A high-resolution transcriptome map identifies small RNA regulation of metabolism in the gut microbe Bacteroides thetaiotaomicron.

Nature Communications
Daniel RyanAlexander J Westermann

Abstract

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.

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Citations

Feb 6, 2021·Biological Chemistry·Daniel RyanAlexander J Westermann
Jan 30, 2021·The Journal of Experimental Biology·Konstantin Schmidt, Philipp Engel
Feb 19, 2021·Nature Reviews. Genetics·Alexander J Westermann, Jörg Vogel
Jun 17, 2021·Proceedings of the National Academy of Sciences of the United States of America·Manuela FuchsFranziska Faber
Jul 2, 2021·Frontiers in Bioengineering and Biotechnology·Monika MortimerPatricia A Holden
Jul 10, 2021·Nature Microbiology·Falk PonathJörg Vogel
Aug 12, 2021·Molecular Microbiology·Gianluca PrezzaAlexander J Westermann
Sep 2, 2021·Annual Review of Biomedical Data Science·Yancong ZhangCurtis Huttenhower
Jul 13, 2021·Journal of Bacteriology·Amanda N D AdamsCarin K Vanderpool
Aug 10, 2021·Journal of Bacteriology·Nicholas A Pudlo, Eric C Martens

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Methods Mentioned

BETA
RNA-seq
dRNA-seq
Ribo-seq
PCR
electrophoretic mobility shift

Software Mentioned

PANTHER Classification System
Plotly
Cutadapt
Integrated Genome Browser
GLAM2
- Base
JBrowse
Illumina
WAR webserver
RNAfold

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