Ontology highlight
ABSTRACT:
PROVIDER: PRJNA982418 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:LF82, an adherent invasive Escherichia coli (AIEC) pathobiont, is associated with Crohn’s disease, an inflammatory bowel disease of unknown etiology. No genetic features have been identified that distinguish AIEC strains, such as LF82, from “commensal” or pathogenic E. coli. We investigated an extremely rare single nucleotide polymorphism (SNP) within the highly conserved rpoD gene, encoding sigma70 [primary sigma factor, RNA polymerase (RNAP)]. We demonstrate that sigma70 D445V results in transcriptome and phenotypic changes consistent with LF82 phenotypes, including increased biofilm formation and antibiotic resistance. The position of D445V within RNAP is predicted to affect spacer interaction; in vitro transcriptions reveal that the variant increases transcription from several promoters with a 16 bp spacer and a -14G:C. Our work demonstrates that a single SNP within the bacterial primary sigma can lead to myriad gene expression changes/ new phenotypes and suggests an underrecognized mechanism by which pathobionts and other strain variants can emerge.
2024-09-30 | GSE253924 | GEO
Project description:In the present study OMICs analysis was employed to investigate the early molecular responses of zebrafish embryos to exposure to the fungicide metalaxyl. Metalaxyl, a nucleic acid metabolism inhibitor according to Fungicide Resistance Action Committee (FRAC) classification, may also induce adverse effects on non-target organisms inhabiting the environment. Early molecular responses in terms of transcriptome and proteome analysis were investigated and refined to select potentially substance specific biomarker candidates for early prediction of metalaxyl toxicity in zebrafish embryos.
2024-01-02 | PXD045444 | Pride
Project description:Lignin accumulates progressively in cell walls during plant development, therefore, we are interested in analyzing the transcriptome and metabolome of engineered sorghum lines at three developmental stages. Results from these analyses will help to understand the metabolic changes (if any) besides lignin synthesis in transgenics and anticipate plants' physiological responses during growth under natural environment in future field trials.
This project will analyze the transcriptome and metabolome in stems of low-lignin sorghum transgenic lines compared to wild-type (WT) control.
The work (proposal:https://doi.org/10.46936/10.25585/60008680) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.
2024-05-14 | MSV000094762 | MassIVE
Project description:Acetylation of lysine residues is conserved across organisms and plays important roles in various cellular functions. Maintaining intracellular pH homeostasis is crucial for the survival of enteric bacteria in acidic gastric tract. However, it remains unkown whether bacteria can utilize reversible protein acetylation system to adapt to acidic environment. Here we demonstrate that the protein acetylation/deacetylation is critical for Salmonella Typhimurium to survive in acidic environment. We first used RNA-seq to analyze the transcriptome patterns under acid stress, and found that the transcriptional levels of genes involved in NAD+/NADH metabolism were significantly changed, leading to the increase of intracellular NAD+/NADH ratio. Moreover, acid stress down-regulated the transcriptional level of pat (encoding an acetyltranseferase) and genes encoding adenylate cyclase and cAMP-regulatory protein (CRP) which regulates pat positively. Acid signal also affects TCA cycle to promote the consumption of Ac-CoA, which reduced the donor of acetylation. Lowered acetylation level is not only bacterial’s response to acid stress, but also positively regulates the survival rate of S. Typhimurium. The deletion mutant of pat had more stable intracellular pH, which paralleled with higher survival rate after acid treatment compared with the wild type strain and deletion mutant of cobB. Our data suggest that bacteria can down-regulate protein acetylation level to prevent intracellular pH further falling in acid stress, and this work may provide a new perspective to understand the bacterial acid resistance mechanism. To use RNA-seq to analyze the transcriptome patterns under acid stress
2015-04-16 | E-GEOD-67925 | biostudies-arrayexpress
Project description:Bacteria that live in the acidic environment face number of growth-related challenges from the intracellular pH changes. In order to survive under acidic environment, Lactic acid bacteria must employ multiple genes and proteins to regulate the relative pathways.
2018-11-20 | GSE107136 | GEO
Project description:Bacteria that live in the acidic environment face number of growth-related challenges from the intracellular pH changes. In order to survive under acidic environment, Lactic acid bacteria must employ multiple genes and proteins to regulate the relative pathways.
2018-11-20 | GSE107135 | GEO
Project description:We aim to compare global transcriptomic analysis of wt and delta-nrdRmutant in Escherichia coli LF82 strain.
2015-02-02 | E-MTAB-2288 | biostudies-arrayexpress
Project description:We aim to compare global transcriptomic analysis of wt and delta nrdRmutant in Escherichia coli LF82 strain.
2016-06-27 | E-MTAB-2295 | biostudies-arrayexpress