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A high-resolution transcriptome map identifies small RNA regulation of metabolism in the gut microbe Bacteroides thetaiotaomicron
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A high-resolution transcriptome map identifies small RNA regulation of metabolism in the gut microbe Bacteroides thetaiotaomicron
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Journal Article
A high-resolution transcriptome map identifies small RNA regulation of metabolism in the gut microbe Bacteroides thetaiotaomicron
2020
Overview
Bacteria of the genus
Bacteroides
are common members of the human intestinal microbiota and important degraders of polysaccharides in the gut. Among them, the species
Bacteroides thetaiotaomicron
has emerged as the model organism for functional microbiota research. Here, we use differential RNA sequencing (dRNA-seq) to generate a single-nucleotide resolution transcriptome map of
B
.
thetaiotaomicron
grown under defined laboratory conditions. An online browser, called ‘Theta-Base’ (
www.helmholtz-hiri.de/en/datasets/bacteroides
), is launched to interrogate the obtained gene expression data and annotations of ~4500 transcription start sites, untranslated regions, operon structures, and 269 noncoding RNA elements. Among the latter is GibS, a conserved, 145 nt-long small RNA that is highly expressed in the presence of
N
-acetyl-
D
-glucosamine as sole carbon source. We use computational predictions and experimental data to determine the secondary structure of GibS and identify its target genes. Our results indicate that sensing of
N
-acetyl-
D
-glucosamine induces GibS expression, which in turn modifies the transcript levels of metabolic enzymes.
Bacteroides thetaiotaomicron
is a human gut microbe and an emergent model organism. Here, Ryan et al. generate single-nucleotide resolution RNA-seq data for this bacterium and map transcription start sites and noncoding RNAs, one of which modulates expression of metabolic enzymes.
Publisher
Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
Subject
/ Acetylglucosamine - metabolism
/ Bacteria
/ Bacterial Proteins - genetics
/ Bacteroides thetaiotaomicron
/ Bacteroides thetaiotaomicron - genetics
/ Bacteroides thetaiotaomicron - growth & development
/ Bacteroides thetaiotaomicron - metabolism
/ Enzymes
/ Gene Expression Regulation, Bacterial
/ Humanities and Social Sciences
/ Humans
/ RNA
/ RNA, Small Untranslated - chemistry
/ RNA, Small Untranslated - genetics
/ RNA, Untranslated - genetics
/ Science
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