Arabidopsis thaliana
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ABSTRACT:
OTHER RELATED OMICS DATASETS IN: E-MEXP-802
PROVIDER: PRJNA100945 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:stem developement-Lignin mutants and UV stress
| PRJNA100947 | ENA
Project description:AtGenExpress: Stress Treatments (UV-B stress)
| PRJNA96931 | ENA
Project description:Second-generation biofuels are generally produced from the polysaccharides in the lignocellulosic plant biomass, mainly cellulose. However, because cellulose is embedded in a matrix of other polysaccharides and lignin, its hydrolysis into the fermentable glucose is hampered. The senesced inflorescence stems of a set of 20 Arabidopsis thaliana mutants in 10 different genes of the lignin biosynthetic pathway were analyzed for cell wall composition and saccharification yield. Saccharification models were built to elucidate which cell wall parameters played a role in cell wall recalcitrance.Although lignin is a key polymer providing the strength necessary for the plant's ability to grow upward, a reduction in lignin content down to 64% of the wild-type level in Arabidopsis was tolerated without any obvious growth penalty. In contrast to common perception, we found that a reduction in lignin was not compensated for by an increase in cellulose, but rather by an increase in matrix polysaccharides. In most lignin mutants, the saccharification yield was improved by up to 88% cellulose conversion for the cinnamoyl-coenzyme A reductase1 mutants under pretreatment conditions, whereas the wild-type cellulose conversion only reached 18%. The saccharification models and Pearson correlation matrix revealed that the lignin content was the main factor determining the saccharification yield. However, also lignin composition, matrix polysaccharide content and composition, and, especially, the xylose, galactose, and arabinose contents influenced the saccharification yield. Strikingly, cellulose content did not significantly affect saccharification yield.Although the lignin content had the main effect on saccharification, also other cell wall factors could be engineered to potentially increase the cell wall processability, such as the galactose content. Our results contribute to a better understanding of the effect of lignin perturbations on plant cell wall composition and its influence on saccharification yield, and provide new potential targets for genetic improvement.
1000-01-01 | S-EPMC3661393 | BioStudies
Project description:Mutation of the lignin biosynthetic gene REF8, which encodes p-coumaroylshikimate 3'-hydroxylase, causes widespread changes in gene expression in Arabidopsis thaliana. Disruption of the genes encoding MED5a and MED5b, subunits of the transcriptional coregulatory complex Mediator, rescue the stunted growth of ref8-1 mutants. By comparing gene expression profiles of wild type, ref8-1, med5a/5b, and med5a/5b ref8-1 mutants, we found that the majority of gene expression changes in ref8-1 mutants depend directly or indirectly on MED5a/5b
2014-05-13 | E-MTAB-4193 | BioStudies
Project description:af09_lignin - dml6 - Transcriptome analysis of lignin mutants and UV stress effect on secondary wall synthesis - DML6 vs S DML6+UV vs S+UV S vs S+UV DML6 vs DML6+UV Keywords: normal vs disease comparison,treated vs untreated comparison Overall design: 2 dye-swap - CATMA arrays
2007-06-20 | GSE8094 | GEO
Project description:Background:Downregulation of genes involved in lignin biosynthesis and related biochemical pathways has been used as a strategy to improve biofuel production. Plant C1 metabolism provides the methyl units used for the methylation reactions carried out by two methyltransferases in the lignin biosynthetic pathway: caffeic acid 3-O-methyltransferase (COMT) and caffeoyl-CoA 3-O-methyltransferase (CCoAOMT). Mutations in these genes resulted in lower lignin levels and altered lignin compositions. Reduced lignin levels can also be achieved by mutations in the C1 pathway gene, folylpolyglutamate synthetase1 (FPGS1), in both monocotyledons and dicotyledons, indicating a link between the C1 and lignin biosynthetic pathways. To test if lignin content can be further reduced by combining genetic mutations in C1 metabolism and the lignin biosynthetic pathway, fpgs1ccoaomt1 double mutants were generated and functionally characterized. Results:Double fpgs1ccoaomt1 mutants had lower thioacidolysis lignin monomer yield and acetyl bromide lignin content than the ccoaomt1 or fpgs1 mutants and the plants themselves displayed no obvious long-term negative growth phenotypes. Moreover, extracts from the double mutants had dramatically improved enzymatic polysaccharide hydrolysis efficiencies than the single mutants: 15.1% and 20.7% higher than ccoaomt1 and fpgs1, respectively. The reduced lignin and improved sugar release of fpgs1ccoaomt1 was coupled with changes in cell-wall composition, metabolite profiles, and changes in expression of genes involved in cell-wall and lignin biosynthesis. Conclusion:Our observations demonstrate that additional reduction in lignin content and improved sugar release can be achieved by simultaneous downregulation of a gene in the C1 (FPGS1) and lignin biosynthetic (CCOAOMT) pathways. These improvements in sugar accessibility were achieved without introducing unwanted long-term plant growth and developmental defects.
2019-01-01 | S-EPMC6498598 | BioStudies
Project description:In plants, environmental perturbations often result in oxidative reactions in the apoplastic space, which are counteracted for by enzymatic and non-enzymatic antioxidative systems, including ascorbate and glutathione. However, the occurrence of the latter and its exact role in the extracellular space are not well documented. In Arabidopsis thaliana, the gamma-glutamyl transferase isoform GGT1 bound to the cell wall takes part in the so-called gamma-glutamyl cycle for extracellular glutathione degradation and recovery, and may be implicated in redox sensing and balance. In this work, oxidative conditions were imposed with UV-B radiation and studied in redox altered ggt1 mutants. Elevated UV-B has detrimental effects on plant metabolism, plasma membranes representing a major target for ROS generated by this harmful radiation. The response of ggt1 knockout Arabidopsis leaves to UV-B radiation was assessed by investigating changes in apoplastic protein composition. We then compared the expression changes resulting from the mutation and from the UV-B treatment. Rearrangements occurring in apoplastic protein composition suggest the involvement of hydrogen peroxide, which may ultimately act as a signal. Other important changes related to hormonal effects, cell wall remodeling, and redox activities are also reported. We argue that oxidative stress conditions imposed by UV-B and by disruption of the gamma-glutamyl cycle result in similar stress-induced responses, to some degree at least. Data shown here are associated with the article from Trentin et al. (2015) [1]; protein data have been deposited to the PRIDE database (Vizcaíno et al., 2014) [2] with identifier PXD001807.
2016-01-01 | S-EPMC4706617 | BioStudies
Project description:Plants coordinate their responses to various biotic and abiotic stresses in order to optimize their developmental and acclimatory programmes. The ultimate response to an excessive amount of stress is local induction of cell death mechanisms. The death of certain cells can help to maintain tissue homeostasis and enable nutrient remobilization, thus increasing the survival chances of the whole organism in unfavourable environmental conditions. UV radiation is one of the environmental factors that negatively affects the photosynthetic process and triggers cell death. The aim of this work was to evaluate a possible role of the red/far-red light photoreceptors phytochrome A (phyA) and phytochrome B (phyB) and their interrelations during acclimatory responses to UV stress. We showed that UV-C treatment caused a disturbance in photosystem II and a deregulation of photosynthetic pigment content and antioxidant enzymes activities, followed by increased cell mortality rate in phyB and phyAB null mutants. We also propose a regulatory role of phyA and phyB in CO2 assimilation, non-photochemical quenching, reactive oxygen species accumulation and salicylic acid content. Taken together, our results suggest a novel role of phytochromes as putative regulators of cell death and acclimatory responses to UV.
1000-01-01 | S-EPMC4623682 | BioStudies
Project description:Ultraviolet-B radiation acts as an environmental stimulus, but in high doses it has detrimental effects on plant metabolism. Plasma membranes represent a major target for Reactive Oxygen Species (ROS) generated by this harmful radiation. Oxidative reactions occurring in the apoplastic space are counteracted by antioxidative systems mainly involving ascorbate and, to some extent, glutathione. The occurrence of the latter and its exact role in the extracellular space are not well documented, however. In Arabidopsis thaliana, the gamma-glutamyl transferase isoform (GGT1) bound to the cell wall takes part in the so-called gamma-glutamyl cycle for extracellular glutathione degradation and recovery, and may be implicated in redox sensing and balance. In this work, oxidative conditions were imposed with Ultraviolet-B radiation (UV-B) and studied in redox altered ggt1 mutants. The response of ggt1 knockout Arabidopsis leaves to UV-B radiation was assessed by investigating changes in extracellular glutathione and ascorbate content and their redox state, and in apoplastic protein composition. Our results show that, on UV-B exposure, soluble antioxidants respond to the oxidative conditions in both genotypes. Rearrangements occur in their apoplastic protein composition, suggesting an involvement of Hydrogen Peroxide (H2O2), which may ultimately act as a signal. Other important changes relating to hormonal effects, cell wall remodeling, and redox activities are discussed. We argue that oxidative stress conditions imposed by UV-B and disruption of the gamma-glutamyl cycle result in similar stress-induced responses, to some degree at least. Data are available via ProteomeXchange with identifier PXD001807.
2015-01-01 | S-EPMC4371699 | BioStudies
Project description:<label>Background</label>Lignocellulosic biomass, such as wood and straw, is an interesting feedstock for the production of fermentable sugars. However, mainly due to the presence of lignin, this type of biomass is recalcitrant to saccharification. In Arabidopsis, lignocellulosic biomass with a lower lignin content or with lignin with an increased fraction of guaiacyl (G) and 5-hydroxyguaiacyl (5H) units shows an increased saccharification efficiency. Here, we stacked these two traits and studied the effect on the saccharification efficiency and biomass yield, by combining either transaldolase (tra2), cinnamate 4-hydroxylase (c4h-3), or 4-coumarate:CoA ligase (4cl1-1) with caffeic acid O-methyltransferase (comt-1 or comt-4) mutants.<label>Results</label>The three double mutants (tra2 comt-1, c4h-3 comt-4, and 4cl1-1 comt-4) had a decreased lignin amount and an increase in G and 5H units in the lignin polymer compared to wild-type (WT) plants. The tra2 comt-1 double mutant had a better saccharification efficiency compared to the parental lines when an acid or alkaline pretreatment was used. For the double mutants, c4h-3 comt-4 and 4cl1-1 comt-4, the saccharification efficiency was significantly higher compared to WT and its parental lines, independent of the pretreatment used. When no pretreatment was used, the saccharification efficiency increased even synergistically for these mutants.<label>Conclusion</label>Our results show that saccharification efficiency can be improved by combining two different mutant lignin traits, leading to plants with an even higher saccharification efficiency, without having a yield reduction of the primary inflorescence stem. This approach can help improve saccharification efficiency in bio-energy crops.
1000-01-01 | S-EPMC6146604 | BioStudies