Transcription profiling of Physcomitrella patens response to red light treatment
Ontology highlight
ABSTRACT:
ORGANISM(S): Physcomitrella patens
SUBMITTER: Stefan Rensing
PROVIDER: E-MTAB-2227 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:comparison of gene expression between UV-B irradiated Physcomitrella patens gametophores with their non-irradiated controls in two different UV irradiation fields.
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Project description:AtGenExpress: A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana (Hybridisations done at NASC). The activity of genes and their encoded products can be regulated in several ways, but transcription is the primary level, since all other modes of regulation (RNA splicing, RNA and protein stability, etc.) are dependent on a gene being transcribed in the first place. The importance of transcriptional regulation has been underscored by the recent flood of global expression analyses, which have confirmed that transcriptional co-regulation of genes that act together is the norm, not the exception. Moreover, many studies suggest that evolutionary change is driven in large part by modifications of transcriptional programs. An essential first step toward deciphering the transcriptional code is to determine the expression pattern of all genes. With this goal in mind, an international effort to develop a gene expression atlas of Arabidopsis has been underway since fall 2003. This project, dubbed AtGenExpress, is funded by the DFG, and will provide the Arabidopsis community with access to a large set of Affymetrix microarray data. As part of this collaboration, we have generated expression data from 80 biologicaly different samples in triplicate. Series 1: Growth conditions: Sterilized seeds will be stratified at 4degreeC for 3 days, exposed to white light for 2 h to induce germination, and grown on MS agar plates (0.9 % agar) without sugar in total darkness for 4 days at 22degreeC. Seedlings will then be transferred to the light conditions described for each slide below for 1 h (to identify early induced genes) and 4 hrs (maximum expression of the first initial light response of most target genes), respectively. All light treatments will be done in parallel to minimize the number of dark controls. All samples will be done in triplicate and only with shoots. Experimenter name = Thomas Kretsch; Experimenter institute = AtGenExpress Experiment Overall Design: 48 samples were used in this experiment
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Project description:Alternative splicing (AS) has a significant potential to impact on the eukaryotic cell transcriptome and proteome. However, the extent of this influence as well as mechanisms, providing the tissue-specific pattern of AS are poorly studied. Here, we analyzed the AS of two life forms, protonema and gametophores, as well as the protoplasts, of a model organism, the Physcomitrella patens moss, using the data of transcriptome and proteome profiling. Altogether, 12,043 genes subjected to alternative splicing were identified. The alternative splicing patterns of 302 genes involved in stress response, growth, and development are changed considerably in the process of the gametophore development, whereas AS of 276 genes involved in transcription regulation, development, cell interactions, and cell response to biotic and abiotic stresses altered upon protoplastitation. Using mass spectrometry analysis, we studied the extent to which AS contributes to proteome diversity and identified 117 isoform-specific peptides for 36 genes with AS events. Our results indicate that AS event have a little impact on the proteome diversity and mostly result in the addition of extra amino acids rather than editing of existing proteins sequences. Among differentially expressed and spliced genes we found serine/arginine-rich (SR) genes, which are known to regulate AS in cells. We identified new isoforms of these genes and data evidencing their translation were obtained at transcriptome and proteome level. We also found that treatment with abscisic and jasmonic acids led to the isoform-specific response in protonema. Besides, we revealed the potential lncRNAmRNA and lncRNApre-mRNA interactions that can influence both the expression and alternative splicing of genes. It can point at an additional level of gene expression and AS regulation by non-coding transcripts in the Physcomitrella patens moss.
2018-01-15 | PXD005223 | Pride
Project description:We studied peptide generation process in moss Physcomitrella patens. For this purpose, analysis of peptidome and transcriptome of two different life forms (gametophores and protonema) and also of protoplasts were made.
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Project description:The establishment of seeds is considered a milestone in plant evolution. A major proportion of the protein networks underpinning desiccation tolerance, the accumulation of storage compounds, and the regulation of dormancy have probably evolved much earlier, however. The same is likely to be the case for the molecular program that drives the transition from heterotrophic offspring to the autotrophic plant. We hypothesized that a comparison with a bryophyte representing a distinct evolutionary lineage to seed plants may reveal the origin of components of the “seed program”. Therefore, we investigated the proteome of five timepoints of moss (P. patens) spore germination as well as protonemata and gametophores, and compared it to Arabidopsis proteome data during seedling establishment. This quantitative comparison showed that not only spores are functionally related to seeds but also the functional similarity of germinating spores and young seedlings. We observed remarkable similarities with regard to desiccation tolerance, lipid droplet proteome composition, control of dormancy, and the metabolic pathways that transform fatty acids into sugars. However, there were also striking differences. For example, the spores of P. patens did not harbor any obvious storage proteins. Furthermore, we did not detect homologs to the main triacylglycerol lipase in Arabidopsis, SUGAR DEPENDENT1. Instead, we discovered a triacylglycerol lipase of the oil body lipase family and a lipoxygenase as being the overall most abundant proteins in spores. This finding indicates an alternative pathway for triacylglycerol degradation via oxylipin intermediates in the moss.
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