Tn-seq of Vibrio cholerae in presence of 0.2% of L-arabinose
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ABSTRACT:
PROVIDER: PRJEB41168 | ENA |
REPOSITORIES: ENA
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Project description:In presence of high concentrations of L-arabinose, Vibrio cholerae enters into a non-proliferative state. In V. cholerae, when L-arabinose in present into the media, it is incorporated and metabolized through the galactose pathway. In the present datasets we show that in presence of L-arabinose, transposon insertions in the galactose pathway confer a resistance to the detrimental effect of L-arabinose.
2020-11-16 | E-MTAB-9747 | biostudies-arrayexpress
Project description:Study of the effect of L-Arabinose on chromosomes replication forks progression in Vibrio cholerae. Processed wig.mat file.
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Project description:In this study, we determined the TfoY regulon of V. cholerae using RNA-seq to better uderstand the protein's function. mRNA profiles of a WT V. cholerae O1 El Tor strain (A1552) and of a TfoY-producing derivative of the WT strain (A1552-TntfoY). 3 independent biological replicates are provided for each bacterial strain. The bacteria were grown to high cell density and in the presence of arabinose (to induce TfoY in strain A1552-TntfoY).
2016-03-22 | E-GEOD-79467 | biostudies-arrayexpress
Project description:Role of L-arabinose on gene expression in E. coli O157:H7 TUV93-0 where CTRL samples were grown in the absence of L-arabinose and ARA samples were grown in the presence of L-arabinose.
2024-03-28 | GSE262155 | GEO
Project description:Genes were differentially expressed in wild-type Salmonella Typhimurium biofilms and an ΔaraE mutant when grown in the presence of 5mM or 40mM L-arabinose. Multiple biological pathways were impacted, including genes involved in arabinose metabolism, curli fimbriae, pentose phosphae pathway, TCA cycle. amino acid synthesis, pyrimidine and purine biosynthesis, and ATP synthesis.
2021-03-31 | GSE171196 | GEO
Project description:AraC is an Escherichia coli transcription factor that regulates genes in response to the presence/absence of arabinose. We used transcription profiling to determine RNA levels in Escherichia coli K-12 strain MG1655 and MG1655 delta araC grown either in the absence or the presence of arabinose. Thus, we identified known and novel AraC-regulated genes. Data presented here are raw .CEL files as well as fully analysed data using GeneSpring
2013-10-19 | E-MTAB-1916 | biostudies-arrayexpress
Project description:In this study, we determined the expression profile of V. cholerae strain A1552 and its varA-deficient mutant at two different growth stages (OD600 of 0.2 or 2.5)
2022-02-08 | GSE196185 | GEO
Project description:Tn antigen (Tn), a single N-acetylgalactosamine (GalNAc) monosaccharide attached to protein Ser and Thr residues, is found on most solid tumors yet rarely detected in adult tissues: featuring it one of the most distinctive signatures of cancers. Although it is prevalent in cancers, Tn-glycosylation sites are not entirely clear owing to the lack of suitable technology. Knowing the Tn-glycosylation sites will spur the development of the new vaccines, diagnostics, and therapeutics of cancers. Here, we report a novel technology named EXoO-Tn for large-scale mapping of Tn-glycosylation sites. EXoO-Tn utilizes glycosyltransferase C1GalT1 and isotopically-labeled UDP-Gal(13C6) to tag and convert Tn to Gal(13C6)-Tn. This exquisite Gal(13C6)-Tn structure is recognized by a human-gut-bacterial enzyme, called OpeRATOR, that specifically cleaves N-termini of the Gal(13C6)-Tn-occupied Ser and Thr residues to yield site-containing glycopeptides. The enzymes C1GalT1 and OpeRATOR could be used concurrently in one-pot. The effectiveness of EXoO-Tn was evaluated by analyzing Jurkat cells, where 947 Tn-glycosylation sites from 480 glycoproteins were mapped. Bioinformatic analysis of the identified site-specific Tn-glycoproteins revealed conserved motif, cellular localization, relative position in proteins, and mapped site-specific Tn-glycoproteome in different studies. Given the significance of Tn in cancers, EXoO-Tn is anticipated to have broad utilities in clinical study of cancers.
2022-02-15 | PXD014390 | Pride
Project description:L-Arabinose occurs at economically relevant levels in lignocellulosic hydrolysates. Especially at low concentrations of L-arabinose, its uptake via the Gal2 galactose transporter is an important rate-controlling step in the complete conversion of these feedstocks by engineered, pentose-metabolizing Saccharomyces cerevisiae strains. Chemostat-based transcriptome analysis yielded 16 putative sugar transporter genes in the filamentous fungus Penicillium chrysogenum whose transcript levels were at least three-fold higher in L-arabinose-limited cultures than in glucose-limited and ethanol-limited cultures. Of five genes that showed an over 30-fold higher transcript level in arabinose-grown cultures, only one (Pc20g01790) restored growth on L-arabinose upon expression in an engineered L-arabinose-fermenting S. cerevisiae strain in which GAL2 had been deleted. Sugar-transport assays indicated that Pc20g01790this transporter, designated as PcAraT, encodes functions as a high-affinity (Km = 0.13 mM) L-arabinose-proton symporter that does not transport xylose or glucose. An L-arabinose-metabolizing S. cerevisiae strain co-expressing Pc20g01790PcAraT and GAL2 showed lower residual substrate concentrations in L-arabinose-limited chemostat cultures (4 mg L-1) than a congenic strain in which L-arabinose import exclusively depended on Gal2 (1.8 g L-1). Inhibition of L-arabinose transport by these sugars was less pronounced than observed with Gal2. A hexose-phosphorylation-deficient, L-arabinose-metabolizing S. cerevisiae strain expressing PcAraT Pc20g0190 grew on 20 g L-1 L-arabinose in the presence of 20 g L-1 glucose, which completely inhibited growth on L-arabinose of a congenic strain dependent on L-arabinose transport via Gal2. Its high affinity and specificity for L-L-arabinose, combined with limited sensitivity to inhibition by glucose and D-D-xylose make PcAraT/ Pc20g01790 a valuable transporter gene for application in metabolic engineering strategies aimed at engineering S. cerevisiae strains for efficient conversion of lignocellulosic hydrolysates.
2017-10-03 | GSE104491 | GEO
Project description:Saccharomyces cerevisiae IMS0002 which, after metabolic and evolutionary engineering, ferments the pentose sugar arabinose. Glucose and arabinose-limited anaerobic chemostat cultures of IMS0002 and its non-evolved ancestor IMS0001 were subjected to transcriptome analysis to identify key genetic changes contributing to efficient arabinose utilization by strain IMS0002.
2011-03-01 | GSE27539 | GEO