Ontology highlight
ABSTRACT:
PROVIDER: PRJNA886999 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Interactions between plants and each neighboring microbial species are fundamental building blocks that collectively determine the structure and function of the plant microbiota, but the molecular basis of such interactions is poorly characterized. Here, we monocolonized Arabidopsis leaves with nine plant-associated bacteria from all major phyla of the plant microbiota and profiled co-transcriptomes of plants and bacteria. These strains elicited quantitatively different plant transcriptional responses including typical pattern-triggered immunity responses. Genes of non-pathogenic bacteria involved in general metabolism and energy production were commonly suppressed in planta in contrast to a virulent pathogen. Various nutrient acquisition pathways that are frequently encoded in the genomes of plant-associated bacteria were induced in planta in a strain-specific manner, shedding light on bacterial adaptation to the plant environment and identifying a potential driving force of niche separation. Integrative analyses of plant and bacterial transcriptomes suggested that the transcriptional reprogramming of plants is largely uncoupled from that of bacteria at an early stage of interactions. This study provides insights into how plants discriminate among bacterial strains and sets the foundation for in-depth mechanistic dissection of plant-microbiota interactions.
2021-04-26 | GSE150422 | GEO
Project description:Pyrimethanil (PYR) is a world-wide used fungicide approved for use in plant protection products in Agriculture, and with some (eco)toxicological concerns.We aimed at finding molecular biomarkers in the model yeast Saccharomyces cerevisiae that may be used to predict potential cytotoxic effects of this xenobiotic while providing mechanistic clues possibly relevant for experimentally less accessible non-target eukaryotes. We used microarrays to carry out a gene expression profiling analysis in S. cereviseae strain BY4741 upon 2 hours exposure to PYR at concentrations exerting moderate to median levels of phenotypic effects (inhibition of yeast growth rate). Two exposure scenarios were analysed, namely the 20% and 50%-inhibitory concentrations of PYR (IC20 and IC50, respectively), compared to control cells not exposed to the fungicide (CT02).
2014-05-23 | GSE53126 | GEO
Project description:In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide difenoconazole, a sterol biosynthesis inhibitor according to Fungicide Resistance Action Committee (FRAC) classification. Zebrafish embryos were exposed to difenoconazole according to OECD guidelines (OECD test No. 236). At the end of exposure time (96 hours), simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally, potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.
2024-01-01 | E-MTAB-13269 | biostudies-arrayexpress
Project description:In the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the fungicide metalaxyl, a nucleic acids metabolism inhibitor according to Fungicide Resistance Action Committee (FRAC) classification. Zebrafish embryos were exposed to metalaxyl according to OECD guidelines (OECD test No. 236). At the end of exposure time (96 hours), simultaneous RNA and protein extraction from 10 embryos was performed using a Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Illumina HiSeq 4000 System and the obtained sequences went through bioinformatic analysis pipeline to Identify and count the detected gene sequences followed by differential gene expression analysis. Finally, potential substance specific biomarker candidates were refined and selected based on the differential expression patterns and the biological functions investigation of the detected DEGs.
2024-01-01 | E-MTAB-13270 | biostudies-arrayexpress
Project description:Nα-terminal acetylation (NTA) ranges among the most abundant protein modifications in higher eukaryotes. Over 40 % of the human and plant proteome are co-translationally acetylated by a single Nα-acetyltransferase (Nat) termed NatA. The core NatA complex consists of the catalytic subunit NAA10 and the ribosome-binding subunit NAA15. In humans, the regulatory subunit HYPK and the acetyltransferase NAA50 join the complex. Even though both are conserved in Arabidopsis thaliana, only AtHYPK is known to interact with AtNatA.
Here we analyse the interactome of AtNAA50 and provide evidence for the association of the enzyme with AtNatA. Moreover we demonstrate that AtNAA50 interacts with ribosome-associated proteins involved in protein translation, folding and translocation. A recent study shows that acetylation protects NatA substrates from proteasomal degradation. In consequence, NatA depletion results in an accelerated protein turnover. We report that this is not true for the depletion of AtNAA50, suggesting that the enzyme is not required for NatA activity. In line with this, novel amiNAA50 knockdown lines do not display the characteristic drought resistance of NatA mutants. Instead, complementary transcriptome and proteome analyses suggest that AtNAA50 is a negative regulator of plant immunity. Pathogen challenges confirm that amiNAA50 plants are resistant to oomycetes and bacteria.
2024-03-01 | PXD040755 | JPOST Repository
Project description:Pyrimethanil (PYR) is a world-wide used fungicide approved for use in plant protection products in Agriculture, and with some (eco)toxicological concerns.We aimed at finding molecular biomarkers in the model yeast Saccharomyces cerevisiae that may be used to predict potential cytotoxic effects of this xenobiotic while providing mechanistic clues possibly relevant for experimentally less accessible non-target eukaryotes. We used microarrays to carry out a gene expression profiling analysis in S. cereviseae strain BY4741 upon 2 hours exposure to PYR at concentrations exerting moderate to median levels of phenotypic effects (inhibition of yeast growth rate). Two exposure scenarios were analysed, namely the 20% and 50%-inhibitory concentrations of PYR (IC20 and IC50, respectively), compared to control cells not exposed to the fungicide (CT02). Exponential standardized cell suspensions of S. cerevisiae BY4741 in minimal growth medium were incubated in the presence of 20 and 110 mg/L of PYR (corresponding to the PYR IC20 and IC50, respectively), or in medium non-supplemented with the fungicide (control cells, CT02) during 2 h, and used for total RNA isolation and hybridization on Affymetrix microarrays. Exposure experiments with both concentrations of PYR and with control cells were carried out together. For each exposure condition, independent biological triplicates were processed and analysed.
2014-05-23 | E-GEOD-53126 | biostudies-arrayexpress
Project description:Because they comprise some of the most efficient wood-decayers, Polyporales fungi impact carbon cycling in forest environment. The transcriptomic trends of selected Polyporales species from the core polyporoid and phlebioid clades during degradation of diverse lignocellulosic substrates led to the discovery of conserved gene sets regulated for plant cell wall degradation. Our results unveil some of the mechanisms underlying Polyporales diversification and pinpoint to yet overlooked proteins that could contribute to the ability of Polyporales to degrade recalcitrant plant cell wall polymers.
2021-08-11 | GSE156164 | GEO