Extension of the Visualization Tool MapMan to Allow Statistical Analysis of Arrays, Display of Coresponding Genes, and Comparison with Known Responses

Usadel, Björn; Nagel, Axel; Thimm, Oliver; Redestig, Henning; Blaesing, Oliver E.; Palacios-Rojas, Natalia; Selbig, Joachim; Hannemann, Jan; Piques, Maria; Steinhauser, Dirk; Scheible, Wolf‐Rüdiger; Gibon, Yves; Morcuende, Rosa; Weicht, Daniel; Meyer, Svenja; Stitt, Mark

doi:10.1104/pp.105.060459

Cited by 575 publications

(594 citation statements)

References 28 publications

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“…Differentially expressed genes were chosen according to a false discovery rate of 0.05 and a 1.5-fold change between SSE genotypes and the wild-type genotype (full probe set, Arabidopsis Genome Initiative list, and calculated ratios are presented in Supplemental Tables S2 and S3). Genes that responded significantly were clustered and classified according to their physiological functions using the enrichment and functional annotation clustering tools embedded in PageMan (http://mapman.mpimp-golm.mpg.de/pageman/; Usadel et al, 2005) and DAVID (http://david.abcc.ncifcrf.gov/; Huang et al, 2009). …”

Section: Microarray Analysismentioning

confidence: 99%

Seed-Specific Expression of a Feedback-Insensitive Form of CYSTATHIONINE-γ-SYNTHASE in Arabidopsis Stimulates Metabolic and Transcriptomic Responses Associated with Desiccation Stress

et al. 2014

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and Tel-Hai College, Upper Galilee 11016, Israel (R.A.) With an aim to elucidate novel metabolic and transcriptional interactions associated with methionine (Met) metabolism in seeds, we have produced transgenic Arabidopsis (Arabidopsis thaliana) seeds expressing a feedback-insensitive form of CYSTATHIONINEg-SYNTHASE, a key enzyme of Met synthesis. Metabolic profiling of these seeds revealed that, in addition to higher levels of Met, the levels of many other amino acids were elevated. The most pronounced changes were the higher levels of stress-related amino acids (isoleucine, leucine, valine, and proline), sugars, intermediates of the tricarboxylic acid cycle, and polyamines and lower levels of polyols, cysteine, and glutathione. These changes reflect stress responses and an altered mitochondrial energy metabolism. The transgenic seeds also had higher contents of total proteins and starch but lower water contents. In accordance with the metabolic profiles, microarray analysis identified a strong induction of genes involved in defense mechanisms against osmotic and drought conditions, including those mediated by the signaling cascades of ethylene and abscisic acid. These changes imply that stronger desiccation processes occur during seed development. The expression levels of transcripts controlling the levels of Met, sugars, and tricarboxylic acid cycle metabolites were also significantly elevated. Germination assays showed that the transgenic seeds had higher germination rates under salt and osmotic stresses and in the presence of ethylene substrate and abscisic acid. However, under oxidative conditions, the transgenic seeds displayed much lower germination rates. Altogether, the data provide new insights on the factors regulating Met metabolism in Arabidopsis seeds and on the mechanisms by which elevated Met levels affect seed composition and behavior.

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Section: Microarray Analysismentioning

confidence: 99%

Seed-Specific Expression of a Feedback-Insensitive Form of CYSTATHIONINE-γ-SYNTHASE in Arabidopsis Stimulates Metabolic and Transcriptomic Responses Associated with Desiccation Stress

et al. 2014

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“…Although, in general, only small fold changes of abundance in friendly relative to the wild type were observed, these changes were determined to be significant using Cybr-T (Baldi and Long, 2001) for 4,121 nonredundant transcripts (Supplemental Table S1). The significantly regulated transcripts were allocated to functional groups using MapMan (Usadel et al, 2005), resulting in the identification of 54 significantly regulated functional groups of genes ( Table I). The functional groups included Protein Synthesis and Protein Degradation, consistent with the observed induction of autophagy.…”

Section: The Roots Of Friendly Contain Significantly Greater Numbers mentioning

confidence: 99%

FRIENDLY Regulates Mitochondrial Distribution, Fusion, and Quality Control in Arabidopsis

et al. 2014

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Mitochondria are defining components of most eukaryotes. However, higher plant mitochondria differ biochemically, morphologically, and dynamically from those in other eukaryotes. FRIENDLY, a member of the CLUSTERED MITOCHONDRIA superfamily, is conserved among eukaryotes and is required for correct distribution of mitochondria within the cell. We sought to understand how disruption of FRIENDLY function in Arabidopsis (Arabidopsis thaliana) leads to mitochondrial clustering and the effects of this aberrant chondriome on cell and whole-plant physiology. We present evidence for a role of FRIENDLY in mediating intermitochondrial association, which is a necessary prelude to mitochondrial fusion. We demonstrate that disruption of mitochondrial association, motility, and chondriome structure in friendly affects mitochondrial quality control and leads to mitochondrial stress, cell death, and strong growth phenotypes.

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“…The differential expression analysis was carried out using Avadis 4.3 (Strand Genomics), while the heat maps, PCAs, and hierarchical clustering were all carried out using Partek Genomics suite software, version 6.3. MapMan (Thimm et al, 2004;Usadel et al, 2005) analyses were performed using a reduced set of unique probe sets (17,722). The mapping file used was generated as described by Howell et al (2009).…”

Section: Microarray Analysesmentioning

confidence: 99%

Defining Core Metabolic and Transcriptomic Responses to Oxygen Availability in Rice Embryos and Young Seedlings

et al. 2009

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Analysis reveals that there is limited overlap in the sets of transcripts that show significant changes in abundance during anaerobiosis in different plant species. This may be due to the fact that a combination of primary effects, changes due to the presence or absence of oxygen, and secondary effects, responses to primary changes or tissue and developmental responses, are measured together and not differentiated from each other. In order to dissect out these responses, the effect of the presence or absence of oxygen was investigated using three different experimental designs using rice (Oryza sativa) as a model system. A total of 110 metabolites and 9,596 transcripts were found to change significantly in response to oxygen availability in at least one experiment. However, only one-quarter of these showed complementary responses to oxygen in all three experiments, allowing the core response to oxygen availability to be defined. A total of 10 metabolites and 1,136 genes could be defined as aerobic responders (up-regulated in the presence of oxygen and down-regulated in its absence), and 13 metabolites and 730 genes could be defined as anaerobic responders (up-regulated in the absence of oxygen and down-regulated in its presence). Defining core sets of transcripts that were sensitive to oxygen provided insights into alterations in metabolism, specifically carbohydrate and lipid metabolism and the putative regulatory mechanisms that allow rice to grow under anaerobic conditions. Transcript abundance of a specific set of transcription factors was sensitive to oxygen availability during all of the different experiments conducted, putatively identifying primary regulators of gene expression under anaerobic conditions. Combined with the possibility of selective transcript degradation, these transcriptional processes are involved in the core response of rice to anaerobiosis.

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Extension of the Visualization Tool MapMan to Allow Statistical Analysis of Arrays, Display of Coresponding Genes, and Comparison with Known Responses

Cited by 575 publications

References 28 publications

Seed-Specific Expression of a Feedback-Insensitive Form of CYSTATHIONINE-γ-SYNTHASE in Arabidopsis Stimulates Metabolic and Transcriptomic Responses Associated with Desiccation Stress

Seed-Specific Expression of a Feedback-Insensitive Form of CYSTATHIONINE-γ-SYNTHASE in Arabidopsis Stimulates Metabolic and Transcriptomic Responses Associated with Desiccation Stress

FRIENDLY Regulates Mitochondrial Distribution, Fusion, and Quality Control in Arabidopsis

Defining Core Metabolic and Transcriptomic Responses to Oxygen Availability in Rice Embryos and Young Seedlings

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