & Environm Sci, EE-51014 Tartu, Estonia Umea Univ, Dept Plant Physiol, SE-90187 Umea, Sweden %G English %0 Journal Article %A Sweetlove, L. J. %A Fell, D. %A Fernie, A. R. %D 2008 %T Getting to grips with the plant metabolic network %J Biochemical Journal %V 409 %P 27-41 %8 Jan 1 %! Getting to grips with the plant metabolic network %@ 0264-6021 %1 Fernie~Central Metabolism~ %3 1 %M ISI:000252414300003 %K arabidopsis metabolic control metabolic flux metabolomics plant metabolic network subcellular compartmentation protein-protein interactions c-13 labeling experiments adp-glucose pyrophosphorylase potato solanum-tuberosum nmr-based fluxomics escherichia-coli flux analysis steady-state amino-acids saccharomyces-cerevisiae %X Research into plant metabolism has a long history, and analytical approaches of ever-increasing breadth and sophistication have been brought to bear. We now have access to vast repositories of data concerning enzymology and regulatory features of enzymes, as well as large-scale datasets containing profiling information of transcripts, protein and metabolite levels. Nevertheless, despite this wealth of data, we remain some way off from being able to rationally engineer plant metabolism or even to predict metabolic responses. Within the past 18 months, rapid progress has been made, with several highly informative plant network interrogations being discussed in the literature. In the present review we will appraise the current state of the art regarding plant metabolic network analysis and attempt to outline what the necessary steps are in order to further our understanding of network regulation. %Z Part 1 251ZJ Times Cited:0 Cited References Count:185 %U ://000252414300003 %+ Sweetlove, LJ Univ Oxford, Dept Plant Sci, S Parks Rd, Oxford OX1 3RB, England Univ Oxford, Dept Plant Sci, Oxford OX1 3RB, England Oxford Brookes Univ, Sch Life Sci, Oxford OX3 0BP, England Max Planck Inst Mol Pflanzenphysiol, D-14476 Potsdam, Germany %G English %0 Journal Article %A Strehmel, N. %A Hummel, J. %A Erban, A. %A Strassburg, K. %A Kopka, J. %D 2008 %T Retention index thresholds for compound matching in GC-MS metabolite profiling %J Journal of Chromatography B-Analytical Technologies in the Biomedical and Life Sciences %V 871 %N 2 %P 182-190 %8 Aug 15 %! Retention index thresholds for compound matching in GC-MS metabolite profiling %@ 1570-0232 %1 Kopka~Root Metabolism~Bioinformatics cig~ %3 1 %M ISI:000259130400005 %K retention index matching gas chromatography gc-ms metabolite profiling metabolomics gas chromatography/mass spectrometry mass-spectrometry functional genomics reporting standards metabolomics database identification derivatization extraction libraries %X The generation of retention index (RI) libraries is an expensive and time-consuming effort. Procedures for the transfer of RI properties between chromatography variants are, therefore, highly relevant for a shared use. The precision of RI determination and accuracy of RI transfer between 8 method variants employing 5%-phenyl-95%-dimethylpolysiloxane capillary columns was investigated using a series of 9 n-alkanes (C-10-C-3G). The precision of the RI determination of 13 exemplary fatty acid methyl esters (C-8 ME-C-30 ME) was 0.22-0.33 standard deviation (S.D.) expressed in RI units in low complexity samples. In the presence of complex biological matrices this precision may deteriorate to 0.75-1.11. Application of the previously proposed Kovats, van den Dool or 3rd-5th order polynomial regression algorithms resulted in similar precision of RI calculation. For transfer of empirical van den Dool-RI properties between the chromatography variants 3rd order regression was found to represent the minimal necessary assumption. The range of typical regression coefficients was r(2) = 0.9988-0.9998 and accuracy of RI prediction between chromatography variants varied between 5.1 and 19.8 (0.29-0.69%) S.D. of residual RI error, RIpredicted - RIdetermined (n > 64). Accuracy of prediction was enhanced when subsets of chemically similar Compound classes were used for regression, for example organic acids and sugars exhibited 0.78 (n = 29) and 3.74 (n = 37) S.D. of residual RI error, respectively. In conclusion, we suggest use of percent RI error rather than absolute RI units for the definition of matching thresholds. Thresholds of 0.5-1.0% may apply to most transfers between chromatography variants. These thresholds will not solve all matching ambiguities in complex samples. Therefore, we recommend co-analysis of reference substances with each GC-MS profiling experiment. Composition of these defined reference mixtures may best approximate or mimic the quantitative and qualitative composition of the biological matrix under investigation. (C) 2008 Elsevier B.V. All rights reserved. %Z 347HE Times Cited:1 Cited References Count:36 %U ://000259130400005 %+ Kopka, J Max Planck Inst Mol Plant Physiol, Dept Prof L Willmitzer, Muehlenberg 1, D-14476 Potsdam, Germany Max Planck Inst Mol Plant Physiol, Dept Prof L Willmitzer, D-14476 Potsdam, Germany %G English %0 Journal Article %A Steinfath, M. %A Groth, D. %A Lisec, J. %A Selbig, J. %D 2008 %T Metabolite profile analysis: from raw data to regression and classification %J Physiologia Plantarum %V 132 %N 2 %P 150-161 %8 Feb %! Metabolite profile analysis: from raw data to regression and classification %@ 0031-9317 %1 Selbig~Bioinformatics crg~ %3 1 %M ISI:000252261900004 %K independent component analysis systems biology peak alignment metabolomics pca identification phenotypes discovery networks samples %X Successful metabolic profile analysis will aid in the fundamental understanding of physiology. Here, we present a possible analysis workflow. Initially, the procedure to transform raw data into a data matrix containing relative metabolite levels for each sample is described. Given that, because of experimental issues in the technical equipment, the levels of some metabolites cannot be universally determined or that different experiments need to be compared, missing value estimation and normalization are presented as helpful preprocessing steps. Regression methods are presented in this review as tools to relate metabolite levels with other physiological properties like biomass and gene expression. As the number of measured metabolites often exceeds the number of samples, dimensionality reduction methods are required. Two of these methods are discussed in detail in this review. Throughout this article, practical examples illustrating the application of the aforementioned methods are given. We focus on the uncovering the relationship between metabolism and growth-related properties. %Z 249WV Times Cited:0 Cited References Count:43 %U ://000252261900004 %+ Steinfath, M Univ Potsdam, Inst Biol & Biochem, Dept Mol Biol, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany Univ Potsdam, Inst Biol & Biochem, Dept Mol Biol, D-14476 Potsdam, Germany Max Planck Inst Mol Plant Physiol, Dept Mol Biol, D-14476 Potsdam, Germany %G English %0 Journal Article %A Sreenivasulu, N. %A Usadel, B. %A Winter, A. %A Radchuk, V. %A Scholz, U. %A Stein, N. %A Weschke, W. %A Strickert, M. %A Close, T. J. %A Stitt, M. %A Graner, A. %A Wobus, U. %D 2008 %T Barley grain maturation and germination: Metabolic pathway and regulatory network commonalities and differences highlighted by new MapMan/PageMan profiling tools %J Plant Physiology %V 146 %N 4 %P 1738-1758 %8 Apr %! Barley grain maturation and germination: Metabolic pathway and regulatory network commonalities and differences highlighted by new MapMan/PageMan profiling tools %@ 0032-0889 %1 Stitt~System Regulation~Usadel~Integrative Carbon Biology~ %3 1 %M ISI:000256417900023 %K arabidopsis seed-germination gene-expression aleurone cells abscisic-acid gibberellin biosynthesis filial tissues messenger-rna distinct dormancy patterns %X Plant seeds prepare for germination already during seed maturation. We performed a detailed transcriptome analysis of barley (Hordeum vulgare) grain maturation, desiccation, and germination in two tissue fractions (starchy endosperm / aleurone and embryo / scutellum) using the Affymetrix Barley1 GeneChip. To aid data evaluation, Arabidopsis thaliana MapMan and PageMan tools were adapted to barley. The analyses allow a number of conclusions: (1) Cluster analysis revealed a smooth transition in transcription programs between late seed maturation and germination within embryo tissues, but not in the endosperm / aleurone. (2) More than 12,000 transcripts are stored in the embryo of dry barley grains, many of which are presumably activated during germination. (3) Transcriptional activation of storage reserve mobilization events occurs at an early stage of germination, well before radicle protrusion. (4) Key genes of gibberellin (GA) biosynthesis are already active during grain maturation at a time when abscisic acid peaks suggesting the formation of an endogenous store of GA in the aleurone. This GA probably acts later during germination in addition to newly synthesized GA. (5) Beside the well-known role of GA in gene activation during germination spatiotemporal expression data and cis-element searches in homologous rice promoters confirm an equally important gene-activating role of abscisic acid during this developmental period. The respective regulatory webs are linked to auxin and ethylene controlled networks. In summary, new bioinformatics PageMan and MapMan tools developed in barley have been successfully used to investigate in detail the transcriptome relationships between seed maturation and germination in an important crop plant. %Z 308VJ Times Cited:4 Cited References Count:55 %U ://000256417900023 %+ Sreenivasulu, N Leibniz Inst Pflanzengenet & Kulturpflanzenforsch, D-06466 Gatersleben, Germany Leibniz Inst Pflanzengenet & Kulturpflanzenforsch, D-06466 Gatersleben, Germany Max Planck Inst Mol Pflanzenphysiol, D-14476 Potsdam, Germany Univ Calif Riverside, Dept Bot & Plant Sci, Riverside, CA 92521 USA %G English %0 Journal Article %A Skirycz, A. %A Radziejwoski, A. %A Busch, W. %A Hannah, M. A. %A Czeszejko, J. %A Kwasniewski, M. %A Zanor, M. I. %A Lohmann, J. U. %A De Veylder, L. %A Witt, I. %A Mueller-Roeber, B. %D 2008 %T The DOF transcription factor OBP1 is involved in cell cycle regulation in Arabidopsis thaliana %J Plant Journal %V 56 %N 5 %P 779-792 %8 Dec %! The DOF transcription factor OBP1 is involved in cell cycle regulation in Arabidopsis thaliana %@ 0960-7412 %1 Mueller-Roeber~Plant Signaling~ %3 1 %M ISI:000261275400008 %K cell cycle dof transcription factor arabidopsis obp1 d-type cyclin genome-wide analysis retinoblastoma-related protein dependent kinase complex gene-expression domain proteins suspension-cultures salicylic-acid tobacco growth division %X In contrast to animal growth, plant growth is largely post-embryonic. Therefore plants have developed new mechanisms to precisely regulate cell proliferation by means of internal and external stimuli whilst the general core cell cycle machinery is conserved between eukaryotes. In this work we demonstrate a role for the Arabidopsis thaliana DNA-binding-with-one-finger (DOF) transcription factor OBP1 in the control of cell division upon developmental signalling. Inducible overexpression of OBP1 resulted in a significant overrepresentation of cell cycle genes among the upregulated transcripts. Direct targets of OBP1, as verified by chromatin immunoprecipitation, include at least the core cell cycle gene CYCD3;3 and the replication-specific transcription factor gene AtDOF2;3. Consistent with our molecular data, short-term activation of OBP1 in cell cultures affected cell cycle re-entry, shortening the duration of the G(1) phase and the overall length of the cell cycle, whilst constitutive overexpression of OBP1 in plants influenced cell size and cell number, leading to a dwarfish phenotype. Expression during embryogenesis, germination and lateral root initiation suggests an important role for OBP1 in cell cycle re-entry, operating as a transcriptional regulator of key cell cycle genes. Our findings provide significant input into our understanding of how cell cycle activity is incorporated into plant growth and development. %Z 377UE Times Cited:0 Cited References Count:55 %U ://000261275400008 %+ Mueller-Roeber, B Max Planck Inst Mol Plant Physiol, Cooperat Res Grp, Muhlenberg 1, D-14476 Potsdam, Germany Max Planck Inst Mol Plant Physiol, Cooperat Res Grp, D-14476 Potsdam, Germany Univ Ghent VIB, Dept Plant Syst Biol, B-9052 Ghent, Belgium Max Planck Inst Dev Biol, Dept Mol Biol, D-72076 Tubingen, Germany Univ Potsdam, Dept Mol Biol, D-14476 Potsdam, Germany Silesian Univ, Dept Genet, PL-40032 Katowice, Poland %G English %0 Journal Article %A Sienkiewicz-Porzucek, A. %A Nunes-Nesi, A. %A Sulpice, R. %A Lisec, J. %A Centeno, D. C. %A Carillo, P. %A Leisse, A. %A Urbanczyk-Wochniak, E. %A Fernie, A. R. %D 2008 %T Mild reductions in mitochondrial citrate synthase activity result in a compromised nitrate assimilation and reduced leaf pigmentation but have no effect on photosynthetic performance or growth %J Plant Physiology %V 147 %N 1 %P 115-127 %8 May %! Mild reductions in mitochondrial citrate synthase activity result in a compromised nitrate assimilation and reduced leaf pigmentation but have no effect on photosynthetic performance or growth %@ 0032-0889 %1 Fernie~Central Metabolism~Genes and small Molecules~System Regulation~ %3 1 %M ISI:000256419400012 %K nadp-isocitrate dehydrogenase transgenic tomato plants organic-acid metabolism transcription factors aluminum tolerance cytosolic phosphoglucomutase antisense inhibition nitrogen deficiency electron-transport gene-expression %X Transgenic tomato (Solanum lycopersicum) plants, expressing a fragment of the mitochondrial citrate synthase gene in the antisense orientation and exhibiting mild reductions in the total cellular activity of this enzyme, displayed essentially no visible phenotypic alteration from the wild type. A more detailed physiological characterization, however, revealed that although these plants were characterized by relatively few changes in photosynthetic parameters they displayed a decreased relative flux through the tricarboxylic acid cycle and an increased rate of respiration. Furthermore, biochemical analyses revealed that the transformants exhibited considerably altered metabolism, being characterized by slight decreases in the levels of organic acids of the tricarboxylic acid cycle, photosynthetic pigments, and in a single line in protein content but increases in the levels of nitrate, several amino acids, and starch. We additionally determined the maximal catalytic activities of a wide range of enzymes of primary metabolism, performed targeted quantitative PCR analysis on all three isoforms of citrate synthase, and conducted a broader transcript profiling using the TOM1 microarray. Results from these studies confirmed that if the lines were somewhat impaired in nitrate assimilation, they were not severely affected by this, suggesting the presence of strategies by which metabolism is reprogrammed to compensate for this deficiency. The results are discussed in the context of carbon-nitrogen interaction and interorganellar coordination of metabolism. %Z 308VV Times Cited:3 Cited References Count:66 %U ://000256419400012 %+ Fernie, AR Max Planck Inst Mol Pflanzenphysiol, D-14476 Golm, Germany Max Planck Inst Mol Pflanzenphysiol, D-14476 Golm, Germany Univ Naples 2, Dipartimento Sci Vita, I-81100 Caserta, Italy %G English %0 Journal Article %A Shao, N. %A Bock, R. %D 2008 %T A codon-optimized luciferase from Gaussia princeps facilitates the in vivo monitoring of gene expression in the model alga Chlamydomonas reinhardtii %J Current Genetics %V 53 %N 6 %P 381-388 %8 Jun %! A codon-optimized luciferase from Gaussia princeps facilitates the in vivo monitoring of gene expression in the model alga Chlamydomonas reinhardtii %@ 0172-8083 %1 Bock~ Organelle Biology, Biotechnology and Molecular Ecophysiology~ %3 1 %M ISI:000256084400006 %K reporter gene chlamydomonas reinhardtii luciferase gaussia princeps heat-inducible expression bioluminescence heat-shock genes light induction reporter gene chloroplast transformation regions hsp70a assay tool %X The unicellular green alga Chlamydomonas reinhardtii has emerged as a superb model species in plant biology. Although the alga is easily transformable, the low efficiency of transgene expression from the Chlamydomonas nuclear genome has severely hampered functional genomics research. For example, poor transgene expression is held responsible for the lack of sensitive reporter genes to monitor gene expression in vivo, analyze subcellular protein localization or study protein-protein interactions. Here, we have tested the luciferase from the marine copepod Gaussia princeps (G-Luc) for its suitability as a sensitive bioluminescent reporter of gene expression in Chlamydomonas. We show that a Gaussia luciferase gene variant, engineered to match the codon usage in the Chlamydomonas nuclear genome, serves as a highly sensitive reporter of gene expression from both constitutive and inducible algal promoters. Its bioluminescence signal intensity greatly surpasses previously developed reporters for Chlamydomonas nuclear gene expression and reaches values high enough for utilizing the reporter as a tool to monitor responses to environmental stresses in vivo and to conduct high-throughput screenings for signaling mutants in Chlamydomonas. %Z 304BG Times Cited:0 Cited References Count:23 %U ://000256084400006 %+ Bock, R Max Planck Inst Mol Pflanzenphysiol, Am Muhlenberg 1, D-14476 Potsdam, Germany Max Planck Inst Mol Pflanzenphysiol, D-14476 Potsdam, Germany %G English %0 Journal Article %A Shao, N. %A Beck, C. F. %A Lemaire, S. D. %A Krieger-Liszkay, A. %D 2008 %T Photosynthetic electron flow affects H2O2 signaling by inactivation of catalase in Chlamydomonas reinhardtii %J Planta %V 228 %N 6 %P 1055-1066 %8 Nov %! Photosynthetic electron flow affects H2O2 signaling by inactivation of catalase in Chlamydomonas reinhardtii %@ 0032-0935 %1 Organelle Biology, Biotechnology and Molecular Ecophysiology~ %3 1 %M ISI:000260782800015 %K catalase chlamydomonas hydrogen peroxide signaling thioredoxin chloroplast gene-expression oxidative stress-response water-water cycle ascorbate peroxidase hydrogen-peroxide arabidopsis-thaliana thioredoxin targets redox regulation cell-death oxygen %X A specific signaling role for H2O2 in Chlamydomonas reinhardtii was demonstrated by the definition of a promoter that specifically responded to this ROS. Expression of a nuclear-encoded reporter gene driven by this promoter was shown to depend not only on the level of exogenously added H2O2 but also on light. In the dark, the induction of the reporter gene by H2O2 was much lower than in the light. This lower induction was correlated with an accelerated disappearance of H2O2 from the culture medium in the dark. Due to a light-induced reduction in catalase activity, H2O2 levels in the light remained higher. Photosynthetic electron transport mediated the light-controlled down-regulation of the catalase activity since it was prevented by 3-(3'4'-dichlorophenyl)-1,1-dimethylurea (DCMU), an inhibitor of photosystem II. In the presence of light and DCMU, expression of the reporter gene was low while the addition of aminotriazole, a catalase inhibitor, led to a higher induction of the reporter gene by H2O2 in the dark. The role of photosynthetic electron transport and thioredoxin in this regulation was investigated by using mutants deficient in photosynthetic electron flow and by studying the correlation between NADP-malate dehydrogenase and catalase activities. It is proposed that, contrary to expectations, a controlled down-regulation of catalase activity occurs upon a shift of cells from dark to light. This down-regulation apparently is necessary to maintain a certain level of H2O2 required to activate H2O2-dependent signaling pathways. %Z 370SG Times Cited:0 Cited References Count:54 %U ://000260782800015 %+ Krieger-Liszkay, A CEA, iBiTecS, Serv Bioenerget Biol Struct & Mecanisme, CNRS URA 2096, F-91191 Gif Sur Yvette, France CEA, iBiTecS, Serv Bioenerget Biol Struct & Mecanisme, CNRS URA 2096, F-91191 Gif Sur Yvette, France Univ Paris 11, CNRS, Inst Biotechnol Plantes, F-91405 Orsay, France Max Planck Inst Mol Pflanzenphysiol, D-14476 Potsdam, Germany Univ Freiburg, Fak Biol, Inst Biol 3, D-79104 Freiburg, Germany %G English %0 Journal Article %A Schweighofer, A. %A Meskiene, I. %D 2008 %T Regulation of stress hormones jasmonates and ethylene by MAPK pathways in plants %J Mol Biosyst %V 4 %N 8 %P 799-803 %8 Aug %! Regulation of stress hormones jasmonates and ethylene by MAPK pathways in plants %O Molecular bioSystems %@ 1742-2051 (Electronic) %1 Integrative Proteomics and Metabolomics~Weckwerth~ %3 1 %M 18633480 %X Plant stress hormones, such as jasmonates (JAs) and ethylene (ET) are essential in plant defence against stress conditions. JAs are used in cosmetics and food flavouring, and the recently demonstrated anti-cancer activity of JAs highlights their potential in health protection. It reinforces the need for a better understanding of biosynthetic regulation of JAs. Which mechanisms are involved in the regulation of the biosynthesis of JAs and ET? Production of stress hormones is induced in plants after wounding or herbivore attack. ET is a gaseous compound and plant JAs are oxylipins structurally similar to prostaglandins that are induced upon inflammation or injury in mammals. Wounding activates protein phosphorylation cascades involving mitogen-activated protein kinases (MAPKs). MAPKs regulate ET production. The induction of JA biosynthesis was suggested to require MAPK activation; however the defined roles of MAPKs in JA production remain unclear. Here we will highlight the most recent findings suggesting the regulation of JA biosynthesis and ethylene production by stress activated MAPKs and phosphatases that inactivate these MAPKs. %Z Journal Article Research Support, Non-U.S. Gov't England %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18633480 %+ Max Planck Institute of Molecular Plant Physiology, Golm, Germany. %G eng %0 Journal Article %A Schippers, J. H. M. %A Nunes-Nesi, A. %A Apetrei, R. %A Hille, J. %A Fernie, A. R. %A Dijkwel, P. P. %D 2008 %T The Arabidopsis onset of leaf death5 Mutation of Quinolinate Synthase Affects Nicotinamide Adenine Dinucleotide Biosynthesis and Causes Early Ageing %J Plant Cell %V 20 %N 10 %P 2909-2925 %8 Oct %! The Arabidopsis onset of leaf death5 Mutation of Quinolinate Synthase Affects Nicotinamide Adenine Dinucleotide Biosynthesis and Causes Early Ageing %@ 1040-4651 %1 Fernie~Central Metabolism~ %3 1 %M ISI:000261378600031 %K programmed cell-death fe-s cluster electron-transfer flavoprotein senescence-associated genes leaf senescence oxidative stress arabidopsis-thaliana cysteine desulfurase alternative oxidase life-span %X Leaf senescence in Arabidopsis thaliana is a strict, genetically controlled nutrient recovery program, which typically progresses in an age-dependent manner. Leaves of the Arabidopsis onset of leaf death5 ( old5) mutant exhibit early developmental senescence. Here, we show that OLD5 encodes quinolinate synthase ( QS), a key enzyme in the de novo synthesis of NAD. The Arabidopsis QS was previously shown to carry a Cys desulfurase domain that stimulates reconstitution of the oxygen-sensitive Fe-S cluster that is required for QS activity. The old5 lesion in this enzyme does not affect QS activity but it decreases its Cys desulfurase activity and thereby the long-term catalytic competence of the enzyme. The old5 mutation causes increased NAD steady state levels that coincide with increased activity of enzymes in the NAD salvage pathway. NAD plays a key role in cellular redox reactions, including those of the tricarboxylic acid cycle. Broad-range metabolite profiling of the old5 mutant revealed that it contains higher levels of tricarboxylic acid cycle intermediates and nitrogen-containing amino acids. The mutant displays a higher respiration rate concomitant with increased expression of oxidative stress markers. We postulate that the alteration in the oxidative state is integrated into the plant developmental program, causing early ageing of the mutant. %Z 379ED Times Cited:0 Cited References Count:114 %U ://000261378600031 %+ Dijkwel, PP Univ Groningen, Groningen Biomol Sci & Biotechnol Inst, NL-9751 NN Haren, Netherlands Univ Groningen, Groningen Biomol Sci & Biotechnol Inst, NL-9751 NN Haren, Netherlands Max Planck Inst Mol Plant Physiol, D-14476 Potsdam, Germany Massey Univ, Inst Mol BioSci, Palmerston North 4442, New Zealand %G English %0 Journal Article %A Schauer, N. %A Semel, Y. %A Balbo, I. %A Steinfath, M. %A Repsilber, D. %A Selbig, J. %A Pleban, T. %A Zamir, D. %A Fernie, A. R. %D 2008 %T Mode of inheritance of primary metabolic traits in tomato %J Plant Cell %V 20 %N 3 %P 509-523 %8 Mar %! Mode of inheritance of primary metabolic traits in tomato %@ 1040-4651 %1 Fernie~Energy Metabolism~Selbig~Bioinformatics crg~ %3 1 %M ISI:000256415500006 %K interspecific introgression lines chromatography-mass spectrometry quantitative trait natural variation arabidopsis-thaliana qtl analysis fruit size lycopersicon-pennellii genetic-variation plant-metabolism %X To evaluate components of fruit metabolic composition, we have previously metabolically phenotyped tomato (Solanum lycopersicum) introgression lines containing segmental substitutions of wild species chromosome in the genetic background of a cultivated variety. Here, we studied the hereditability of the fruit metabolome by analyzing an additional year's harvest and evaluating the metabolite profiles of lines heterozygous for the introgression (ILHs), allowing the evaluation of putative quantitative trait locus (QTL) mode of inheritance. These studies revealed that most of the metabolic QTL (174 of 332) were dominantly inherited, with relatively high proportions of additively (61 of 332) or recessively (80 of 332) inherited QTL and a negligible number displaying the characteristics of overdominant inheritance. Comparison of the mode of inheritance of QTL revealed that several metabolite pairs displayed a similar mode of inheritance of QTL at the same chromosomal loci. Evaluation of the association between morphological and metabolic traits in the ILHs revealed that this correlation was far less prominent, due to a reduced variance in the harvest index within this population. These data are discussed in the context of genomics-assisted breeding for crop improvement, with particular focus on the exploitation of wide biodiversity. %Z 308UM Times Cited:1 Cited References Count:85 %U ://000256415500006 %+ Fernie, AR Max Planck Inst Mol Plant Physiol, D-14476 Potsdam, Germany Max Planck Inst Mol Plant Physiol, D-14476 Potsdam, Germany Hebrew Univ Jerusalem, Inst Plant Sci & Genet, IL-76100 Rehovot, Israel Hebrew Univ Jerusalem, Fac Agr, Otto Warburg Ctr Biotechnol, IL-76100 Rehovot, Israel Univ Potsdam, Inst Biochem & Biol, Dept Bioinformat, D-14476 Potsdam, Germany Res Inst Biol Farm Anim, D-18196 Dummerstorf, Germany %G English %0 Journal Article %A Scarpeci, T. E. %A Zanor, M. I. %A Carrillo, N. %A Mueller-Roeber, B. %A Valle, E. M. %D 2008 %T Generation of superoxide anion in chloroplasts of Arabidopsis thaliana during active photosynthesis: a focus on rapidly induced genes %J Plant Molecular Biology %V 66 %N 4 %P 361-378 %8 Mar %! Generation of superoxide anion in chloroplasts of Arabidopsis thaliana during active photosynthesis: a focus on rapidly induced genes %@ 0167-4412 %1 Central Metabolism~Mueller-Roeber~ %3 1 %M ISI:000253129900003 %K antioxidant response chloroplast hsp oxidative stress wrky shock transcription factor finger protein zat12 reactive oxygen heat-stress high light oxidative stress hypersensitive response glutamine-synthetase environmental-stress signal-transduction %X The antioxidant defense system involves complex functional coordination of multiple components in different organelles within the plant cell. Here, we have studied the Arabidopsis thaliana early response to the generation of superoxide anion in chloroplasts during active photosynthesis. We exposed plants to methyl viologen (MV), a superoxide anion propagator in the light, and performed biochemical and expression profiling experiments using Affymetrix ATH1 GeneChip(R) microarrays under conditions in which photosynthesis and antioxidant enzymes were active. Data analysis identified superoxide-responsive genes that were compared with available microarray results. Examples include genes encoding proteins with unknown function, transcription factors and signal transduction components. A common GAAAAGTCAAAC motif containing the W-box consensus sequence of WRKY transcription factors, was found in the promoters of genes highly up-regulated by superoxide. Band shift assays showed that oxidative treatments enhanced the specific binding of leaf protein extracts to this motif. In addition, GUS reporter gene fused to WRKY30 promoter, which contains this binding motif, was induced by MV and H2O2. Overall, our study suggests that genes involved in signalling pathways and with unknown functions are rapidly activated by superoxide anion generated in photosynthetically active chloroplasts, as part of the early antioxidant response of Arabidopsis leaves. %Z 262DT Times Cited:0 Cited References Count:59 %U ://000253129900003 %+ Valle, EM Univ Nacl Rosario, Inst Biol Mol & Celular Rosario IBR CONICET, Fac Ciencias Bioquim & Farmaceut, Suipacha 531, Rosario, Argentina Univ Nacl Rosario, Inst Biol Mol & Celular Rosario IBR CONICET, Fac Ciencias Bioquim & Farmaceut, Rosario, Argentina Max Planck Inst Mol Plant Physiol, D-14476 Golm, Germany Univ Potsdam, Inst Biochem & Biol, D-14476 Golm, Germany %G English %0 Journal Article %A Sanchez, D. H. %A Siahpoosh, M. R. %A Roessner, U. %A Udvardi, M. %A Kopka, J. %D 2008 %T Plant metabolomics reveals conserved and divergent metabolic responses to salinity %J Physiologia Plantarum %V 132 %N 2 %P 209-219 %8 Feb %! Plant metabolomics reveals conserved and divergent metabolic responses to salinity %@ 0031-9317 %1 Kopka~Root Metabolism~ %3 1 %M ISI:000252261900009 %K arabidopsis-thaliana salt tolerance component analysis water-stress drought profiles database genes nmr %X New metabolic profiling technologies provide data on a wider range of metabolites than traditional targeted approaches. Metabolomic technologies currently facilitate acquisition of multivariate metabolic data using diverse, mostly hyphenated, chromatographic detection systems, such as GC-MS or liquid chromatography coupled to mass spectrometry, Fourier-transformed infrared spectroscopy or NMR-based methods. Analysis of the resulting data can be performed through a combination of non-supervised and supervised statistical methods, such as independent component analysis and analysis of variance, respectively. These methods reduce the complex data sets to information, which is relevant for the discovery of metabolic markers or for hypothesis-driven, pathway-based analysis. Plant responses to salinity involve changes in the activity of genes and proteins, which invariably lead to changes in plant metabolism. Here, we highlight a selection of recent publications in the salt stress field, and use gas chromatography time-of-flight mass spectrometry profiles of polar fractions from the plant models, Arabidopsis thaliana, Lotus japonicus and Oryza sativa to demonstrate the power of metabolite profiling. We present evidence for conserved and divergent metabolic responses among these three species and conclude that a change in the balance between amino acids and organic acids may be a conserved metabolic response of plants to salt stress. %Z 249WV Times Cited:0 Cited References Count:36 %U ://000252261900009 %+ Kopka, J Max Planck Inst Mol Plant Physiol, Am Muehlenberg 1, D-14476 Potsdam, Germany Max Planck Inst Mol Plant Physiol, D-14476 Potsdam, Germany Univ Melbourne, Sch Bot, Australian Ctr Plant Funct Genom, Melbourne, Vic 3010, Australia Samuel Roberts Noble Fdn Inc, Ardmore, OK 73401 USA %G English %0 Journal Article %A Sanchez, D.H. %A Redestig, H. %A Kraemer, U. %A Udvardi, M.K. %A Kopka, J. %D 2008 %T Metabolome-ionome-biomass interactions: What can we learn about salt stress by multiparallel phenotyping? %J Plant Signaling and Behavior %V 3 %N 8 %P 598 - 600 %! Metabolome-ionome-biomass interactions: What can we learn about salt stress by multiparallel phenotyping? %1 Kopka~Root Metabolism~ %3 1 %X Long-term exposure of plants to saline soil results in mineral ion imbalance, altered metabolism, and reduced growth. Currently, the interaction between ion content and plant metabolism under salt-stress is poorly understood. Here we present a multivariate correlation study on the metabolome, ionome, and biomass changes of Lotus japonicus challenged by salt stress. Using latent variable models, we show that increasing salinity leads to reproducible changes of metabolite, ion and nutrient pools. Strong correlations between the metabolome and the ionome or biomass may allow one to estimate the degree of salt stress experienced by a plant based on metabolite profiles. Despite the apparently high predictive power of the models, it remains to be investigated whether such metabolite profiles of non- or moderately-stressed plants can be used by breeding programs as ideal ideotypes for the selection of enhanced salt-tolerant %+ Max Planck Institute for Molecular Plant Physiology, Wissenschaftspark Golm, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany Bioquant Center, University of Heidelberg, Im Neuenheimer Feld 267, Heidelberg, D-69120, Germany Samuel Roberts Noble Foundation, 2510 Sam Noble Pky., Ardmore, OK 73401, USA %0 Journal Article %A Sanchez, D. H. %A Lippold, F. %A Redestig, H. %A Hannah, M. A. %A Erban, A. %A Kraemer, U. %A Kopka, J. %A Udvardi, M. K. %D 2008 %T Integrative functional genomics of salt acclimatization in the model legume Lotus japonicus %J Plant Journal %V 53 %N 6 %P 973-987 %8 Mar 7 %! Integrative functional genomics of salt acclimatization in the model legume Lotus japonicus %O Plant J %@ 0960-7412 (Print) %1 Kopka~Root Metabolism~ %3 1 %M 18047558 %X The model legume Lotus japonicus was subjected to non-lethal long-term salinity and profiled at the ionomic, transcriptomic and metabolomic levels. Two experimental designs with various stress doses were tested: a gradual step acclimatization and an initial acclimatization approach. Ionomic profiling by inductively coupled plasma/atomic emission spectrometry (ICP-AES) revealed salt stress-induced reductions in potassium, phosphorus, sulphur, zinc and molybdenum. Microarray profiling using the Lotus Genechip((R)) allowed the identification of 912 probesets that were differentially expressed under the acclimatization regimes. Gas chromatography/mass spectrometry-based metabolite profiling identified 147 differentially accumulated soluble metabolites, indicating a change in metabolic phenotype upon salt acclimatization. Metabolic changes were characterized by a general increase in the steady-state levels of many amino acids, sugars and polyols, with a concurrent decrease in most organic acids. Transcript and metabolite changes exhibited a stress dose-dependent response within the range of NaCl concentrations used, although threshold and plateau behaviours were also observed. The combined observations suggest a successive and increasingly global requirement for the reprogramming of gene expression and metabolic pathways to maintain ionic and osmotic homeostasis. A simple qualitative model is proposed to explain the systems behaviour of plants during salt acclimatization. %Z Journal article for cell and molecular biology %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18047558 %+ Max Planck Institute for Molecular Plant Physiology, Wissenschaftspark Golm, Am Muhlenberg 1, Potsdam-Golm, D-14 476, Germany. %G Eng %0 Journal Article %A Rumpler, M. %A Woesz, A. %A Dunlop, J. W. C. %A van Dongen, J. T. %A Fratzl, P. %D 2008 %T The effect of geometry on three-dimensional tissue growth %J Journal of the Royal Society Interface %V 5 %N 27 %P 1173-1180 %8 Oct 6 %! The effect of geometry on three-dimensional tissue growth %@ 1742-5689 %1 van Dongen~Energy Metabolism~ %3 1 %M ISI:000258530600004 %K three-dimensional tissue formation scaffold channels bone tissue engineering curvature-driven growth osteoblasts mc3t3-e1 cells matrix adhesion hydroxyapatite scaffolds differentiation organization mechanisms substratum patterns %X Tissue formation is determined by uncountable biochemical signals between cells; in addition, physical parameters have been shown to exhibit significant effects on the level of the single cell. Beyond the cell, however, there is still no quantitative understanding of how geometry affects tissue growth, which is of much significance for bone healing and tissue engineering. In this paper, it is shown that the local growth rate of tissue formed by osteoblasts is strongly influenced by the geometrical features of channels in an artificial three-dimensional matrix. Curvature-driven effects and mechanical forces within the tissue may explain the growth patterns as demonstrated by numerical simulation and confocal laser scanning microscopy. This implies that cells within the tissue surface are able to sense and react to radii of curvature much larger than the size of the cells themselves. This has important implications towards the understanding of bone remodelling and defect healing as well as towards scaffold design in bone tissue engineering. %Z 338TB Times Cited:0 Cited References Count:38 %U ://000258530600004 %+ Fratzl, P Max Planck Inst Colloids & Interfaces, Dept Biomat, D-14424 Potsdam, Germany Max Planck Inst Colloids & Interfaces, Dept Biomat, D-14424 Potsdam, Germany Max Planck Inst Mol Plant Physiol, Dept Organelle Biol Biotechnol & Mol Ecophysiol, Energy Metabolism Res Grp, D-14424 Potsdam, Germany %G English %0 Journal Article %A Rumpler, M. %A Woesz, A. %A Dunlop, J. %A van Dongen, J. %A Klaushofer, K. %A Fratzl, P. %D 2008 %T Three-dimensional geometry determines the tissue formation kinetics in vitro %J Calcified Tissue International %V 82 %P S76-S76 %! Three-dimensional geometry determines the tissue formation kinetics in vitro %@ 0171-967X %1 van Dongen~Energy Metabolism~ %3 1 %$ abstract %M ISI:000256258300163 %Z Suppl. 1 306OS Times Cited:0 Cited References Count:0 %U ://000256258300163 %+ Ludwig Boltzmann Inst Osteol, Dept Med 4, Vienna, Austria Max Planck Inst Colloids & Interfaces, Dept Biomat, Potsdam, Germany Max Planck Inst Mol Plant Physiol, Dept Organelle Biol Biotechnol & Mol Ecophysiol, Potsdam, Germany %G English %0 Journal Article %A Ruffel, S. %A Freixes, S. %A Balzergue, S. %A Tillard, P. %A Jeudy, C. %A Martin-Magniette, M. L. %A van der Merwe, M. J. %A Kakar, K. %A Gouzy, J. %A Fernie, A. R. %A Udvardi, M. %A Salon, C. %A Gojon, A. %A Lepetit, M. %D 2008 %T Systemic signaling of the plant nitrogen status triggers specific transcriptome responses depending on the nitrogen source in Medicago truncatula %J Plant Physiology %V 146 %N 4 %P 2020-2035 %8 Apr %! Systemic signaling of the plant nitrogen status triggers specific transcriptome responses depending on the nitrogen source in Medicago truncatula %@ 0032-0889 %1 Fernie~Central Metabolism~Udvardi~Molecular Plant Nutrition~System Regulation~ %3 1 %M ISI:000256417900044 %K affinity nitrate transporter arabidopsis-thaliana gene-expression protein family long-distance n-2 fixation no3-uptake feedback mechanism genomic analysis ammonium uptake %X Legumes can acquire nitrogen (N) from NO3-, NH4+, and N-2 (through symbiosis with Rhizobium bacteria); however, the mechanisms by which uptake and assimilation of these N forms are coordinately regulated to match the N demand of the plant are currently unknown. Here, we find by use of the split-root approach in Medicago truncatula plants that NO3- uptake, NH4+ uptake, and N-2 fixation are under general control by systemic signaling of plant N status. Indeed, irrespective of the nature of the N source, N acquisition by one side of the root system is repressed by high N supply to the other side. Transcriptome analysis facilitated the identification of over 3,000 genes that were regulated by systemic signaling of the plant N status. However, detailed scrutiny of the data revealed that the observation of differential gene expression was highly dependent on the N source. Localized N starvation results, in the unstarved roots of the same plant, in a strong compensatory up-regulation of NO3- uptake but not of either NH4+ uptake or N-2 fixation. This indicates that the three N acquisition pathways do not always respond similarly to a change in plant N status. When taken together, these data indicate that although systemic signals of N status control root N acquisition, the regulatory gene networks targeted by these signals, as well as the functional response of the N acquisition systems, are predominantly determined by the nature of the N source. %Z 308VJ Times Cited:0 Cited References Count:76 %U ://000256417900044 %+ Lepetit, M INRA, CNRS Sup, Agro UM2,Inst Biol Integrat Plantes, UMR Biochim & Physiol Mol Plantes 5004, F-34060 Montpellier, France INRA, CNRS Sup, Agro UM2,Inst Biol Integrat Plantes, UMR Biochim & Physiol Mol Plantes 5004, F-34060 Montpellier, France INRA, UMR, Unite Genet & Ecophysiol Legumineuses, F-21065 Dijon, France INRA, CNRS, UMR 1165, UEVE 8114,Unite Rech Genom Vegetale, F-91057 Evry, France Max Planck Inst Mol Pflanzenphys, D-14476 Potsdam, Germany INRA, CNRS, UMR 441 2594, Lab Interact Plantes Microorgan, F-31326 Castanet Tolosan, France INRA, UMR AgroParisTech MIA 518, F-75231 Paris, France %G English %0 Journal Article %A Rogato, A. %A D'Apuzzo, E. %A Barbulova, A. %A Omrane, S. %A Stedel, C. %A Simon-Rosin, U. %A Katinakis, P. %A Flemetakis, M. %A Udvardi, M. %A Chiurazzi, M. %D 2008 %T Tissue-specific down-regulation of LjAMT1;1 compromises nodule function and enhances nodulation in Lotus japonicus %J Plant Molecular Biology %V 68 %N 6 %P 585-595 %8 Dec %! Tissue-specific down-regulation of LjAMT1;1 compromises nodule function and enhances nodulation in Lotus japonicus %@ 0167-4412 %1 Udvardi~Molecular Plant Nutrition~ %3 1 %M ISI:000260378600005 %K ammonium transport nitrogen fixation nodule symbiosis affinity ammonium transporters nitrogen-fixation root-nodules phosphoenolpyruvate carboxylase peribacteroid membrane symbiosome membrane soybean nodules legume nodules plant expression %X Plant ammonium transporters of the AMT1 family are involved in N-uptake from the soil and ammonium transport, and recycling within the plant. Although AMT1 genes are known to be expressed in nitrogen-fixing nodules of legumes, their precise roles in this specialized organ remain unknown. We have taken a reverse-genetic approach to decipher the physiological role of LjAMT1;1 in Lotus japonicus nodules. LjAMT1;1 is normally expressed in both the infected zone and the vascular tissue of Lotus nodules. Inhibition of LjAMT1;1 gene expression, using an antisense gene construct driven by a leghemoglobin promoter resulted in a substantial reduction of LjAMT1;1 transcript in the infected tissue but not the vascular bundles of transgenic plants. As a result, the nitrogen-fixing activity of nodules was partially impaired and nodule number increased compared to control plants. Expression of LjAMT1;1-GFP fusion protein in plant cells indicated a plasma-membrane location for the LjAMT1;1 protein. Taken together, the results are consistent with a role of LjAMT1;1 in retaining ammonium derived from symbiotic nitrogen fixation in plant cells prior to its assimilation. %Z 365AP Times Cited:0 Cited References Count:51 %U ://000260378600005 %+ Chiurazzi, M Inst Genet & Biophys A Buzzati Traverso, Via P Castellino 12, I-80131 Naples, Italy Inst Genet & Biophys A Buzzati Traverso, I-80131 Naples, Italy Max Planck Inst Mol Plant Physiol, Mol Plant Nutr Grp, D-14476 Potsdam, Germany Agr Univ Athens, Dept Agr Biotechnol, Athens 11855, Greece %G English %0 Journal Article %A Rogalski, M. %A Schoettler, M. A. %A Thiele, W. %A Schulze, W. X. %A Bock, R. %D 2008 %T Rpl33, a nonessential plastid-encoded ribosomal protein in tobacco, is required under cold stress conditions %J Plant Cell %V 20 %N 8 %P 2221-2237 %8 Aug %! Rpl33, a nonessential plastid-encoded ribosomal protein in tobacco, is required under cold stress conditions %@ 1040-4651 %1 Schoettler~Photosynthesis Research~Bock~Organelle Biology, Biotechnology and Molecular Ecophysiology~Schulze~Signaling Proteomics~ %3 1 %M ISI:000259703300019 %K cytochrome b(6)f complex reading frame reveals photosystem-i chloroplast ribosome escherichia-coli higher-plants gene-transfer targeted inactivation arabidopsis-thaliana electron-transport %X Plastid genomes contain a conserved set of genes encoding components of the translational apparatus. While knockout of plastid translation is lethal in tobacco (Nicotiana tabacum), it is not known whether each individual component of the plastid ribosome is essential. Here, we used reverse genetics to test whether several plastid genome-encoded ribosomal proteins are essential. We found that, while ribosomal proteins Rps2, Rps4, and Rpl20 are essential for cell survival, knockout of the gene encoding ribosomal protein Rpl33 did not affect plant viability and growth under standard conditions. However, when plants were exposed to low temperature stress, recovery of Rpl33 knockout plants was severely compromised, indicating that Rpl33 is required for sustaining sufficient plastid translation capacity in the cold. These findings uncover an important role for plastid translation in plant tolerance to chilling stress. %Z 355IT Times Cited:0 Cited References Count:69 %U ://000259703300019 %+ Bock, R Max Planck Inst Mol Pflanzenphysiol, D-14476 Potsdam, Germany Max Planck Inst Mol Pflanzenphysiol, D-14476 Potsdam, Germany %G English %0 Journal Article %A Rogalski, M. %A Karcher, D. %A Bock, R. %D 2008 %T Superwobbling facilitates translation with reduced tRNA sets %J Nature structural and molecular biology %V 15 %N 2 %P 192-8 %8 Feb %! Superwobbling facilitates translation with reduced tRNA sets %O Nature Structural and Molecular Biology %@ 1545-9985 (Electronic) %1 Bock~Organelle Biology, Biotechnology and Molecular Ecophysiology~ %3 1 %M 18193063 %X Some bacterial and most organelle genomes do not encode the full set of 32 tRNA species required to read all codons according to Crick's wobble rules. 'Superwobble', in which a tRNA species with an unmodified U in the wobble position reads all four nucleotides in the third codon position, represents one possible mechanism for how a reduced tRNA set could still suffice. We have tested the superwobble hypothesis by producing knockout mutants for the pair of plastid glycine tRNA genes. Here we show that, whereas the tRNA gene with U in the wobble position is essential, the gene with G in this position is nonessential, demonstrating that the U-containing anticodon can indeed read all four glycine triplets. We also show that the price for superwobbling is a reduced translational efficiency, which explains why most organisms prefer pairs of isoaccepting tRNAs over the superwobbling mechanism. %Z Journal Article Research Support, Non-U.S. Gov't United States %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18193063 %+ Max-Planck-Institut fur Molekulare Pflanzenphysiologie, Am Muhlenberg 1, D-14476 Potsdam-Golm, Germany. %G eng %0 Journal Article %A Rinder, J. %A Casazza, A. P. %A Hoefgen, R. %A Hesse, H. %D 2008 %T Regulation of aspartate-derived amino acid homeostasis in potato plants (Solanum tuberosum L.) by expression of E-coli homoserine kinase %J Amino Acids %V 34 %N 2 %P 213-222 %8 Feb %! Regulation of aspartate-derived amino acid homeostasis in potato plants (Solanum tuberosum L.) by expression of E-coli homoserine kinase %@ 0939-4451 %1 Hoefgen~Amino Acid and Sulfur Metabolism~ %3 1 %M ISI:000253000900005 %K aspartate family homoserine kinase methionine threonine potato cystathionine gamma-synthase pisum-sativum-l threonine synthase methionine biosynthesis arabidopsis-thaliana s-adenosylmethionine tissue-cultures beta-lyase metabolism gene %X The availability of the carbon backbone O-phosphohomoserine (OPHS) is critical to methionine (met) and threonine (thr) synthesis. OPHS derives from homoserine and is formed by homoserine kinase (HSK). To clarify the function of HSK in cellular metabolism, the E. coli HSK ortholog thrB was expressed in potato plants targeting the EcHSK protein to chloroplasts and to the cytosol. Both approaches resulted in up to 11 times increased total HSK enzyme activity. Transgenic plants exhibited reduced homoserine levels while met and thr did not accumulate significantly. However, the precursor cysteine and upstream intermediates of met such as cystathionine and homocysteine did indicating an accelerated carbon flow towards the end products. Coincidently, plants with elevated cytosolic levels of EcHSK exhibited a reduction in transcript levels of the endogenous HSK, as well as of threonine synthase (TS), cystathionine beta-lyase (CbL), and met synthase (MS). In all plants, cystathionine gamma-synthase (CgS) expression remained relatively unchanged from wild type levels, while S-adenosylmethionine synthetase (SAMS) expression increased. Feeding studies with externally supplied homoserine fostered the synthesis of met and thr but the regulation of synthesis of both amino acids retained the wild type regulation pattern. The results indicate that excess of plastidial localised HSK activity does not influence the de novo synthesis of met and thr. However, expression of HSK in the cytosol resulted in the down-regulation of gene expression of pathway genes probably mediated via OPHS. We integrated these data in a novel working model describing the regulatory mechanism of met and thr homeostasis. %Z 260HH Times Cited:0 Cited References Count:41 %U ://000253000900005 %+ Hesse, H Max Planck Inst Mol Pflanzenphysiol, Dept Mol Physiol, Muhlenberg 1, D-14476 Golm, Germany Max Planck Inst Mol Pflanzenphysiol, Dept Mol Physiol, D-14476 Golm, Germany Univ Milan, Sect Plant Physiol & Biochem, Dept Biol, Milan, Italy %G English %0 Journal Article %A Riewe, D. %A Grosman, L. %A Zauber, H. %A Wucke, C. %A Fernie, A. R. %A Geigenberger, P. %D 2008 %T Metabolic and developmental adaptations of growing potato tubers in response to specific manipulations of the adenylate energy status %J Plant Physiology %V 146 %N 4 %P 1579-1598 %8 Apr %! Metabolic and developmental adaptations of growing potato tubers in response to specific manipulations of the adenylate energy status %@ 0032-0889 %1 Fernie~Central Metabolism~Geigenberger~Storage Carbohydrate Metabolism~ %3 1 %M ISI:000256417900011 %K adp-glucose pyrophosphorylase posttranslational redox-activation low internal oxygen starch synthesis solanum-tuberosum carbon metabolism sucrose synthase inorganic pyrophosphate ethanolic fermentation antisense inhibition %X Heterotrophic carbon metabolism has been demonstrated to be limited by oxygen availability in a variety of plant tissues, which in turn inevitably affects the adenylate status. To study the effect of altering adenylate energy metabolism, without changing the oxygen supply, we expressed a plastidially targeted ATP/ADP hydrolyzing phosphatase (apyrase) in tubers of growing potato (Solanum tuberosum) plants under the control of either inducible or constitutive promoters. Inducible apyrase expression in potato tubers, for a period of 24 h, resulted in a decrease in the ATP-content and the ATP-ADP ratio in the tubers. As revealed by metabolic profiling, this was accompanied by a decrease in the intermediates of sucrose to starch conversion and several plastidially synthesized amino acids, indicating a general depression of tuber metabolism. Constitutive tuber-specific apyrase expression did not lead to a reduction of ATP, but rather a decrease in ADP and an increase in AMP levels. Starch accumulation was strongly inhibited and shifted to the production of amylopectin instead of amylose in these tubers. Furthermore, the levels of almost all amino acids were decreased, although soluble sugars and hexose-Ps were highly abundant. Respiration was elevated in the constitutively expressing lines indicating a compensation for the dramatic increase in ATP hydrolysis. The increase in respiration did not affect the internal oxygen tensions in the tubers. However, the tubers developed a ginger-like phenotype having an elevated surface-volume ratio and a reduced mass per tuber. Decreased posttranslational redox activation of ADP-glucose pyrophosphorylase and a shift in the ratio of soluble starch synthase activity to granule-bound starch synthase activity were found to be partially responsible for the alterations in starch structure and abundance. The activity of alcohol dehydrogenase was decreased and pyruvate decarboxylase was induced, but this was neither reflected by an increase in fermentation products nor in the cellular redox state, indicating that fermentation was not yet induced in the transgenic lines. When taken together the combined results of these studies allow the identification of both short-and long-term adaptation of plant metabolism and development to direct changes in the adenylate status. %Z 308VJ Times Cited:2 Cited References Count:80 %U ://000256417900011 %+ Geigenberger, P Max Planck Inst Mol Plant Physiol, D-14476 Potsdam, Germany Max Planck Inst Mol Plant Physiol, D-14476 Potsdam, Germany %G English %0 Journal Article %A Riewe, D. %A Grosman, L. %A Fernie, A. R. %A Zauber, H. %A Wucke, C. %A Geigenberger, P. %D 2008 %T A Cell Wall-Bound Adenosine Nucleosidase is Involved in the Salvage of Extracellular ATP in Solanum tuberosum %J Plant and Cell Physiology %V 49 %N 10 %P 1572-1579 %8 Oct %! A Cell Wall-Bound Adenosine Nucleosidase is Involved in the Salvage of Extracellular ATP in Solanum tuberosum %@ 0032-0781 %1 Central Metabolism~Fernie~Geigenberger~Storage Carbohydrate Metabolism~ %3 1 %M ISI:000260154500016 %K adenosine nucleosidase apoplast apyrase cell wall extracellular atp solanum tuberosum acid-phosphatase potato-tubers arabidopsis metabolism expression family growth localization purification triphosphate %X Extracellular ATP (eATP) has recently been demonstrated to play a crucial role in plant development and growth. To investigate the fate of eATP within the apoplast, we used intact potato (Solanum tuberosum) tuber slices as an experimental system enabling access to the apoplast without interference of cytosolic contamination. (i) Incubation of intact tuber slices with ATP led to the formation of ADP, AMP, adenosine, adenine and ribose, indicating operation of apyrase, 5'-nucleotidase and nucleosidase. (ii) Measurement of apyrase, 5'-nucleotidase and nucleosidase activities in fractionated tuber tissue confirmed the apoplastic localization for apyrase and phosphatase in potato and led to the identification of a novel cell wall-bound adenosine nucleosidase activity. (iii) When intact tuber slices were incubated with saturating concentrations of adenosine, the conversion of adenosine into adenine was much higher than adenosine import into the cell, suggesting a potential bypass of adenosine import. Consistent with this, import of radiolabeled adenine into tuber slices was inhibited when ATP, ADP or AMP were added to the slices. (iv) In wild-type plants, apyrase and adenosine nucleosidase activities were found to be co-regulated, indicating functional linkage of these enzymes in a shared pathway. (v) Moreover, adenosine nucleosidase activity was reduced in transgenic lines with strongly reduced apoplastic apyrase activity. When taken together, these results suggest that a complete ATP salvage pathway is present in the apoplast of plant cells. %Z 361VE Times Cited:1 Cited References Count:29 %U ://000260154500016 %+ Geigenberger, P Max Planck Inst Mol Plant Physiol, Muhlenberg 1, D-14476 Potsdam, Germany Max Planck Inst Mol Plant Physiol, D-14476 Potsdam, Germany Leibniz Inst Vegetable & Ornamental Crops, D-14979 Grossbeeren, Germany %G English %0 Journal Article %A Riewe, D. %A Grosman, L. %A Fernie, A. R. %A Wucke, C. %A Geigenberger, P. %D 2008 %T The potato-specific apyrase is apoplastically localized and has influence on gene expression, growth, and development %J Plant Physiol %V 147 %N 3 %P 1092-109 %8 Jul %! The potato-specific apyrase is apoplastically localized and has influence on gene expression, growth, and development %O Plant physiology %@ 0032-0889 (Print) %1 Central Metabolism~Fernie~Geigenberger~Storage Carbohydrate Metabolism~ %3 1 %M 18480378 %K Apyrase/genetics/*metabolism Cloning, Molecular Consensus Sequence Gene Expression Gene Expression Profiling Gene Expression Regulation, Plant Green Fluorescent Proteins/metabolism Plant Epidermis/enzymology Plant Leaves/enzymology Plant Tubers/*enzymology/growth & development Plants, Genetically Modified/enzymology Promoter Regions (Genetics) RNA, Messenger/metabolism Solanum tuberosum/*enzymology/genetics/growth & development %X Apyrases hydrolyze nucleoside triphosphates and diphosphates and are found in all eukaryotes and a few prokaryotes. Although their enzymatic properties have been well characterized, relatively little is known regarding their subcellular localization and physiological function in plants. In this study, we used reverse genetic and biochemical approaches to investigate the role of potato (Solanum tuberosum)-specific apyrase. Silencing of the apyrase gene family with RNA interference constructs under the control of the constitutive 35S promoter led to a strong decrease in apyrase activity to below 10% of the wild-type level. This decreased activity led to phenotypic changes in the transgenic lines, including a general retardation in growth, an increase in tuber number per plant, and differences in tuber morphology. Silencing of apyrase under the control of a tuber-specific promoter led to similar changes in tuber morphology; however, there were no direct effects of apyrase inhibition on tuber metabolism. DNA microarrays revealed that decreased expression of apyrase leads to increased levels of transcripts coding for cell wall proteins involved in growth and genes involved in energy transfer and starch synthesis. To place these results in context, we determined the subcellular localization of the potato-specific apyrase. Using a combination of approaches, we were able to demonstrate that this enzyme is localized to the apoplast. We describe the evidence that underlies both this fact and that potato-specific apyrase has a crucial role in regulating growth and development. %Z Journal Article Research Support, Non-U.S. Gov't United States %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18480378 %+ Max-Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany. %G eng %0 Journal Article %A Riano-Pachon, D. M. %A Correa, L. G. %A Trejos-Espinosa, R. %A Mueller-Roeber, B. %D 2008 %T Green transcription factors: a chlamydomonas overview %J Genetics %V 179 %N 1 %P 31-9 %8 May %! Green transcription factors: a chlamydomonas overview %O Genetics %@ 0016-6731 (Print) %1 Bioinformatics~Mueller-Roeber~Plant Signaling~Walther~ %3 1 %M 18493038 %K Angiosperms/*genetics Animals Chlamydomonas reinhardtii/*genetics Computational Biology Genes, Protozoan/*genetics Genomics *Phylogeny Species Specificity Transcription Factors/*genetics %X Transcription factors (TFs) control gene expression by interacting with cis-elements in target gene promoters. Transcription regulators (TRs) assist in controlling gene expression through interaction with TFs, chromatin remodeling, or other mechanisms. Both types of proteins thus constitute master controllers of dynamic transcriptional networks. To uncover such control elements in the photosynthetic green alga Chlamydomonas reinhardtii, we performed a comprehensive analysis of its genome sequence. In total, we identified 234 genes encoding 147 TFs and 87 TRs of approximately 40 families. The set of putative TFs and TRs, including their transcript and protein sequences, domain architectures, and supporting information about putative orthologs, is available at http://plntfdb.bio.uni-potsdam.de/v2.0/. Twelve of 34 plant-specific TF families were found in at least one algal species, indicating their early evolutionary origin. Twenty-two plant-specific TF families and one plant-specific TR family were not observed in algae, suggesting their specific association with developmental or physiological processes characteristic to multicellular plants. We also analyzed the occurrence of proteins that constitute the light-regulated transcriptional network in angiosperms and found putative algal orthologs for most of them. Our analysis provides a solid ground for future experimental studies aiming at deciphering the transcriptional regulatory networks in green algae. %Z Comparative Study Journal Article United States %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18493038 %+ Department of Molecular Biology, University of Potsdam, 14476 Potsdam-Golm, Germany. %G eng %0 Journal Article %A Rautengarten, C. %A Usadel, B. %A Neumetzler, L. %A Hartmann, J. %A Buessis, D. %A Altmann, T. %D 2008 %T A subtilisin-like serine protease essential for mucilage release from Arabidopsis seed coats %J Plant Journal %V 54 %N 3 %P 466-480 %8 May %! A subtilisin-like serine protease essential for mucilage release from Arabidopsis seed coats %@ 0960-7412 %1 Usadel~Integrative Carbon Biology~Altmann~Developmental Physiology and Genomics~Plant Cell Walls - Persson~ %3 1 %M ISI:000255955300010 %K cell wall seed coat mucilage subtilase pectin methylesterase arabidopsis thaliana pectin methylesterase inhibitors glycoprotein inhibitor secretory pathway gene encodes kiwi fruit thaliana differentiation trichome DNA transparent-testa-glabra1 %X During Arabidopsis seed development large quantities of mucilage, composed of pectins, are deposited into the apoplast underneath the outer wall of the seed coat. Upon imbibition of mature seeds, the stored mucilage expands through hydration and breaks the outer cell wall that encapsulates the whole seed. Mutant seeds carrying loss-of-function alleles of AtSBT1.7 that encodes one of 56 Arabidopsis thaliana subtilisin-like serine proteases (subtilases) do not release mucilage upon hydration. Microscopic analysis of the mutant seed coat revealed no visible structural differences compared with wild-type seeds. Weakening of the outer primary wall using cation chelators; triggered mucilage release from the seed coats of mutants. However, in contrast to mature wild-type seeds, the mutant's outer cell walls did not rupture at the radial walls of the seed coat epidermal cells, but instead opened at the chalazal end of the seed, and were released in one piece. In atsbt1.7, the total rhamnose and galacturonic acid contents, representing the backbone of mucilage, remained unchanged compared with wild-type seeds. Thus, extrusion and solubility, but not the initial deposition of mucilage, are affected in atsbt1.7 mutants. AtSBT1.7 is localized in the developing seed coat, indicating a role in testa development or maturation. The altered mode of rupture of the outer seed coat wall and mucilage release indicate that AtSBT1.7 triggers the accumulation, and/or activation, of cell wall modifying enzymes necessary either for the loosening of the outer primary cell wall, or to facilitate swelling of the mucilage, as indicated by elevated pectin methylesterase activity in developing atsbt1.7 mutant seeds. %Z 302FX Times Cited:0 Cited References Count:63 %U ://000255955300010 %+ Rautengarten, C Univ Potsdam, Inst Biochem & Biol, D-14476 Golm, Germany Univ Potsdam, Inst Biochem & Biol, D-14476 Golm, Germany Max Planck Inst Mol Physiol, D-14476 Golm, Germany Max Planck Inst Colloids & Interfaces, D-14476 Golm, Germany %G English %0 Journal Article %A Paredez, A. R. %A Persson, S. %A Ehrhardt, D. W. %A Somerville, C. R. %D 2008 %T Genetic evidence that cellulose synthase activity influences microtubule cortical array organization %J Plant Physiology %V 147 %N 4 %P 1723-1734 %8 Aug %! Genetic evidence that cellulose synthase activity influences microtubule cortical array organization %@ 0032-0889 %1 Persson~Plant Cell Walls - Persson~ %3 1 %M ISI:000258184800025 %K cell elongation arabidopsis-thaliana plasma-membrane phospholipase-d microfibril alignment plant-cells in-vivo tubulin growth mutants %X To identify factors that influence cytoskeletal organization we screened for Arabidopsis ( Arabidopsis thaliana) mutants that show hypersensitivity to the microtubule destabilizing drug oryzalin. We cloned the genes corresponding to two of the 131 mutant lines obtained. The genes encoded mutant alleles of PROCUSTE1 and KORRIGAN, which both encode proteins that have previously been implicated in cellulose synthesis. Analysis of microtubules in the mutants revealed that both mutants have altered orientation of root cortical microtubules. Similarly, isoxaben, an inhibitor of cellulose synthesis, also altered the orientation of cortical microtubules while exogenous cellulose degradation did not. Thus, our results substantiate that proteins involved in cell wall biosynthesis influence cytoskeletal organization and indicate that this influence on cortical microtubule stability and orientation is correlated with cellulose synthesis rather than the integrity of the cell wall. %Z 333WR Times Cited:4 Cited References Count:60 %U ://000258184800025 %+ Somerville, CR Carnegie Inst Washington, Dept Plant Biol, 290 Panama St, Stanford, CA 94305 USA Carnegie Inst Washington, Dept Plant Biol, Stanford, CA 94305 USA Univ Calif Berkeley, Dept Mol & Cell Biol, Berkeley, CA 94720 USA Stanford Univ, Dept Biol Sci, Stanford, CA 94305 USA Max Planck Inst Mol Pflanzenphysiol, D-14476 Glom, Germany %G English %0 Journal Article %A Pant, B. D. %A Buhtz, A. %A Kehr, J. %A Scheible, W. R. %D 2008 %T MicroRNA399 is a long-distance signal for the regulation of plant phosphate homeostasis %J Plant Journal %V 53 %N 5 %P 731-738 %8 Mar %! MicroRNA399 is a long-distance signal for the regulation of plant phosphate homeostasis %@ 0960-7412 %1 Kehr~Micro- and Protein-Analysis~Scheible~Molecular Genomics~ %3 1 %M ISI:000253484600003 %K microrna phosphate homeostasis long-distance signaling nutrient arabidopsis brassica arabidopsis-thaliana inorganic-phosphate messenger-rna root-system rt-pcr phloem gene availability transport architecture %X The presence of microRNA species in plant phloem sap suggests potential signaling roles by long-distance regulation of gene expression. Proof for such a role for a phloem-mobile microRNA is lacking. Here we show that phosphate (Pi) starvation-induced microRNA399 (miR399) is present in the phloem sap of two diverse plant species, rapeseed and pumpkin, and levels are strongly and specifically increased in phloem sap during Pi deprivation. By performing micro-grafting experiments using Arabidopsis, we further show that chimeric plants constitutively over-expressing miR399 in the shoot accumulate mature miR399 species to very high levels in their wild-type roots, while corresponding primary transcripts are virtually absent in roots, demonstrating shoot-to-root transport. The chimeric plants exhibit (i) down-regulation of the miR399 target transcript (PHO2), which encodes a critical component for maintenance of Pi homeostasis, in the wild-type root, and (ii) Pi accumulation in the shoot, which is the phenotype of pho2 mutants, miR399 over-expressers or chimeric plants with a genetic knock-out of PHO2 in the root. Hence the transported miR399 molecules retain biological activity. This is a demonstration of systemic control of a biological process, i.e. maintenance of plant Pi homeostasis, by a phloem-mobile microRNA. %Z 267BY Times Cited:8 Cited References Count:49 %U ://000253484600003 %+ Scheible, WR Max Planck Inst Mol Plant Physiol, Sci Pk Golm,Muhlenberg 1, D-14476 Potsdam, Germany Max Planck Inst Mol Plant Physiol, D-14476 Potsdam, Germany %G English %0 Journal Article %A Palmieri, L. %A Santoro, A. %A Carrari, F. %A Blanco, E. %A Nunes-Nesi, A. %A Arrigoni, R. %A Genchi, F. %A Fernie, A. R. %A Palmieri, F. %D 2008 %T Identification and Characterization of ADNT1, a Novel Mitochondrial Adenine Nucleotide Transporter from Arabidopsis %J Plant Physiology %V 148 %N 4 %P 1797-1808 %8 Dec %! Identification and Characterization of ADNT1, a Novel Mitochondrial Adenine Nucleotide Transporter from Arabidopsis %@ 0032-0889 %1 Fernie~Central Metabolism~ %3 1 %M ISI:000261501500007 %K functional-characterization bacterial expression saccharomyces-cerevisiae plant-mitochondria tissue distribution electron-transport uncoupling protein molecular-identification thiamine pyrophosphate bovine mitochondria %X Despite the fundamental importance and high level of compartmentation of mitochondrial nucleotide metabolism in plants, our knowledge concerning the transport of nucleotides across intracellular membranes remains far from complete. Study of a previously uncharacterized Arabidopsis (Arabidopsis thaliana) gene (At4g01100) revealed it to be a novel adenine nucleotide transporter, designated ADNT1, belonging to the mitochondrial carrier family. The ADNT1 gene shows broad expression at the organ level. Green fluorescent protein-based cell biological analysis demonstrated targeting of ADNT1 to mitochondria. While analysis of the expression of b-glucuronidase fusion proteins suggested that it was expressed across a broad range of tissue types, it was most highly expressed in root tips. Direct transport assays with recombinant and reconstituted ADNT1 were utilized to demonstrate that this protein displays a relatively narrow substrate specificity largely confined to adenylates and their closest analogs. ATP uptake was markedly inhibited by the presence of other adenylates and general inhibitors of mitochondrial transport but not by bongkrekate or carboxyatractyloside, inhibitors of the previously characterized ADP/ATP carrier. Furthermore, the kinetics are substantially different from those of this carrier, with ADNT1 preferring AMP to ADP. Finally, isolation and characterization of a T-DNA insertional knockout mutant of ADNT1, alongside complementation and antisense approaches, demonstrated that although deficiency of this transporter did not seem to greatly alter photosynthetic metabolism, it did result in reduced root growth and respiration. These findings are discussed in the context of a potential function for ADNT1 in the provision of the energy required to support growth in heterotrophic plant tissues. %Z 380YH Times Cited:0 Cited References Count:66 %U ://000261501500007 %+ Fernie, AR Max Planck Inst Mol Pflanzenphysiol, Dept Willmitzer, D-14476 Potsdam, Germany Max Planck Inst Mol Pflanzenphysiol, Dept Willmitzer, D-14476 Potsdam, Germany Univ Bari, Dept Pharmacobiol, Biochem & Mol Biol Lab, I-70125 Bari, Italy Consiglio Nazl Ric Inst Biomembranes & Bioenerget, I-70125 Bari, Italy %G English %0 Journal Article %A Oliver, S. N. %A Tiessen, A. %A Fernie, A. R. %A Geigenberger, P. %D 2008 %T Decreased expression of plastidial adenylate kinase in potato tubers results in an enhanced rate of respiration and a stimulation of starch synthesis that is attributable to post-translational redox-activation of ADP-glucose pyrophosphorylase %J Journal of experimental botany %V 59 %N 2 %P 315-25 %! Decreased expression of plastidial adenylate kinase in potato tubers results in an enhanced rate of respiration and a stimulation of starch synthesis that is attributable to post-translational redox-activation of ADP-glucose pyrophosphorylase %O J Exp Bot %@ 1460-2431 (Electronic) %1 Geigenberger~Storage Carbohydrate Metabolism~Fernie~Central Metabolism~ %3 1 %M 18252705 %X Adenine nucleotides are of general importance for many aspects of cell function, but their role in the regulation of biosynthetic processes is still unclear. It was previously reported that decreased expression of plastidial adenylate kinase, catalysing the interconversion of ATP and AMP to ADP, leads to increased adenylate pools and starch content in transgenic potato tubers. However, the underlying mechanisms were not elucidated. Here, it is shown that decreased expression of plastidial adenylate kinase in growing tubers leads to increased rates of respiratory oxygen consumption and increased carbon fluxes into starch. Increased rates of starch synthesis were accompanied by post-translational redox-activation of ADP-glucose pyrophosphorylase (AGPase), catalysing the key regulatory step of starch synthesis in the plastid, while there were no substantial changes in metabolic intermediates or sugar levels. A similar increase in post-translational redox-activation of AGPase was found after supplying adenine to wild-type potato tuber discs to increase adenine nucleotide levels. Results provide first evidence for a link between redox-activation of AGPase and adenine nucleotide levels in plants. %Z Journal Article Research Support, Non-U.S. Gov't England %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18252705 %+ Max-Planck-Institute of Molecular Plant Physiology, Am Muehlenberg 1, D-14476 Potsdam-Golm, Germany. %G eng %0 Journal Article %A Oliver, S. N. %A Lunn, J. E. %A Urbanczyk-Wochniak, E. %A Lytovchenko, A. %A van Dongen, J. T. %A Faix, B. %A Schmalzlin, E. %A Fernie, A. R. %A Geigenberger, P. %D 2008 %T Decreased Expression of Cytosolic Pyruvate Kinase in Potato Tubers Leads to a Decline in Pyruvate Resulting in an in Vivo Repression of the Alternative Oxidase %J Plant Physiology %V 148 %N 3 %P 1640-1654 %8 Nov %! Decreased Expression of Cytosolic Pyruvate Kinase in Potato Tubers Leads to a Decline in Pyruvate Resulting in an in Vivo Repression of the Alternative Oxidase %@ 0032-0889 %1 Central Metabolism~Fernie~Energy Metabolism~Geigenberger~Storage Carbohydrate Metabolism~van Dongen~ %3 1 %M ISI:000260719500037 %K higher-plant mitochondria transgenic tobacco plants low internal oxygen nad malic enzyme sucrose synthase phosphoenolpyruvate carboxylase nitrogen assimilation regulatory properties arabidopsis-thaliana malate-dehydrogenase %X The aim of this work was to investigate the effect of decreased cytosolic pyruvate kinase (PKc) on potato (Solanum tuberosum) tuber metabolism. Transgenic potato plants with strongly reduced levels of PKc were generated by RNA interference gene silencing under the control of a tuber-specific promoter. Metabolite profiling showed that decreased PKc activity led to a decrease in the levels of pyruvate and some other organic acids involved in the tricarboxylic acid cycle. Flux analysis showed that this was accompanied by changes in carbon partitioning, with carbon flux being diverted from glycolysis toward starch synthesis. However, this metabolic shift was relatively small and hence did not result in enhanced starch levels in the tubers. Although total respiration rates and the ATP to ADP ratio were largely unchanged, transgenic tubers showed a strong decrease in the levels of alternative oxidase (AOX) protein and a corresponding decrease in the capacity of the alternative pathway of respiration. External feeding of pyruvate to tuber tissue or isolated mitochondria resulted in activation of the AOX pathway, both in the wild type and the PKc transgenic lines, providing direct evidence for the regulation of AOX by changes in pyruvate levels. Overall, these results provide evidence for a crucial role of PKc in the regulation of pyruvate levels as well as the level of the AOX in heterotrophic plant tissue, and furthermore reveal that these parameters are interlinked in vivo. %Z 369UN Times Cited:0 Cited References Count:87 %U ://000260719500037 %+ Geigenberger, P Max Planck Inst Mol Plant Physiol, D-14476 Potsdam Golm, Germany Max Planck Inst Mol Plant Physiol, D-14476 Potsdam Golm, Germany Leibniz Inst Vegetable & Ornamental Crops, D-14979 Grossbeeren, Germany Univ Potsdam, Inst Chem, D-14476 Potsdam Golm, Germany Interdisciplinary Ctr Photon, D-14476 Potsdam Golm, Germany %G English %0 Journal Article %A Nunes-Nesi, A. %A Sulpice, R. %A Gibon, Y. %A Fernie, A. R. %D 2008 %T The enigmatic contribution of mitochondrial function in photosynthesis %J Journal of Experimental Botany %V 59 %N 7 %P 1675-1684 %8 May %! The enigmatic contribution of mitochondrial function in photosynthesis %@ 0022-0957 %1 Fernie~Central Metabolism~System Regulation~ %3 1 %M ISI:000256274800020 %K ascorbate biosynthesis mitochondrial function photorespiration photosynthesis gamma-lactone dehydrogenase ascorbate-glutathione cycle l-galactose phosphorylase electron-transport chain last unknown enzyme arabidopsis-thaliana uncoupling-protein serine hydroxymethyltransferase respiratory metabolism glycine decarboxylase %X Considerable cumulative evidence has accrued suggesting a vital role for mitochondrial function in optimizing photosynthesis. Both pharmacological approaches using respiratory inhibitors and reverse genetic approaches have recently underscored the high degree of interconnection between photosynthesis and respiration-the major pathways of energy production which are largely confined to the plastid and mitochondria, respectively. Here recent studies into the nature of these interactions are reviewed, with particular focus on (i) the recently described link between the mitochondrial electron transport chain activity, ascorbate biosynthesis, and photosynthesis; and (ii) the contribution of mitochondrial metabolism to the photorespiratory process. Whilst there is increasing evidence of a role for ascorbate in co-ordinating the rates of respiration and photosynthesis, some data are presented here for plants grown under extreme environmental conditions that suggest that this relationship is not absolute. It thus seems likely that interactions between these compartments are perhaps more numerous and complicated than previously thought. This observation suggests that although the elucidation of the genetic bases of both photorespiration and the Wheeler-Smirnoff pathway of ascorbate biosynthesis has recently been completed, much further research is probably necessary in order to understand fully how energy metabolism is co-ordinated in the illuminated leaf. %Z 306VB Times Cited:1 Cited References Count:76 %U ://000256274800020 %+ Nunes-Nesi, A Max Planck Inst Mol Pflanzenphysiol, Muhlenberg 1, D-14476 Potsdam, Germany Max Planck Inst Mol Pflanzenphysiol, D-14476 Potsdam, Germany %G English %0 Journal Article %A Nikoloski, Z. %A Grimbs, S. %A Selbig, J. %A Ebenhoeh, O. %D 2008 %T Hardness and Approximability of the Inverse Scope Problem %J Algorithms in Bioinformatics, Wabi 2008 %V 5251 %P 99-112 %! Hardness and Approximability of the Inverse Scope Problem %@ 0302-9743 %1 Ebenhoeh~Systems Biology and Mathematical Modeling~Selbig~Bioinformatics crg~ %3 1 %M ISI:000260069100009 %K scope metabolic networks completeness metabolic networks %X For a given metabolic network, we address the problem of determining the minimum cardinality set of substrate compounds necessary for synthesizing a set of target metabolites, called the inverse scope problem. We define three variants of the inverse scope problem whose solutions may indicate minimal nutritional requirements that must be met to ensure sustenance of an organism, with or without some side products. Here, we show that the inverse scope problems are NP-hard oil general graphs and directed acyclic graphs (DAGs). Moreover, we show that the general inverse scope problem cannot be approximated within n(1/2-epsilon) for any constant epsilon > 0 unless P = NP. Our results have direct implications for identifying the biosynthetic capabilities of a given organism and for designing biochemical experiments. %Z Bij46 Times Cited:0 Cited References Count:21 Lecture Notes in Bioinformatics %U ://000260069100009 %+ Nikoloski, Z Univ Potsdam, Inst Biochem & Biol, Potsdam, Brandenburg, Germany Univ Potsdam, Inst Biochem & Biol, Potsdam, Brandenburg, Germany %G English %0 Journal Article %A Nikoloski, Z. %A Grimbs, S. %A May, P. %A Selbig, J. %D 2008 %T Metabolic networks are NP-hard to reconstruct %J Journal of Theoretical Biology %V 254 %N 4 %P 807-816 %8 Oct 21 %! Metabolic networks are NP-hard to reconstruct %@ 0022-5193 %1 Selbig~Bioinformatics crg~ %3 1 %M ISI:000260023600012 %K reconstruction metabolic networks completeness approximation chlamydomonas-reinhardtii genome annotation pathways enzymes databases model %X High-throughput data from various omics and sequencing techniques have rendered the automated metabolic network reconstruction a highly relevant problem. Our approach reflects the inherent probabilistic nature of the steps involved in metabolic network reconstruction. Here, the goal is to arrive at networks which combine probabilistic information with the possibility to obtain a small number of disconnected network constituents by reduction of a given preliminary probabilistic metabolic network. We define automated metabolic network reconstruction as an optimization problem on four-partite graph (nodes representing genes, enzymes, reactions, and metabolites) which integrates: (1) probabilistic information obtained from the existing process for metabolic reconstruction from a given genome, (2) connectedness of the raw metabolic network, and (3) clustering of components in the reconstructed metabolic network. The practical implications of our theoretical analysis refer to the quality of reconstructed metabolic networks and shed light on the problem of finding more efficient and effective methods for automated reconstruction. Our main contributions include: a completeness result for the defined problem, polynomial-time approximation algorithm, and an optimal polynomial-time algorithm for trees. Moreover, we exemplify our approach by the reconstruction of the sucrose biosynthesis pathway in Chlamydomonas reinhardtii. (C) 2008 Elsevier Ltd. All rights reserved. %Z 359YG Times Cited:0 Cited References Count:30 %U ://000260023600012 %+ Nikoloski, Z Univ Potsdam, Inst Biochem & Biol, Karl Liebknecht Str 24-25,Haus 20, D-14476 Potsdam, Germany Univ Potsdam, Inst Biochem & Biol, D-14476 Potsdam, Germany Max Planck Inst Mol Plant Physiol, D-14476 Potsdam, Germany %G English %0 Journal Article %A Neupert, J. %A Karcher, D. %A Bock, R. %D 2008 %T Design of simple synthetic RNA thermometers for temperature-controlled gene expression in Escherichia coli %J Nucleic Acids Research %V 36 %N 19 %P - %8 Nov %! Design of simple synthetic RNA thermometers for temperature-controlled gene expression in Escherichia coli %@ 0305-1048 %1 Bock~Organelle Biology, Biotechnology and Molecular Ecophysiology~ %3 1 %M ISI:000260983000003 %K thermosensor controls expression translation transformation riboswitches %X RNA thermometers are thermosensors that regulate gene expression by temperature-induced changes in RNA conformation. Naturally occurring RNA thermometers exhibit complex secondary structures which are believed to undergo a series of gradual structural changes in response to temperature shifts. Here, we report the de novo design of considerably simpler RNA thermometers that provide useful RNA-only tools to regulate bacterial gene expression by a shift in the growth temperature. We show that a single small stem-loop structure containing the ribosome binding site is sufficient to construct synthetic RNA thermometers that work efficiently at physiological temperatures. Our data suggest that the thermometers function by a simple melting mechanism and thus provide minimum size on/off switches to experimentally induce or repress gene expression by temperature. %Z 373PA Times Cited:0 Cited References Count:19 %U ://000260983000003 %+ Bock, R Max Planck Inst Mol Pflanzenphysiol, Muhlenberg 1, D-14476 Potsdam, Germany Max Planck Inst Mol Pflanzenphysiol, D-14476 Potsdam, Germany %G English %0 Journal Article %A Neigenfind, J. %A Gyetvai, G. %A Basekow, R. %A Diehl, S. %A Achenbach, U. %A Gebhardt, C. %A Selbig, J. %A Kersten, B. %D 2008 %T Haplotype inference from unphased SNP data in heterozygous polyploids based on SAT %J BMC Genomics %V 9 %N 1 %P 356 %8 Jul 30 %! Haplotype inference from unphased SNP data in heterozygous polyploids based on SAT %O BMC genomics %@ 1471-2164 (Electronic) %1 Bioinformatics crg~ Selbig~ %3 1 %M 18667059 %X ABSTRACT: BACKGROUND: Haplotype inference based on unphased SNP markers is an important task in population genetics. Although there are different approaches to the inference of haplotypes in diploid species, the existing software is not suitable for inferring haplotypes from unphased SNP data in polyploid species, such as the cultivated potato (Solanum tuberosum). Potato species are tetraploid and highly heterozygous. RESULTS: Here we present the software SATlotyper which is able to handle polyploid and polyallelic data. SATlotyper uses the Boolean satisfiability problem to formulate Haplotype Inference by Pure Parsimony. The software excludes existing haplotype inferences, thus allowing for calculation of alternative inferences. As it is not known which of the multiple haplotype inferences are best supported by the given unphased data set, we use a bootstrapping procedure that allows for scoring of alternative inferences. Finally, by means of the bootstrapping scores, it is possible to optimise the phased genotypes belonging to a given haplotype inference. The program is evaluated with simulated and experimental SNP data generated for heterozygous tetraploid populations of potato. We show that, instead of taking the first haplotype inference reported by the program, we can significantly improve the quality of the final result by applying additional methods that include scoring of the alternative haplotype inferences and genotype optimisation. For a sub-population of nineteen individuals, the predicted results computed by SATlotyper were directly compared with results obtained by experimental haplotype inference via sequencing of cloned amplicons. Prediction and experiment gave similar results regarding the inferred haplotypes and phased genotypes. CONCLUSIONS: Our results suggest that Haplotype Inference by Pure Parsimony can be solved efficiently by the SAT approach, even for data sets of unphased SNP from heterozygous polyploids. SATlotyper is freeware and is distributed as a Java JAR file. The software can be downloaded from the webpage of the GABI Primary Database at http://www.gabipd.org/projects/satlotyper/. The application of SATlotyper will provide haplotype information, which can be used in haplotype association mapping studies of polyploid plants. %Z Journal article %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18667059 %G Eng %0 Journal Article %A Mutwil, M. %A Obro, J. %A Willats, W. G. %A Persson, S. %D 2008 %T GeneCAT--novel webtools that combine BLAST and co-expression analyses %J Nucleic Acids Res %V 36 %N Web Server issue %P W320-6 %8 Jul 1 %! GeneCAT--novel webtools that combine BLAST and co-expression analyses %O Nucleic acids research %@ 1362-4962 (Electronic) %1 Plant Cell Walls - Persson~Persson~ %3 1 %M 18480120 %X The gene co-expression analysis toolbox (GeneCAT) introduces several novel microarray data analyzing tools. First, the multigene co-expression analysis, combined with co-expressed gene networks, provides a more powerful data mining technique than standard, single-gene co-expression analysis. Second, the high-throughput Map-O-Matic tool matches co-expression pattern of multiple query genes to genes present in user-defined subdatabases, and can therefore be used for gene mapping in forward genetic screens. Third, Rosetta combines co-expression analysis with BLAST and can be used to find 'true' gene orthologs in the plant model organisms Arabidopsis thaliana and Hordeum vulgare (Barley). GeneCAT is equipped with expression data for the model plant A. thaliana, and first to introduce co-expression mining tools for the monocot Barley. GeneCAT is available at http://genecat.mpg.de. %Z Journal Article Research Support, Non-U.S. Gov't England %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18480120 %+ Department of Molecular Biology, University of Copenhagen, Ole Maaloes vej 5, 2200 Copenhagen N, Denmark. %G eng %0 Journal Article %A Mutwil, M. %A Debolt, S. %A Persson, S. %D 2008 %T Cellulose synthesis: a complex complex %J Curr Opin Plant Biol %V 11 %N 3 %P 252-7 %8 Jun %! Cellulose synthesis: a complex complex %O Current opinion in plant biology %@ 1369-5266 (Print) %1 Plant Cell Walls - Persson~Persson~ %3 1 %M 18485800 %X Cellulose is the world's most abundant biopolymer and a key structural component of the plant cell wall. Cellulose is comprised of hydrogen-bonded beta-1,4-linked glucan chains that are synthesized at the plasma membrane by large cellulose synthase (CESA) complexes. Recent advances in visualization of fluorescently labelled complexes have facilitated exploration of regulatory modes of cellulose production. For example, several herbicides, such as isoxaben and 2,6-dichlorobenzonitrile that inhibit cellulose production appear to affect different aspects of synthesis. Dual-labelling of cytoskeletal components and CESAs has revealed dynamic feedback regulation between cellulose synthesis and microtubule orientation and organization. In addition, fluorescently tagged CESA2 subunits may substitute for another subunit, CESA6, which suggests both plasticity and specificity for one of the components of the CESA complex. %Z Journal Article Research Support, Non-U.S. Gov't England %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18485800 %+ Max-Planck-Institute for Molecular Plant Physiology, Am Muehlenberg 2, Potsdam, Germany. %G eng %0 Journal Article %A Musialak, M. %A Morcuende, R. %A Scheible, W. %D 2008 %T Investigating novel potential regulators and signalling components in phosphate stress responses of Arabidopsis thaliana %J Comparative Biochemistry and Physiology a-Molecular & Integrative Physiology %V 150 %N 3 %P S193-S193 %8 Jul %! Investigating novel potential regulators and signalling components in phosphate stress responses of Arabidopsis thaliana %@ 1095-6433 %1 Scheible~Molecular Genomics~ %3 1 %$ abstract %M ISI:000257631500495 %Z Suppl. S 326AY Times Cited:0 Cited References Count:3 %U ://000257631500495 %+ Max Planck Inst Mol Plant Physiol, Golm, Germany Inst Nat Resources & Agr Biol Salamanca, Salamanca, Spain %G English %0 Journal Article %A Morgan, M. J. %A Lehmann, M. %A Schwarzlander, M. %A Baxter, C. J. %A Sienkiewicz-Porzucek, A. %A Williams, T. C. R. %A Schauer, N. %A Fernie, A. R. %A Fricker, M. D. %A Ratcliffe, R. G. %A Sweetlove, L. J. %A Finkemeier, I. %D 2008 %T Decrease in manganese superoxide dismutase leads to reduced root growth and affects tricarboxylic acid cycle flux and mitochondrial redox homeostasis %J Plant Physiology %V 147 %N 1 %P 101-114 %8 May %! Decrease in manganese superoxide dismutase leads to reduced root growth and affects tricarboxylic acid cycle flux and mitochondrial redox homeostasis %@ 0032-0889 %1 Fernie~Central Metabolism~ %3 1 %M ISI:000256419400011 %K oxidative stress reactive oxygen plant-mitochondria ascorbate peroxidase arabidopsis-thaliana isocitrate dehydrogenases spinach-chloroplasts transgenic plants yeast mutants active oxygen %X Superoxide dismutases (SODs) are key components of the plant antioxidant defense system. While plastidic and cytosolic isoforms have been extensively studied, the importance of mitochondrial SOD at a cellular and whole-plant level has not been established. To address this, transgenic Arabidopsis (Arabidopsis thaliana) plants were generated in which expression of AtMSD1, encoding the mitochondrial manganese (Mn) SOD, was suppressed by antisense. The strongest antisense line showed retarded root growth even under control growth conditions. There was evidence for a specific disturbance of mitochondrial redox homeostasis in seedlings grown in liquid culture: a mitochondrially targeted redox-sensitive green fluorescent protein was significantly more oxidized in the MnSOD-antisense background. In contrast, there was no substantial change in oxidation of cytosolically targeted redox-sensitive green fluorescent protein, nor changes in antioxidant defense components. The consequences of altered mitochondrial redox status of seedlings were subtle with no widespread increase of mitochondrial protein carbonyls or inhibition of mitochondrial respiratory complexes. However, there were specific inhibitions of tricarboxylic acid (TCA) cycle enzymes (aconitase and isocitrate dehydrogenase) and an inhibition of TCA cycle flux in isolated mitochondria. Nevertheless, total respiratory CO2 output of seedlings was not decreased, suggesting that the inhibited TCA cycle enzymes can be bypassed. In older, soil-grown plants, redox perturbation was more pronounced with changes in the amount and/or redox poise of ascorbate and glutathione. Overall, the results demonstrate that reduced MnSOD affects mitochondrial redox balance and plant growth. The data also highlight the flexibility of plant metabolism with TCA cycle inhibition having little effect on overall respiratory rates. %Z 308VV Times Cited:3 Cited References Count:70 %U ://000256419400011 %+ Sweetlove, LJ Univ Oxford, Dept Plant Sci, S Parks Rd, Oxford OX1 3RB, England Univ Oxford, Dept Plant Sci, Oxford OX1 3RB, England Max Planck Inst Mol Plant Physiol, D-14476 Potsdam, Germany %G English %0 Journal Article %A Mendoza-Cozatl, D. G. %A Butko, E. %A Springer, F. %A Torpey, J. W. %A Komives, E. A. %A Kehr, J. %A Schroeder, J. I. %D 2008 %T Identification of high levels of phytochelatins, glutathione and cadmium in the phloem sap of Brassica napus. A role for thiol-peptides in the long-distance transport of cadmium and the effect of cadmium on iron translocation %J Plant Journal %V 54 %N 2 %P 249-259 %8 Apr %! Identification of high levels of phytochelatins, glutathione and cadmium in the phloem sap of Brassica napus. A role for thiol-peptides in the long-distance transport of cadmium and the effect of cadmium on iron translocation %@ 0960-7412 %1 Kehr~Micro- and Protein-Analysis~ %3 1 %M ISI:000254792700006 %K cadmium translocation iron content in xylem long-distance transport heavy metals thiol-peptides mass spectrometry toxic metals arabidopsis synthase plants tolerance yeast roots acid mechanisms synthetase %X Phytochelatins (PCs) are glutathione-derived peptides that function in heavy metal detoxification in plants and certain fungi. Recent research in Arabidopsis has shown that PCs undergo long-distance transport between roots and shoots. However, it remains unknown which tissues or vascular systems, xylem or phloem, mediate PC translocation and whether PC transport contributes to physiologically relevant long-distance transport of cadmium (Cd) between shoots and roots. To address these questions, xylem and phloem sap were obtained from Brassica napus to quantitatively analyze which thiol species are present in response to Cd exposure. High levels of PCs were identified in the phloem sap within 24 h of Cd exposure using combined mass spectrometry and fluorescence HPLC analyses. Unexpectedly, the concentration of Cd was more than four-fold higher in phloem sap compared to xylem sap. Cadmium exposure dramatically decreased iron levels in xylem and phloem sap whereas other essential heavy metals such as zinc and manganese remained unchanged. Data suggest that Cd inhibits vascular loading of iron but not nicotianamine. The high ratios [PCs]/[Cd] and [glutathione]/[Cd] in the phloem sap suggest that PCs and glutathione (GSH) can function as long-distance carriers of Cd. In contrast, only traces of PCs were detected in xylem sap. Our results suggest that, in addition to directional xylem Cd transport, the phloem is a major vascular system for long-distance source to sink transport of Cd as PC-Cd and glutathione-Cd complexes. %Z 285RA Times Cited:3 Cited References Count:44 %U ://000254792700006 %+ Schroeder, JI Univ Calif San Diego, Div Biol Sci, Cell & Dev Biol Sect, La Jolla, CA 92093 USA Univ Calif San Diego, Div Biol Sci, Cell & Dev Biol Sect, La Jolla, CA 92093 USA Univ Calif San Diego, Ctr Genet Mol, La Jolla, CA 92093 USA Max Planck Inst Mol Plant Physiol, D-14476 Potsdam Ot Golm, Germany Univ Calif San Diego, Dept Chem & Biochem, La Jolla, CA 92093 USA %G English %0 Journal Article %A Melotto-Passarin, D. M. %A Berger, I. J. %A Dressano, K. %A De Martin, V. D. %A Oliveira, G. C. X. %A Bock, R. %A Carrer, H. %D 2008 %T Phylogenetic relationships in Solanaceae and related species based on cpDNA sequence from plastid trnE-trnT region %J Crop Breeding and Applied Biotechnology %V 8 %N 1 %P 85-95 %8 Mar %! Phylogenetic relationships in Solanaceae and related species based on cpDNA sequence from plastid trnE-trnT region %@ 1518-7853 %1 Bock~Organelle Biology, Biotechnology and Molecular Ecophysiology~ %3 1 %M ISI:000258198000012 %K intergenic spacer multiple alignment of DNA nucleotide polymorphism taxonomic levels maximum parsimony chloroplast DNA molecular evolution plant systematics genome ndhf convolvulaceae classification nuclear %X Intergenic spacers of chloroplast DNA (cpDNA) are very useful in phylogenetic and population genetic studies of plant species, to study their potential integration in phylogenetic analysis. The non-coding trnE-trnT intergenic spacer of cpDNA was analyzed to assess the nucleotide sequence polymorphism of 16 Solanaceae species and to estimate its ability to contribute to the resolution of phylogenetic studies of this group. Multiple alignments of DNA sequences of trnE-trnT intergenic spacer made the identification of nucleotide variability in this region possible and the phylogeny was estimated by maximum parsimony and rooted with Convolvulaceae Ipomoea batalas, the most closely related family. Besides, this intergenic spacer was tested for the phylogenetic ability to differentiate taxonomic levels. For this purpose, species from four other families were analyzed and compared with Solanaceae species. Results confirmed polymorphism in the trnE-trnT region at different taxonomic levels. %Z 334BT Times Cited:0 Cited References Count:39 %U ://000258198000012 %+ Melotto-Passarin, DM Univ Sao Paulo, ESALQ, Dept Ciencias Biol, Lab Biotecnol Agricola, Ave Padua Dias 11, BR-13418900 Piracicaba, SP, Brazil Univ Sao Paulo, ESALQ, Dept Ciencias Biol, Lab Biotecnol Agricola, BR-13418900 Piracicaba, SP, Brazil Companhia Cigarros Souza Cruz, Rio Negro, PR, Brazil USP, ESALQ, Dept Genet, BR-13418900 Piracicaba, SP, Brazil Max Planck Inst Mol Plant Physiol, D-14476 Potsdam, Golm, Germany %G English %0 Journal Article %A McKhann, H. I. %A Gery, C. %A Berard, A. %A Leveque, S. %A Zuther, E. %A Hincha, D. K. %A De Mita, S. %A Brunel, D. %A Teoule, E. %D 2008 %T Natural variation in CBF gene sequence, gene expression and freezing tolerance in the Versailles core collection of Arabidopsis thaliana %J Bmc Plant Biology %V 8 %P - %8 Oct 15 %! Natural variation in CBF gene sequence, gene expression and freezing tolerance in the Versailles core collection of Arabidopsis thaliana %@ 1471-2229 %1 Hincha~Transcript Profiling~ %3 1 %M ISI:000260828400001 %K cold-response pathway low-temperature transcription factors duplicated genes brassica-napus acclimation drought accessions regulator elements %X Background: Plants from temperate regions are able to withstand freezing temperatures due to a process known as cold acclimation, which is a prior exposure to low, but non-freezing temperatures. During acclimation, a large number of genes are induced, bringing about biochemical changes in the plant, thought to be responsible for the subsequent increase in freezing tolerance. Key regulatory proteins in this process are the CBF1, 2 and 3 transcription factors which control the expression of a set of target genes referred to as the "CBF regulon". Results: To assess the role of the CBF genes in cold acclimation and freezing tolerance of Arabidopsis thaliana, the CBF genes and their promoters were sequenced in the Versailles core collection, a set of 48 accessions that maximizes the naturally-occurring genetic diversity, as well as in the commonly used accessions Col-0 and WS. Extensive polymorphism was found in all three genes. Freezing tolerance was measured in all accessions to assess the variability in acclimated freezing tolerance. The effect of sequence polymorphism was investigated by evaluating the kinetics of CBF gene expression, as well as that of a subset of the target COR genes, in a set of eight accessions with contrasting freezing tolerance. Our data indicate that CBF genes as well as the selected COR genes are cold induced in all accessions, irrespective of their freezing tolerance. Although we observed different levels of expression in different accessions, CBF or COR gene expression was not closely correlated with freezing tolerance. Conclusion: Our results indicate that the Versailles core collection contains significant natural variation with respect to freezing tolerance, polymorphism in the CBF genes and CBF and COR gene expression. Although there tends to be more CBF and COR gene expression in tolerant accessions, there are exceptions, reinforcing the idea that a complex network of genes is involved in freezing tolerance and that the CBF genes alone cannot explain all differences in phenotype. Our study also highlights the difficulty in assessing the function of single transcription factors that are members of closely related gene families. %Z 371JU Times Cited:0 Cited References Count:57 %U ://000260828400001 %+ McKhann, HI CNG, INRA, EPGV, 2 Rue Gaston Cremieux, F-91057 Evry, France CNG, INRA, EPGV, F-91057 Evry, France INRA, SGAP, F-78026 Versailles, France Max Planck Inst Mol Plant Physiol, D-14476 Potsdam, Germany INRA, UMR Divers & Adaptat Plantes Cultivees 1097, F-34130 Domaine De Melgueil, Mauguio, France UPMC, F-75252 Paris 05, France %G English %0 Journal Article %A McCabe, M. S. %A Klaas, M. %A Gonzalez-Rabade, N. %A Poage, M. %A Badillo-Corona, J. A. %A Zhou, F. %A Karcher, D. %A Bock, R. %A Gray, J. C. %A Dix, P. J. %D 2008 %T Plastid transformation of high-biomass tobacco variety Maryland Mammoth for production of human immunodeficiency virus type 1 (HIV-1) p24 antigen %J Plant Biotechnology Journal %V 6 %N 9 %P 914-929 %8 Dec %! Plastid transformation of high-biomass tobacco variety Maryland Mammoth for production of human immunodeficiency virus type 1 (HIV-1) p24 antigen %@ 1467-7644 %1 Bock~Organelle Biology, Biotechnology and Molecular Ecophysiology~ %3 1 %M ISI:000261079600005 %K chloroplast transformation high-biomass tobacco human immunodeficiency virus type 1 (hiv-1) p24 antigen end rule pathway transgenic chloroplasts plant chloroplasts protective antigen escherichia-coli protein expression vaccine gene purification %X Chloroplast transformation of the high-biomass tobacco variety Maryland Mammoth has been assessed as a production platform for the human immunodeficiency virus type 1 (HIV-1) p24 antigen. Maryland Mammoth offers the prospect of higher yields of intact functional protein per unit floor area of contained glasshouse per unit time prior to flowering. Two different transformation constructs, pZSJH1p24 (for the insertion of a native p24 cDNA between the rbcL and accD genes) and pZF5 (for the insertion of a chloroplast-codon-optimized p24 gene between trnfM and trnG) were examined for the production of p24. Plants generated with construct pZSJH1p24 exhibited a normal green phenotype, but p24 protein accumulated only in the youngest leaves (up to approximately 350 mu g/g fresh weight or 2.5% total soluble protein) and was undetectable in mature leaves. In contrast, some of the plants generated with pZF5 exhibited a yellow phenotype (pZF5-yellow) with detectable p24 accumulation (up to approximately 450 mu g/g fresh weight or 4.5% total soluble protein) in all leaves, regardless of age. Total protein in pZF5-yellow leaves was reduced by 40%. The pZF5-yellow phenotype was associated with recombination between native and introduced direct repeat sequences of the rbcL 3' untransformed region in the plastid genome. Chloroplast-expressed p24 was recognized by a conformation-dependent monoclonal antibody to p24, and p24 protein could be purified from pZF5-yellow leaves using a simple procedure, involving ammonium sulphate precipitation and ion-exchange chromatography, without the use of an affinity tag. The purified p24 was shown to be full length with no modifications, such as glycosylation or phosphorylation, using N-terminal sequencing and mass spectrometry. %Z 374YM Times Cited:1 Cited References Count:60 %U ://000261079600005 %+ Dix, PJ Natl Univ Ireland Maynooth, Dept Biol, Maynooth, Kildare, Ireland Natl Univ Ireland Maynooth, Dept Biol, Maynooth, Kildare, Ireland Univ Cambridge, Dept Plant Sci, Cambridge CB2 3EA, England Max Planck Inst Mol Pflanzenphysiol, D-14476 Potsdam, Germany %G English %0 Journal Article %A Mazzella, M. A. %A Zanor, M. I. %A Fernie, A. R. %A Casal, J. J. %D 2008 %T Metabolic responses to red/far-red ratio and ontogeny show poor correlation with the growth rate of sunflower stems %J Journal of Experimental Botany %V 59 %N 9 %P 2469-2477 %8 Jun %! Metabolic responses to red/far-red ratio and ontogeny show poor correlation with the growth rate of sunflower stems %@ 0022-0957 %1 Fernie~Central Metabolism~ %3 1 %M ISI:000256760400018 %K carbohydrates metabolic profile phytochrome shade avoidance sunflower shade-avoidance-response arabidopsis-thaliana lipid-composition extension-growth glyoxylate cycle gene-expression light quality potato-tuber phytochrome mustard %X In sparse canopies, low red to far-red (R/FR) ratios reach only vertically-oriented stems, which respond with faster rates of extension. It is shown here that this signal also promotes stem dry matter accumulation in sunflower (Helianthus annuus) but not in mustard (Sinapis alba L.). Physically blocking internode extension growth also blocked internode recovery of labelled carbon fed to the leaves, indicating that increased carbon accumulation is partially a consequence of increased extension growth in sunflower. However, low R/FR also promoted carbon accumulation in the lower section of the internode, where extension growth was unaffected. Although the levels of many soluble metabolites and of cell-wall carbohydrates increased in the stem in response to low R/FR, allowing conservation of their concentration, sucrose was present at a lower concentration under low R/FR. This change is anticipated to favour carbon unloading from the stem phloem. Low R/FR also reduced the levels of selected fatty acids, fatty acid alcohols, and sterols. Compared with the lower section, the upper section of the internode showed higher levels of organic acids, amino acids, fatty acids, and sterols. It is concluded that the promotion of stem extension growth by low R/FR ratios causes increased dry matter gain in sunflower internodes by a mechanism that is largely independent of changes in metabolism, since, whilst both low R/FR and ontogeny alter the metabolic profile, the changes do not correlate with the observed growth responses. %Z 313SN Times Cited:0 Cited References Count:31 %U ://000256760400018 %+ Casal, JJ Univ Buenos Aires, Fac Agron, IFEVA, RA-1417 Buenos Aires, DF, Argentina Univ Buenos Aires, Fac Agron, IFEVA, RA-1417 Buenos Aires, DF, Argentina Consejo Nacl Invest Cient & Tecn, RA-1417 Buenos Aires, DF, Argentina Inst Invest Ingn Genet & Biol, INGEBI, RA-1428 Buenos Aires, DF, Argentina Max Planck Inst Mol Pflanzenphysiol, D-14476 Potsdam, Germany %G English %0 Journal Article %A May, P. %A Wienkoop, S. %A Kempa, S. %A Usadel, B. %A Christian, N. %A Rupprecht, J. %A Weiss, J. %A Recuenco-Munoz, L. %A Ebenhoeh, O. %A Weckwerth, W. %A Walther, D. %D 2008 %T Metabolomics- and proteomics-assisted genome annotation and analysis of the draft metabolic network of Chlamydomonas reinhardtii %J Genetics %V 179 %N 1 %P 157-166 %8 May %! Metabolomics- and proteomics-assisted genome annotation and analysis of the draft metabolic network of Chlamydomonas reinhardtii %@ 0016-6731 %1 Ebenhoeh~Systems Biology and Mathematical Modeling~Usadel~Integrative Carbon Biology~Weckwerth~Integrative Proteomics and Metabolomics~Walther~Bioinformatics cig~ %3 1 %M ISI:000256312000015 %K bioenergetic pathways protein identification evolution database server plants sets kegg %X We present an integrated analysis of the molecular repertoire of Chlamydomonas reinhardtii under reference conditions. Bioinformatics annotation methods combined with GCxGC/MS-based metabolomics and LC/MS-based shotgun proteomics profiling technologies have been applied to characterize abundant proteins and metabolites, resulting in the detection of 1069 proteins and 159 metabolites. Of the measured proteins, 204 currently do not have EST sequence support; thus a significant portion of the proteomics-detected proteins provide evidence for the validity of in silico gene models. Furthermore, the generated peptide data lend support to the validity of a number of proteins currently in the proposed model stage. By integrating genomic annotation information with experimentally identified metabolites and proteins, we constructed a draft metabolic network for Chlamydomonas. Computational metabolic modeling allowed an identification of missing enzymatic links. Sonic experimentally detected metabolites are not producible by the currently known and annotated enzyme set, thus suggesting entry points for further targeted gene discovery or biochemical pathway research. All data sets are made available as supplementary material as well as web-accessible databases and within the functional context via the Chlamydomonas-adapted MapMan annotation platform. Information of identified peptides is also available directly via the JGI-Chlamydomonas genomic resource database (http://genome.jgi-psf.org/Chlre3/Chlre3.home.html). %Z 307IG Times Cited:4 Cited References Count:35 %U ://000256312000015 %+ Walther, D Max Planck Inst Mol Plant Physiol, Muhlenberg 1, D-14424 Potsdam, Germany Max Planck Inst Mol Plant Physiol, D-14424 Potsdam, Germany Univ Potsdam, Inst Biochem & Biol, GoFORSYS, D-14424 Potsdam, Germany %G English %0 Journal Article %A Matthaeus, F. %A Salazar, C. %A Ebenhoeh, O. %D 2008 %T Biosynthetic potentials of metabolites and their hierarchical organization %J Plos Computational Biology %V 4 %N 4 %P - %8 Apr %! Biosynthetic potentials of metabolites and their hierarchical organization %@ 1553-734X %1 Systems Biology and Mathematical Modeling~Ebenhoeh~ %3 1 %M ISI:000255411400019 %K escherichia-coli networks evolution pathways world DNA %X A major challenge in systems biology is to understand how complex and highly connected metabolic networks are organized. The structure of these networks is investigated here by identifying sets of metabolites that have a similar biosynthetic potential. We measure the biosynthetic potential of a particular compound by determining all metabolites than can be produced from it and, following a terminology introduced previously, call this set the scope of the compound. To identify groups of compounds with similar scopes, we apply a hierarchical clustering method. We find that compounds within the same cluster often display similar chemical structures and appear in the same metabolic pathway. For each cluster we define a consensus scope by determining a set of metabolites that is most similar to all scopes within the cluster. This allows for a generalization from scopes of single compounds to scopes of a chemical family. We observe that most of the resulting consensus scopes overlap or are fully contained in others, revealing a hierarchical ordering of metabolites according to their biosynthetic potential. Our investigations show that this hierarchy is not only determined by the chemical complexity of the metabolites, but also strongly by their biological function. As a general tendency, metabolites which are necessary for essential cellular processes exhibit a larger biosynthetic potential than those involved in secondary metabolism. A central result is that chemically very similar substances with different biological functions may differ significantly in their biosynthetic potentials. Our studies provide an important step towards understanding fundamental design principles of metabolic networks determined by the structural and functional complexity of metabolites. %Z 294MY Times Cited:0 Cited References Count:26 %U ://000255411400019 %+ Matthaus, F Univ Heidelberg, Interdisciplinary Ctr Sci Comp, Heidelberg, Germany Univ Heidelberg, Interdisciplinary Ctr Sci Comp, Heidelberg, Germany German Canc Res Ctr, D-6900 Heidelberg, Germany Max Planck Inst Mol Plant Physiol, Potsdam, Germany Univ Potsdam, Inst Biochem & Biol, Potsdam, Germany %G English %0 Journal Article %A Luedemann, A. %A Strassburg, K. %A Erban, A. %A Kopka, J. %D 2008 %T TagFinder for the quantitative analysis of gas chromatography - mass spectrometry (GC-MS)-based metabolite profiling experiments %J Bioinformatics %V 24 %N 5 %P 732-737 %8 Mar 1 %! TagFinder for the quantitative analysis of gas chromatography - mass spectrometry (GC-MS)-based metabolite profiling experiments %@ 1367-4803 %1 Kopka~Root Metabolism~ %3 1 %M ISI:000253746400025 %K gc-tof-ms functional genomics plant metabolomics identifying differences reporting standards data-management gc/ms identification tool extraction %X Motivation: Typical GC-MS-based metabolite profiling experiments may comprise hundreds of chromatogram files, which each contain up to 1000 mass spectral tags (MSTs). MSTs are the characteristic patterns of similar to 25-250 fragment ions and respective isotopomers, which are generated after gas chromatography (GC) by electron impact ionization (EI) of the separated chemical molecules. These fragment ions are subsequently detected by time-of-flight (TOF) mass spectrometry (MS). MSTs of profiling experiments are typically reported as a list of ions, which are characterized by mass, chromatographic retention index (RI) or retention time (RT), and arbitrary abundance. The first two parameters allow the identification, the later the quantification of the represented chemical compounds. Many software tools have been reported for the pre-processing, the so-called curve resolution and deconvolution, of GC-(EI-TOF)-MS files. Pre-processing tools generate numerical data matrices, which contain all aligned MSTs and samples of an experiment. This process, however, is error prone mainly due to (i) the imprecise RI or RT alignment of MSTs and (ii) the high complexity of biological samples. This complexity causes co-elution of compounds and as a consequence non-selective, in other words impure MSTs. The selection and validation of optimal fragment ions for the specific and selective quantification of simultaneously eluting compounds is, therefore, mandatory. Currently validation is performed in most laboratories under human supervision. So far no software tool supports the non-targeted and user-independent quality assessment of the data matrices prior to statistical analysis. TagFinder may fill this gap. Strategy: TagFinder facilitates the analysis of all fragment ions, which are observed in GC-(EI-TOF)-MS profiling experiments. The non-targeted approach allows the discovery of novel and unexpected compounds. In addition, mass isotopomer resolution is maintained by TagFinder processing. This feature is essential for metabolic flux analyses and highly useful, but not required for metabolite profiling. Whenever possible, TagFinder gives precedence to chemical means of standardization, for example, the use of internal reference compounds for retention time calibration or quantitative standardization. In addition, external standardization is supported for both compound identification and calibration. The workflow of TagFinder comprises, (i) the import of fragment ion data, namely mass, time and arbitrary abundance (intensity), from a chromatography file interchange format or from peak lists provided by other chromatogram pre-processing software, (ii) the annotation of sample information and grouping of samples into classes, (iii) the RI calculation, (iv) the binning of observed fragment ions of equal mass from different chromatograms into RI windows, (v) the combination of these bins, so-called mass tags, into time groups of co-eluting fragment ions, (vi) the test of time groups for intensity correlated mass tags, (vii) the data matrix generation and (viii) the extraction of selective mass tags supported by compound identification. Thus, TagFinder supports both non-targeted fingerprinting analyses and metabolite targeted profiling. %Z 270UT Times Cited:0 Cited References Count:51 %U ://000253746400025 %+ Kopka, J Max Planck Inst Mol Plant Physiol, Dept Prof L Willmitzer, Muehlenberg 1, D-14476 Potsdam, Germany Max Planck Inst Mol Plant Physiol, Dept Prof L Willmitzer, D-14476 Potsdam, Germany %G English %0 Journal Article %A Lohse, M. %A Krüger, P. %A Hannemann, J. %A Nagel, A. %A Stitt, M. %A Walther, D. %A Usadel, B. %D 2008 %T Robin - Microarray Experimentanalyse leicht gemacht %J GenomXPress %V 3 %P 16-17 %! Robin - Microarray Experimentanalyse leicht gemacht %1 Stitt~System Regulation~Walther~Bioinformatics cig~Usadel~Integrative Carbon Biology~ %3 1 %0 Journal Article %A Lisec, J. %A Meyer, R. C. %A Steinfath, M. %A Redestig, H. %A Becher, M. %A Witucka-Wall, H. %A Fiehn, O. %A Torjek, O. %A Selbig, J. %A Altmann, T. %A Willmitzer, L. %D 2008 %T Identification of metabolic and biomass QTL in Arabidopsis thaliana in a parallel analysis of RIL and IL populations %J Plant Journal %V 53 %N 6 %8 Nov 28 %! Identification of metabolic and biomass QTL in Arabidopsis thaliana in a parallel analysis of RIL and IL populations %O Plant J %@ 0960-7412 (Print) %1 Willmitzer~Genes and small Molecules~Altmann~Developmental Physiology and Genomics~Selbig~Bioinformatics crg~ %3 1 %M 18047556 %X Plant growth and development are tightly linked to primary metabolism and they are subject to natural variation. In order to get insight into the genetic factors controlling biomass and primary metabolism and to determine their relations, two Arabidopsis thaliana populations - 429 Recombinant Inbred Lines (RIL) and 97 Introgression Lines (IL), derived from accessions Col-0 and C24 - were analyzed with respect to biomass and metabolic composition using a mass spectrometry based metabolic profiling approach. Six and 157 Quantitative Trait Loci (QTL) were found for biomass and metabolic content, respectively. Two biomass QTL coincide with significantly more metabolic QTL (mQTL) than statistically expected supporting the notion that the metabolic profile and biomass accumulation of a plant are linked. Along the same line three out of six biomass QTL can be simulated purely on the basis of metabolic composition. QTL based on the analysis of the ILs were in substantial agreement with the RIL based results: five of six biomass QTL and 55% of mQTL found in the RIL population were also found in the IL population at a significance level of p://000261728800005 %+ Levine, LH Dynamac Corp, Space Life Sci Lab, Kennedy Space Ctr, FL 32899 USA Dynamac Corp, Space Life Sci Lab, Kennedy Space Ctr, FL 32899 USA Hokkaido Tokai Univ, Sch Engn, Dept Biosci & Technol, Sapporo, Hokkaido, Japan Max Planck Inst Mol Pflanzenphysiol, D-14476 Golm, Germany Univ Florida, Dept Environm Hort, Plant Mol & Cellular Biol Program, Gainesville, FL 32611 USA Univ Florida, Inst Food & Agr Sci, Dept Stat, Gainesville, FL 32611 USA NASA, Sustainable Syst Div, Kennedy Space Ctr, FL 32899 USA %G English %0 Journal Article %A Lejay, L. %A Wirth, J. %A Pervent, M. %A Cross, J. M. F. %A Tillard, P. %A Gojon, A. %D 2008 %T Oxidative pentose phosphate pathway-dependent sugar sensing as a mechanism for regulation of root ion transporters by photosynthesis %J Plant Physiology %V 146 %N 4 %P 2036-2053 %8 Apr %! Oxidative pentose phosphate pathway-dependent sugar sensing as a mechanism for regulation of root ion transporters by photosynthesis %@ 0032-0889 %1 System Regulation~ %3 1 %M ISI:000256417900045 %K arabidopsis-thaliana nitrate transporter no3-uptake signaling pathways diurnal regulation higher-plants nonphotosynthetic organs carbon assimilation nitrite reduction sulfur nutrition %X Root ion transport systems are regulated by light and/or sugars, but the signaling mechanisms are unknown. We showed previously that induction of the NRT2.1 NO3- transporter gene by sugars was dependent on carbon metabolism downstream hexokinase (HXK) in glycolysis. To gain further insights on this signaling pathway and to explore more systematically the mechanisms coordinating root nutrient uptake with photosynthesis, we studied the regulation of 19 light-/ sugar-induced ion transporter genes. A combination of sugar, sugar analogs, light, and CO2 treatments provided evidence that these genes are not regulated by a common mechanism and unraveled at least four different signaling pathways involved: regulation by light per se, by HXK-dependent sugar sensing, and by sugar sensing upstream or downstream HXK, respectively. More specific investigation of sugar-sensing downstream HXK, using NRT2.1 and NRT1.1 NO3- transporter genes as models, highlighted a correlation between expression of these genes and the concentration of glucose-6-P in the roots. Furthermore, the phosphogluconate dehydrogenase inhibitor 6-aminonicotinamide almost completely prevented induction of NRT2.1 and NRT1.1 by sucrose, indicating that glucose-6-P metabolization within the oxidative pentose phosphate pathway is required for generating the sugar signal. Out of the 19 genes investigated, most of those belonging to the NO3-, NH4+, and SO42- transporter families were regulated like NRT2.1 and NRT1.1. These data suggest that a yet-unidentified oxidative pentose phosphate pathway-dependent sugar-sensing pathway governs the regulation of root nitrogen and sulfur acquisition by the carbon status of the plant to coordinate the availability of these three elements for amino acid synthesis. %Z 308VJ Times Cited:2 Cited References Count:87 %U ://000256417900045 %+ Lejay, L Agro M CNRS INRA SupAgro UM2, UMR Biochim & Physiol Mol Plantes 5004, Inst Biol Integrat Plantes, F-34060 Montpellier, France Agro M CNRS INRA SupAgro UM2, UMR Biochim & Physiol Mol Plantes 5004, Inst Biol Integrat Plantes, F-34060 Montpellier, France Agro M INRA SupAgro, UMR Ecophysiol Plantes Sous Stress Environnementa, Inst Biol Integrat Plantes, F-34060 Montpellier, France Max Planck Inst Mol Plant Physiol, D-14476 Potsdam, Germany %G English %0 Journal Article %A Lein, W. %A Usadel, B. %A Stitt, M. %A Reindl, A. %A Ehrhardt, T. %A Sonnewald, U. %A Boernke, F. %D 2008 %T Large-scale phenotyping of transgenic tobacco plants (Nicotiana tabacum) to identify essential leaf functions %J Plant Biotechnology Journal %V 6 %N 3 %P 246-263 %8 Apr %! Large-scale phenotyping of transgenic tobacco plants (Nicotiana tabacum) to identify essential leaf functions %@ 1467-7644 %1 Stitt~System Regulation~Lein~Gene Function~Usadel~Integrative Carbon Biology~ %3 1 %M ISI:000253760500004 %K arabidopsis thaliana essential genes expressed sequence tag (est) gene silencing nicotiana tabacum phenotyping chalcone synthase gene antisense rna chlorophyll biosynthesis arabidopsis-thaliana potato plants t-DNA insertional mutagenesis chelatase activity mutant phenotypes atp synthase %X Two of the major challenges in functional genomics are to identify genes that play a key role in biological processes, and to elucidate the biological role of the large numbers of genes whose function is poorly characterized or still completely unknown. In this study, a combination of large-scale expressed sequence tag sequencing, high-throughput gene silencing and visual phenotyping was used to identify genes in which partial inhibition of expression leads to marked phenotypic changes, mostly on leaves. Three normalized tobacco (Nicotiana tabacum) cDNA libraries were prepared directly in a binary vector using different tissues of tobacco as an RNA source, randomly sequenced and clustered. The Agrobacterium-tobacco leaf disc transformation system was used to generate sets of antisense or co-suppression transgenic tobacco plants for over 20 000 randomly chosen clones, each representing an independent cluster. After transfer to the glasshouse, transgenic plants were scored visually after 10-14 days for changes in growth, leaf form and chlorosis or necrosis. Putative hits were validated by repeating the transformation. This procedure is more stringent than the analysis of knockout mutants, because it requires that even a partial decrease in expression generates a phenotype. This procedure identified 88 validated gene/phenotype relations. These included several previously characterized gene/phenotype relationships, demonstrating the validity of the approach. For about one-third, a function could be inferred, but a loss-of-function phenotype had not been described previously. Strikingly, almost one-half of the validated genes were poorly annotated, or had no known function. For 77 of these tobacco sequences, a single or small number of potential orthologues were identified in Arabidopsis. The genes for which orthologues were identified in Arabidopsis included about one-half of the genes whose function was completely unknown. Comparison with published gene/phenotype relations for Arabidopsis knockout mutants revealed surprisingly little overlap with the present study. Our results indicate that partial gene silencing identifies novel gene/phenotype relationships, which are distinct from those uncovered by knockout screens. They also show that it is possible to perform these analyses in a crop species in which full genome sequence information is lacking, and subsequently to transfer the information to a reference species in which functional studies can be performed more effectively. %Z 271AE Times Cited:0 Cited References Count:67 %U ://000253760500004 %+ Lein, W Max Planck Inst Mol Plant Physiol, Muhlenberg 1, D-14476 Golm, Germany Max Planck Inst Mol Plant Physiol, D-14476 Golm, Germany BASF AG, D-67056 Ludwigshafen, Germany Inst Pflanzengenet & Kulturpflanzenforsch, D-06466 Gatersleben, Germany %G English %0 Journal Article %A Lehmann, U. %A Wienkoop, S. %A Tschoep, H. %A Weckwerth, W. %D 2008 %T If the antibody fails - a mass Western approach %J Plant Journal %V 55 %N 6 %P 1039-1046 %8 Sep %! If the antibody fails - a mass Western approach %@ 0960-7412 %1 Weckwerth~Integrative Proteomics and Metabolomics~System Regulation~ %3 1 %M ISI:000259221900012 %K proteomics mass spectrometry systems biology plant systems biology isozymes stable isotope dilution sucrose-phosphate synthase carbohydrate-metabolism arabidopsis-thaliana gene-expression low-temperature proteins sugar plants starch leaves %X Sucrose-phosphate synthase (SPS) has attracted the interest of plant scientists for decades. It is the key enzyme in sucrose metabolism and is under investigation in various plant species, e.g. spinach, tobacco, poplar, resurrection plants, maize, rice, kiwi and Arabidopsis thaliana. In A. thaliana, there are four distinct SPS isoforms. Their expression is thought to depend on environmental conditions and plant tissue. However, these data were derived from mRNA expression levels only. No data on SPS protein identification from crude extracts have been available until now. An antibody approach failed to distinguish the four isoforms. Therefore, we developed a method for SPS quantification and isoform-specific identification in A. thaliana complex protein samples. Samples were separated on SDS-PAGE, digested and directly applied to liquid chromatography/triple-stage quadrupole mass spectrometry (LC/TSQ-MS). In this approach, known as mass Western, samples were analysed in multi-reaction monitoring (MRM) mode, so that all four SPS isoforms could be measured in one experiment. In addition to the relative quantification, stable isotope-labelled internal peptide standards allowed absolute quantification of SPS proteins. Protein extracts from various plant tissues, samples harvested during the day or the night, and cold-stressed plants were analysed. The stress-specific SPS5a isoform showed increased concentrations in cold-stressed leaf material. %Z 348PH Times Cited:0 Cited References Count:38 %U ://000259221900012 %+ Weckwerth, W Max Planck Inst Mol Plant Physiol, Muhlenberg 1, D-14424 Potsdam, Germany Max Planck Inst Mol Plant Physiol, D-14424 Potsdam, Germany Univ Potsdam, Inst Biochem & Biol, Potsdam, Germany Univ Vienna, Dept Melecular Syst Biol, A-1010 Vienna, Austria %G English %0 Journal Article %A Leboeuf, E. %A Immerzeel, P. %A Gibon, Y. %A Steup, M. %A Pauly, M. %D 2008 %T High-throughput functional assessment of polysaccharide-active enzymes using matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry as exemplified on plant cell wall polysaccharides %J Analytical Biochemistry %V 373 %N 1 %P 9-17 %8 Feb 1 %! High-throughput functional assessment of polysaccharide-active enzymes using matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry as exemplified on plant cell wall polysaccharides %@ 0003-2697 %1 System Regulation~ %3 1 %M ISI:000252069000002 %K glycosyltransferase esterase substrate specificity maldi-tof mass spectrometry fucosyl-transferase carbohydrate microarrays assay specificity inhibitors binding %X Despite a wealth of sequence information on genes encoding carbohydrate-active enzymes (e.g., transferases, esterases, hydrolases), very few of these enzymes have been described in detail, particularly regarding substrate specificities. A facile and rapid method for the characterization of substrate specificities of polysaccharide-active enzymes that uses matrix-assisted laser desorption-time of flight mass spectrometry (MALDI-TOF MS) has been developed. This method has been applied to characterize a xyloglucan fucosyltransferase and a pectin methyl-esterase. Reactions were performed in liquid phase, and aliquots of the reaction mixtures were spotted on a polyvinylidene fluoride (PVDF) membrane. Reaction products were precipitated onto the membrane and cleaned by treatment with an ethanol-water mixture. Subsequently, the reaction products were hydrolyzed by specific endoglycanases, and the resulting oligosaccharides were directly analyzed onto the PVDF membrane by MALDI-TOF MS. The new method is amenable to high-throughput analysis and, thus, constitutes an emerging avenue to rapidly fill the gap in our knowledge of the specificities of polysaccharide-active enzymes. (c) 2007 Elsevier Inc. All rights reserved. %Z 247HM Times Cited:0 Cited References Count:28 %U ://000252069000002 %+ Pauly, M Michigan State Univ, MSU DOE Plant Res Lab, E Lansing, MI 48824 USA Michigan State Univ, MSU DOE Plant Res Lab, E Lansing, MI 48824 USA Univ Potsdam, Inst Biochem & Biol, Dept Plant Physiol, D-14476 Potsdam, Germany Max Planck Inst Mol Plant Physiol, D-14476 Potsdam, Germany %G English %0 Journal Article %A Le, Q. M. %A Hincha, D. %D 2008 %T Natural genetic variation of sub-zero cold acclimation in Arabidopsis thaliana %J Cryoletters %V 29 %N 1 %P 80-81 %8 Jan-Feb %! Natural genetic variation of sub-zero cold acclimation in Arabidopsis thaliana %@ 0143-2044 %1 Hincha~Transcript Profiling~ %3 1 %M ISI:000254484100027 %Z 281GE Times Cited:0 Cited References Count:1 %U ://000254484100027 %+ Max Planck Inst Mol Plants Physiol, Transcript Profiling Grp, D-14476 Potsdam, Germany %G English %0 Journal Article %A Le, M. Q. %A Engelsberger, W. R. %A Hincha, D. K. %D 2008 %T Natural genetic variation in acclimation capacity at sub-zero temperatures after cold acclimation at 4 degrees C in different Arabidopsis thaliana accessions %J Cryobiology %V 57 %N 2 %P 104-112 %8 Oct %! Natural genetic variation in acclimation capacity at sub-zero temperatures after cold acclimation at 4 degrees C in different Arabidopsis thaliana accessions %@ 0011-2240 %1 Hincha~Transcript Profiling~Signaling Proteomics~ %3 1 %M ISI:000260407000004 %K arabidospis thaliana cbf transcription factors cold acclimation compatible solutes cor genes freezing tolerance gene expression sub-zero acclimation freezing tolerance transcription factors response pathway winter oat expression stress metabolome plants mechanisms activators %X Freezing tolerance is an important factor in the geographical distribution of plants and strongly influences crop yield. Many plants increase their freezing tolerance during exposure to low, nonfreezing temperatures (cold acclimation) and acclimation may continue at mild freezing temperatures in a process termed sub-zero acclimation. There is considerable natural variation in the cold acclimation capacity of Arabidopsis that has been used to study the molecular basis of this trait, but much less is known about the molecular basis of sub-zero acclimation. Freezing tolerance of detached leaves from the accessions C24, Columbia-0, Rschew, and Tenela was investigated using an electrolyte leakage assay. Sub-zero acclimation could be achieved by shifting plants from 4 degrees C to -3 degrees C, or by using detached leaves, either in the presence or absence of ice nucleation. The magnitude of the increase in freezing tolerance depended on both temperature and duration of sub-zero acclimation and while Columbia-0 showed no significant increase in freezing tolerance, the other three accessions increased their freezing tolerance significantly. The levels of several sugars that have been shown to be induced during cold acclimation at nonfreezing temperatures were not strongly changed during sub-zero acclimation and there was no correlation between the increases in freezing tolerance and sugar levels in the different accessions. Expression of the three cold induced OF transcription factor genes and five of their representative target CUR genes was moderately increased during sub-zero acclimation, but again there was no correlation to changes in freezing tolerance, indicating that the genetic and molecular basis of sub-zero acclimation is most likely different from that of cold acclimation at above freezing temperatures. Further studies will be needed to reveal novel signal transduction pathways and protective mechanisms important in sub-zero acclimation. (C) 2008 Elsevier Inc. All rights reserved. %Z 365LD Times Cited:0 Cited References Count:42 %U ://000260407000004 %+ Hincha, DK Max Planck Inst Mol Pflanzenphysiol, Muhlenberg 1, D-14476 Potsdam, Germany Max Planck Inst Mol Pflanzenphysiol, D-14476 Potsdam, Germany %G English %0 Journal Article %A Lange, P. R. %A Geserick, C. %A Tischendorf, G. %A Zrenner, R. %D 2008 %T Functions of chloroplastic adenylate kinases in Arabidopsis %J Plant Physiology %V 146 %N 2 %P 492-504 %8 Feb %! Functions of chloroplastic adenylate kinases in Arabidopsis %@ 0032-0889 %1 Zrenner~Nucleotides and Sugars~Developmental Physiology and Genomics~ %3 1 %M ISI:000252892700014 %K energy-charge escherichia-coli mitochondrial proteome spinach-chloroplasts purine biosynthesis molecular analysis gene-expression ump/cmp kinase potato-tubers higher-plants %X Adenosine monophosphate kinase (AMK; adenylate kinase) catalyses the reversible formation of ADP by the transfer of one phosphate group from ATP to AMP, thus equilibrating adenylates. The Arabidopsis (Arabidopsis thaliana) genome contains 10 genes with an adenylate/ cytidylate kinase signature; seven of these are identified as putative adenylate kinases. Encoded proteins of at least two members of this Arabidopsis adenylate kinase gene family are targeted to plastids. However, when the individual genes are disrupted, the phenotypes of both mutants are strikingly different. Although absence of AMK2 causes only 30% reduction of total adenylate kinase activity in leaves, there is loss of chloroplast integrity leading to small, pale-looking plantlets from embryo to seedling development. In contrast, no phenotype for disruption of the second plastid adenylate kinase was found. From this analysis, we conclude that AMK2 is the major activity for equilibration of adenylates and de novo synthesis of ADP in the plastid stroma. %Z 258TP Times Cited:0 Cited References Count:67 %U ://000252892700014 %+ Zrenner, R Max Planck Inst Mol Pflanzenphysiol, D-14476 Golm, Germany Max Planck Inst Mol Pflanzenphysiol, D-14476 Golm, Germany Free Univ Berlin, Inst Biol Pflanzenphysiol, D-14195 Berlin, Germany %G English %0 Journal Article %A Kryvych, S. %A Nikiforova, V. %A Herzog, M. %A Perazza, D. %A Fisahn, J. %D 2008 %T Gene expression profiling of the different stages of Arabidopsis thaliana trichome development on the single cell level %J Plant Physiology and Biochemistry %V 46 %N 2 %P 160-173 %8 Feb %! Gene expression profiling of the different stages of Arabidopsis thaliana trichome development on the single cell level %@ 0981-9428 %1 Nikiforova~System Integration~Fisahn~Biophysical Analysis~ %3 1 %M ISI:000254149700006 %K arabidopsis thaliana single cell level gene expression profiling cell cycle plant hormones leaf trichomes trichome initial cells microrna family endoreduplication identification biosynthesis gibberellins homeostasis siamese leaves growth %X Leaf hairs (trichomes) of Arabidopsis thaliana are a model system for studying cell development, differentiation and cell cycle regulation. To exploit this model system with ultimate spatial resolution we applied single cell sampling, thus avoiding the averaging effect induced by complex tissue mixtures. In particular, we analysed gene expression profiles of two selected stages of the developing trichome: trichome initial cells and mature trichomes, as well as pavement cells. Ten single cells per sample were collected by glass microcapillaries and used for the generation of radioactive probes for subsequent hybridization to nylon filters representing approximately 8000 genes of A. thaliana. Functional categorization of genes transcribed in trichome initials, mature trichomes and pavement cells demonstrated involvement of these surface cells in the stress response. In silico promoter analysis of genes preferentially expressed in trichome initials revealed enrichment in MYB-binding sites and presence of elements involved in hormonal, metal, sulphur response and cell cycle regulation. Three candidate genes preferentially expressed in trichome initials were selected for further analysis: At3g16980 (putative RNA polymerase 11), At5g15230 (GASA4) and At4g27260 (GH3.5, WES1). Promoter:GUS studies confirmed expression of the putative RNA polymerase 11 and the gibberellin responsive GASA4 in trichome initials and partially in mature trichomes. Functional implication of the three selected candidates in trichome development and hence in cell cycle regulation in A. thaliana is discussed. We suggest that these genes are involved in differentiation and initiation of endocycling during trichome development. (c) 2007 Elsevier Masson SAS. All rights reserved. %Z 276NR Times Cited:0 Cited References Count:43 %U ://000254149700006 %+ Kryvych, S Max Planck Inst Mol Plant Physiol, D-14476 Potsdam, Germany Max Planck Inst Mol Plant Physiol, D-14476 Potsdam, Germany Univ Grenoble 1, Lab Plastes & Differenciat Cellulaire, Ctr Natl Rech Sci, Unite Mixte Rech 5575, F-38041 Grenoble, France %G English %0 Journal Article %A Kruse, K. %A Ebenhoeh, O. %D 2008 %T Comparing flux balance analysis to network expansion: Producibility, sustainability and the scope of compounds %J Genome Informatics %V 20 %P 91–101 %! Comparing flux balance analysis to network expansion: Producibility, sustainability and the scope of compounds %1 Ebenhoeh~Systems Biology and Mathematical Modeling~ %3 1 %K statistical correlation Pearson coefficient non-linear correlation mutual information knearest neighbor entropy metabolomics Arabidopsis thaliana. %X Non-linear correlations based on mutual information are evaluated to measure statistical dependencies among data points measured from metabolism in two dimensional space. While the Pearson correlation coefficient is only rigorously applicable to characterize strictly linear correlations with Gaussian noise, the mutual information coefficient is more generally valid. Here, we use recent distribution-free (non-parametric) mutual information estimators based on k-nearest neighbor distances. The mutual information algorithm of Kraskov et al. is found to yield estimates with low systematic and statistical error. The significance of the different methods is probed for artificial sets of tens to hundreds of data points, a size currently typical for metabolomic data. We analyze experimental data on metabolite concentrations from Arabidopsis thaliana by using these procedures. The mutual information was able to detect additional non-linear correlations undetectable for the Pearson coefficient. %+ Max Planck Inst Mol Plant Physiol, Muhlenberg 1, D-14424 Potsdam, Germany Max Planck Inst Mol Plant Physiol, D-14424 Potsdam, Germany %G English %0 Journal Article %A Koslowsky, S. %A Riegler, H. %A Bergmuller, E. %A Zrenner, R. %D 2008 %T Higher biomass accumulation by increasing phosphoribosylpyrophosphate synthetase activity in Arabidopsis thaliana and Nicotiana tabacum %J Plant Biotechnology Journal %V 6 %N 3 %P 281-294 %8 Apr %! Higher biomass accumulation by increasing phosphoribosylpyrophosphate synthetase activity in Arabidopsis thaliana and Nicotiana tabacum %@ 1467-7644 %1 Zrenner~Nucleotides and Sugars~ %3 1 %M ISI:000253760500006 %K metabolic regulation phosphoribosylpyrophosphate synthetase plant growth transgenic plant potato solanum-tuberosum diphosphate synthase enzyme-activities plant-growth biosynthesis pyrimidine metabolism protein phosphoribosyltransferase degradation %X Plants are able to produce all the organic compounds required for development and growth. As developmental processes and metabolic pathways use a common resource pool, the tight regulation of the distribution of metabolites between growth, production of defence compounds and storage products can be assumed. A transgenic approach was used to investigate the importance of supplying the key intermediate phosphoribosylpyrophosphate (PRPP) for plant growth and biomass accumulation in the model plant Arabidopsis thaliana and in Nicotiana tabacum. For this purpose, the Ashbya gossypii genes coding for either PRPP synthetase (PRS) or a mutated variant of the same gene were over-expressed under the control of a constitutive promoter. It was shown that increased PRS activity in A. thaliana or N. tabacum leads to a substantial increase in biomass accumulation under different standardized growth conditions. Growth enhancement was accompanied by significant changes in the amount of sugars and other metabolites. This study provides evidence that the supply of PRPP co-limits growth rates, and has obvious implications for biotechnological strategies aiming to increase plant biomass as an alternative renewable energy source. %Z 271AE Times Cited:0 Cited References Count:35 %U ://000253760500006 %+ Zrenner, R Max Planck Inst Mol Pflanzenphysiol, Muhlenberg 1, D-14476 Potsdam GOLM, Germany Max Planck Inst Mol Pflanzenphysiol, D-14476 Potsdam GOLM, Germany %G English %0 Journal Article %A Korn, M. %A Peterek, S. %A Mock, H. P. %A Heyer, A. G. %A Hincha, D. K. %D 2008 %T Heterosis in the freezing tolerance, and sugar and flavonoid contents of crosses between Arabidopsis thaliana accessions of widely varying freezing tolerance %J Plant Cell and Environment %V 31 %N 6 %P 813-827 %8 Jun %! Heterosis in the freezing tolerance, and sugar and flavonoid contents of crosses between Arabidopsis thaliana accessions of widely varying freezing tolerance %@ 0140-7791 %1 Hincha~Transcript Profiling~System Regulation~ %3 1 %M ISI:000255661700010 %K cold acclimation compatible solutes cold-acclimation low-temperature genetic-variation natural variation molecular-basis water-stress plants metabolome establishment transcriptome %X Heterosis is defined as the increased vigour of hybrids in comparison to their parents. We investigated 24 F-1 hybrid lines of Arabidopsis thaliana generated by reciprocally crossing either C24 or Col with six other parental accessions (Can, Co, Cvi, Ler, Rsch, Te) that differ widely in their freezing tolerance. The crosses differed in the degree of heterosis for freezing tolerance, both in the non-acclimated state and after a 14 d cold acclimation period. Crosses with C24 showed more heterosis than crosses with Col, and heterosis was stronger in acclimated than in non-acclimated plants. Leaf content of soluble sugars and proline showed more deviation from mid-parent values in crosses involving C24 than in those involving Col, and deviations were larger in acclimated than in non-acclimated plants. There were significant correlations between the content of different sugars and leaf freezing tolerance, as well as between heterosis effects in freezing tolerance and sugar content. Flavonoid content and composition varied between accessions, and between non-acclimated and acclimated plants. In the crosses, large deviations from the mid-parent values in the contents of different flavonols occurred, and there were strikingly strong correlations between both flavonol content and freezing tolerance, and between heterosis effects in freezing tolerance and flavonol content. %Z 298BP Times Cited:2 Cited References Count:48 %U ://000255661700010 %+ Hincha, DK Max Planck Inst Mol Pflanzenphysiol, Muhlenberg 1, D-14476 Potsdam, Germany Max Planck Inst Mol Pflanzenphysiol, D-14476 Potsdam, Germany Leibniz Inst Pflanzengenet & Kulturpflanzenforsch, D-06466 Gatersleben, Germany Univ Stuttgart, Inst Biol, D-70569 Stuttgart, Germany %G English %0 Journal Article %A Koehl, K. I. %A Basler, G. %A Luedemann, A. %A Selbig, J. %A Walther, D. %D 2008 %T A plant resource and experiment management system based on the Golm Plant Database as a basic tool for omics research %J Plant Methods %V 4 %P 11 %! A plant resource and experiment management system based on the Golm Plant Database as a basic tool for omics research %O Plant methods %@ 1746-4811 (Electronic) %1 Bioinformatics crg~Bioinformatics cig~Selbig~Walther~Koehl~Green team~ %3 1 %M 18495032 %X ABSTRACT: BACKGROUND: For omics experiments, detailed characterisation of experimental material with respect to its genetic features, its cultivation history and its treatment history is a requirement for analyses by bioinformatics tools and for publication needs. Furthermore, meta-analysis of several experiments in systems biology based approaches make it necessary to store this information in a standardised manner, preferentially in relational databases. In the Golm Plant Database System, we devised a data management system based on a classical Laboratory Information Management System combined with web-based user interfaces for data entry and retrieval to collect this information in an academic environment. RESULTS: The database system contains modules representing the genetic features of the germplasm, the experimental conditions and the sampling details. In the germplasm module, genetically identical lines of biological material are generated by defined workflows, starting with the import workflow, followed by further workflows like genetic modification (transformation), vegetative or sexual reproduction. The latter workflows link lines and thus create pedigrees. For experiments, plant objects are generated from plant lines and united in so-called cultures, to which the cultivation conditions are linked. Materials and methods for each cultivation step are stored in a separate ACCESS database of the plant cultivation unit. For all cultures and thus every plant object, each cultivation site and the culture's arrival time at a site are logged by a barcode-scanner based system. Thus, for each plant object, all site-related parameters, e.g. automatically logged climate data, are available. These life history data and genetic information for the plant objects are linked to analytical results by the sampling module, which links sample components to plant object identifiers. This workflow uses controlled vocabulary for organs and treatments. Unique names generated by the system and barcode labels facilitate identification and management of the material. Web pages are provided as user interfaces to facilitate maintaining the system in an environment with many desktop computers and a rapidly changing user community. Web based search tools are the basis for joint use of the material by all researchers of the institute. CONCLUSION: The Golm Plant Database system, which is based on a relational database, collects the genetic and environmental information on plant material during its production or experimental use at the Max-Planck-Institute of Molecular Plant Physiology. It thus provides information according to the MIAME standard for the component 'Sample' in a highly standardised format. The Plant Database system thus facilitates collaborative work and allows efficient queries in data analysis for systems biology research. %Z Journal Article England %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18495032 %+ Max-Planck-Institute of Molecular Plant Physiology, Am Muhlenberg 1, 14476 Golm, Germany. koehl@mpimp-golm.mpg.de. %G eng %0 Journal Article %A Kloosterman, B. %A De Koeyer, D. %A Griffiths, R. %A Flinn, B. %A Steuernagel, B. %A Scholz, U. %A Sonnewald, S. %A Sonnewald, U. %A Bryan, G. J. %A Prat, S. %A Banfalvi, Z. %A Hammond, J. P. %A Geigenberger, P. %A Nielsen, K. L. %A Visser, R. G. F. %A Bachem, C. W. B. %D 2008 %T Genes driving potato tuber initiation and growth: identification based on transcriptional changes using the POCI array %J Functional & Integrative Genomics %V 8 %N 4 %P 329-340 %8 Nov %! Genes driving potato tuber initiation and growth: identification based on transcriptional changes using the POCI array %@ 1438-793X %1 Geigenberger~Storage Carbohydrate Metabolism~ %3 1 %M ISI:000259247800003 %K potato unigene oligo array tuber development expression profiling expressed sequence tags libraries search %X The increasing amount of available expressed gene sequence data makes whole-transcriptome analysis of certain crop species possible. Potato currently has the second largest number of publicly available expressed sequence tag (EST) sequences among the Solanaceae. Most of these ESTs, plus other proprietary sequences, were combined and used to generate a unigene assembly. The set of 246,182 sequences produced 46,345 unigenes, which were used to design a 44K 60-mer oligo array (Potato Oligo Chip Initiative: POCI). In this study, we attempt to identify genes controlling and driving the process of tuber initiation and growth by implementing large-scale transcriptional changes using the newly developed POCI array. Major gene expression profiles could be identified exhibiting differential expression at key developmental stages. These profiles were associated with functional roles in cell division and growth. A subset of genes involved in the regulation of the cell cycle, based on their Gene Ontology classification, exhibit a clear transient upregulation at tuber onset indicating increased cell division during these stages. The POCI array allows the study of potato gene expression on a much broader level than previously possible and will greatly enhance analysis of transcriptional control mechanisms in a wide range of potato research areas. POCI sequence and annotation data are publicly available through the POCI database (http://pgrc.ipk-gatersleben.de/poci). %Z 348ZE Times Cited:0 Cited References Count:23 %U ://000259247800003 %+ Kloosterman, B Univ Wageningen & Res Ctr, Wageningen UR Plant Breeding, POB 386, NL-6700 AJ Wageningen, Netherlands Univ Wageningen & Res Ctr, Wageningen UR Plant Breeding, NL-6700 AJ Wageningen, Netherlands Agr & Agri Food Canada, Potato Res Ctr, Fredericton, NB E3B 4Z7, Canada BioAtlantech, Fredericton, NB E3B 6Z9, Canada Leibniz Inst Pflanzengenet & Kulturpflanzenforsch, D-06466 Gatersleben, Germany Univ Erlangen Nurnberg, Lehrstuhl Biochem, D-91058 Erlangen, Germany Scottish Crop Res Inst, Dundee DD2 5DA, Scotland CSIC, Ctr Nacl Biotecnol, E-28049 Madrid, Spain Agr Biotechnol Ctr, H-2101 Godollo, Hungary Univ Warwick, Warwick HRI, Warwick CV35 9EF, England Max Planck Inst Mol Pflanzenphysiol, D-14476 Golm, Germany Univ Aalborg, Dept Biotechnol Chem & Environm Engn, Aalborg, Denmark %G English %0 Journal Article %A Khomyakova, E. %A Livshits, M. A. %A Steinhauser, M. C. %A Dauphinot, L. %A Cohen-Kaminsky, S. %A Rossier, J. %A Soussaline, F. %A Potier, M. C. %D 2008 %T On-chip hybridization kinetics for optimization of gene expression experiments %J Biotechniques %V 44 %N 1 %P 109-117 %8 Jan %! On-chip hybridization kinetics for optimization of gene expression experiments %@ 0736-6205 %1 System Regulation~ %3 1 %M ISI:000252842100024 %K surface hybridization DNA hybridization microarray duplexes reveals oligonucleotides equilibrium microchips behavior arrays %X DNA microarray technology is a powerful tool for getting an overview of gene expression in biological samples. Although the successful use of microarray-based expression analysis was demonstrated in a number of applications, the main problem with this approach is the fact that expression levels deduced from hybridization experiments do not necessarily correlate with RNA concentrations. Moreover oligonucleotide probes corresponding to the same gene can give different hybridization signals. Apart from cross-hybridizations and differential splicing, this could be due to secondary structures of probes or targets. In addition, for low-copy genes, hybridization equilibrium maybe reached after hybridization times much longer than the one commonly used (overnight, i.e., 15 h). Thus, hybridization signals could depend on kinetic properties of the probe, which may vary between different oligonucleotide probes immobilized on the same microarray. To validate this hypothesis, on-chip hybridization kinetics and duplex thermostability analysis were performed using oligonucleotide microarrays containing 50-mer probes corresponding to 10 mouse genes. We demonstrate that differences in hybridization kinetics between the probes exist and can influence the interpretation of expression data. In addition, we show that using on-chip hybridization kinetics, quantification of targets is feasible using calibration curves. %Z 258AZ Times Cited:0 Cited References Count:24 %U ://000252842100024 %+ Khomyakova, E Max Planck Inst, Inst Mol Plant Physiol, Am Muehlenberg 1, D-14476 Golm, Germany IMSTAR, Paris, France EIMB, Moscow, Russia CNRS, UMR 7637, F-75005 Paris, France CNRS, UMR 8078, Le Plessis Robinson, France %G English %0 Journal Article %A Keurentjes, J. J. B. %A Sulpice, R. %A Gibon, Y. %A Steinhauser, M. C. %A Fu, J. Y. %A Koornneef, M. %A Stitt, M. %A Vreugdenhil, D. %D 2008 %T Integrative analyses of genetic variation in enzyme activities of primary carbohydrate metabolism reveal distinct modes of regulation in Arabidopsis thaliana %J Genome Biology %V 9 %N 8 %P - %! Integrative analyses of genetic variation in enzyme activities of primary carbohydrate metabolism reveal distinct modes of regulation in Arabidopsis thaliana %@ 1474-760X %1 Stitt~System Regulation~ %3 1 %M ISI:000259701400014 %K quantitative trait loci nitrogen use efficiency inbred line population cytosolic phosphoglucomutase glucose pyrophosphorylase transpiration efficiency secondary metabolism carbon metabolism parallel analysis natural variation %X Background: Plant primary carbohydrate metabolism is complex and flexible, and is regulated at many levels. Changes of transcript levels do not always lead to changes in enzyme activities, and these do not always affect metabolite levels and fluxes. To analyze interactions between these three levels of function, we have performed parallel genetic analyses of 15 enzyme activities involved in primary carbohydrate metabolism, transcript levels for their encoding structural genes, and a set of relevant metabolites. Quantitative analyses of each trait were performed in the Arabidopsis thaliana Ler x Cvi recombinant inbred line (RIL) population and subjected to correlation and quantitative trait locus (QTL) analysis. Results: Traits affecting primary metabolism were often correlated, possibly due to developmental control affecting multiple genes, enzymes, or metabolites. Moreover, the activity QTLs of several enzymes co-localized with the expression QTLs (eQTLs) of their structural genes, or with metabolite accumulation QTLs of their substrates or products. In addition, many trait-specific QTLs were identified, revealing that there is also specific regulation of individual metabolic traits. Regulation of enzyme activities often occurred through multiple loci, involving both cis-and trans-acting transcriptional or post-transcriptional control of structural genes, as well as independently of the structural genes. Conclusion: Future studies of the regulatory processes in primary carbohydrate metabolism will benefit from an integrative genetic analysis of gene transcription, enzyme activity, and metabolite content. The multiparallel QTL analyses of the various interconnected transducers of biological information flow, described here for the first time, can assist in determining the causes and consequences of genetic regulation at different levels of complex biological systems. %Z 355IA Times Cited:0 Cited References Count:77 %U ://000259701400014 %+ Keurentjes, JJB Univ Wageningen & Res Ctr, Genet Lab, Arboretumlaan, NL-6703 BD Wageningen, Netherlands Univ Wageningen & Res Ctr, Genet Lab, NL-6703 BD Wageningen, Netherlands Univ Wageningen & Res Ctr, Lab Plant Physiol, NL-6703 BD Wageningen, Netherlands Ctr Biosyst Genom, NL-6708 PB Wageningen, Netherlands Max Planck Inst Mol Plant Physiol, D-14476 Potsdam, Germany Univ Groningen, Groningen Biomol Sci & Biotechnol Inst, Groningen Bioinformat Ctr, NL-9751 NN Groningen, Netherlands Max Planck Inst Plant Breeding Res, D-50829 Cologne, Germany %G English %0 Book Section %A Kersten, B. %A Wanker, E.E. %D 2008 %T Klinische Proteomik %E Ganten, D. %E Ruckpaul, K. %B Grundlagen der Molekularen Medizin:Section 3.1 %C Berlin, Heidelberg, New York %I Springer %! Klinische Proteomik %1 Walther~Bioinformatics cig~ %3 1 %G german %0 Journal Article %A Kersten, B. %A Nagel, A. %A Riano-Pachon, D.M. %A Neigenfind, J. %A Weber, E. %A Wagner, R. %A Diehl, S. %D 2008 %T Die GABI-Primaerdatenbank GabiPD - Komplexe Integration von GABI-Daten aus Modell- und Nutzpflanzen %J GenomXPress %V 1 %P 17-19 %! Die GABI-Primaerdatenbank GabiPD - Komplexe Integration von GABI-Daten aus Modell- und Nutzpflanzen %3 1 %G deutsch %0 Book Section %A Kersten, B. %D 2008 %T Time to search for kinase substrates %E Rakwal, R. %E Agrawal, G.K. %B Plant Proteomics: Technologies, Strategies, and Applications %C Hoboken, USA %I Wiley-Interscience %P 485-498 %! Time to search for kinase substrates %1 Walther~Bioinformatics cig~ %3 1 %0 Journal Article %A Kempa, S. %A Krasensky, J. %A Dal Santo, S. %A Kopka, J. %A Jonak, C. %D 2008 %T A central role of abscisic acid in stress-regulated carbohydrate metabolism %J PLoS ONE %V 3 %N 12 %P e3935 %! A central role of abscisic acid in stress-regulated carbohydrate metabolism %O PLoS ONE %@ 1932-6203 (Electronic) %1 Kopka~Root Metabolism~ %3 1 %M 19081841 %K Abscisic Acid/*pharmacology Arabidopsis/*drug effects/genetics/*physiology Carbohydrate Metabolism/*drug effects Gene Expression Regulation, Plant/drug effects Genes, Plant Salinity Sodium Chloride/pharmacology Stress, Physiological/*drug effects Time Factors Transcription, Genetic/drug effects %X BACKGROUND: Abiotic stresses adversely affect plant growth and development. The hormone abscisic acid (ABA) plays a central role in the response and adaptation to environmental constraints. However, apart from the well established role of ABA in regulating gene expression programmes, little is known about its function in plant stress metabolism. PRINCIPAL FINDINGS: Using an integrative multiparallel approach of metabolome and transcriptome analyses, we studied the dynamic response of the model glyophyte Arabidopsis thaliana to ABA and high salt conditions. Our work shows that salt stress induces complex re-adjustment of carbohydrate metabolism and that ABA triggers the initial steps of carbon mobilisation. SIGNIFICANCE: These findings open new perspectives on how high salinity and ABA impact on central carbohydrate metabolism and highlight the power of iterative combinatorial approaches of non-targeted and hypothesis-driven experiments in stress biology. %Z Journal Article Research Support, Non-U.S. Gov't United States %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19081841 %+ Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria. %G eng %0 Journal Article %A Kehr, J. %A Buhtz, A. %D 2008 %T Long distance transport and movement of RNA through the phloem %J Journal of Experimental Botany %V 59 %P 85-92 %8 Sep 27 %! Long distance transport and movement of RNA through the phloem %@ 0022-0957 (Print) %1 Kehr~Micro- and Protein-Analysis~ %3 1 %M 17905731 %X Cell-to-cell communication is essential for plant development and adaptation to environmental changes. As a strategy for efficient intercellular communication, plants have evolved a plant-specific symplasmic network connected via plasmodesmata that allows a locally restricted information exchange from cell to cell. A rapid information transfer over long distances is enabled via the phloem transport tubes that pervade the complete plant and thus connect even the most distant organs. While communication by small molecules like metabolites and phytohormones is comparably well studied, the intercellular trafficking of proteins and RNAs has only recently emerged as a novel mechanism of cell-to-cell and long-distance signalling in plants. In particular the non-cell-autonomous and systemic transport pathway for specific RNAs seems to play a key role in the co-ordination of important physiological processes, including virus defence, gene silencing, regulation of development, and nutrient allocation. This review is a summary of the current knowledge on RNAs contained in the phloem long-distance transport system, their transport mechanism, and their potential functions. %Z Journal article %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17905731 %+ Max Planck Institute of Molecular Plant Physiology, Department Lothar Willmitzer, Am Muhlenberg 1, 14424 Golm/Potsdam, Germany. %G Eng %0 Book Section %A Kartal, O. %A Ebenhoeh, O. %D 2008 %T The glucan, water dikinase - a kinetic model to understand the initial step in starch mobilization in plant leaves %E Hansmann, U.H.E. %E Meinke, J.H. %E Mohanty, S. %E Nadler, W. %E Zimmermann, O. %B From Computational Biophysics to Systems Biology %C Juelich %I John von Neumann Institute for Computing %V 40 of NIC Series %P 245–248 %! The glucan, water dikinase - a kinetic model to understand the initial step in starch mobilization in plant leaves %1 Ebenhoeh~Systems Biology and Mathematical Modeling~ %3 1 %0 Journal Article %A Karcher, D. %A Kahlau, S. %A Bock, R. %D 2008 %T Faithful editing of a tomato-specific mRNA editing site in transgenic tobacco chloroplasts %J Rna-a Publication of the Rna Society %V 14 %N 2 %P 217-224 %8 Feb %! Faithful editing of a tomato-specific mRNA editing site in transgenic tobacco chloroplasts %@ 1355-8382 %1 Bock~Organelle Biology, Biotechnology and Molecular Ecophysiology~ %3 1 %M ISI:000252929400004 %K nicotiana tabacum solanum lycopersicum plastid evolution rps12 rna editing plastid transformation pentatricopeptide repeat protein in-vivo hornwort chloroplasts nicotiana-tabacum plastid genomes transcript gene recognition maize identification %X RNA editing sites and their site-specific trans-acting recognition factors are thought to have coevolved. Hence, evolutionary loss of an editing site by a genomic mutation is normally followed by the loss of the specific recognition factor for this site, due to the absence of selective pressure for its maintenance. Here, we have tested this scenario for the only tomato-specific plastid RNA editing site. A single C-to-U editing site in the tomato rps12 gene is absent from the tobacco and nightshade plastid genomes, where the presence of a genomic T nucleotide obviates the need for editing of the rps12 mRNA. We have introduced the tomato editing site into the tobacco rps12 gene by plastid transformation and find that, surprisingly, this heterologous site is efficiently edited in the transplastomic plants. This suggests that the trans-acting recognition factor for the rps12 editing site has been maintained, presumably because it serves another function in tobacco plastids. Bioinformatics analyses identified an editing site in the rpoB gene of tobacco and tomato whose sequence context exhibits striking similarity to that of the tomato rps12 editing site. This may suggest that requirement for rpoB editing resulted in maintenance of the rps12 editing activity or, alternatively, the pre-existing rpoB editing activity facilitated the evolution of a novel editing site in rps12. %Z 259HC Times Cited:0 Cited References Count:49 %U ://000252929400004 %+ Rock, R Max Planck Inst Mol Pflanzenphysiol, Am Muhlenberg 1, D-14476 Potsdam, Germany Max Planck Inst Mol Pflanzenphysiol, D-14476 Potsdam, Germany %G English %0 Journal Article %A Kakar, K. %A Wandrey, M. %A Czechowski, T. %A Gaertner, T. %A Scheible, W. R. %A Stitt, M. %A Torres-Jerez, I. %A Xiao, Y. %A Redman, J. C. %A Wu, H. C. %A Cheung, F. %A Town, C. D. %A Udvardi, M. K. %D 2008 %T A community resource for high-throughput quantitative RT-PCR analysis of transcription factor gene expression in Medicago truncatula %J Plant Methods %V 4 %P 18 %! A community resource for high-throughput quantitative RT-PCR analysis of transcription factor gene expression in Medicago truncatula %O Plant methods %@ 1746-4811 (Electronic) %1 Molecular Genomics~Molecular Plant Nutrition~Scheible~Stitt~System Regulation~Udvardi~ %3 1 %M 18611268 %X ABSTRACT: BACKGROUND: Medicago truncatula is a model legume species that is currently the focus of an international genome sequencing effort. Although several different oligonucleotide and cDNA arrays have been produced for genome-wide transcript analysis of this species, intrinsic limitations in the sensitivity of hybridization-based technologies mean that transcripts of genes expressed at low-levels cannot be measured accurately with these tools. Amongst such genes are many encoding transcription factors (TFs), which are arguably the most important class of regulatory proteins. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) is the most sensitive method currently available for transcript quantification, and one that can be scaled up to analyze transcripts of thousands of genes in parallel. Thus, qRT-PCR is an ideal method to tackle the problem of TF transcript quantification in Medicago and other plants. RESULTS: We established a bioinformatics pipeline to identify putative TF genes in Medicago truncatula and to design gene-specific oligonucleotide primers for qRT-PCR analysis of TF transcripts. We validated the efficacy and gene-specificity of over 1000 TF primer pairs and utilized these to identify sets of organ-enhanced TF genes that may play important roles in organ development or differentiation in this species. This community resource will be developed further as more genome sequence becomes available, with the ultimate goal of producing validated, gene-specific primers for all Medicago TF genes. CONCLUSION: High-throughput qRT-PCR using a 384-well plate format enables rapid, flexible, and sensitive quantification of all predicted Medicago transcription factor mRNAs. This resource has been utilized recently by several groups in Europe, Australia, and the USA, and we expect that it will become the 'gold-standard' for TF transcript profiling in Medicago truncatula. %Z Journal Article England %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18611268 %+ Max-Planck Institute of Molecular Plant Physiology, Am Muhlenberg 1, 14476 Potsdam-Golm, Germany. mudvardi@noble.org. %G eng %0 Journal Article %A Kahlau, S. %A Bock, R. %D 2008 %T Plastid transcriptomics and translatomics of tomato fruit development and chloroplast-to-chromoplast differentiation: Chromoplast gene expression largely serves the production of a single protein %J Plant Cell %V 20 %N 4 %P 856-874 %8 Apr %! Plastid transcriptomics and translatomics of tomato fruit development and chloroplast-to-chromoplast differentiation: Chromoplast gene expression largely serves the production of a single protein %@ 1040-4651 %1 Bock~Organelle Biology, Biotechnology and Molecular Ecophysiology~ %3 1 %M ISI:000256416200008 %K tobacco nicotiana-tabacum acetyl-coa carboxylase intron splicing factor cyclic electron flow open reading frames group-ii higher-plants chlamydomonas-reinhardtii rna-polymerases capsicum-annuum %X Plastid genes are expressed at high levels in photosynthetically active chloroplasts but are generally believed to be drastically downregulated in nongreen plastids. The genome-wide changes in the expression patterns of plastid genes during the development of nongreen plastid types as well as the contributions of transcriptional versus translational regulation are largely unknown. We report here a systematic transcriptomics and translatomics analysis of the tomato (Solanum lycopersicum) plastid genome during fruit development and chloroplast-to-chromoplast conversion. At the level of RNA accumulation, most but not all plastid genes are strongly downregulated in fruits compared with leaves. By contrast, chloroplast-to-chromoplast differentiation during fruit ripening is surprisingly not accompanied by large changes in plastid RNA accumulation. However, most plastid genes are translationally downregulated during chromoplast development. Both transcriptional and translational downregulation are more pronounced for photosynthesis-related genes than for genes involved in gene expression, indicating that some low-level plastid gene expression must be sustained in chromoplasts. High-level expression during chromoplast development identifies accD, the only plastid-encoded gene involved in fatty acid biosynthesis, as the target gene for which gene expression activity in chromoplasts is maintained. In addition, we have determined the developmental patterns of plastid RNA polymerase activities, intron splicing, and RNA editing and report specific developmental changes in the splicing and editing patterns of plastid transcripts. %Z 308UT Times Cited:2 Cited References Count:110 %U ://000256416200008 %+ Bock, R Max Planck Inst Mol Pflanzenphysiol, D-14476 Potsdam, Germany Max Planck Inst Mol Pflanzenphysiol, D-14476 Potsdam, Germany %G English %0 Journal Article %A Jensen, J. K. %A Sorensen, S. O. %A Harholt, J. %A Geshi, N. %A Sakuragi, Y. %A Moller, I. %A Zandleven, J. %A Bernal, A. J. %A Jensen, N. B. %A Sorensen, C. %A Pauly, M. %A Beldman, G. %A Willats, W. G. T. %A Scheller, H. V. %D 2008 %T Identification of a xylogalacturonan xylosyltransferase involved in pectin biosynthesis in Arabidopsis %J Plant Cell %V 20 %N 5 %P 1289-1302 %8 May %! Identification of a xylogalacturonan xylosyltransferase involved in pectin biosynthesis in Arabidopsis %@ 1040-4651 %1 Pauly~Plant Cell Walls~ %3 1 %M ISI:000257320600010 %K polysaccharide rhamnogalacturonan-ii cell-wall polysaccharides monoclonal-antibody xyloglucan galactosyltransferase enzymatic degradation rapid method gene homogalacturonan thaliana encodes %X Xylogalacturonan (XGA) is a class of pectic polysaccharide found in plant cell walls. The Arabidopsis thaliana locus At5g33290 encodes a predicted Type II membrane protein, and insertion mutants of the At5g33290 locus had decreased cell wall xylose. Immunological studies, enzymatic extraction of polysaccharides, monosaccharide linkage analysis, and oligosaccharide mass profiling were employed to identify the affected cell wall polymer. Pectic XGA was reduced to much lower levels in mutant than in wild-type leaves, indicating a role of At5g33290 in XGA biosynthesis. The mutated gene was designated xylogalacturonan deficient1 (xgd1). Transformation of the xgd1-1 mutant with the wild-type gene restored XGA to wild-type levels. XGD1 protein heterologously expressed in Nicotiana benthamiana catalyzed the transfer of xylose from UDP-xylose onto oligogalacturonides and endogenous acceptors. The products formed could be hydrolyzed with an XGA-specific hydrolase. These results confirm that the XGD1 protein is a XGA xylosyltransferase. The protein was shown by expression of a fluorescent fusion protein in N. benthamiana to be localized in the Golgi vesicles as expected for a glycosyltransferase involved in pectin biosynthesis. %Z 321QC Times Cited:2 Cited References Count:52 %U ://000257320600010 %+ Scheller, HV Univ Copenhagen, Fac Life Sci, Dept Plant Biol, Plant Mol Biol Lab, DK-1871 Frederiksberg C, Denmark Univ Copenhagen, Fac Life Sci, Dept Plant Biol, Plant Mol Biol Lab, DK-1871 Frederiksberg C, Denmark Univ Copenhagen, Dept Mol Biol, Fac Sci, DK-1353 Copenhagen, Denmark Univ Wageningen & Res Ctr, Dept Agrotechnol & Food Sci, Food Chem Lab, NL-6700 EV Wageningen, Netherlands Max Planck Inst Mol Physiol, D-14476 Golm, Germany Joint Bioenergy Inst, Feedstocks Div, Emeryville, CA 94608 USA %G English %0 Journal Article %A Hundertmark, M. %A Hincha, D. K. %D 2008 %T LEA (Late Embryogenesis Abundant) proteins and their encoding genes in Arabidopsis thaliana %J Bmc Genomics %V 9 %P - %8 Mar 4 %! LEA (Late Embryogenesis Abundant) proteins and their encoding genes in Arabidopsis thaliana %@ 1471-2164 %1 Hincha~Transcript Profiling~ %3 1 %M ISI:000254891600001 %K plant craterostigma-plantagineum intrinsically unstructured proteins natively unfolded proteins amino-acid-sequence oryza-sativa l. freezing tolerance water-deficit saccharomyces-cerevisiae cryoprotective activity functional divergence %X Background: LEA (late embryogenesis abundant) proteins have first been described about 25 years ago as accumulating late in plant seed development. They were later found in vegetative plant tissues following environmental stress and also in desiccation tolerant bacteria and invertebrates. Although they are widely assumed to play crucial roles in cellular dehydration tolerance, their physiological and biochemical functions are largely unknown. Results: We present a genome-wide analysis of LEA proteins and their encoding genes in Arabidopsis thaliana. We identified 51 LEA protein encoding genes in the Arabidopsis genome that could be classified into nine distinct groups. Expression studies were performed on all genes at different developmental stages, in different plant organs and under different stress and hormone treatments using quantitative RT-PCR. We found evidence of expression for all 51 genes. There was only little overlap between genes expressed in vegetative tissues and in seeds and expression levels were generally higher in seeds. Most genes encoding LEA proteins had abscisic acid response (ABRE) and/ or low temperature response (LTRE) elements in their promoters and many genes containing the respective promoter elements were induced by abscisic acid, cold or drought. We also found that 33% of all Arabidopsis LEA protein encoding genes are arranged in tandem repeats and that 43% are part of homeologous pairs. The majority of LEA proteins were predicted to be highly hydrophilic and natively unstructured, but some were predicted to be folded. Conclusion: The analyses indicate a wide range of sequence diversity, intracellular localizations, and expression patterns. The high fraction of retained duplicate genes and the inferred functional diversification indicate that they confer an evolutionary advantage for an organism under varying stressful environmental conditions. This comprehensive analysis will be an important starting point for future efforts to elucidate the functional role of these enigmatic proteins. %Z 287BO Times Cited:0 Cited References Count:129 %U ://000254891600001 %+ Hincha, DK Max Planck Inst Mol Pflanzenphysiol, Am Muhlenberg, D-14476 Potsdam, Germany Max Planck Inst Mol Pflanzenphysiol, D-14476 Potsdam, Germany %G English %0 Journal Article %A Hufton, A. L. %A Groth, D. %A Vingron, M. %A Lehrach, H. %A Poustka, A. J. %A Panopoulou, G. %D 2008 %T Early vertebrate whole genome duplications were predated by a period of intense genome rearrangement %J Genome Research %V 18 %N 10 %P 1582-1591 %8 Oct %! Early vertebrate whole genome duplications were predated by a period of intense genome rearrangement %@ 1088-9051 %1 Bioinformatics cig~ %3 1 %M ISI:000259700800005 %K segmental duplications ciona-intestinalis animal genomes evolution gene divergence polyploidy amphioxus perspectives tetraploidy %X Researchers, supported by data from polyploid plants, have suggested that whole genome duplication (WGD) may induce genomic instability and rearrangement, an idea which could have important implications for vertebrate evolution. Benefiting from the newly released amphioxus genome sequence (Branchiostoma floridae), an invertebrate that researchers have hoped is representative of the ancestral chordate genome, we have used gene proximity conservation to estimate rates of genome rearrangement throughout vertebrates and some of their invertebrate ancestors. We find that, while amphioxus remains the best single source of invertebrate information about the early chordate genome, its genome structure is not particularly well conserved and it cannot be considered a fossilization of the vertebrate preduplication genome. In agreement with previous reports, we identify two WGD events in early vertebrates and another in teleost fish. However, we find that the early vertebrate WGD events were not followed by increased rates of genome rearrangement. Indeed, we measure massive genome rearrangement prior to these WGD events. We propose that the vertebrate WGD events may have been symptoms of a preexisting predisposition toward genomic structural change. %Z 355HU Times Cited:1 Cited References Count:54 %U ://000259700800005 %+ Panopoulou, G Max Planck Inst Mol Genet, D-12169 Berlin, Germany Max Planck Inst Mol Genet, D-12169 Berlin, Germany Univ Potsdam, Bioinformat Grp, Max Planck Inst Mol Plant Physiol, D-14476 Potsdam, Germany %G English %0 Journal Article %A Huang, C. Y. %A Roessner, U. %A Eickmeier, I. %A Genc, Y. %A Callahan, D. L. %A Shirley, N. %A Langridge, P. %A Bacic, A. %D 2008 %T Metabolite profiling reveals distinct changes in carbon and nitrogen metabolism in phosphate-deficient barley plants (Hordeum vulgare L.) %J Plant and Cell Physiology %V 49 %N 5 %P 691-703 %8 May %! Metabolite profiling reveals distinct changes in carbon and nitrogen metabolism in phosphate-deficient barley plants (Hordeum vulgare L.) %@ 0032-0781 %3 1 %M ISI:000256173400002 %K ammonium barley (hordeum vulgare l.) carbohydrate metabolite profile phosphate deficiency arabidopsis-thaliana phosphorus stress amino-acids roots expression gene rice deprivation responses systems %X Plants modify metabolic processes for adaptation to low phosphate (P) conditions. Whilst transcriptomic analyses show that P deficiency changes hundreds of genes related to various metabolic processes, there is limited information available for global metabolite changes of P-deficient plants, especially for cereals. As changes in metabolites are the ultimate 'readout' of changes in gene expression, we profiled polar metabolites from both shoots and roots of P-deficient barley (Hordeum vulgare) using gas chromatography-mass spectrometry (GC-MS). The results showed that mildly P-deficient plants accumulated di- and trisaccharides (sucrose, maltose, raffinose and 6-kestose), especially in shoots. Severe P deficiency increased the levels of metabolites related to ammonium metabolism in addition to di- and trisaccharides, but reduced the levels of phosphorylated intermediates (glucose-6-P, fructose-6-P, inositol-1-P and glycerol-3-P) and organic acids (alpha-ketoglutarate, succinate, fumarate and malate). The results revealed that P-deficient plants modify carbohydrate metabolism initially to reduce P consumption, and salvage P from small P-containing metabolites when P deficiency is severe, which consequently reduced levels of organic acids in the tricarboxylic acid (TCA) cycle. The extent of the effect of severe P deficiency on ammonium metabolism was also revealed by liquid chromatography-mass spectrometry (LC-MS) quantitative analysis of free amino acids. A sharp increase in the concentrations of glutamine and asparagine was observed in both shoots and roots of severely P-deficient plants. Based on these data, a strategy for improving the ability of cereals to adapt to low P environments is proposed that involves alteration in partitioning of carbohydrates into organic acids and amino acids to enable more efficient utilization of carbon in P-deficient plants. %Z 305JD Times Cited:0 Cited References Count:53 %U ://000256173400002 %+ Huang, CY Univ Adelaide, Australian Ctr Plant Funct Genom, Waite Campus,PMB1, Glen Osmond, SA 5064, Australia Univ Adelaide, Australian Ctr Plant Funct Genom, Glen Osmond, SA 5064, Australia Univ Melbourne, Australian Ctr Plant Funct Genom, Sch Bot, Melbourne, Vic 3010, Australia Max Planck Inst Mol Pflanzenphys, D-14476 Golm, Germany Univ Adelaide, Mol Plant Breeding Cooperat Res Ctr, Adelaide, SA 5005, Australia %G English %0 Journal Article %A Hoehenwarter, W. %A van Dongen, J. T. %A Wienkoop, S. %A Steinfath, M. %A Hummel, J. %A Erban, A. %A Sulpice, R. %A Regierer, B. %A Kopka, J. %A Geigenberger, P. %A Weckwerth, W. %D 2008 %T A rapid approach for phenotype-screening and database independent detection of cSNP/protein polymorphism using mass accuracy precursor alignment %J Proteomics %V 8 %N 20 %P 4214-4225 %8 Oct %! A rapid approach for phenotype-screening and database independent detection of cSNP/protein polymorphism using mass accuracy precursor alignment %@ 1615-9853 %1 van Dongen~Energy Metabolism~Kopka~Root Metabolism~Weckwerth~Integrative Carbon Biology~Geigenberger~Storage Carbohydrate Metabolism~System Regulation~Bioinformatics cig~ %3 1 %M ISI:000260717300009 %K expressed nucleic acid polymorphism label-free shotgun proteomics multivariate data mining potato tuber spectral sampling shotgun proteomics pattern-recognition biomarker selection variable selection complex peptide spectrometry proteins enolase identification metabolites %X The dynamics of a proteome can only be addressed with large-scale, high-throughput methods. To cope with the inherent complexity, techniques based on targeted quantification using proteotypic peptides are arising. This is an essential systems biology approach; however, for the exploratory discovery of unexpected markers, nontargeted detection of proteins, and protein modifications is indispensable. We present a rapid label-free shotgun proteomics approach that extracts relevant phenotype-specific peptide product ion spectra in an automated workflow without prior identification. These product ion spectra are subsequently sequenced with database search and de novo prediction algorithms. We analyzed six potato tuber cultivars grown on three plots of two geographically separated fields in Germany. For data mining about 1.5 million spectra from 107 analyses were aligned and statistically examined in approximately 1 day. Several cultivar-specific protein markers were detected. Based on de novo-sequencing a dominant protein polymorphism not detectable in the available EST-databases was assigned exclusively to a specific potato cultivar. The approach is applicable to organisms with unsequenced or incomplete genomes and to the automated extraction of relevant mass spectra that potentially cannot be identified by genome/EST-based search algorithms. %Z 369TR Times Cited:0 Cited References Count:28 %U ://000260717300009 %+ Weckwerth, W Max Planck Inst Mol Pflanzenphysiol, Am Muhlenberg 1, D-14424 Potsdam, Germany Max Planck Inst Mol Pflanzenphysiol, D-14424 Potsdam, Germany Univ Potsdam, Inst Biochem & Biol, Golm, Germany Univ Potsdam, Inst Biochem & Biol, GoFORSYS, Golm, Germany Univ Vienna, Dept Mol Syst Biol, A-1010 Vienna, Austria %G English %0 Journal Article %A Hoefgen, R. %A Nikiforova, V. J. %D 2008 %T Metabolomics integrated with transcriptomics: assessing systems response to sulfur-deficiency stress %J Physiologia Plantarum %V 132 %N 2 %P 190-198 %8 Feb %! Metabolomics integrated with transcriptomics: assessing systems response to sulfur-deficiency stress %@ 0031-9317 %1 Hoefgen~Amino Acid and Sulfur Metabolism~Nikiforova~System Integration~ %3 1 %M ISI:000252261900007 %K acetyl-l-serine sulfate transporter genes lateral root development arabidopsis-thaliana metabolite expression nitrogen nutrition biology profiles %X Sulfur-containing amino acids, cysteine and methionine synthesized in plants are essential for human and animal nutrition. That is why understanding of how inorganic sulfur is taken up by plants and built into the organic molecules in the process of sulfur assimilation is important. As complex biological systems, plants subsist as integrated molecular, organelle, cell, tissue and organ entities, being in permanent synergistic coordination. The process of sulfur uptake and assimilation is an integral part of this dense network of influences, its reconstruction may help in manipulating the bioproduction of organic sulfur-containing compounds. New high-throughput technologies allow the systems' view on the coordination of complex processes in living organisms. Among them, transcriptomics and metabolomics studies were applied to Arabidopsis plants subjected to sulfur-deficiency stress. From the integrated analysis of the obtained data, the mosaic picture of distinct sulfur stress response events and processes are starting to be assembled into the whole systems' network of sulfur assimilation. At the time trajectory of sulfur stress response, two system states can be distinguished. The first state of short-term responses is characterized by the development of enhanced lateral roots exploring the space in search for the lacking nutrient. When this physiological reaction cannot be accomplished by bringing the system back to the initial state of sulfur sufficiency, a new program is toggled aiming at saving the organismal resources for vital seed production. Here, we describe the biological reasoning in these two system states and the process of state transition between them. %Z 249WV Times Cited:0 Cited References Count:50 %U ://000252261900007 %+ Nikiforova, VJ Max Planck Inst Mol Pflanzenphysiol, Abt Mol Physiol 1, Am Muhlenberg 1, D-14476 Potsdam, Germany Max Planck Inst Mol Pflanzenphysiol, Abt Mol Physiol 1, D-14476 Potsdam, Germany Russian Acad Sci, KA Timiryazev Plant Physiol Inst, Moscow 127276, Russia %G English %0 Book Section %A Hoefgen, R. %A Hesse, H. %D 2008 %T Sulfur and Cysteine Metabolism %E Jez, Joseph %B Sulfur: A Missing Link between Soils, Crops and Nutritions %C Madison %I American Society of Agronomy %V 50 %P 83-104 %S Agronomy Monograph %! Sulfur and Cysteine Metabolism %1 Amino Acid and Sulfur Metabolism~Hoefgen~ %3 1 %M 978-0-89118-168-2 %+ Max-Planck -Institut für Molekulare Pflanzenphysiologie Am Mühlenberg 1 14476 Potsdam %G English %0 Journal Article %A Hincha, D. K. %A Rennecke, P. %A Oliver, A. E. %D 2008 %T Protection of liposomes against fusion during drying by oligosaccharides is not predicted by the calorimetric glass transition temperatures of the dry sugars %J European Biophysics Journal with Biophysics Letters %V 37 %N 4 %P 503-508 %8 Apr %! Protection of liposomes against fusion during drying by oligosaccharides is not predicted by the calorimetric glass transition temperatures of the dry sugars %@ 0175-7571 %1 Hincha~Transcript Profiling~ %3 1 %M ISI:000254235700015 %K model membranes d-sorbitol stability water phosphatidylcholine anhydrobiotes stabilization vitrification preservation tolerance %X Sugars play an important role in the desiccation tolerance of most anhydrobiotic organisms. It has been shown in previous studies that different structural families of oligosaccharides have different efficacies to interact with phospholipid headgroups and protect membranes from solute leakage during drying. Here, we have compared three families of linear oligosaccharides (fructans (inulins), malto-oligosaccharides, manno-oligosaccharides) for their chain-length dependent protection of egg phosphatidylcholine liposomes against membrane fusion. We found increased protection with chain length up to a degree of polymerization (DP) of 5 for malto-oligosaccharides, and a decrease for inulins and manno-oligosaccharides. Differential scanning calorimetry measurements showed that for all sugars the glass transition temperature (T-g) increased with DP, although to different degrees for the different oligosaccharide families. Higher T-g values resulted in reduced membrane fusion only for malto-oligosaccharides below DP5. Contrary to expectation, for inulins, manno-oligosaccharides and malto-oligosaccharides of a DP above five, fusion increased with increasing T-g, indicating that other physical parameters are more important in determining the ability of different sugars to protect membranes against fusion during drying. Further research will be necessary to experimentally define such parameters. %Z 277ST Times Cited:0 Cited References Count:32 %U ://000254235700015 %+ Hincha, DK Max Planck Inst Mol Pflanzenphysiol, Am Muhlenberg 1, D-14424 Potsdam, Germany Max Planck Inst Mol Pflanzenphysiol, D-14424 Potsdam, Germany Univ Calif Davis, Sch Vet Med, Davis, CA 95616 USA Univ Calif Davis, Dept Appl Sci, Davis, CA 95616 USA %G English %0 Journal Article %A Hincha, D. K. %D 2008 %T Effects of alpha-tocopherol (vitamin E) on the stability and lipid dynamics of model membranes mimicking the lipid composition of plant chloroplast membranes %J Febs Letters %V 582 %N 25-26 %P 3687-3692 %8 Oct 29 %! Effects of alpha-tocopherol (vitamin E) on the stability and lipid dynamics of model membranes mimicking the lipid composition of plant chloroplast membranes %@ 0014-5793 %1 Hincha~Transcript Profiling~ %3 1 %M ISI:000260807500020 %K alpha-tocopherol chloroplast lipid compatible solute freezing stress liposome vitamin e freeze-thaw damage thylakoid membranes molecular-dynamics bilayers trehalose liposomes tocotrienols solute probes glycolipids %X Tocopherol ( vitamin E) is widely recognized as a cellular antioxidant. It is essential for human and animal health, but only synthesized in photosynthetic organisms, where it is localized in chloroplast membranes. While many studies have investigated non-antioxidative effects of tocopherol on phospholipid membranes, nothing is known about its effects on membranes containing chloroplast glycolipids. Here, liposomes resembling plant chloroplast membranes were used to investigate the effects of alpha-tocopherol on vesicle stability during freezing and on lipid dynamics. alpha-Tocopherol had a pronounced influence on membrane dynamics and showed strong interactions in its effects on membrane stability during freezing with the cryoprotectant sucrose. alpha-Tocopherol showed maximal effects at low concentrations ( around 2 mol%), close to its contents in chloroplast membranes. (c) 2008 Published by Elsevier B. V. on behalf of the Federation of European Biochemical Societies. %Z 371BT Times Cited:0 Cited References Count:40 %U ://000260807500020 %+ Hincha, DK Max Planck Inst Mol Pflanzenphysiol, Muhlenberg 1, D-14476 Potsdam, Germany Max Planck Inst Mol Pflanzenphysiol, D-14476 Potsdam, Germany %G English %0 Journal Article %A Hartmann, S. %A Vision, T. J. %D 2008 %T Using ESTs for phylogenomics: Can one accurately infer a phylogenetic tree from a gappy alignment? %J Bmc Evolutionary Biology %V 8 %P - %8 Mar 26 %! Using ESTs for phylogenomics: Can one accurately infer a phylogenetic tree from a gappy alignment? %@ 1471-2148 %1 Bioinformatics crg~ %3 1 %M ISI:000255712600002 %K obligate pollination mutualism incomplete distance matrices multiple sequence alignment missing data bat phylogeny taxa euphorbiaceae supertrees genomics sites %X Background: While full genome sequences are still only available for a handful of taxa, large collections of partial gene sequences are available for many more. The alignment of partial gene sequences results in a multiple sequence alignment containing large gaps that are arranged in a staggered pattern. The consequences of this pattern of missing data on the accuracy of phylogenetic analysis are not well understood. We conducted a simulation study to determine the accuracy of phylogenetic trees obtained from gappy alignments using three commonly used phylogenetic reconstruction methods (Neighbor Joining, Maximum Parsimony, and Maximum Likelihood) and studied ways to improve the accuracy of trees obtained from such datasets. Results: We found that the pattern of gappiness in multiple sequence alignments derived from partial gene sequences substantially compromised phylogenetic accuracy even in the absence of alignment error. The decline in accuracy was beyond what would be expected based on the amount of missing data. The decline was particularly dramatic for Neighbor Joining and Maximum Parsimony, where the majority of gappy alignments contained 25% to 40% incorrect quartets. To improve the accuracy of the trees obtained from a gappy multiple sequence alignment, we examined two approaches. In the first approach, alignment masking, potentially problematic columns and input sequences are excluded from from the dataset. Even in the absence of alignment error, masking improved phylogenetic accuracy up to 100-fold. However, masking retained, on average, only 83% of the input sequences. In the second approach, alignment subdivision, the missing data is statistically modelled in order to retain as many sequences as possible in the phylogenetic analysis. Subdivision resulted in more modest improvements to alignment accuracy, but succeeded in including almost all of the input sequences. Conclusion: These results demonstrate that partial gene sequences and gappy multiple sequence alignments can pose a major problem for phylogenetic analysis. The concern will be greatest for high-throughput phylogenomic analyses, in which Neighbor Joining is often the preferred method due to its computational efficiency. Both approaches can be used to increase the accuracy of phylogenetic inference from a gappy alignment. The choice between the two approaches will depend upon how robust the application is to the loss of sequences from the input set, with alignment masking generally giving a much greater improvement in accuracy but at the cost of discarding a larger number of the input sequences. %Z 298UM Times Cited:2 Cited References Count:51 %U ://000255712600002 %+ Vision, TJ Univ N Carolina, Dept Biol, CB 3280, Chapel Hill, NC 27599 USA Univ N Carolina, Dept Biol, Chapel Hill, NC 27599 USA Univ Potsdam, Inst Biochem & Biol, D-14476 Potsdam, Germany %G English %0 Journal Article %A Hannah, M. A. %A Redestig, H. %A Leisse, A. %A Willmitzer, L. %D 2008 %T Global mRNA changes in microarray experiments %J Nature Biotechnology %V 26 %N 7 %P 741-742 %8 Jul %! Global mRNA changes in microarray experiments %@ 1087-0156 %1 Willmitzer~Genes and small Molecules~ %3 1 %M ISI:000257491600015 %K performance expression %Z 324BC Times Cited:0 Cited References Count:13 %U ://000257491600015 %+ Hannah, MA Bayer Cropsci NV, Technol Pk 38, B-9000 Ghent, Belgium Max Planck Inst Mol Pflanzenphysiol, D-14424 Potsdam, Germany %G English %0 Journal Article %A Hanikenne, M. %A Talke, I. N. %A Haydon, M. J. %A Lanz, C. %A Nolte, A. %A Motte, P. %A Kroymann, J. %A Weigel, D. %A Kraemer, U. %D 2008 %T Evolution of metal hyperaccumulation required cis-regulatory changes and triplication of HMA4 %J Nature %V 453 %N 7193 %P 391-5 %8 May 15 %! Evolution of metal hyperaccumulation required cis-regulatory changes and triplication of HMA4 %O Nature %@ 1476-4687 (Electronic) %1 Kraemer~Metal Homeostasis~ %3 1 %M 18425111 %K Adaptation, Physiological/genetics/physiology Adenosine Triphosphatases/*genetics/metabolism Arabidopsis/*genetics/*metabolism Arabidopsis Proteins/*genetics/metabolism Cadmium/metabolism *Evolution, Molecular Gene Dosage/*genetics Gene Expression Regulation, Plant/genetics Genome, Plant/genetics Metals/*metabolism Molecular Sequence Data Organ Specificity Promoter Regions (Genetics)/*genetics RNA Interference Transcription, Genetic/genetics Zinc/metabolism %X Little is known about the types of mutations underlying the evolution of species-specific traits. The metal hyperaccumulator Arabidopsis halleri has the rare ability to colonize heavy-metal-polluted soils, and, as an extremophile sister species of Arabidopsis thaliana, it is a powerful model for research on adaptation. A. halleri naturally accumulates and tolerates leaf concentrations as high as 2.2% zinc and 0.28% cadmium in dry biomass. On the basis of transcriptomics studies, metal hyperaccumulation in A. halleri has been associated with more than 30 candidate genes that are expressed at higher levels in A. halleri than in A. thaliana. Some of these genes have been genetically mapped to broad chromosomal segments of between 4 and 24 cM co-segregating with Zn and Cd hypertolerance. However, the in planta loss-of-function approaches required to demonstrate the contribution of a given candidate gene to metal hyperaccumulation or hypertolerance have not been pursued to date. Using RNA interference to downregulate HMA4 (HEAVY METAL ATPASE 4) expression, we show here that Zn hyperaccumulation and full hypertolerance to Cd and Zn in A. halleri depend on the metal pump HMA4. Contrary to a postulated global trans regulatory factor governing high expression of numerous metal hyperaccumulation genes, we demonstrate that enhanced expression of HMA4 in A. halleri is attributable to a combination of modified cis-regulatory sequences and copy number expansion, in comparison to A. thaliana. Transfer of an A. halleri HMA4 gene to A. thaliana recapitulates Zn partitioning into xylem vessels and the constitutive transcriptional upregulation of Zn deficiency response genes characteristic of Zn hyperaccumulators. Our results demonstrate the importance of cis-regulatory mutations and gene copy number expansion in the evolution of a complex naturally selected extreme trait. The elucidation of a natural strategy for metal hyperaccumulation enables the rational design of technologies for the clean-up of metal-contaminated soils and for bio-fortification. %Z Journal Article Research Support, Non-U.S. Gov't England %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18425111 %+ Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam, Germany. %G eng %0 Generic %A Handorf, T. %A Christian, N. %A Ebenhoeh, O. %A Kahn, D. %D 2008 %T An environmental perspective on metabolism %B Journal of Theoretical Biology %V 252 %N 3 %P 530-537 %8 Jun 7 %! An environmental perspective on metabolism %@ 0022-5193 %1 Ebenhoeh~Systems Biology and Mathematical Modeling~ %3 1 %M ISI:000256771500019 %K nutrient scope metabolic network networks evolution %X In principle the knowledge of an organism's metabolic network allows to infer its biosynthetic capabilities. Handorf et al. [2005. Expanding metabolic networks: scopes of compounds, robustness, and evolution. J. Mol. Evol. 61, 498-512] developed a method of network expansion generating the set of all possible metabolites that can be produced from a set of compounds, given the structure of a metabolic network. Here we investigate the inverse problem: which chemical compounds or sets of compounds must be provided as external resources in order to sustain the growth or maintenance of an organism, given the structure of its metabolic network? Although this problem is highly combinatorial, we show that it is possible to calculate locally minimal nutrient sets that can be interpreted in terms of resource types. Using these types we predict broad nutritional requirements for 447 organisms, providing clues for possible environments from the knowledge of their metabolic networks. (c) 2007 Elsevier Ltd. All rights reserved. %Z 313WU Times Cited:0 Cited References Count:14 %U ://000256771500019 %+ Handorf, T Humboldt Univ, Dept Biol, Invalidenstr 42, D-10115 Berlin, Germany Humboldt Univ, Dept Biol, D-10115 Berlin, Germany Max Planck Inst Mol Plant Physiol, D-14476 Potsdam Golm, Germany Univ Lyon 1, CNRS, INRIA, UMR 5558,Lab Biometr & Biol Evolut, F-69622 Villeurbanne, France %G English %0 Journal Article %A Guy, C. %A Kopka, J. %A Moritz, T. %D 2008 %T Plant metabolomics coming of age %J Physiologia Plantarum %V 132 %N 2 %P 113-116 %8 Feb %! Plant metabolomics coming of age %@ 0031-9317 %1 Kopka~Root Metabolism~ %3 1 %M ISI:000252261900001 %K metabolites spectrometry metabonomics h-1-nmr systems %Z 249WV Times Cited:0 Cited References Count:31 %U ://000252261900001 %+ Guy, C Univ Florida, Plant Mol & Cellular Biol Program, Dept Environm Hort, Gainesville, FL 32611 USA Univ Florida, Plant Mol & Cellular Biol Program, Dept Environm Hort, Gainesville, FL 32611 USA Max Planck Inst Mol Plant Physiol, D-14476 Potsdam, Germany Swedish Univ Agr Sci, Dept Forest Genet & Plant Physiol, Umea Plant Sci Ctr, SE-90187 Umea, Sweden %G English %0 Journal Article %A Guy, C. %A Kaplan, F. %A Kopka, J. %A Selbig, J. %A Hincha, D. K. %D 2008 %T Metabolomics of temperature stress %J Physiologia Plantarum %V 132 %N 2 %P 220-235 %8 Feb %! Metabolomics of temperature stress %@ 0031-9317 %1 Hincha~Transcript Profiling~Kopka~Root Metabolism~Selbig~Bioinformatics crg~ %3 1 %M ISI:000252261900010 %K plant cold-acclimation freezing tolerance arabidopsis-thaliana systems biology heat-stress transcription factors chilling sensitivity signaling networks pathways genes %X Plants possess inducible tolerance mechanisms that extend the temperature range for survival during acute temperature stress. The inducible mechanisms of cold acclimation and acquired thermotolerance involve highly complex processes. These include perception and signal transduction of non-optimal temperatures or their physical consequences on cellular components that program extensive modification of the transcriptome, proteome, metabolome and composition and physical structure of the cytoplasm, membranes and cell walls. Therefore, a systems biology approach will be necessary to advance the understanding of plant stress responses and tolerance mechanisms. One promise of systems biology is that it will greatly enhance our understanding of individual and collective functions and thereby provide a more holistic view of plant stress responses. Past studies have found that several metabolites that could functionally contribute to induced stress tolerance have been associated with stress responses. Recent metabolite-profiling studies have refocused attention on these and other potentially important components found in the 'temperature-stress metabolome'. These metabolomic studies have demonstrated that active reconfiguration of the metabolome is regulated in part by changes in gene expression initiated by temperature-stress-activated signaling and stress-related transcription factors. One aspect of metabolism that is consistent across all of the temperature-stress metabolomic studies to date is the prominent role of central carbohydrate metabolism, which seems to be a major feature of the reprogramming of the metabolome during temperature stress. Future metabolomic studies of plant temperature-stress responses should reveal additional metabolic pathways that have important functions in temperature-stress tolerance mechanisms. %Z 249WV Times Cited:0 Cited References Count:74 %U ://000252261900010 %+ Guy, C Univ Florida, Dept Environm Hort, Plant Mol & Cellular Biol Program, Gainesville, FL 32611 USA Univ Florida, Dept Environm Hort, Plant Mol & Cellular Biol Program, Gainesville, FL 32611 USA Univ Florida, Coll Med, Dept Biochem & Mol Biol, Gainesville, FL 32610 USA Max Planck Inst Mol Plant Physiol, D-14476 Potsdam, Germany %G English %0 Journal Article %A Grigston, J. C. %A Osuna, D. %A Scheible, W. R. %A Liu, C. %A Stitt, M. %A Jones, A. M. %D 2008 %T D-Glucose sensing by a plasma membrane regulator of G signaling protein, AtRGS1 %J Febs Letters %V 582 %N 25-26 %P 3577-3584 %8 Oct 29 %! D-Glucose sensing by a plasma membrane regulator of G signaling protein, AtRGS1 %@ 0014-5793 %1 Stitt~System Regulation~Scheible~Molecular Genomics~ %3 1 %M ISI:000260807500002 %K arabidopsis thaliana regulator of g-protein signaling protein 1 glucose sensing heterotrimeric g protein complex regulator of g signaling protein 1 arabidopsis heterotrimeric g-protein arabidopsis seed-germination abscisic-acid regulation probe level data alpha-subunit cell-proliferation beta-subunit guard-cells rgs protein sugar %X Plants use sugars as signaling molecules and possess mechanisms to detect and respond to changes in sugar availability, ranging from the level of secondary signaling molecules to altered gene transcription. G-protein-coupled pathways are involved in sugar signaling in plants. The Arabidopsis thaliana regulator of G-protein signaling protein 1 (AtRGS1) combines a receptor-like seven transmembrane domain with an RGS domain, interacts with the Arabidopsis G alpha subunit (AtGPA1) in a D-glucose-regulated manner, and stimulates AtGPA1 GTPase activity. We determined that AtRGS1 interacts with additional components, genetically defined here, to serve as a plasma membrane sensor for D-glucose. This interaction between AtRGS1 and AtGPA1 involves, in part, the seven-transmembrane domain of AtRGS1. %Z 371BT Times Cited:0 Cited References Count:60 %U ://000260807500002 %+ Jones, AM Univ N Carolina, Dept Biol, CB 3280, Chapel Hill, NC 27599 USA Univ N Carolina, Dept Biol, Chapel Hill, NC 27599 USA Univ N Carolina, Dept Pharmacol, Chapel Hill, NC 27599 USA Max Planck Inst Mol Plant Physiol, D-14476 Potsdam, Germany %G English %0 Journal Article %A Gorzka, G. %A Nikiforova, V. %D 2008 %T German-Russian Cooperation Network Biotechnology: The Project continues %J BIOforum Europe %V 12 %N 9 %P 24-25 %! German-Russian Cooperation Network Biotechnology: The Project continues %1 Nikiforova~System Integration~ %3 1 %0 Journal Article %A Giavalisco, P. %A Hummel, J. %A Lisec, J. %A Inostroza, A. C. %A Catchpole, G. %A Willmitzer, L. %D 2008 %T High-Resolution Direct Infusion-Based Mass Spectrometry in Combination with Whole C-13 Metabolome Isotope Labeling Allows Unambiguous Assignment of Chemical Sum Formulas %J Analytical Chemistry %V 80 %N 24 %P 9417-9425 %8 Dec 15 %! High-Resolution Direct Infusion-Based Mass Spectrometry in Combination with Whole C-13 Metabolome Isotope Labeling Allows Unambiguous Assignment of Chemical Sum Formulas %@ 0003-2700 %1 Willmitzer~Genes and small Molecules~Bioinformatics cig~ %3 1 %M ISI:000261728900006 %K systems biology functional genomics elemental compositions personalized medicine plant metabolomics nmr-spectroscopy ion suppression database protein tool %X A new strategy for direct infusion-based metabolite analysis employing a combination of high-resolution mass spectrometry and C-13-isotope labeling of entire metabolomes is described. Differentially isotope labeled metabolite extracts from otherwise identically grown reference plants were prepared and infused into a Fourier transform ion cyclotron resonance mass spectrometer. The derived accurate mass lists from each extract were searched, using an in-house-developed database search tool, against a number of comprehensive metabolite databases. Comparison of the retrieved chemical formulas from both, the C-12 and C-13 samples, leads to two major advantages compared to nonisotope-based metabolite fingerprinting: first, removal of background contaminations from the result list, due to the C-12/C-13 peak pairing principle and therefore positive identification of compounds of true biological origin; second, elimination of ambiguity in chemical formula assignment due to the same principle, leading to the clear association of one measured mass to only one chemical formula. Applying this combination of strategies to metabolite extracts of the model plant Arabidopsis thaliana therefore resulted in the reproducible identification of more than 1000 unambiguous chemical sum formulas of biological origin of which more than 80% have not been associated to Arabidopsis before. %Z 384FE Times Cited:0 Cited References Count:58 %U ://000261728900006 %+ Giavalisco, P Max Planck Inst Mol Pflanzenphysiol, Muhlenberg 1, D-14476 Potsdam, Germany Max Planck Inst Mol Pflanzenphysiol, D-14476 Potsdam, Germany %G English %0 Journal Article %A Geisler, D. A. %A Sampathkumar, A. %A Mutwil, M. %A Persson, S. %D 2008 %T Laying down the bricks: logistic aspects of cell wall biosynthesis %J Current opinion in plant biology %V 11 %N 6 %P 647-52 %8 Dec %! Laying down the bricks: logistic aspects of cell wall biosynthesis %O Curr Opin Plant Biol %@ 1369-5266 (Print) %1 Persson~Plant Cell Walls - Persson~ %3 1 %M 18818118 %X Plant cell wall polysaccharides are synthesised at the plasma membrane and in the Golgi apparatus. Current research efforts mainly try to address how these molecules are synthesised or modified. However, it is clear that polysaccharide synthesis in the two compartments needs to be carried out in a coordinated fashion, and that carbohydrates and proteins that are delivered from the Golgi to the cell surface have to undergo a range of modifications. Consequently, there appears to be a need for a fine-tuned system that coalesces signals from the wall, synthesis of carbohydrate-based molecules and vesicle shuttling. Several recent papers have scratched the surface for an initial understanding of these linked processes. For example, the impairment of the proton pumping activity in the trans-Golgi network, which is part of the cell's trafficking system, results in growth defects, changes in Golgi stack morphology and cellulose deficiency. An increased understanding of how cell wall synthesis is coordinated with the secretory machinery may facilitate avenues for modulating cell wall contents and therefore overall plant biomass. %Z Journal Article Research Support, Non-U.S. Gov't England %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18818118 %+ Max Planck Institute for Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam, Germany. %G eng %0 Journal Article %A Gaupels, F. %A Buhtz, A. %A Knauer, T. %A Deshmukh, S. %A Waller, F. %A van Bel, A. J. E. %A Kogel, K. H. %A Kehr, J. %D 2008 %T Adaptation of aphid stylectomy for analyses of proteins and mRNAs in barley phloem sap %J Journal of Experimental Botany %V 59 %N 12 %P 3297-3306 %8 Sep %! Adaptation of aphid stylectomy for analyses of proteins and mRNAs in barley phloem sap %@ 0022-0957 %1 Kehr~Micro- and Protein-Analysis~ %3 1 %M ISI:000259202900007 %K aphid barley cdna-aflp mrna phloem protein rhopalosiphum padi signalling stylectomy two-dimensional gel electrophoresis long-distance transport sieve-tube exudate ricinus-communis macromolecular trafficking in-vivo plants rice movement defense gene %X Sieve tubes are transport conduits not only for photoassimilates but also for macromolecules and other compounds that are involved in sieve tube maintenance and systemic signalling. In order to gain sufficient amounts of pure phloem exudates from barley plants for analyses of the protein and mRNA composition, a previously described stylectomy set-up was optimized. Aphids were placed in sealed cages, which, immediately after microcauterization of the stylets, were flooded with water-saturated silicon oil. The exuding phloem sap was collected with a capillary connected to a pump. Using up to 30 plants and 600 aphids (Rhopalosiphum padi) in parallel, an average of 10 mu l of phloem sap could be obtained within 6 h of sampling. In first analyses of the macromolecular content, eight so far unknown phloem mRNAs were identified by cDNA-amplified fragment length polymorphism. Transcripts in barley phloem exudates are related to metabolism, signalling, and pathogen defence, for example coding for a protein kinase and a pathogen- and insect-responsive WIR1A (wheat-induced resistance 1A)-like protein. Further, one-dimensional gel electrophoresis and subsequent partial sequencing by mass spectrometry led to the identification of seven major proteins with putative functions in stress responses and transport of mRNAs, proteins, and sugars. Two of the discovered proteins probably represent isoforms of a new phloem-mobile sucrose transporter. Notably, two-dimensional electrophoresis confirmed that there are > 250 phloem proteins awaiting identification in future studies. %Z 348HZ Times Cited:0 Cited References Count:56 %U ://000259202900007 %+ Gaupels, F Univ Verona, Dipartimento Sci & Tecnol, Str Grazie 15, I-37134 Verona, Italy IFZ, Inst Phytopathol & Appl Zool, D-35392 Giessen, Germany Inst Gen Bot, Plant Cell Biol Res Grp, D-35390 Giessen, Germany Max Planck Inst Mol Plant Physiol, Dept Lothar Willmitzer, D-14424 Golm, Germany %G English %0 Journal Article %A Gaude, N. %A Nakamura, Y. %A Scheible, W. R. %A Ohta, H. %A Doermann, P. %D 2008 %T Phospholipase C5 (NPC5) is involved in galactolipid accumulation during phosphate limitation in leaves of Arabidopsis %J Plant Journal %V 56 %N 1 %P 28-39 %8 Oct %! Phospholipase C5 (NPC5) is involved in galactolipid accumulation during phosphate limitation in leaves of Arabidopsis %@ 0960-7412 %1 Doermann~Molecular Genomics~Plant Lipids~Scheible~ %3 1 %M ISI:000259526700003 %K galactolipid phosphate phospholipase phospholipid sulfolipid digalactosyldiacylglycerol synthase limited growth plant gene starvation thaliana expression cells biosynthesis deprivation %X The replacement of phospholipids by galacto- and sulfolipids in plant membranes represents an important adaptive process for growth on phosphate-limiting soils. Gene expression and lipid analyses revealed that the MYB transcription factor PHR1 that has been previously shown to regulate phosphate responses is not a major factor controlling membrane lipid changes. Candidate genes for phospholipid degradation were selected based on induction of expression during phosphate deprivation. Lipid measurements in the corresponding Arabidopsis mutants revealed that the non-specific phospholipase C5 (NPC5) is required for normal accumulation of digalactosyldiacylglycerol (DGDG) during phosphate limitation in leaves. The growth and DGDG content of a double mutant npc5 pho1 (between npc5 and the phosphate-deficient pho1 mutant) are reduced compared to parental lines. The amount of DGDG increases from approximately 15 mol% to 22 mol% in npc5, compared to 28 mol% in wild-type, indicating that NPC5 is responsible for approximately 50% of the DGDG synthesized during phosphate limitation in leaves. Expression in Escherichia coli revealed that NPC5 shows phospholipase C activity on phosphatidylcholine and phosphatidylethanolamine. A double mutant of npc5 and pld zeta 2 (carrying a mutation in the phospholipase D zeta 2 gene) was generated. Lipid measurements in npc5 pld zeta 2 indicated that the contribution of PLD zeta 2 to DGDG production in leaves is negligible. In contrast to the chloroplast envelope localization of galactolipid synthesis enzymes, NPC5 localizes to the cytosol, suggesting that, during phosphate limitation, soluble NPC5 associates with membranes where it contributes to the conversion of phospholipids to diacylglycerol, the substrate for galactolipid synthesis. %Z 352VY Times Cited:0 Cited References Count:51 %U ://000259526700003 %+ Dormann, P Max Planck Inst Mol Plant Physiol, Muhlenberg 1, D-14476 Potsdam, Germany Max Planck Inst Mol Plant Physiol, D-14476 Potsdam, Germany Tokyo Inst Technol, Grad Sch Biosci & Biotechnol, Midori Ku, Yokohama, Kanagawa 2268501, Japan Tokyo Inst Technol, Ctr Biol Resources & Informat, Yokohama, Kanagawa 2268501, Japan Tokyo Inst Technol, Res Ctr Evolving Earth & Planets, Yokohama, Kanagawa 2268501, Japan %G English %0 Journal Article %A Fischer, U. %A Kuhlmann, M. %A Pecinka, A. %A Schmidt, R. %A Mette, M. F. %D 2008 %T Local DNA features affect RNA-directed transcriptional gene silencing and DNA methylation %J Plant Journal %V 53 %N 1 %P 1-10 %8 Jan %! Local DNA features affect RNA-directed transcriptional gene silencing and DNA methylation %@ 0960-7412 %1 Schmidt~ %3 1 %M ISI:000252109300001 %K transgene expression transcriptional gene silencing DNA methylation heterochromatin position effect repetitive sequences genome-wide analysis double-stranded-rna arabidopsis-thaliana expression promoters transformants integration transgenes plants level %X Transcription of a nopaline synthase promoter (pNOS) inverted repeat provides an RNA signal that can trigger transcriptional gene silencing and methylation of pNOS promoters in trans. The degree of silencing is influenced by the local DNA features close to the target promoter integration sites. Among 26 transgenic Arabidopsis thaliana lines harbouring single copies of a T-DNA including a pNOS-NPTII reporter gene at different chromosomal loci, NPTII RNA levels showed limited variation. When challenged by the silencer transgene providing the pNOS RNA signal, reduction of the NPTII RNA levels in the F-1 generation varied by more than 100-fold, ranging from no reduction to reduction to < 1% of the non-silenced level. Silencing was generally correlated with proportional DNA methylation in the pNOS region, except for one target transgene showing substantial DNA methylation without adequate silencing. Silencing was progressive through generations. Differences in the degree of silencing among the target transgenes were transmitted at least to the F-3 generation, and seemed to be influenced by transgene-flanking sequences. Apparently, close-by repeats promoted, whereas close-by functional genes diminished, the response to the silencing signal. %Z 247UY Times Cited:0 Cited References Count:33 %U ://000252109300001 %+ Mette, MF Leibniz Inst Plant Genet & Crop Plant Res, Corrensstr 3, D-06466 Gatersleben, Germany Leibniz Inst Plant Genet & Crop Plant Res, D-06466 Gatersleben, Germany Max Plank Inst Mol Plant Physiol, D-14476 Golm, Germany %G English %0 Journal Article %A Fey, H. %A Piano, D. %A Horn, R. %A Fischer, D. %A Schmidt, M. %A Ruf, S. %A Schroeder, W. P. %A Bock, R. %A Buechel, C. %D 2008 %T Isolation of highly active photosystem II core complexes with a His-tagged Cyt b559 subunit from transplastomic tobacco plants %J Biochim Biophys Acta %V 1777 %N 12 %P 1501-9 %8 Dec %! Isolation of highly active photosystem II core complexes with a His-tagged Cyt b559 subunit from transplastomic tobacco plants %O Biochimica et biophysica acta %@ 0006-3002 (Print) %1 Bock~Organelle Biology, Biotechnology and Molecular Ecophysiology~ %3 1 %M 18973745 %X Photosystem II (PSII) is a huge multi-protein-complex consisting, in higher plants and green algae, of the PS II core and the adjacent light harvesting proteins. In the study reported here, N-terminal His-tags were added to the plastome-encoded alpha-subunit of cytochrome b559, PsbE, in tobacco plants, thus facilitating rapid, mild purification of higher plant PSII. Biolistic chloroplast transformation was used to replace the wildtype psbE gene by His-tagged counterparts. Transgenic plants did not exhibit an obvious phenotype. However, the oxygen evolution capacity of thylakoids prepared from the mutants compared to the wildtype was reduced by 10-30% depending on the length of the His-tag, although Fv/Fm values differed only slightly. Homoplasmic F1 plants were used to isolate PSII cores complexes. The cores contained no detectable traces of LHC or PsaA/B polypeptides, but the main core subunits of PSII could be identified using immunodetection and mass spectroscopy. In addition, Psb27 and PsbS were detected. The presence of the former was presumably due to the preparation method, since PSII complexes located in the stroma are also isolated. In contrast to previous reports, PsbS was solely found as a monomer on SDS-PAGE in the PSII core complexes of tobacco. %Z Journal Article Research Support, Non-U.S. Gov't Netherlands %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18973745 %+ Institute of Molecular Biosciences, University of Frankfurt, Siesmayerstr. 70, D60323 Frankfurt, Germany. %G eng %0 Journal Article %A Fettke, J. %A Nunes-Nesi, A. %A Alpers, J. %A Szkop, M. %A Fernie, A. R. %A Steup, M. %D 2008 %T Alterations in Cytosolic Glucose-Phosphate Metabolism Affect Structural Features and Biochemical Properties of Starch-Related Heteroglycans %J Plant Physiology %V 148 %N 3 %P 1614-1629 %8 Nov %! Alterations in Cytosolic Glucose-Phosphate Metabolism Affect Structural Features and Biochemical Properties of Starch-Related Heteroglycans %@ 0032-0889 %1 Central Metabolism~Fernie~ %3 1 %M ISI:000260719500035 %K growing potato-tubers pho-2 phosphorylase isozyme arabidopsis-thaliana l water dikinase plastidial phosphoglucomutase subcellular-localization antisense repression maltose metabolism beta-amylases wild-type %X The cytosolic pools of glucose-1-phosphate (Glc-1-P) and glucose-6-phosphate are essential intermediates in several biosynthetic paths, including the formation of sucrose and cell wall constituents, and they are also linked to the cytosolic starch-related heteroglycans. In this work, structural features and biochemical properties of starch-related heteroglycans were analyzed as affected by the cytosolic glucose monophosphate metabolism using both source and sink organs from wild-type and various transgenic potato (Solanum tuberosum) plants. In leaves, increased levels of the cytosolic phosphoglucomutase (cPGM) did affect the cytosolic heteroglycans, as both the glucosyl content and the size distribution were diminished. By contrast, underexpression of cPGM resulted in an unchanged size distribution and an unaltered or even increased glucosyl content of the heteroglycans. Heteroglycans prepared from potato tubers were found to be similar to those from leaves but were not significantly affected by the level of cPGM activity. However, external glucose or Glc-1-P exerted entirely different effects on the cytosolic heteroglycans when added to tuber discs. Glucose was directed mainly toward starch and cell wall material, but incorporation into the constituents of the cytosolic heteroglycans was very low and roughly reflected the relative monomeric abundance. By contrast, Glc-1-P was selectively taken up by the tuber discs and resulted in a fast increase in the glucosyl content of the heteroglycans that quantitatively reflected the level of the cytosolic phosphorylase activity. Based on C-14 labeling experiments, we propose that in the cytosol, glucose and Glc-1-P are metabolized by largely separated paths. %Z 369UN Times Cited:0 Cited References Count:57 %U ://000260719500035 %+ Steup, M Univ Potsdam, Dept Plant Physiol, D-14476 Potsdam Golm, Germany Univ Potsdam, Dept Plant Physiol, D-14476 Potsdam Golm, Germany Univ Potsdam, Max Planck Inst Mol Plant Physiol, D-14476 Potsdam Golm, Germany %G English %0 Journal Article %A Farre, E. M. %A Fernie, A. R. %A Willmitzer, L. %D 2008 %T Analysis of subcellular metabolite levels of potato tubers (Solanum tuberosum) displaying alterations in cellular or extracellular sucrose metabolism %J Metabolomics %V 4 %N 2 %P 161-170 %8 Jun %! Analysis of subcellular metabolite levels of potato tubers (Solanum tuberosum) displaying alterations in cellular or extracellular sucrose metabolism %@ 1573-3882 %1 Fernie~Central Metabolism~Willmitzer~Genes and small Molecules~ %3 1 %M ISI:000255680200007 %K compartmentation plant heterotrophic carbon metabolism maltose biosynthesis metabolite profiling pho-2 phosphorylase isozyme yeast-derived invertase nonaqueous fractionation starch synthesis systems biology amino-acids leaves accumulation expression leads %X The expression of a heterologous invertase in potato tubers (Solanum tuberosum) in either the cytosol or apoplast leads to a decrease in total sucrose content and to an increase in glucose. Depending on the targeting of the enzyme different changes in phenotype and metabolism of the tubers occur: the cytosolic invertase expressing tubers show an increase in the glycolytic flux, accumulation of amino acids and organic acids, and the appearance of novel disaccharides; however, these changes are not observed when the enzyme is expressed in the apoplast [Roessner et al. (2001). Plant Cell, 13, 11-29]. The analysis of these lines raised several questions concerning the regulation of compartmentation of metabolites in potato tubers. In the current study we addressed these questions by performing comparative subcellular metabolite profiling. We demonstrate that: (i) hexoses accumulate in the vacuole independently of their site of production, but that the cytosolic invertase expression led to a strong increase in the cytosolic glucose concentration and decrease in cytosolic sucrose, whereas these effects were more moderate in the apoplastic expressors; (ii) three out of four of the novel compounds found in the cytosolic overexpressors accumulate in the same compartment; (iii) despite changes in absolute cellular content the subcellular distribution of amino acids was invariant in the invertase overexpressing tubers. These results are discussed in the context of current models of the compartmentation of primary metabolism in heterotrophic plant tissues. %Z 298IA Times Cited:0 Cited References Count:31 %U ://000255680200007 %+ Farre, EM Univ Calif San Diego, Dept Dev & Cell Biol, 9500 Gilman Dr, La Jolla, CA 92093 USA Max Planck Inst Mol Pflanzenphysiol, D-14476 Potsdam, Germany %G English %0 Journal Article %A Falkenberg, B. %A Witt, I. %A Zanor, M. I. %A Steinhauser, D. %A Mueller-Roeber, B. %A Hesse, H. %A Hoefgen, R. %D 2008 %T Transcription factors relevant to auxin signalling coordinate broad-spectrum metabolic shifts including sulphur metabolism %J Journal of Experimental Botany %V 59 %N 10 %P 2831-2846 %8 Jul %! Transcription factors relevant to auxin signalling coordinate broad-spectrum metabolic shifts including sulphur metabolism %@ 0022-0957 %1 Hoefgen~Amino Acid and Sulfur Metabolism~Mueller-Roeber~Plant Signaling~Plant Lipids~Genes and small Molecules~ %3 1 %M ISI:000257401500022 %K auxin sulphur metabolism systems biology transcription factors transgenic potato plants bacterial serine acetyltransferase arabidopsis-thaliana aux/iaa proteins methionine biosynthesis nitrogen assimilation regulatory networks response factors amino-acids gene %X A systems approach has previously been used to follow the response behaviour of Arabidopsis thaliana plants upon sulphur limitation. A response network was reconstructed from a time series of transcript and metabolite profiles, integrating complex metabolic and transcript data in order to investigate a potential causal relationship. The resulting scale-free network allowed potential transcriptional regulators of sulphur metabolism to be identified. Here, three sulphur-starvation responsive transcription factors, IAA13, IAA28, and ARF-2 (ARF1-(B) under bar inding (P) under bar rotein), all of which are related to auxin signalling, were selected for further investigation. IAA28 overexpressing and knock-down lines showed no major morphological changes, whereas IAA13- and ARF1-BP-overexpressing plants grew more slowly than the wild type. Steady-state metabolite levels and expression of pathway-relevant genes were monitored under normal and sulphate-depleted conditions. For all lines, changes in transcript and metabolite levels were observed, yet none of these changes could exclusively be linked to sulphur stress. Instead, up- or down-regulation of the transcription factors caused metabolic changes which in turn affected sulphur metabolism. Auxin-relevant transcription factors are thus part of a complex response pattern to nutrient starvation that serve as coordinators of the metabolic shifts driving sulphur homeostasis rather then as direct effectors of the sulphate assimilation pathway. This study provides the first evidence ever presented that correlates auxin-related transcriptional regulators with primary plant metabolism. %Z 322UT Times Cited:1 Cited References Count:68 %U ://000257401500022 %+ Hesse, H Max Planck Inst Mol Pflanzenphysiol, Wissensch Pk Golm, D-14424 Potsdam, Germany Max Planck Inst Mol Pflanzenphysiol, D-14424 Potsdam, Germany Univ Potsdam, Inst Biochem & Biol, D-14476 Potsdam, Germany %G English %0 Journal Article %A Fait, A. %A Hanhineva, K. %A Beleggia, R. %A Dai, N. %A Rogachev, I. %A Nikiforova, V. J. %A Fernie, A. R. %A Aharoni, A. %D 2008 %T Reconfiguration of the achene and receptacle metabolic networks during strawberry fruit development %J Plant Physiology %V 148 %N 2 %P 730-750 %8 Oct %! Reconfiguration of the achene and receptacle metabolic networks during strawberry fruit development %@ 0032-0889 %1 Fernie~Central Metabolism~Nikiforova~System Integration~ %3 1 %M ISI:000259810400006 %K fragaria x ananassa transgenic tomato plants seed development gene-expression in-vitro phenylpropanoid metabolism o-methyltransferase phenolic-compounds mass-spectrometry cv chandler %X The anatomy of strawberry (Fragaria 3 ananassa) fruit, in which the achene is found on the outer part of the fruit, makes it an excellent species for studying the regulation of fruit development. It can provide a model for the cross talk between primary and secondary metabolism, whose role is of pivotal importance in the process. By combining gas chromatography-mass spectrometry and liquid chromatography-mass spectrometry with the aim of addressing the metabolic regulation underlying fruit seed development, we simultaneously analyzed the composition of primary and secondary metabolites, separately, in achene and receptacle during fruit ripening of strawberry cultivar Herut. The results from these analyses suggest that changes in primary and secondary metabolism reflect organ and developmental specificities. For instance, the receptacle was characterized by increases in sugars and their direct derivatives, while the achene was characterized by a major decrease in the levels of carbon- and nitrogen-rich compounds, with the exception of storage-related metabolites (e. g. raffinose). Furthermore, the receptacle, and to a lesser extent the achene, exhibited dynamic fluctuations in the levels and nature of secondary metabolites across the ripening process. In the receptacle, proanthocyanidins and flavonol derivatives characterized mainly early developmental stages, while anthocyanins were abundant in the mature red stage; in the achene, ellagitannin and flavonoids were abundant during early and late development, respectively. Correlation-based network analysis suggested that metabolism is substantially coordinated during early development in either organ. Nonetheless, a higher degree of connectivity within and between metabolic pathways was measured in the achenes. The data are discussed within the context of current models both of the interaction of primary and secondary metabolism and of the metabolic interaction between the different plant organs. %Z 356XH Times Cited:1 Cited References Count:98 %U ://000259810400006 %+ Fait, A Ben Gurion Univ Negev, Jacob Blaustein Inst Desert Res, Dept Dryland Biotechnol, IL-84990 Midreshet Ben Gurion, Israel Univ Kuopio, Dept Biosci, Kuopio 70210, Finland CRA Cereal Res Ctr, I-71100 Foggia, Italy Agr Res Org, Volcani Ctr, IL-50250 Bet Dagan, Israel Weizmann Inst Sci, Dept Plant Sci, IL-76100 Rehovot, Israel Max Planck Inst Mol Pflanzenphysiol, Abt Willmitzer, D-14476 Potsdam, Germany %G English %0 Journal Article %A Fait, A. %A Fromm, H. %A Walter, D. %A Galili, G. %A Fernie, A. R. %D 2008 %T Highway or byway: the metabolic role of the GABA shunt in plants %J Trends in Plant Science %V 13 %N 1 %P 14-19 %8 Jan %! Highway or byway: the metabolic role of the GABA shunt in plants %@ 1360-1385 %1 Walther~Bioinformatics~Fernie~Central Metabolism~ %3 1 %M ISI:000253002800004 %K gamma-aminobutyric-acid succinic-semialdehyde dehydrogenase glutamate-decarboxylase amino-acids wheat seedlings arabidopsis catabolism expression leaves tomato %X Much of the recent work on the gamma-aminobutyrate (GABA) shunt in plants has concentrated on stress/pest-associated and signalling roles. However, fifty years after the structural elucidation of the pathway, aspects of its regulation and even of its biological significance remain largely obscure. Here, we assess the importance of GABA metabolism in plants, reviewing relevant biological circumstances and taking advantage of high-throughput data accessibility and computational approaches. We discuss the premise that GABA metabolism plays a major role in carbon and nitrogen primary metabolism. We further evaluate technological developments that will likely allow us to address the quantitative importance of this shunt within the biological processes to which it contributes. %Z 260IA Times Cited:0 Cited References Count:62 %U ://000253002800004 %+ Fait, A Max Planck Inst Mol Pflanzenphysiol, Dept Willmitzer, Am Muhlenberg 1, D-14476 Potsdam, Germany Max Planck Inst Mol Pflanzenphysiol, Dept Willmitzer, D-14476 Potsdam, Germany Tel Aviv Univ, Fac Life Sci, Dept Plant Sci, Tel Aviv, Israel Max Planck Inst Mol Pflanzenphysiol, Bioinformat Grp, D-14476 Potsdam, Germany Weizmann Inst Sci, Dept Plant Sci, IL-76100 Rehovot, Israel %G English %0 Journal Article %A Eisenhut, M. %A Huege, J. %A Schwarz, D. %A Bauwe, H. %A Kopka, J. %A Hagemann, M. %D 2008 %T Metabolome Phenotyping of Inorganic Carbon Limitation in Cells of the Wild Type and Photorespiratory Mutants of the Cyanobacterium Synechocystis sp Strain PCC 6803 %J Plant Physiology %V 148 %N 4 %P 2109-2120 %8 Dec %! Metabolome Phenotyping of Inorganic Carbon Limitation in Cells of the Wild Type and Photorespiratory Mutants of the Cyanobacterium Synechocystis sp Strain PCC 6803 %@ 0032-0889 %1 Kopka~Root Metabolism~ %3 1 %M ISI:000261501500029 %K flux analysis sp pcc-6803 protein pcc-7942 genomics cycle microorganisms purification spectrometry phosphatase %X The amount of inorganic carbon represents one of the main environmental factors determining productivity of photoautotrophic organisms. Using the model cyanobacterium Synechocystis sp. PCC 6803, we performed a first metabolome study with cyanobacterial cells shifted from high CO2 (5% in air) into conditions of low CO2 (LC; ambient air with 0.035% CO2). Using gas chromatography-mass spectrometry, 74 metabolites were reproducibly identified under different growth conditions. Shifting wild-type cells into LC conditions resulted in a global metabolic reprogramming and involved increases of, for example, 2-oxoglutarate (2OG) and phosphoenolpyruvate, and reductions of, for example, sucrose and fructose-1,6-bisphosphate. A decrease in Calvin-Benson cycle activity and increased usage of associated carbon cycling routes, including photorespiratory metabolism, was indicated by synergistic accumulation of the fumarate, malate, and 2- phosphoglycolate pools and a transient increase of 3-phosphoglycerate. The unexpected accumulation of 2OG with a concomitant decrease of glutamine pointed toward reduced nitrogen availability when cells are confronted with LC. Despite the increase in 2OG and low amino acid pools, we found a complete dephosphorylation of the PII regulatory protein at LC characteristic for nitrogen-replete conditions. Moreover, mutants with defined blocks in the photorespiratory metabolism leading to the accumulation of glycolate and glycine, respectively, exhibited features of LC-treated wild-type cells such as the changed 2OG to glutamine ratio and PII phosphorylation state already under high CO2 conditions. Thus, metabolome profiling demonstrated that acclimation to LC involves coordinated changes of carbon and interacting nitrogen metabolism. We hypothesize that Synechocystis has a temporal lag of acclimating carbon versus nitrogen metabolism with carbon leading. %Z 380YH Times Cited:0 Cited References Count:41 %U ://000261501500029 %+ Hagemann, M Univ Rostock, Inst Biowissensch, D-18051 Rostock, Germany Univ Rostock, Inst Biowissensch, D-18051 Rostock, Germany Max Planck Inst Mol Pflanzenphysiol, D-14476 Golm, Germany %G English %0 Journal Article %A Ehlert, B. %A Schoettler, M. A. %A Tischendorf, G. %A Ludwig-Mueller, J. %A Bock, R. %D 2008 %T The paramutated SULFUREA locus of tomato is involved in auxin biosynthesis %J Journal of Experimental Botany %V 59 %N 13 %P 3635-3647 %8 Oct %! The paramutated SULFUREA locus of tomato is involved in auxin biosynthesis %@ 0022-0957 %1 Schoettler~Photosynthesis Research~Bock~Organelle Biology, Biotechnology and Molecular Ecophysiology~ %3 1 %M ISI:000259973800013 %K auxin auxin biosynthesis paramutation photosynthesis solanum lycopersicum sulfurea cytochrome b(6)f complex reading frame reveals indole-3-acetic-acid biosynthesis targeted inactivation tropaeolum-majus plastid genome maize arabidopsis tobacco tryptophan %X The tomato (Solanum lycopersicum) sulfurea mutation displays trans-inactivation of wild-type alleles in heterozygous plants, a phenomenon referred to as paramutation. Homozygous mutant plants and paramutated leaf tissue of heterozygous plants show a pigment-deficient phenotype. The molecular basis of this phenotype and the function of the SULFUREA gene (SULF) are unknown. Here, a comprehensive physiological analysis of the sulfurea mutant is reported which suggests a molecular function for the SULFUREA locus. It is found that the sulf mutant is auxin-deficient and that the pigment-deficient phenotype is likely to represent only a secondary consequence of the auxin deficiency. This is most strongly supported by the isolation of a suppressor mutant which shows an auxin overaccumulation phenotype and contains elevated levels of indole-3-acetic acid (IAA). Several lines of evidence point to a role of the SULF gene in tryptophan-independent auxin biosynthesis, a pathway whose biochemistry and enzymology is still completely unknown. Thus, the sulfurea mutant may provide a promising entry point into elucidating the tryptophan-independent pathway of IAA synthesis. %Z 359GG Times Cited:0 Cited References Count:56 %U ://000259973800013 %+ Bock, R Max Planck Inst Mol Pflanzenphysiol, Muhlenberg 1, D-14476 Potsdam, Germany Max Planck Inst Mol Pflanzenphysiol, D-14476 Potsdam, Germany Free Univ Berlin, Inst Biol, D-14195 Berlin, Germany Tech Univ Dresden, Inst Bot, D-01062 Dresden, Germany %G English %0 Journal Article %A Ebert, B. %A Melle, C. %A Lieckfeldt, E. %A Zoeller, D. %A von Eggeling, F. %A Fisahn, J. %D 2008 %T Protein profiling of single epidermal cell types from Arabidopsis thaliana using surface-enhanced laser desorption and ionization technology %J Journal of plant physiology %V 165 %N 12 %P 1227-37 %8 Aug %! Protein profiling of single epidermal cell types from Arabidopsis thaliana using surface-enhanced laser desorption and ionization technology %O J Plant Physiol %@ 0176-1617 (Print) %1 Biophysical Analysis~Fisahn~ %3 1 %M 18423788 %X Here, we describe a novel approach for investigating differential protein expression within three epidermal cell types. In particular, 3000 single pavement, basal, and trichome cells from leaves of Arabidopsis thaliana were harvested by glass micro-capillaries. Subsequently, these single cell samples were joined to form pools of 100 individual cells and analyzed using the ProteinChip technology; SELDI: surface-enhanced laser desorption and ionization. As a result, numerous protein signals that were differentially expressed in the three epidermal cell types could be detected. One of these proteins was characterized by tryptical digestion and subsequent identification via tandem quadrupole-time of flight (Q-TOF) mass spectrometry. Down regulation of this sequenced small subunit precursor of ribulose-1,5 bisphophate carboxylase(C) oxygenase(O) (RuBisCo) in trichome and basal cells indicates the sink status of these cell types that are located on the surface of A. thaliana source leaves. Based on the obtained protein profiles, we suggest a close functional relationship between basal and trichome cells at the protein level. %Z Journal Article Germany %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18423788 %+ Max-Planck-Institute of Molecular Plant Physiology, 14776 Potsdam OT Golm, Germany. %G eng %0 Journal Article %A Dworschak, S. %A Grell, S. %A Nikiforova, V. J. %A Schaub, T. %A Selbig, J. %D 2008 %T Modeling biological networks by action languages via answer set programming %J Constraints %V 13 %N 1-2 %P 21-65 %8 Jun %! Modeling biological networks by action languages via answer set programming %@ 1383-7133 %1 Selbig~Bioinformatics crg~Nikiforova~System Integration~ %3 1 %M ISI:000255408000003 %K biological network model action language answer set programming logic programs arabidopsis-thaliana sulfur systems knowledge inference semantics pathways %X We describe an approach to modeling biological networks by action languages via answer set programming. To this end, we propose an action language for modeling biological networks, building on previous work by Baral et al. We introduce its syntax and semantics along with a translation into answer set programming, an efficient Boolean Constraint Programming Paradigm. Finally, we describe one of its applications, namely, the sulfur starvation response-pathway of the model plant Arabidopsis thaliana and sketch the functionality of our system and its usage. %Z 294LR Times Cited:0 Cited References Count:49 %U ://000255408000003 %+ Dworschak, S Univ Potsdam, Inst Informat, August Bebel Str 89, D-14482 Potsdam, Germany Univ Potsdam, Inst Informat, D-14482 Potsdam, Germany Max Planck Inst Mol Pflanzenphysiol, D-14424 Potsdam, Germany Univ Potsdam, Inst Biol Biochem, D-14439 Potsdam, Germany Russian Acad Sci, KA Timiryazev Plant Physiol Inst, Moscow 127276, Russia %G English %0 Journal Article %A Durek, P. %A Walther, D. %D 2008 %T The integrated analysis of metabolic and protein interaction networks reveals novel molecular organization principles %J BMC Syst Biol %V 2 %! The integrated analysis of metabolic and protein interaction networks reveals novel molecular organization principles %1 Walther~Bioinformatics cig~ %3 1 %< doi:10.1186/1752-0509-2-100 %0 Journal Article %A Doehlemann, G. %A Wahl, R. %A Horst, R. J. %A Voll, L. M. %A Usadel, B. %A Poree, F. %A Stitt, M. %A Pons-Kuhnemann, J. %A Sonnewald, U. %A Kahmann, R. %A Kamper, J. %D 2008 %T Reprogramming a maize plant: transcriptional and metabolic changes induced by the fungal biotroph Ustilago maydis %J Plant Journal %V 56 %N 2 %P 181-195 %8 Oct %! Reprogramming a maize plant: transcriptional and metabolic changes induced by the fungal biotroph Ustilago maydis %@ 0960-7412 %1 Stitt~System Regulation~Usadel~Integrative Carbon Biology~ %3 1 %M ISI:000259914500001 %K microarray biotrophy zea mays ustilago maydis metabolite profiling defence signalling glutathione-s-transferases programmed cell-death corn smut fungus disease resistance pathogenic development lignin biosynthesis signal-transduction response pathways stress responses jasmonic acid %X The fungal pathogen Ustilago maydis establishes a biotrophic relationship with its host plant maize (Zea mays). Hallmarks of the disease are large plant tumours in which fungal proliferation occurs. Previous studies suggested that classical defence pathways are not activated. Confocal microscopy, global expression profiling and metabolic profiling now shows that U. maydis is recognized early and triggers defence responses. Many of these early response genes are downregulated at later time points, whereas several genes associated with suppression of cell death are induced. The interplay between fungus and host involves changes in hormone signalling, induction of antioxidant and secondary metabolism, as well as the prevention of source leaf establishment. Our data provide novel insights into the complexity of a biotrophic interaction. %Z 358KA Times Cited:0 Cited References Count:79 %U ://000259914500001 %+ Kahmann, R Max Planck Inst Terr Microbiol, D-35043 Marburg, Germany Max Planck Inst Terr Microbiol, D-35043 Marburg, Germany Univ Erlangen Nurnberg, Dept Biochem, D-91058 Erlangen, Germany Max Planck Inst Plant Physiol, D-14476 Potsdam, Germany Univ Giessen, D-35392 Giessen, Germany %G English %0 Journal Article %A D'Antuono, A. L. %A Ott, T. %A Krusell, L. %A Voroshilova, V. %A Ugalde, R. A. %A Udvardi, M. %A Lepek, V. C. %D 2008 %T Defects in rhizobial cyclic glucan and lipopolysaccharide synthesis alter legume gene expression during nodule development %J Molecular Plant-Microbe Interactions %V 21 %N 1 %P 50-60 %8 Jan %! Defects in rhizobial cyclic glucan and lipopolysaccharide synthesis alter legume gene expression during nodule development %@ 0894-0282 %1 Udvardi~Molecular Plant Nutrition~ %3 1 %M ISI:000251660600005 %K competitiveness infection threads lotus glaber nod factor perception phenolic compounds symbiotic nitrogen-fixation subtractive hybridization approach receptor kinase gene medicago-truncatula sinorhizobium-meliloti lotus-japonicus model legume plant defense root-nodules potential regulators %X cDNA array technology was used to compare transcriptome profiles of Lotus japonicus roots inoculated with a Mesorhizobium loti wild-type and two mutant strains affected in cyclic beta(1-2) glucan synthesis (cgs) and in lipopolysaccharide synthesis (lps beta 2). Expression of genes associated with the development of a fully functional nodule was significantly affected in plants inoculated with the cgs mutant. Array results also revealed that induction of marker genes for nodule development was delayed when plants were inoculated with the lps beta 2 mutant. Quantitative real-time reverse-transcriptase polymerase chain reaction was used to quantify gene expression of a subset of genes involved in plant defense response, redox metabolism, or genes that encode for nodulins. The majority of the genes analyzed in this study were more highly expressed in roots inoculated with the wild type compared with those inoculated with the cgs mutant strain. Some of the genes exhibited a transient increase in transcript levels during intermediate steps of normal nodule development while others displayed induced expression during the final steps of nodule development. Ineffective nodules induced by the glucan mutant showed higher expression of phenylalanine ammonia lyase than wild-type nodules. Differences in expression pattern of genes involved in early recognition and signaling were observed in plants inoculated with the M. loti mutant strain affected in the synthesis of cyclic glucan. %Z 241MN Times Cited:0 Cited References Count:67 %U ://000251660600005 %+ Lepek, VC Univ Nacl Gen San Martin, CONICET, INTECH, Inst Investigac Biotecnol, Buenos Aires, DF, Argentina Univ Nacl Gen San Martin, CONICET, INTECH, Inst Investigac Biotecnol, Buenos Aires, DF, Argentina Max Planck Inst Mol Plant Physiol, Golm, Germany %G English %0 Journal Article %A DaMatta, F. M. %A Cunha, R. L. %A Antunes, W. C. %A Martins, S. C. V. %A Araujo, W. L. %A Fernie, A. R. %A Moraes, G. A. B. K. %D 2008 %T In field-grown coffee trees source-sink manipulation alters photosynthetic rates, independently of carbon metabolism, via alterations in stomatal function %J New Phytologist %V 178 %N 2 %P 348-357 %! In field-grown coffee trees source-sink manipulation alters photosynthetic rates, independently of carbon metabolism, via alterations in stomatal function %@ 0028-646X %1 Fernie~Central Metabolism~ %3 1 %M ISI:000254385100014 %K carbon metabolism coffea arabica gas exchange photosynthesis source-sink manipulation stomatal conductance leaf photosynthesis fruit load carbohydrate-metabolism down-regulation ring-barking peach-trees arabica plants canephora starch %X Perturbations of the source-sink balances were performed in field-grown coffee (Coffea arabica) trees to investigate the possible role of carbohydrates in feedback regulation of photosynthesis. Four treatments were applied at the whole-plant level: (i) complete defruiting and maintenance of the full leaf area, (ii) the half crop load and full leaf area, (iii) the full crop load and full leaf area and (iv) the full crop load and half leaf area. Sampling and measurements were performed twice during the phase of dry matter accumulation of fruits. Gas exchange, chlorophyll a fluorescence, carbon isotope labelling and steady-state metabolite measurements were assessed in source leaves. The average rate of net photosynthetic rate (A) and stomatal conductance (g(s)) were larger (> 50%), and carbon isotope composition ratio was lower, in trees with a full crop load and half leaf area than in defruited trees, with individuals of the other two treatments showing intermediate values. However, differences in A seem unlikely to have been caused either by photochemical impairments or a direct end-product-mediated feedback down-regulation of photosynthesis. It is proposed that the decreased A in defruited coffee trees was independent of carbon metabolism and was rather directly related to a lower CO2 availability coupled to lower g(s). %Z 279WE Times Cited:0 Cited References Count:35 %U ://000254385100014 %+ DaMatta, FM Univ Fed Vicosa, Dept Biol Vegetal, BR-36570000 Vicosa, MG, Brazil Univ Fed Vicosa, Dept Biol Vegetal, BR-36570000 Vicosa, MG, Brazil Max Planck Inst Mol Plant Physiol, D-14476 Potsdam, Germany %G English %0 Journal Article %A Crowhurst, R. N. %A Gleave, A. P. %A MacRae, E. A. %A Ampomah-Dwamena, C. %A Atkinson, R. G. %A Beuning, L. L. %A Bulley, S. M. %A Chagne, D. %A Marsh, K. B. %A Matich, A. J. %A Montefiori, M. %A Newcomb, R. D. %A Schaffer, R. J. %A Usadel, B. %A Allan, A. C. %A Boldingh, H. L. %A Bowen, J. H. %A Davy, M. W. %A Eckloff, R. %A Ferguson, A. R. %A Fraser, L. G. %A Gera, E. %A Hellens, R. P. %A Janssen, B. J. %A Klages, K. %A Lo, K. R. %A MacDiarmid, R. M. %A Nain, B. %A McNeilage, M. A. %A Rassam, M. %A Richardson, A. C. %A Rikkerink, E. H. A. %A Ross, G. S. %A Schroder, R. %A Snowden, K. C. %A Souleyre, E. J. F. %A Templeton, M. D. %A Walton, E. F. %A Wang, D. %A Wang, M. Y. %A Wang, Y. Y. %A Wood, M. %A Wu, R. M. %A Yauk, Y. K. %A Laing, W. A. %D 2008 %T Analysis of expressed sequence tags from Actinidia: Applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening %J Bmc Genomics %V 9 %P - %8 Jul 27 %! Analysis of expressed sequence tags from Actinidia: Applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening %@ 1471-2164 %1 Usadel~Integrative Carbon Biology~ %3 1 %M ISI:000258552400001 %K kiwi-fruit biochemical-characterization cell-wall shikimate dehydrogenase microsatellite markers arabidopsis-thaliana beta-galactosidase cysteine protease fleshed kiwifruit storage proteins %X Background: Kiwifruit (Actinidia spp.) are a relatively new, but economically important crop grown in many different parts of the world. Commercial success is driven by the development of new cultivars with novel consumer traits including flavor, appearance, healthful components and convenience. To increase our understanding of the genetic diversity and gene-based control of these key traits in Actinidia, we have produced a collection of 132,577 expressed sequence tags ( ESTs). Results: The ESTs were derived mainly from four Actinidia species ( A. chinensis, A. deliciosa, A. arguta and A. eriantha) and fell into 41,858 non redundant clusters ( 18,070 tentative consensus sequences and 23,788 EST singletons). Analysis of flavor and fragrance-related gene families ( acyltransferases and carboxylesterases) and pathways (terpenoid biosynthesis) is presented in comparison with a chemical analysis of the compounds present in Actinidia including esters, acids, alcohols and terpenes. ESTs are identified for most genes in color pathways controlling chlorophyll degradation and carotenoid biosynthesis. In the health area, data are presented on the ESTs involved in ascorbic acid and quinic acid biosynthesis showing not only that genes for many of the steps in these pathways are represented in the database, but that genes encoding some critical steps are absent. In the convenience area, genes related to different stages of fruit softening are identified. Conclusion: This large EST resource will allow researchers to undertake the tremendous challenge of understanding the molecular basis of genetic diversity in the Actinidia genus as well as provide an EST resource for comparative fruit genomics. The various bioinformatics analyses we have undertaken demonstrates the extent of coverage of ESTs for genes encoding different biochemical pathways in Actinidia. %Z 339BF Times Cited:0 Cited References Count:100 %U ://000258552400001 %+ Laing, WA Hort & Food Res Inst New Zealand Ltd, PB 92169, Auckland, New Zealand Hort & Food Res Inst New Zealand Ltd, Auckland, New Zealand Max Planck Inst Mol Plant Physiol, D-14476 Potsdam, Germany %G English %0 Journal Article %A Correa, L. G. %A Riano-Pachon, D. M. %A Schrago, C. G. %A dos Santos, R. V. %A Mueller-Roeber, B. %A Vincentz, M. %D 2008 %T The role of bZIP transcription factors in green plant evolution: adaptive features emerging from four founder genes %J PLoS ONE %V 3 %N 8 %P e2944 %! The role of bZIP transcription factors in green plant evolution: adaptive features emerging from four founder genes %O PLoS ONE %@ 1932-6203 (Electronic) %1 Bioinformatics~Mueller-Roeber~Plant Signaling~Walther~ %3 1 %M 18698409 %X BACKGROUND: Transcription factors of the basic leucine zipper (bZIP) family control important processes in all eukaryotes. In plants, bZIPs are regulators of many central developmental and physiological processes including photomorphogenesis, leaf and seed formation, energy homeostasis, and abiotic and biotic stress responses. Here we performed a comprehensive phylogenetic analysis of bZIP genes from algae, mosses, ferns, gymnosperms and angiosperms. METHODOLOGY/PRINCIPAL FINDINGS: We identified 13 groups of bZIP homologues in angiosperms, three more than known before, that represent 34 Possible Groups of Orthologues (PoGOs). The 34 PoGOs may correspond to the complete set of ancestral angiosperm bZIP genes that participated in the diversification of flowering plants. Homologous genes dedicated to seed-related processes and ABA-mediated stress responses originated in the common ancestor of seed plants, and three groups of homologues emerged in the angiosperm lineage, of which one group plays a role in optimizing the use of energy. CONCLUSIONS/SIGNIFICANCE: Our data suggest that the ancestor of green plants possessed four bZIP genes functionally involved in oxidative stress and unfolded protein responses that are bZIP-mediated processes in all eukaryotes, but also in light-dependent regulations. The four founder genes amplified and diverged significantly, generating traits that benefited the colonization of new environments. %Z Journal Article Research Support, Non-U.S. Gov't United States %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18698409 %+ Centro de Biologia Molecular e Engenharia Genetica, Departamento de Genetica e Evolucao, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil. %G eng %0 Journal Article %A Christensen, A. %A Svensson, K. %A Persson, S. %A Jung, J. %A Michalak, M. %A Widell, S. %A Sommarin, M. %D 2008 %T Functional characterization of Arabidopsis calreticulin1a: A key alleviator of endoplasmic reticulum stress %J Plant and Cell Physiology %V 49 %N 6 %P 912-924 %8 Jun %! Functional characterization of Arabidopsis calreticulin1a: A key alleviator of endoplasmic reticulum stress %@ 0032-0781 %1 Plant Cell Walls - Persson~Persson~ %3 1 %M ISI:000256764900005 %K endoplasmic reticulum plant arabidopsis tunicamycin bradykinin calcium plant-cells ca2+ influx expression binding protein identification thaliana calnexin overexpression inhibition %X The chaperone calreticulin plays important roles in a variety of processes in the endoplasmic reticulum (ER) of animal cells, such as Ca2+ signaling and protein folding. Although the functions of calreticulin are well characterized in animals, only indirect evidence is available for plants. To increase our understanding of plant calreticulins we introduced one of the Arabidopsis isoforms, AtCRT1a, into calreticulin-deficient (crt(-/-)) mouse embryonic fibroblasts. As a result of calreticulin deficiency, the mouse crt(-/-) fibroblasts have decreased levels of Ca2+ in the ER and impaired protein folding abilities. Expression of the AtCRT1a in mouse crt(-/-) fibroblasts rescued these phenotypes, i.e. AtCRT1a restored the Ca2+-holding capacity and chaperone functions in the ER of the mouse crt(-/-) fibroblasts, demonstrating that the animal sorting machinery was also functional for a plant protein, and that basic calreticulin functions are conserved across the Kingdoms. Expression analyses using a beta-glucuronidase (GUS)AtCRT1a promoter construct revealed high expression of CRT1a in root tips, floral tissues and in association with vascular bundles. To assess the impact of AtCRT1a in planta, we generated Atcrt1a mutant plants. The Atcrt1a mutants exhibited increased sensitivity to the drug tunicamycin, an inducer of the unfolded protein response. We therefore conclude that AtCRT1a is an alleviator of the tunicamycin-induced unfolded protein response, and propose that the use of the mouse crt(-/-) fibroblasts as a calreticulin expression system may prove useful to assess functionalities of calreticulins from different species. %Z 313UG Times Cited:1 Cited References Count:49 %U ://000256764900005 %+ Persson, S Max Planck Inst Mol Plant Physiol, Muehlenberg 1, DE-14476 Potsdam, Germany Max Planck Inst Mol Plant Physiol, DE-14476 Potsdam, Germany Lund Univ, Dept Biochem, Ctr Chem & Chem Engn, SE-22100 Lund, Sweden Lund Univ, Dept Cell & Organism Biol, SE-22362 Lund, Sweden Univ Alberta, Dept Biochem, Edmonton, AB T6G 2H7, Canada Umea Univ, Dept Plant Physiol, Umea Plant Sci Ctr, SE-90187 Umea, Sweden %G English %0 Journal Article %A Chincinska, I. A. %A Liesche, J. %A Krugel, U. %A Michalska, J. %A Geigenberger, P. %A Grimm, B. %A Kuhn, C. %D 2008 %T Sucrose transporter StSUT4 from potato affects flowering, tuberization, and shade avoidance response %J Plant Physiology %V 146 %N 2 %P 515-528 %8 Feb %! Sucrose transporter StSUT4 from potato affects flowering, tuberization, and shade avoidance response %@ 0032-0889 %1 Geigenberger~Storage Carbohydrate Metabolism~ %3 1 %M ISI:000252892700016 %K enucleate sieve elements phytochrome-b affects arabidopsis expression gibberellins plants light gene time photoperiod %X Sucrose (Suc) transporters belong to a large gene family. The physiological role of SUT1 proteins has been intensively investigated in higher plants, whereas that of SUT4 proteins is so far unknown. All three known Suc transporters from potato (Solanum tuberosum), SUT1, SUT2, and SUT4, are colocalized and their RNA levels not only follow a diurnal rhythm, but also oscillate in constant light. Here, we examined the physiological effects of transgenic potato plants on RNA interference (RNAi)inactivated StSUT4 expression. The phenotype of StSUT4-RNAi plants includes early flowering, higher tuber production, and reduced sensitivity toward light enriched in far-red wavelength (i. e. in canopy shade). Inhibition of StSUT4 led to tuber production of the strict photoperiodic potato subsp. andigena even under noninductive long-day conditions. Accumulation of soluble sugars and Suc efflux from leaves of transgenic plants are modified in StSUT4-RNAi plants, leading to modified Suc levels in sink organs. StSUT4 expression of wild-type plants is induced by gibberellins and ethephon, and external supply of gibberellic acid leads to even more pronounced differences between wild-type and StSUT4-RNAi plants regarding tuber yield and internode elongation, indicating a reciprocal regulation of StSUT4 and gibberellins. %Z 258TP Times Cited:0 Cited References Count:42 %U ://000252892700016 %+ Kuhn, C Humboldt Univ, Inst Biol Plant Physiol, D-10115 Berlin, Germany Humboldt Univ, Inst Biol Plant Physiol, D-10115 Berlin, Germany Max Planck Inst Mol Pflanzenphysiol, D-14476 Potsdam, Germany %G English %0 Journal Article %A Chen, S. %A Hajirezaei, M. R. %A Zanor, M. I. %A Hornyik, C. %A Debast, S. %A Lacomme, C. %A Fernie, A. R. %A Sonnewald, U. %A Bornke, F. %D 2008 %T RNA interference-mediated repression of sucrose-phosphatase in transgenic potato tubers (Solanum tuberosum) strongly affects the hexose-to-sucrose ratio upon cold storage with only minor effects on total soluble carbohydrate accumulation %J Plant Cell and Environment %V 31 %N 1 %P 165-176 %8 Jan %! RNA interference-mediated repression of sucrose-phosphatase in transgenic potato tubers (Solanum tuberosum) strongly affects the hexose-to-sucrose ratio upon cold storage with only minor effects on total soluble carbohydrate accumulation %O Plant Cell Environment %@ 0140-7791 %1 Fernie~Central Metabolism~ %3 1 %M ISI:000251387100013 %K cold sweetening hexogenesis sucrose sugar-signalling sucrose-6-phosphate vacuolar invertase decreased expression low-temperature arabidopsis-thaliana freezing tolerance plant-tissues water-stress synthase starch gene metabolism %X Storage of potato tubers at low temperatures leads to the accumulation of glucose and fructose in a process called 'cold sweetening'. The aim of this work was to investigate the role of sucrose-phosphatase (SPP) in potato tuber carbohydrate metabolism at low temperature (4 degrees C). To this end, RNA interference (RNAi) was used to reduce SPP expression in transgenic potato tubers. Analysis of SPP specific small interfering RNAs (siRNAs), SPP protein accumulation and enzyme activity indicated that SPP silencing in transgenic tubers was stable during the cold treatment. Analysis of soluble carbohydrates showed that in transgenic tubers, cold-induced hexogenesis was inhibited while, despite strongly reduced SPP activity, sucrose levels exceeded wild-type (WT) values four- to fivefold after 34 d of cold treatment. This led to a drastic change in the hexose-to-sucrose ratio from 1.9 in WT tubers to 0.15 to 0.11 in transgenic tubers, while the total amount of soluble sugars was largely unchanged in both genotypes. Sucrose-6(F)-phosphate (Suc6P), the substrate of SPP, accumulated in transgenic tubers in the cold which most likely enables the residual enzyme to operate with maximal catalytic activity in vivo and thus, in the long term, counterbalances reduced SPP activity in the transformants. Northern analysis revealed that cold-induced expression of vacuolar invertase (VI) was blocked in SPP-silenced tubers explaining a reduced sucrose-to-hexose conversion. Suc6P levels were found to negatively correlate with VI expression. A possible role of Suc6P in regulating VI expression is discussed. %Z 237PH Times Cited:0 Cited References Count:54 %U ://000251387100013 %+ Bornke, F Univ Dundee, Sch Life Sci, MRC Phosphorylat Unit, Dundee DD1 5EH, Scotland Univ Dundee, Sch Life Sci, MRC Phosphorylat Unit, Dundee DD1 5EH, Scotland Univ Erlangen Nurnberg, Lehrstuhl Biochem, Erlangen, Germany Leibniz Inst Pflanzengenet & Kulturpflanzenforsch, D-06466 Gatersleben, Germany Scottish Crop Res Inst, Dundee DD2 5DA, Scotland Univ Edinburgh, Inst Mol Plant Sci, Edinburgh EH9 3JH, Midlothian, Scotland Max Planck Inst Mol Pflanzenphysiol, Am Muhlenberg 1, D-14476 Potsdam, Germany %G English %0 Journal Article %A Centeno, D. C. %A Oliver, S. N. %A Nunes-Nesi, A. %A Geigenberger, P. %A Machado, D. N. %A Loureiro, M. E. %A Silva, M. A. P. %A Fernie, A. R. %D 2008 %T Metabolic regulation of pathways of carbohydrate oxidation in potato (Solanum tuberosum) tubers %J Physiologia Plantarum %V 133 %N 4 %P 744-754 %8 Aug %! Metabolic regulation of pathways of carbohydrate oxidation in potato (Solanum tuberosum) tubers %@ 0031-9317 %1 Fernie~Central Metabolism~Geigenberger~Storage Carbohydrate Metabolism~ %3 1 %M ISI:000257515300011 %K mitochondrial malate-dehydrogenase adp-glucose pyrophosphorylase pentose-phosphate pathway low internal oxygen starch synthesis sucrose degradation alternative oxidase plant respiration citrate synthase redox activation %X In the present article we evaluate the consequence of tuber-specific expression of yeast invertase, on the pathways of carbohydrate oxidation, in potato (Solanum tuberosum L. cv. Desiree). We analysed the relative rates of glycolysis and the oxidative pentose phosphate pathway that these lines exhibited as well as the relative contributions of the cytochrome and alternative pathways of mitochondrial respiration. Enzymatic and protein abundance analysis revealed concerted upregulation of the glycolytic pathway and of specific enzymes of the tricarboxylic acid cycle and the alternative oxidase but invariant levels of enzymes of the oxidative pentose phosphate pathway and proteins of the cytochrome pathway. When taken together these experiments suggest that the overexpression of a cytosolic invertase (EC 3.2.1.26) results in a general upregulation of carbohydrate oxidation with increased flux through both the glycolytic and oxidative pentose phosphate pathways as well as the cytochrome and alternative pathways of oxidative phosphorylation. Moreover these data suggest that the upregulation of respiration is a consequence of enhanced efficient mitochondrial metabolism. %Z 324JQ Times Cited:1 Cited References Count:77 %U ://000257515300011 %+ Fernie, AR Max Planck Inst Mol Pflanzenphysiol, Muhlenberg 1, D-14476 Potsdam, Germany Max Planck Inst Mol Pflanzenphysiol, D-14476 Potsdam, Germany Univ Fed Vicosa, Dept Biol Vegetal, Minas Gerais, Brazil %G English %0 Journal Article %A Cavalier, D. M. %A Lerouxel, O. %A Neumetzler, L. %A Yamauchi, K. %A Reinecke, A. %A Freshour, G. %A Zabotina, O. A. %A Hahn, M. G. %A Burgert, I. %A Pauly, M. %A Raikhel, N. V. %A Keegstra, K. %D 2008 %T Disrupting two Arabidopsis thaliana xylosyltransferase genes results in plants deficient in xyloglucan, a major primary cell wall component %J Plant Cell %V 20 %N 6 %P 1519-1537 %8 Jun %! Disrupting two Arabidopsis thaliana xylosyltransferase genes results in plants deficient in xyloglucan, a major primary cell wall component %@ 1040-4651 %1 Pauly~Plant Cell Walls~ %3 1 %M ISI:000258061200008 %K cultured soybean cells sycamore extracellular xyloglucan root hair morphogenesis monoclonal-antibodies udp-xylose fucosyl-transferase structural-analysis golgi membranes polysaccharides biosynthesis %X Xyloglucans are the main hemicellulosic polysaccharides found in the primary cell walls of dicots and nongraminaceous monocots, where they are thought to interact with cellulose to form a three-dimensional network that functions as the principal load-bearing structure of the primary cell wall. To determine whether two Arabidopsis thaliana genes that encode xylosyltransferases, XXT1 and XXT2, are involved in xyloglucan biosynthesis in vivo and to determine how the plant cell wall is affected by the lack of expression of XXT1, XXT2, or both, we isolated and characterized xxt1 and xxt2 single and xxt1 xxt2 double T-DNA insertion mutants. Although the xxt1 and xxt2 mutants did not have a gross morphological phenotype, they did have a slight decrease in xyloglucan content and showed slightly altered distribution patterns for xyloglucan epitopes. More interestingly, the xxt1 xxt2 double mutant had aberrant root hairs and lacked detectable xyloglucan. The reduction of xyloglucan in the xxt2 mutant and the lack of detectable xyloglucan in the xxt1 xxt2 double mutant resulted in significant changes in the mechanical properties of these plants. We conclude that XXT1 and XXT2 encode xylosyltransferases that are required for xyloglucan biosynthesis. Moreover, the lack of detectable xyloglucan in the xxt1 xxt2 double mutant challenges conventional models of the plant primary cell wall. %Z 332DD Times Cited:2 Cited References Count:102 %U ://000258061200008 %+ Keegstra, K Michigan State Univ, Dept Energy, Plant Res Lab, E Lansing, MI 48824 USA Michigan State Univ, Dept Energy, Plant Res Lab, E Lansing, MI 48824 USA Max Planck Inst Mol Plant Phys, D-14476 Potsdam, Germany Max Planck Inst Colloids & Interfaces, Dept Biomat, D-14424 Potsdam, Germany Univ Calif Riverside, Dept Bot & Plant Sci, Ctr Plant Cell Biol, Inst Integrat Genome Biol, Riverside, CA 92521 USA Univ Georgia, Complex Carbohydrate Res Ctr, Athens, GA 30602 USA Michigan State Univ, Dept Plant Biol, E Lansing, MI 48824 USA Michigan State Univ, Dept Biochem & Mol Biol, E Lansing, MI 48824 USA %G English %0 Journal Article %A Cartieaux, F. %A Contesto, C. %A Gallou, A. %A Desbrosses, G. %A Kopka, J. %A Taconnat, L. %A Renou, J. P. %A Touraine, B. %D 2008 %T Simultaneous interaction of Arabidopsis thaliana with Bradyrhizobium sp strain ORS278 and Pseudomonas syriugae pv. tomato DC3000 leads to complex transcriptome changes %J Molecular Plant-Microbe Interactions %V 21 %N 2 %P 244-259 %8 Feb %! Simultaneous interaction of Arabidopsis thaliana with Bradyrhizobium sp strain ORS278 and Pseudomonas syriugae pv. tomato DC3000 leads to complex transcriptome changes %@ 0894-0282 %1 Kopka~Root Metabolism~ %3 1 %M ISI:000252458600010 %K induced systemic resistance chromatography-mass spectrometry salicylic-acid functional genomics acquired-resistance gene-expression fusarium-wilt photosynthetic bradyrhizobia microarray experiments biocontrol bacteria %X Induced systemic resistance (ISR) is a process elicited by telluric microbes, referred to as plant growth-promoting rhizobacteria (PGPR), that protect the host plant against pathogen attacks. ISR has been defined from studies using Pseudomonas strains as the biocontrol agent. Here, we show for the first time that a photosynthetic Bradyrhizobium sp. strain, ORS278, also exhibits the ability to promote ISR in Arabidopsis thaliana, indicating that the ISR effect may be a widespread ability. To investigate the molecular bases of this response, we performed a transcriptome analysis designed to reveal the changes in gene expression induced by the PGPR, the pathogen alone, or by both. The results confirm the priming pattern of ISR described previously, meaning that a set of genes, of which the majority was predicted to be influenced by jasmonic acid or ethylene, was induced upon pathogen attack when plants were previously colonized by PGPR. The analysis and interpretation of transcriptome data revealed that 12-oxo-phytodienoic acid, an intermediate of the jasmonic acid biosynthesis pathway, is likely to be an actor in the signaling cascade involved in ISR. In addition, we show that the PGPR counterbalanced the pathogen-induced changes in expression of a series of genes. %Z 252PO Times Cited:0 Cited References Count:68 %U ://000252458600010 %+ Touraine, B Univ Montpellier 2, Lab Symbioses Trop & Mediterraneennes, Inst Rech Dev,Inst Natl Rech Agron,UMR 113, Ecole Natl Super Agron Montpellier, CC 002,Pl Eugene Bataillon, F-34095 Montpellier 5, France Univ Montpellier 2, Lab Symbioses Trop & Mediterraneennes, Inst Rech Dev,Inst Natl Rech Agron,UMR 113, Ecole Natl Super Agron Montpellier, F-34095 Montpellier 5, France Max Planck Inst Mol Plant Physiol, D-14476 Golm, Germany Univ Evry Val Essonne, Inst Natl Rech Agron, CNRS, UMR 8114,Unite Rech Genom Vegetale, F-91057 Evry, France %G English %0 Journal Article %A Buhtz, A. %A Springer, F. %A Chappell, L. %A Baulcombe, D. C. %A Kehr, J. %D 2008 %T Identification and characterization of small RNAs from the phloem of Brassica napus %J Plant Journal %V 53 %N 5 %P 739-749 %8 Mar %! Identification and characterization of small RNAs from the phloem of Brassica napus %@ 0960-7412 %1 Kehr~Micro- and Protein-Analysis~ %3 1 %M ISI:000253484600004 %K brassica napus microrna phloem sap copper starvation phosphate starvation sulphur starvation arabidopsis-thaliana computational identification plant micrornas interfering rna stress biogenesis targets protein genes mirna %X Systemic signalling is indispensable for the coordination of diverse physiological processes during development, defence and nutrient allocation. Indirect evidence suggests that plant small RNAs (smRNAs) could be involved in long-distance information transfer via the vasculature of the plant. Analyses of the smRNA complements of vascular exudates from oilseed rape (Brassica napus) showed that xylem sap is devoid of RNA, whereas phloem sap contained a large number of smRNAs. In addition to 32 annotated microRNAs (miRNAs) from 18 different families that could be identified and approved, a set of unknown smRNAs, predominantly of 21 and 24 nucleotides in length, was obtained, and selected candidates were found to be highly abundant in phloem sap. Moreover, we could demonstrate that the levels of three miRNAs known to respond to nutrient deprivation in non-vascular tissue, miR395 (sulphate), miR398 (copper) and miR399 (phosphate), were increased in phloem sap during the growth of plants under the respective starvation conditions. Interestingly, only mature miRNA molecules were found to be stress responsive, demonstrating that single-stranded sense miRNAs are most likely to represent the physiologically relevant molecules. The strong responses in the phloem suggest a role of miRNAs in systemic information transfer via this long-distance transport system. %Z 267BY Times Cited:8 Cited References Count:53 %U ://000253484600004 %+ Kehr, J Max Planck Inst Mol Plant Physiol, Dept Lothar Willmitzer, D-14476 Potsdam, Germany Max Planck Inst Mol Plant Physiol, Dept Lothar Willmitzer, D-14476 Potsdam, Germany John Innes Inst, Sainsbury Lab, Norwich NR4 7UH, Norfolk, England %G English %0 Journal Article %A Brandes, U. %A Delling, D. %A Gaertler, M. %A Gorke, R. %A Hoefer, M. %A Nikoloski, Z. %A Wagner, D. %D 2008 %T On modularity clustering %J IEEE Transactions on Knowledge and Data Engineering %V 20 %N 2 %P 172-188 %8 Feb %! On modularity clustering %@ 1041-4347 %1 Bioinformatics~ %3 1 %M ISI:000251686000003 %K graph clustering graph partitioning modularity community structure greedy algorithm community %X Modularity is a recently introduced quality measure for graph clusterings. It has immediately received considerable attention in several disciplines, particularly in the complex systems literature, although its properties are not well understood. We study the problem of finding clusterings with maximum modularity, thus providing theoretical foundations for past and present work based on this measure. More precisely, we prove the conjectured hardness of maximizing modularity both in the general case and with the restriction to cuts and give an Integer Linear Programming formulation. This is complemented by first insights into the behavior and performance of the commonly applied greedy agglomerative approach. %Z 241WH Times Cited:0 Cited References Count:29 %U ://000251686000003 %+ Brandes, U Univ Konstanz, Dept Comp & Informat Sci, Box D 67, D-78457 Constance, Germany Univ Konstanz, Dept Comp & Informat Sci, D-78457 Constance, Germany Univ Karlsruhe, Fac Informat, TH, ITI Wagner, D-76128 Karlsruhe, Germany Rhein Westfal TH Aachen, Dept Comp Sci, Lehrstuhl Informat 1, D-52074 Aachen, Germany Max Planck Inst Mol Plant Physiol, Bioinformat Grp, D-14476 Potsdam, Germany %G English %0 Journal Article %A Boettcher, C. %A Centeno, D. %A Freitag, J. %A Hoefgen, R. %A Koehl, K. %A Kopka, J. %A Kroymann, J. %A Matros, A. %A Mock, H. P. %A Neumann, S. %A Pfalz, M. %A Von Roepenack-Lahaye, E. %A Schauer, N. %A Trenkamp, S. %A Zurbriggen, M. %A Fernie, A. R. %D 2008 %T Teaching (and learning from) metabolomics: The 2006 PlantMetaNet ETNA Metabolomics Research School %J Physiologia Plantarum %V 132 %N 2 %P 136-149 %8 Feb %! Teaching (and learning from) metabolomics: The 2006 PlantMetaNet ETNA Metabolomics Research School %@ 0031-9317 %1 Fernie~Central Metabolism~Hoefgen~Amino Acid and Sulfur Metabolism~Kopka~Root Metabolism~Koehl~Green team~ %3 1 %M ISI:000252261900003 %K flight-mass-spectrometry plant secondary metabolism arabidopsis-thaliana functional genomics systems biology liquid-chromatography transcription factor medicago-truncatula positive selection quantitative trait %X Under the auspices of the European Training and Networking Activity programme of the European Union, a 'Metabolic Profiling and Data Analysis' Plant Genomics and Bioinformatics Summer School was hosted in Potsdam, Germany between 20 and 29 September 2006. Sixteen early career researchers were invited from the European Union partner nations and the so-called developing nations (Appendix). Lectures from invited leading European researchers provided an overview of the state of the art of these fields and seeded discussion regarding major challenges for their future advancement. Hands-on experience was provided by an example experiment - that of defining the metabolic response of Arabidopsis to treatment of a commercial herbicide of defined mode of action. This experiment was performed throughout the duration of the course in order to teach the concepts underlying extraction and machine handling as well as to provide a rich data set with which the required computation and statistical skills could be illustrated. Here we review the state of the field by describing both key lectures given at and practical aspects taught at the summer school. In addition, we disclose results that were obtained using the four distinct technical platforms at the different participating institutes. While the effects of the chosen herbicide are well documented, this study looks at a broader number of metabolites than in previous investigations. This allowed, on the one hand, not only to characterise further effects of the herbicide than previously observed but also to detect molecules other than the herbicide that were obviously present in the commercial formulation. These data and the workshop in general are all discussed in the context of the teaching of metabolomics. %Z 249WV Times Cited:0 Cited References Count:96 %U ://000252261900003 %+ Fernie, AR Leibniz Inst Plant Biochem, Weinberg 3, D-06120 Halle, Germany Leibniz Inst Plant Biochem, D-06120 Halle, Germany Max Planck Inst Mol Plant Physiol, D-14476 Potsdam, Germany Leibniz Inst Pflanzengenet & Kulturpflanzenforsch, D-06466 Gatersleben, Germany Max Planck Inst Chem Ecol, D-07745 Jena, Germany %G English %0 Journal Article %A Bock, R. %A Timmis, J. N. %D 2008 %T Reconstructing evolution: gene transfer from plastids to the nucleus %J Bioessays %V 30 %N 6 %P 556-566 %8 Jun %! Reconstructing evolution: gene transfer from plastids to the nucleus %@ 0265-9247 %1 Bock~Organelle Biology, Biotechnology and Molecular Ecophysiology~ %3 1 %M ISI:000256608700006 %K chloroplast DNA ribulose-1,5-bisphosphate carboxylase mitochondrial gene small-subunit higher-plants chlamydomonas-reinhardtii saccharomyces-cerevisiae angiosperm evolution flowering plants leaf development %X During evolution, the genomes of eukaryotic cells have undergone major restructuring to meet the new regulatory challenges associated with compartmentalization of the genetic material in the nucleus and the organelles acquired by endosymbiosis (mitochondria and plastids). Restructuring involved the loss of dispensable or redundant genes and the massive translocation of genes from the ancestral organelles to the nucleus. Genomics and bioinformatic data suggest that the process of DNA transfer from organelles to the nucleus still continues, providing raw material for evolutionary tinkering in the nuclear genome. Recent reconstruction of these events in the laboratory has provided a unique tool to observe genome evolution in real time and to study the molecular mechanisms by which plastid genes are converted into functional nuclear genes. Here, we summarize current knowledge about plastid-to-nuclear gene transfer in the context of genome evolution and discuss new insights gained from experiments that recapitulate endosymbiotic gene transfer in the laboratory. %Z 311OE Times Cited:2 Cited References Count:62 %U ://000256608700006 %+ Bock, R Max Planck Inst Mol Pflanzenphysiol, Muhlenberg 1, D-14476 Potsdam, Germany Max Planck Inst Mol Pflanzenphysiol, D-14476 Potsdam, Germany Univ Adelaide, Sch Mol & Biomed Sci Genet, Adelaide, SA, Australia %G English %0 Journal Article %A Boch, A. %A Trampczynska, A. %A Simm, C. %A Taudte, N. %A Kraemer, U. %A Clemens, S. %D 2008 %T Loss of Zhf and the tightly regulated zinc-uptake system SpZrt1 in Schizosaccharomyces pombe reveals the delicacy of cellular zinc balance %J Fems Yeast Research %V 8 %N 6 %P 883-896 %8 Sep %! Loss of Zhf and the tightly regulated zinc-uptake system SpZrt1 in Schizosaccharomyces pombe reveals the delicacy of cellular zinc balance %@ 1567-1356 %1 Kraemer~Metal Homeostasis~ %3 1 %M ISI:000258403500007 %K metal homeostasis fission yeast zinc transport zinc uptake heavy-metal detoxification fission yeast saccharomyces-cerevisiae endoplasmic-reticulum phytochelatin synthases transporter protein gene-expression cadmium tolerance iron %X Zinc is an essential micronutrient, and yet it can be toxic when present in excess. Zinc acquisition and distribution are dependent on tightly controlled transport of Zn2+ ions. Schizosaccharomyces pombe represents a second eukaryotic model to study cellular metal homeostasis. In several ways its micronutrient metabolism is fundamentally different from Saccharomyces cerevisiae. We identified the first Zn2+-uptake system in S. pombe and named it SpZrt1. Knock-out strains for all three ZIP (Zrt, Irt-like protein) transporters in fission yeast were constructed. Only zrt1 Delta cells were unable to grow at low Zn2+ and showed reduced Zn-65(2+) uptake. Elemental profiles revealed a strong decrease in zinc accumulation. Cd2+ ions inhibited uptake but Fe2+ or Mn2+ did not. Both mRNA abundance and protein amount are tightly regulated. Zrt1 activity is rapidly shut down upon transfer of zinc-deficient cells to zinc-replete conditions. In cells lacking Zhf, a transporter mediating endoplasmic reticulum storage of zinc, this response is about 100-fold more sensitive. Thus, removal of excess of zinc from the cytosol is largely Zhf dependent. Moreover, cells deficient for both transporters are no longer able to adjust to changing external Zn2+ concentrations. Optimal growth is restricted to a narrow range of Zn2+ concentrations, illustrating the fine balance between micronutrient deficiency and toxicity. %Z 336YU Times Cited:0 Cited References Count:47 %U ://000258403500007 %+ Clemens, S Univ Bayreuth, Dept Plant Physiol, Univ Str 30, D-95440 Bayreuth, Germany Univ Bayreuth, Dept Plant Physiol, D-95440 Bayreuth, Germany Leibniz Inst Plant Biochem, Halle, Germany Univ Halle Wittenberg, Dept Microbiol, D-4010 Halle, Germany Max Planck Inst Mol Plant Physiol, Golm, Germany %G English %0 Journal Article %A Bischoff, V. %A Cookson, S. %A Hofte, H. %A Scheible, W. %A Vernhettes, S. %D 2008 %T CESA-Complex motility and expression of cell wall relevant genes is altered in Thaxtomin A treated Arabidopsis seedlings %J Comparative Biochemistry and Physiology a-Molecular & Integrative Physiology %V 150 %N 3 %P S147-S147 %8 Jul %! CESA-Complex motility and expression of cell wall relevant genes is altered in Thaxtomin A treated Arabidopsis seedlings %@ 1095-6433 %1 Scheible~Molecular Genomics~ %3 1 %$ abstract %M ISI:000257631500352 %Z Suppl. S 326AY Times Cited:0 Cited References Count:0 %U ://000257631500352 %+ INRA Versailles, Versailles, France Max Planck Inst Mol Plant Physiol, D-14476 Golm, Germany %G English %0 Journal Article %A Bieniawska, Z. %A Espinoza, C. %A Schlereth, A. %A Sulpice, R. %A Hincha, D. K. %A Hannah, M. A. %D 2008 %T Disruption of the Arabidopsis circadian clock is responsible for extensive variation in the cold-responsive transcriptome %J Plant Physiology %V 147 %N 1 %P 263-279 %8 May %! Disruption of the Arabidopsis circadian clock is responsible for extensive variation in the cold-responsive transcriptome %@ 0032-0889 %1 Hincha~Transcript Profiling~System Regulation~ %3 1 %M ISI:000256419400025 %K regulated gene-expression freezing tolerance natural variation signal-transduction temperature pathway acclimation microarray growth model %X In plants, low temperature causes massive transcriptional changes, many of which are presumed to be involved in the process of cold acclimation. Given the diversity of developmental and environmental factors between experiments, it is surprising that their influence on the identification of cold-responsive genes is largely unknown. Asystematic investigation of genes responding to 1d of cold treatment revealed that diurnal- and circadian-regulated genes are responsible for the majority of the substantial variation between experiments. This is contrary to the widespread assumption that these effects are eliminated using paired diurnal controls. To identify the molecular basis for this variation, we performed targeted expression analyses of diurnal and circadian time courses in Arabidopsis (Arabidopsis thaliana). We show that, after a short initial cold response, in diurnal conditions cold reduces the amplitude of cycles for clock components and dampens or disrupts the cycles of output genes, while in continuous light all cycles become arrhythmic. This means that genes identified as cold-responsive are dependent on the time of day the experiment was performed and that a control at normal temperature will not correct for this effect, as was postulated up to now. Time of day also affects the number and strength of expression changes for a large number of transcription factors, and this likely further contributes to experimental differences. This reveals that interactions between cold and diurnal regulation are major factors in shaping the cold-responsive transcriptome and thus will be an important consideration in future experiments to dissect transcriptional regulatory networks controlling cold acclimation. In addition, our data revealed differential effects of cold on circadian output genes and a unique regulation of an oscillator component, suggesting that cold treatment could also be an important tool to probe circadian and diurnal regulatory mechanisms. %Z 308VV Times Cited:2 Cited References Count:74 %U ://000256419400025 %+ Hannah, MA Max Planck Inst Mol Pflanzenphysiol, D-14424 Potsdam, Germany Max Planck Inst Mol Pflanzenphysiol, D-14424 Potsdam, Germany %G English %0 Journal Article %A Bermudez, L. %A Urias, U. %A Milstein, D. %A Kamenetzky, L. %A Asis, R. %A Fernie, A. R. %A Van Sluys, M. A. %A Carrari, F. %A Rossi, M. %D 2008 %T A candidate gene survey of quantitative trait loci affecting chemical composition in tomato fruit %J Journal of Experimental Botany %V 59 %N 10 %P 2875-2890 %8 Jul %! A candidate gene survey of quantitative trait loci affecting chemical composition in tomato fruit %@ 0022-0957 %1 Fernie~Central Metabolism~ %3 1 %M ISI:000257401500025 %K candidate genes introgressed lines metabolite content quantitative trait loci solanum lycopersicum solanum pennelli tomato carbohydrate-metabolism introgression line sequence qtls map biosynthesis transcript methionine expression evolution %X In tomato, numerous wild-related species have been demonstrated to be untapped sources of valuable genetic variability, including pathogen-resistance genes, nutritional, and industrial quality traits. From a collection of S. pennellii introgressed lines, 889 fruit metabolic loci (QML) and 326 yield-associated loci (YAL), distributed across the tomato genome, had been identified previously. By using a combination of molecular marker sequence analysis, PCR amplification and sequencing, analysis of allelic variation, and evaluation of co-response between gene expression and metabolite composition traits, the present report, provides a comprehensive list of candidate genes co-localizing with a subset of 106 QML and 20 YAL associated either with important agronomic or nutritional characteristics. This combined strategy allowed the identification and analysis of 127 candidate genes located in 16 regions of the tomato genome. Eighty-five genes were cloned and partially sequenced, totalling 45 816 and 45 787 bases from S. lycopersicum and S. pennellii , respectively. Allelic variation at the amino acid level was confirmed for 37 of these candidates. Furthermore, out of the 127 gene-metabolite co-locations, some 56 were recovered following correlation of parallel transcript and metabolite profiling. Results obtained here represent the initial steps in the integration of genetic, genomic, and expressional patterns of genes co-localizing with chemical compositional traits of the tomato fruit. %Z 322UT Times Cited:0 Cited References Count:41 %U ://000257401500025 %+ Rossi, M IB USP, Dept Bot, GaTE Lab, Brasil Rua Matao 277, BR-05508900 Sao Paulo, Brazil IB USP, Dept Bot, GaTE Lab, BR-05508900 Sao Paulo, Brazil IB INTA, Castelar, Argentina Univ Nacl Cordoba, Fac Ciencias Quim, RA-5000 Cordoba, Argentina Max Planck Inst Mol Plant Physiol, D-14476 Potsdam, Germany %G English %0 Journal Article %A Basler, G. %A Nikoloski, Z. %A Ebenhoeh, O. %A Handorf, T. %D 2008 %T Biosynthetic potentials from species-specific metabolic networks %J Genome Informatics %V 20 %P 135–148 %! Biosynthetic potentials from species-specific metabolic networks %1 Ebenhoeh~Systems Biology and Mathematical Modeling~ %3 1 %K biosynthetic capabilities clustering scope species-specific %X Studies of genome-scale metabolic networks allow for qualitative and quantitative descriptions of an organism’s capability to convert nutrients into products. The set of synthesizable products strongly depends on the provided nutrients as well as on the structure of the metabolic network. Here, we apply the method of network expansion and the concept of scopes, describing the synthesizing capacities of an organism when certain nutrients are provided. We analyze the biosynthetic properties of four species: Arabidopsis thaliana, Saccharomyces cerevisiae, Buchnera aphidicola, and Escherichia coli. Matth¨aus et al. [12] have recently developed a method to identify clusters of scopes, reflecting specific biological functions and exhibiting a hierarchical arrangement, using the network comprising all reactions in KEGG. We extend this method by considering random sets of nutrients on well-curated networks of the investigated species from Bio-Cyc. We identify structural properties of the networks that allow to differentiate their biosynthetic capabilities. Furthermore, we evaluate the quality of the clustering of scopes applied to the species-specific networks. Our study provides a novel assessment of the biosynthetic properties of different species. %+ Max Planck Inst Mol Plant Physiol, Muhlenberg 1, D-14424 Potsdam, Germany Max Planck Inst Mol Plant Physiol, D-14424 Potsdam, Germany %G English %0 Journal Article %A Balazadeh, S. %A Riano-Pachon, D. M. %A Mueller-Roeber, B. %D 2008 %T Transcription factors regulating leaf senescence in Arabidopsis thaliana %J Plant Biol (Stuttg) %V 10 Suppl 1 %P 63-75 %8 Sep %! Transcription factors regulating leaf senescence in Arabidopsis thaliana %O Plant biology (Stuttgart, Germany) %@ 1435-8603 (Print) %1 Mueller-Roeber~Plant Signaling~ %3 1 %M 18721312 %X Senescence is a highly regulated process, eventually leading to cell and tissue disintegration: a physiological process associated with nutrient (e.g. nitrogen) redistribution from leaves to reproductive organs. Senescence is not observed in young leaves, indicating that repressors efficiently act to suppress cell degradation during early leaf development and/or that senescence activators are switched on when a leaf ages. Thus, massive regulatory network re-wiring likely constitutes an important component of the pre-senescence process. Transcription factors (TFs) have been shown to be central elements of such regulatory networks. Here, we used quantitative real-time polymerase chain reaction (qRT-PCR) analysis to study the expression of 1880 TF genes during pre-senescence and early-senescence stages of leaf development, using Arabidopsis thaliana as a model. We show that the expression of 185 TF genes changes when leaves develop from half to fully expanded leaves and finally enter partial senescence. Our analysis identified 41 TF genes that were gradually up-regulated as leaves progressed through these developmental stages. We also identified 144 TF genes that were down-regulated during senescence. A considerable number of the senescence-regulated TF genes were found to respond to abiotic stress, and salt stress appeared to be the major factor controlling their expression. Our data indicate a peculiar fine-tuning of developmental shifts during late-leaf development that is controlled by TFs. %Z Journal Article Research Support, Non-U.S. Gov't Germany %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18721312 %+ Max-Planck Institute of Molecular Plant Physiology, Am Muhlenberg 1, Potsdam-Golm, Germany. %G eng %0 Journal Article %A Balazadeh, S. %A Parlitz, S. %A Mueller-Roeber, B. %A Meyer, R. C. %D 2008 %T Natural developmental variations in leaf and plant senescence in Arabidopsis thaliana %J Plant Biology %V 10 %P 136-147 %8 Sep %! Natural developmental variations in leaf and plant senescence in Arabidopsis thaliana %@ 1435-8603 %1 Mueller-Roeber~Plant Signaling~ %3 1 %M ISI:000258078400013 %K accessions arabidopsis thaliana bolting natural variation sag12 senescence wrky53 gene-expression leaves identification reveals metabolism longevity pathways stress trait %X Leaf senescence is a developmentally regulated process that contributes to nutrient redistribution during reproductive growth and finally leads to tissue death. Manipulating leaf senescence through breeding or genetic engineering may help to improve important agronomic traits, such as crop yield and the storage life of harvested organs. Here, we studied natural variations in the regulation of plant senescence among 16 Arabidopsis thaliana accessions. Chlorophyll content and the proportion of yellow leaves were used as indicator parameters to determine leaf and plant senescence respectively. Our study indicated significant genotype effects on the onset and development of senescence. We selected three late- and five early-senescence accessions for further physiological studies. The relationship between leaf and plant senescence was accession-dependent. There was a significant correlation between plant senescence and the total number of leaves, siliques and plant bolting age. We monitored expression of two senescence marker genes, SAG12 and WRKY53, to evaluate progression of senescence. Our data revealed that chlorophyll content does not fully reflect leaf age, because even fully green leaves had already commenced senescence at the molecular level. Integrating senescence parameters, such as the proportion of senescent leaves, at the whole plant level provided a better indication of the molecular status of the plant than single leaf senescence parameters. %Z Suppl. 1 332JD Times Cited:1 Cited References Count:48 %U ://000258078400013 %+ Mueller-Roeber, B Univ Potsdam, Dept Mol Biol, Inst Biochem & Biol, Karl Liebknecht Str 24-25,Haus 20, D-14476 Potsdam, Germany Univ Potsdam, Dept Mol Biol, Inst Biochem & Biol, D-14476 Potsdam, Germany Max Planck Inst Mol Plant Physiol, Potsdam, Germany Leibniz Inst Plant Genet & Crop Plant Res, Gatersleben, Germany %G English %0 Journal Article %A Arvidsson, S. %A Kwasniewski, M. %A Riano-Pachon, D. M. %A Mueller-Roeber, B. %D 2008 %T QuantPrime - a flexible tool for reliable high-throughput primer design for quantitative PCR %J Bmc Bioinformatics %V 9 %P - %8 Nov 1 %! QuantPrime - a flexible tool for reliable high-throughput primer design for quantitative PCR %@ 1471-2105 %1 Mueller-Roeber~Plant Signaling~Bioinformatics cig~ %3 1 %M ISI:000262158700001 %K real-time pcr transcription factors annotation resource genome annotation database sequence reveals genes %X Background: Medium- to large-scale expression profiling using quantitative polymerase chain reaction (qPCR) assays are becoming increasingly important in genomics research. A major bottleneck in experiment preparation is the design of specific primer pairs, where researchers have to make several informed choices, often outside their area of expertise. Using currently available primer design tools, several interactive decisions have to be made, resulting in lengthy design processes with varying qualities of the assays. Results: Here we present QuantPrime, an intuitive and user-friendly, fully automated tool for primer pair design in small- to large-scale qPCR analyses. QuantPrime can be used online through the internet http://www.quantprime.de/or on a local computer after download; it offers design and specificity checking with highly customizable parameters and is ready to use with many publicly available transcriptomes of important higher eukaryotic model organisms and plant crops (currently 295 species in total), while benefiting from exon-intron border and alternative splice variant information in available genome annotations. Experimental results with the model plant Arabidopsis thaliana, the crop Hordeum vulgare and the model green alga Chlamydomonas reinhardtii show success rates of designed primer pairs exceeding 96%. Conclusion: QuantPrime constitutes a flexible, fully automated web application for reliable primer design for use in larger qPCR experiments, as proven by experimental data. The flexible framework is also open for simple use in other quantification applications, such as hydrolyzation probe design for qPCR and oligonucleotide probe design for quantitative in situ hybridization. Future suggestions made by users can be easily implemented, thus allowing QuantPrime to be developed into a broad-range platform for the design of RNA expression assays. %Z 390IY Times Cited:0 Cited References Count:33 %U ://000262158700001 %+ Mueller-Roeber, B Max Planck Inst Mol Plant Physiol, Muhlenberg 1, D-14476 Potsdam, Germany Max Planck Inst Mol Plant Physiol, D-14476 Potsdam, Germany Univ Potsdam, Inst Biochem & Biol, D-14476 Potsdam, Germany Silesian Univ, Dept Genet, PL-40032 Katowice, Poland %G English %0 Journal Article %A Aronsson, H. %A Schoettler, M. A. %A Kelly, A. A. %A Sundqvist, C. %A Doermann, P. %A Karim, S. %A Jarvis, P. %D 2008 %T Monogalactosyldiacylglycerol deficiency in Arabidopsis affects pigment composition in the prolamellar body and impairs thylakoid membrane energization and photoprotection in leaves %J Plant Physiology %V 148 %N 1 %P 580-592 %8 Sep %! Monogalactosyldiacylglycerol deficiency in Arabidopsis affects pigment composition in the prolamellar body and impairs thylakoid membrane energization and photoprotection in leaves %@ 0032-0889 %1 Doermann~Plant Lipids~Schoettler~Photosynthesis Research~ %3 1 %M ISI:000258947600050 %K nadph-protochlorophyllide oxidoreductase photosynthetic electron-transport transit peptide photosystem-ii outer envelope dgd1 mutant chlorophyll fluorescence protein import inner envelope in-vivo %X Monogalactosyldiacylglycerol (MGDG) is the major lipid constituent of chloroplast membranes and has been proposed to act directly in several important plastidic processes, particularly during photosynthesis. In this study, the effect of MGDG deficiency, as observed in the monogalactosyldiacylglycerol synthase1-1 (mgd1-1) mutant, on chloroplast protein targeting, phototransformation of pigments, and photosynthetic light reactions was analyzed. The targeting of plastid proteins into or across the envelope, or into the thylakoid membrane, was not different from wild-type in the mgd1 mutant, suggesting that the residual amount of MGDG in mgd1 was sufficient to maintain functional targeting mechanisms. In dark-grown plants, the ratio of bound protochlorophyllide (Pchlide, F656) to free Pchlide (F631) was increased in mgd1 compared to the wild type. Increased levels of the photoconvertible pigment-protein complex (F656), which is photoprotective and suppresses photooxidative damage caused by an excess of free Pchlide, may be an adaptive response to the mgd1 mutation. Leaves of mgd1 suffered from a massively impaired capacity for thermal dissipation of excess light due to an inefficient operation of the xanthophyll cycle; the mutant contained less zeaxanthin and more violaxanthin than wild type after 60 min of high-light exposure and suffered from increased photosystem II photoinhibition. This is attributable to an increased conductivity of the thylakoid membrane at high light intensities, so that the proton motive force is reduced and the thylakoid lumen is less acidic than in wild type. Thus, the pH-dependent activation of the violaxanthin de-epoxidase and of the PsbS protein is impaired. %Z 344SM Times Cited:0 Cited References Count:63 %U ://000258947600050 %+ Aronsson, H Univ Gothenburg, Dept Plant & Environm Sci, SE-40530 Gothenburg, Sweden Univ Gothenburg, Dept Plant & Environm Sci, SE-40530 Gothenburg, Sweden Max Planck Inst Mol Plant Physiol, D-14476 Golm, Germany Stockholm Univ, Dept Biochem & Biophys, Arrhenius Labs Nat Sci, SE-10691 Stockholm, Sweden Univ Leicester, Dept Biol, Leicester LE1 7RH, Leics, England %G English %0 Journal Article %A Araujo, W. L. %A Nunes-Nesi, A. %A Trenkamp, S. %A Bunik, V. I. %A Fernie, A. R. %D 2008 %T Inhibition of 2-Oxoglutarate Dehydrogenase in Potato Tuber Suggests the Enzyme Is Limiting for Respiration and Confirms Its Importance in Nitrogen Assimilation %J Plant Physiology %V 148 %N 4 %P 1782-1796 %8 Dec %! Inhibition of 2-Oxoglutarate Dehydrogenase in Potato Tuber Suggests the Enzyme Is Limiting for Respiration and Confirms Its Importance in Nitrogen Assimilation %@ 0032-0889 %1 Fernie~Central Metabolism~ %3 1 %M ISI:000261501500006 %K alpha-ketoglutarate-dehydrogenase pigeon breast muscle lipoate succinyltransferase complex electron-transfer flavoprotein low internal oxygen plant-mitochondria isocitrate dehydrogenases oxidative stress photosynthetic performance ammonium assimilation %X The 2-oxoglutarate dehydrogenase complex constitutes a mitochondrially localized tricarboxylic acid cycle multienzyme system responsible for the conversion of 2-oxoglutarate to succinyl-coenzyme A concomitant with NAD+ reduction. Although regulatory mechanisms of plant enzyme complexes have been characterized in vitro, little is known concerning their role in plant metabolism in situ. This issue has recently been addressed at the cellular level in nonplant systems via the use of specific phosphonate inhibitors of the enzyme. Here, we describe the application of these inhibitors for the functional analysis of the potato (Solanum tuberosum) tuber 2-oxoglutarate dehydrogenase complex. In vitro experiments revealed that succinyl phosphonate (SP) and a carboxy ethyl ester of SP are slow-binding inhibitors of the 2-oxoglutarate dehydrogenase complex, displaying greater inhibitory effects than a diethyl ester of SP, a phosphono ethyl ester of SP, or a triethyl ester of SP. Incubation of potato tuber slices with the inhibitors revealed that they were adequately taken up by the tissue and produced the anticipated effects on the in situ enzyme activity. In order to assess the metabolic consequences of the 2-oxoglutarate dehydrogenase complex inhibition, we evaluated the levels of a broad range of primary metabolites using an established gas chromatography-mass spectrometry method. We additionally analyzed the rate of respiration in both tuber discs and isolated mitochondria. Finally, we evaluated the metabolic fate of radiolabeled acetate, 2-oxoglutarate or glucose, and C-13-labeled pyruvate and glutamate following incubation of tuber discs in the presence or absence of either SP or the carboxy ethyl ester of SP. The data obtained are discussed in the context of the roles of the 2-oxoglutarate dehydrogenase complex in respiration and carbon-nitrogen interactions. %Z 380YH Times Cited:0 Cited References Count:93 %U ://000261501500006 %+ Fernie, AR Max Planck Inst Mol Pflanzenphysiol, D-14476 Potsdam, Germany Max Planck Inst Mol Pflanzenphysiol, D-14476 Potsdam, Germany Moscow MV Lomonosov State Univ, AN Belozersly Inst Physicochem Biol, Moscow 119899, Russia %G English %0 Journal Article %A Allen, A. E. %A LaRoche, J. %A Maheswari, U. %A Lommer, M. %A Schauer, N. %A Lopez, P. J. %A Finazzi, G. %A Fernie, A. R. %A Bowler, C. %D 2008 %T Whole-cell response of the pennate diatom Phaeodactylum tricornutum to iron starvation %J Proceedings of the National Academy of Sciences of the United States of America %V 105 %N 30 %P 10438-10443 %8 Jul 29 %! Whole-cell response of the pennate diatom Phaeodactylum tricornutum to iron starvation %@ 0027-8424 %1 Fernie~Central Metabolism~ %3 1 %M ISI:000258211600031 %K genome metabalomics photosynthesis transcriptomics nutrients 2 marine diatoms thalassiosira-pseudonana photosynthetic apparatus elemental stoichiometry electron-transport dunaliella-salina oxidative stress oceanic diatoms pacific-ocean phytoplankton %X Marine primary productivity is iron (Fe)-limited in vast regions of the contemporary oceans, most notably the high nutrient low chlorophyll (HNLC) regions. Diatoms often form large blooms upon the relief of Fe limitation in HNLC regions despite their prebloom low cell density. Although Fe plays an important role in controlling diatom distribution, the mechanisms of Fe uptake and adaptation to low iron availability are largely unknown. Through a combination of nontargeted transcriptomic and metabolomic approaches, we have explored the biochemical strategies preferred by Phaeodactylum tricornutum at growth-limiting levels of dissolved Fe. Processes carried out by components rich in Fe, such as photosynthesis, mitochondrial electron transport, and nitrate assimilation, were down-regulated. Our results show that this retrenchment is compensated by nitrogen (N) and carbon (C) reallocation from protein and carbohydrate degradation, adaptations to chlorophyll biosynthesis and pigment metabolism, removal of excess electrons by mitochondrial alternative oxidase (AOX) and non-photochemical quenching (NPQ), and augmented Fe-independent oxidative stress responses. Iron limitation leads to the elevated expression of at least three gene clusters absent from the Thalassiosira pseudonana genome that encode for components of iron capture and uptake mechanisms. %Z 334GZ Times Cited:2 Cited References Count:46 %U ://000258211600031 %+ LaRoche, J Leibniz Inst Meereswissensch, D-24105 Kiel, Germany Leibniz Inst Meereswissensch, D-24105 Kiel, Germany Ecole Normale Super, Ctr Natl Rech Sci Unite Mixte Rech 8186, Dept Biol, F-75005 Paris, France Max Planck Inst Mol Physiol, D-14476 Potsdam, Germany Univ Paris 06, Ctr Natl Rech Sci Unite Mixte Rech 7141, Inst Biol Physicochim, F-75005 Paris, France Stn Zool, I-80121 Naples, Italy %G English %0 Journal Article %A Ainsworth, E. A. %A Beier, C. %A Calfapietra, C. %A Ceulemans, R. %A Durand-Tardif, M. %A Farquhar, G. D. %A Godbold, D. L. %A Hendrey, G. R. %A Hickler, T. %A Kaduk, J. %A Karnosky, D. F. %A Kimball, B. A. %A Koerner, C. %A Koornneef, M. %A Lafarge, T. %A Leakey, A. D. B. %A Lewin, K. F. %A Long, S. P. %A Manderscheid, R. %A Mcneil, D. L. %A Mies, T. A. %A Miglietta, F. %A Morgan, J. A. %A Nagy, J. %A Norby, R. J. %A Norton, R. M. %A Percy, K. E. %A Rogers, A. %A Soussana, J. F. %A Stitt, M. %A Weigel, H. J. %A White, J. W. %D 2008 %T Next generation of elevated [CO2] experiments with crops: a critical investment for feeding the future world %J Plant Cell and Environment %V 31 %N 9 %P 1317-1324 %8 Sep %! Next generation of elevated [CO2] experiments with crops: a critical investment for feeding the future world %@ 0140-7791 %1 Stitt~System Regulation~ %3 1 %M ISI:000258410600011 %K climate change crop yield face genetic variation atmospheric carbon-dioxide open-air elevation climate-change stomatal conductance enrichment system photosynthesis responses yield growth face %X A rising global population and demand for protein-rich diets are increasing pressure to maximize agricultural productivity. Rising atmospheric [CO2] is altering global temperature and precipitation patterns, which challenges agricultural productivity. While rising [CO2] provides a unique opportunity to increase the productivity of C-3 crops, average yield stimulation observed to date is well below potential gains. Thus, there is room for improving productivity. However, only a fraction of available germplasm of crops has been tested for CO2 responsiveness. Yield is a complex phenotypic trait determined by the interactions of a genotype with the environment. Selection of promising genotypes and characterization of response mechanisms will only be effective if crop improvement and systems biology approaches are closely linked to production environments, that is, on the farm within major growing regions. Free air CO2 enrichment (FACE) experiments can provide the platform upon which to conduct genetic screening and elucidate the inheritance and mechanisms that underlie genotypic differences in productivity under elevated [CO2]. We propose a new generation of large-scale, low-cost per unit area FACE experiments to identify the most CO2-responsive genotypes and provide starting lines for future breeding programmes. 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