Cell wall biogenesis of Arabidopsis thaliana elongating cells: transcriptomics complements proteomics Export

@article{citeulike:6048067, abstract = {BACKGROUND:Plant growth is a complex process involving cell division and elongation. Arabidopsis thaliana hypocotyls undergo a 100-fold length increase mainly by cell elongation. Cell enlargement implicates significant changes in the composition and structure of the cell wall. In order to understand cell wall biogenesis during cell elongation, mRNA profiling was made on half- (active elongation) and fully-grown (after growth arrest) etiolated hypocotyls.RESULTS:Transcriptomic analysis was focused on two sets of genes. The first set of 856 genes named cell wall genes (CWGs) included genes known to be involved in cell wall biogenesis. A significant proportion of them has detectable levels of transcripts (55.5\%), suggesting that these processes are important throughout hypocotyl elongation and after growth arrest. Genes encoding proteins involved in substrate generation or in synthesis of polysaccharides, and extracellular proteins were found to have high transcript levels. A second set of 2927 genes labeled secretory pathway genes (SPGs) was studied to search for new genes encoding secreted proteins possibly involved in wall expansion. Based on transcript level, 433 genes were selected. Genes not known to be involved in cell elongation were found to have high levels of transcripts. Encoded proteins were proteases, protease inhibitors, proteins with interacting domains, and proteins involved in lipid metabolism. In addition, 125 of them encoded proteins of unknown function. Finally, comparison with results of a cell wall proteomic study on the same material revealed that 48 out of the 137 identified proteins were products of the genes having high or moderate level of transcripts. About 15\% of the genes encoding proteins identified by proteomics showed levels of transcripts below background.CONCLUSIONS:Members of known multigenic families involved in cell wall biogenesis, and new genes that might participate in cell elongation were identified. Significant differences were shown in the expression of such genes in half- and fully-grown hypocotyls. No clear correlation was found between the abundance of transcripts (transcriptomic data) and the presence of the proteins (proteomic data) demonstrating (i) the importance of post-transcriptional events for the regulation of genes during cell elongation and (ii) that transcriptomic and proteomic data are complementary.}, author = {Jamet, Elisabeth and Roujol, David and San Clemente, Helene and Irshad, Muhammad and Taconnat, Ludivine S. and Renou, Jean P. and Lezica, Rafael P.}, citeulike-article-id = {6048067}, citeulike-linkout-0 = {http://dx.doi.org/10.1186/1471-2164-10-505}, day = {31}, doi = {10.1186/1471-2164-10-505}, issn = {1471-2164}, journal = {BMC Genomics}, keywords = {cell\_wall, dataset, plants, proteomics, transcriptome}, month = {October}, number = {1}, pages = {505+}, posted-at = {2009-11-03 17:56:29}, priority = {2}, title = {Cell wall biogenesis of Arabidopsis thaliana elongating cells: transcriptomics complements proteomics}, url = {http://dx.doi.org/10.1186/1471-2164-10-505}, volume = {10}, year = {2009} }

TY - JOUR ID - citeulike:6048067 L3 - citeulike-article-id:6048067 N2 - BACKGROUND:Plant growth is a complex process involving cell division and elongation. Arabidopsis thaliana hypocotyls undergo a 100-fold length increase mainly by cell elongation. Cell enlargement implicates significant changes in the composition and structure of the cell wall. In order to understand cell wall biogenesis during cell elongation, mRNA profiling was made on half- (active elongation) and fully-grown (after growth arrest) etiolated hypocotyls.RESULTS:Transcriptomic analysis was focused on two sets of genes. The first set of 856 genes named cell wall genes (CWGs) included genes known to be involved in cell wall biogenesis. A significant proportion of them has detectable levels of transcripts (55.5%), suggesting that these processes are important throughout hypocotyl elongation and after growth arrest. Genes encoding proteins involved in substrate generation or in synthesis of polysaccharides, and extracellular proteins were found to have high transcript levels. A second set of 2927 genes labeled secretory pathway genes (SPGs) was studied to search for new genes encoding secreted proteins possibly involved in wall expansion. Based on transcript level, 433 genes were selected. Genes not known to be involved in cell elongation were found to have high levels of transcripts. Encoded proteins were proteases, protease inhibitors, proteins with interacting domains, and proteins involved in lipid metabolism. In addition, 125 of them encoded proteins of unknown function. Finally, comparison with results of a cell wall proteomic study on the same material revealed that 48 out of the 137 identified proteins were products of the genes having high or moderate level of transcripts. About 15% of the genes encoding proteins identified by proteomics showed levels of transcripts below background.CONCLUSIONS:Members of known multigenic families involved in cell wall biogenesis, and new genes that might participate in cell elongation were identified. Significant differences were shown in the expression of such genes in half- and fully-grown hypocotyls. No clear correlation was found between the abundance of transcripts (transcriptomic data) and the presence of the proteins (proteomic data) demonstrating (i) the importance of post-transcriptional events for the regulation of genes during cell elongation and (ii) that transcriptomic and proteomic data are complementary. IS - 1 JF - BMC Genomics SN - 1471-2164 TI - Cell wall biogenesis of Arabidopsis thaliana elongating cells: transcriptomics complements proteomics VL - 10 SP - 505 KW - cell_wall KW - dataset KW - plants KW - proteomics KW - transcriptome AU - Jamet, Elisabeth AU - Roujol, David AU - San Clemente, Helene AU - Irshad, Muhammad AU - Taconnat, Ludivine AU - Renou, Jean AU - Lezica, Rafael PY - 2009/10/31/ UR - http://dx.doi.org/10.1186/1471-2164-10-505 ER -