Transcriptomic analysis of Arabidopsis developing stems: a close-up on cell wall genes

<p>Abstract</p> <p>Background</p> <p>Different strategies (genetics, biochemistry, and proteomics) can be used to study proteins involved in cell biogenesis. The availability of the complete sequences of several plant genomes allowed the development of transcriptomic studies. Although the expression patterns of some <it>Arabidopsis thaliana </it>genes involved in cell wall biogenesis were identified at different physiological stages, detailed microarray analysis of plant cell wall genes has not been performed on any plant tissues. Using transcriptomic and bioinformatic tools, we studied the regulation of cell wall genes in <it>Arabidopsis </it>stems, <it>i.e. </it>genes encoding proteins involved in cell wall biogenesis and genes encoding secreted proteins.</p> <p>Results</p> <p>Transcriptomic analyses of stems were performed at three different developmental stages, <it>i.e.</it>, young stems, intermediate stage, and mature stems. Many genes involved in the synthesis of cell wall components such as polysaccharides and monolignols were identified. A total of 345 genes encoding predicted secreted proteins with moderate or high level of transcripts were analyzed in details. The encoded proteins were distributed into 8 classes, based on the presence of predicted functional domains. Proteins acting on carbohydrates and proteins of unknown function constituted the two most abundant classes. Other proteins were proteases, oxido-reductases, proteins with interacting domains, proteins involved in signalling, and structural proteins. Particularly high levels of expression were established for genes encoding pectin methylesterases, germin-like proteins, arabinogalactan proteins, fasciclin-like arabinogalactan proteins, and structural proteins. Finally, the results of this transcriptomic analyses were compared with those obtained through a cell wall proteomic analysis from the same material. Only a small proportion of genes identified by previous proteomic analyses were identified by transcriptomics. Conversely, only a few proteins encoded by genes having moderate or high level of transcripts were identified by proteomics.</p> <p>Conclusion</p> <p>Analysis of the genes predicted to encode cell wall proteins revealed that about 345 genes had moderate or high levels of transcripts. Among them, we identified many new genes possibly involved in cell wall biogenesis. The discrepancies observed between results of this transcriptomic study and a previous proteomic study on the same material revealed post-transcriptional mechanisms of regulation of expression of genes encoding cell wall proteins.</p

Transcriptomic analysis of Arabidopsis developing stems: a close-up on cell wall genes

<p>Abstract</p> <p>Background</p> <p>Different strategies (genetics, biochemistry, and proteomics) can be used to study proteins involved in cell biogenesis. The availability of the complete sequences of several plant genomes allowed the development of transcriptomic studies. Although the expression patterns of some <it>Arabidopsis thaliana </it>genes involved in cell wall biogenesis were identified at different physiological stages, detailed microarray analysis of plant cell wall genes has not been performed on any plant tissues. Using transcriptomic and bioinformatic tools, we studied the regulation of cell wall genes in <it>Arabidopsis </it>stems, <it>i.e. </it>genes encoding proteins involved in cell wall biogenesis and genes encoding secreted proteins.</p> <p>Results</p> <p>Transcriptomic analyses of stems were performed at three different developmental stages, <it>i.e.</it>, young stems, intermediate stage, and mature stems. Many genes involved in the synthesis of cell wall components such as polysaccharides and monolignols were identified. A total of 345 genes encoding predicted secreted proteins with moderate or high level of transcripts were analyzed in details. The encoded proteins were distributed into 8 classes, based on the presence of predicted functional domains. Proteins acting on carbohydrates and proteins of unknown function constituted the two most abundant classes. Other proteins were proteases, oxido-reductases, proteins with interacting domains, proteins involved in signalling, and structural proteins. Particularly high levels of expression were established for genes encoding pectin methylesterases, germin-like proteins, arabinogalactan proteins, fasciclin-like arabinogalactan proteins, and structural proteins. Finally, the results of this transcriptomic analyses were compared with those obtained through a cell wall proteomic analysis from the same material. Only a small proportion of genes identified by previous proteomic analyses were identified by transcriptomics. Conversely, only a few proteins encoded by genes having moderate or high level of transcripts were identified by proteomics.</p> <p>Conclusion</p> <p>Analysis of the genes predicted to encode cell wall proteins revealed that about 345 genes had moderate or high levels of transcripts. Among them, we identified many new genes possibly involved in cell wall biogenesis. The discrepancies observed between results of this transcriptomic study and a previous proteomic study on the same material revealed post-transcriptional mechanisms of regulation of expression of genes encoding cell wall proteins.</p

Effects of mti-2

Overexpressed in transgenic plants, protease inhibitors showed insecticidal effects against several insect taxa. We transformed potato internodes with the mustard trypsin inhibitor mti-2 gene. Among the 35 independent transgenic potato lines obtained via Agrobacterium tumefasciens transformation, four (DM6, DM7, DM11, and DM19) were selected for their high level of MTI-2 (at least to 30% of trypsin activity inhibition). Feeding assays were carried out to evaluate their effects on the green-peach aphid, Myzus persicae (Sternorrhyncha: Aphididae). Prereproductive period, nymphal mortality, adult fecundity, and doubling time of M. persicae populations were monitored on nontransformed potato plants (NT) and the four selected DM lines. Compared to NT plants, DM19 did not induce any effect on M. persicae. In contrast, DM7 and DM11 increased nymphal survival by approximately 20%. DM6 and DM11 lines slightly enhanced M. persicae daily fecundity and intrinsic rate of natural increase, leading to a reduction of the doubling time of the populations by 1 day. DM6 did not impact nymphal mortality, whereas with the DM11 almost all the nymphs survived. Potato plants transformed with the mti-2 gene variably affected the life history of M. persicae but did not show any insecticidal effect on the aphid

Imbalanced Lignin Biosynthesis Promotes the Sexual Reproduction of Homothallic Oomycete Pathogens

Lignin is incorporated into plant cell walls to maintain plant architecture and to ensure long-distance water transport. Lignin composition affects the industrial value of plant material for forage, wood and paper production, and biofuel technologies. Industrial demands have resulted in an increase in the use of genetic engineering to modify lignified plant cell wall composition. However, the interaction of the resulting plants with the environment must be analyzed carefully to ensure that there are no undesirable side effects of lignin modification. We show here that Arabidopsis thaliana mutants with impaired 5-hydroxyguaiacyl O-methyltransferase (known as caffeate O-methyltransferase; COMT) function were more susceptible to various bacterial and fungal pathogens. Unexpectedly, asexual sporulation of the downy mildew pathogen, Hyaloperonospora arabidopsidis, was impaired on these mutants. Enhanced resistance to downy mildew was not correlated with increased plant defense responses in comt1 mutants but coincided with a higher frequency of oomycete sexual reproduction within mutant tissues. Comt1 mutants but not wild-type Arabidopsis accumulated soluble 2-O-5-hydroxyferuloyl-l-malate. The compound weakened mycelium vigor and promoted sexual oomycete reproduction when applied to a homothallic oomycete in vitro. These findings suggested that the accumulation of 2-O-5-hydroxyferuloyl-l-malate accounted for the observed comt1 mutant phenotypes during the interaction with H. arabidopsidis. Taken together, our study shows that an artificial downregulation of COMT can drastically alter the interaction of a plant with the biotic environment

Arbres transgéniques, quels risques ?

National audienc