BNB-BSM
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB16757 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Woody plant material represents a renewable resource that has the potential to produce biofuels and/or novel materials with greatly reduced CO2 emissions. The study of viral infection in plants has largely focussed on detrimental symptoms, such as leaf yellowing or cell death that result in reduced crop yields. Apple rubbery wood (ARW) disease is the result of a viral infection that causes woody stems to exhibit increased flexibility. Biochemical and histochemical studies suggest the phenotype is a result of reduced lignification, specifically within the fibre cells of woody xylem. Expression analysis and proteomic data suggests that the downregulation of phenylalanine ammonia lyase (PAL) is responsible for decreased lignification. PAL is required for the first committed step in the phenylpropanoid pathway that leads to lignin biosynthesis. This is consistent with a large increase in soluble phenolics, including the lignin precursor phenylalanine, in symptomatic xylem. Downregulation of PAL appears to result from a widespread siRNA induction by the infected host, triggered by the virus. Symptomatic wood exhibited increased digestibility comparable to those seen in genetically engineered plants that alter lignin biosynthesis. To our knowledge this is the first example of a virus that alters lignin metabolism and offers a unique route to address the problem of the recalcitrant nature of plant biomass and a possible route to generating wood with altered mechanical properties.
2023-01-12 | E-MTAB-11409 | biostudies-arrayexpress
Project description:Woody plant material represents a renewable resource that has the potential to produce biofuels and/or novel materials with greatly reduced CO2 emissions. The study of viral infection in plants has largely focussed on detrimental symptoms, such as leaf yellowing or cell death that result in reduced crop yields. Apple rubbery wood (ARW) disease is the result of a viral infection that causes woody stems to exhibit increased flexibility. Biochemical and histochemical studies suggest the phenotype is a result of reduced lignification, specifically within the fibre cells of woody xylem. Expression analysis and proteomic data suggests that the downregulation of phenylalanine ammonia lyase (PAL) is responsible for decreased lignification. PAL is required for the first committed step in the phenylpropanoid pathway that leads to lignin biosynthesis. This is consistent with a large increase in soluble phenolics, including the lignin precursor phenylalanine, in symptomatic xylem. Downregulation of PAL appears to result from a widespread siRNA induction by the infected host, triggered by the virus. Symptomatic wood exhibited increased digestibility comparable to those seen in genetically engineered plants that alter lignin biosynthesis. To our knowledge this is the first example of a virus that alters lignin metabolism and offers a unique route to address the problem of the recalcitrant nature of plant biomass and a possible route to generating wood with altered mechanical properties.
2023-01-12 | E-MTAB-11410 | biostudies-arrayexpress
Project description:Backgroud: microRNA (miRNA) is implicated in plant development processes, playing pivotal roles in plant adaptation to environmental stresses. Salicornia europaea, a salt mash euhalophyte, is a good model plant to study salt adaptation mechanisms. It is also attractive in being vegetables, forage and oilseed that can be used for saline land reclamation and biofuel precursor production on marginal lands. However, none of the miRNAs from S. europaea have been identified so far. Results: Deep sequencing was performed to investigate small RNA transcriptome of S. europaea. Two hundred and twelve conserved miRNAs comprising 51 families and 31 novel miRNAs (including 7 miRNA star sequences) belonging to 30 families were identified. Interestingly, about half (13 out of 31) of the novel miRNAs were only detected in salt-treated samples. The expression of 43 conserved and 13 novel miRNAs changed significantly in response to salinity. In addition, 53 conserved miRNAs and 13 novel miRNAs were differentially expressed between shoots and roots. Furthermore, a total of 306 and 195 S. europaea unigenes were predicted to be targets of 41 conserved and 29 novel miRNA families, respectively. These targets encode a wide range of proteins, and genes involved in transcription regulation constitute the largest category. Four of them, which encode laccase, F-box family protein, SAC3/GANP family protein, and nadph-cytochrome P450 oxydoreductase, were validated using 5'-RACE. Conclusions: Our results indicate specific miRNAs are tightly regulated by salinity in shoots and/or roots of S. europaea, which play important roles in salt adaptation of this euhalophyte. The S. europaea salt-responsive miRNAs and miRNAs that target transcription factors, nucleotide binding site-leucine-rich repeat proteins and enzymes involved in lignin biosynthesis as well as carbon and nitrogen metabolism may be applied in genetic engineering of crops with higher stress tolerance, and genetic modification of biofuel crops with higher biomass and regulatable lignin biosynthesis.
2017-02-09 | GSE62521 | GEO
Project description:3-hydroxybutyrate fermenting bacterium
| PRJNA32577 | ENA
Project description:Genome sequences of Clostridium phytofermentans ISDg strains subjected to long-term growth selection in an GM3 automat with increasing concentrations of ferulic acid.
| PRJEB16745 | ENA
Project description:O antigen acts as a shield to delay early plant immune recognition of the pathogenic bacterium, Xylella fastidiosa
2020-04-06 | E-GEOD-87643 | ExpressionAtlas
Project description:H. seropedicae is a diazotrophic and endophytic bacterium that associates with economically important grasses promoting plant growth and increasing productivity. To identify genes related to bacterial ability to colonize and promote plant growth wheat seedlings growing hydroponically in Hoaglandâs medium were inoculated with H. seropedicae the bacteria and incubated for 3 days. mRNA from the bacteria present in the root surface and in the plant medium were purified, depleted from rRNA and used for RNA-seq profiling. RT-qPCR analyses were conducted to confirm regulation of selected genes. Comparison of RNA profile of bacteria attached to the root and planktonic revealed an extensive metabolic adaptation to the epiphytic life style.
2016-07-03 | E-MTAB-3646 | biostudies-arrayexpress
Project description:Lignin is a biopolymer found in plant cell walls that accounts for 30% of the organic carbon in the biosphere. White-rot fungi (WRF) are considered the most efficient organisms at degrading lignin in Nature. While lignin depolymerization by WRF has been exhaustively studied, the possibility that WRF are able to utilize lignin as a carbon source is still a matter of controversy. Here we employ 13C-labeling and systems biology approaches to demonstrate that two WRF, Trametes versicolor and Gelatoporia subvermispora, funnel lignin-derived aromatic compounds into central carbon metabolism via intracellular catabolic pathways. These results provide insights into global carbon cycling in soil ecosystems, and furthermore establishes a foundation for employing WRF in simultaneous lignin depolymerization and bioconversion to bioproducts – a key step towards enabling a sustainable bioeconomy.
2021-01-15 | GSE151629 | GEO
Project description:The fungus Polyporus brumalis is a wood decay fungus previously evidenced as efficient lignin degrader with high potential for plant biomass pre-treatment before conversion into bio-energy. Here we used an RNASeq approach that highlighted the active transcription of an unparalleled number of lignin active peroxidases and H2O2 generating enzymes during growth on wheat straw. These enzymes, together with metabolic processes related to detoxification appear as key determinants of the fungal adaption to lignin degradation.
2018-12-21 | GSE112011 | GEO