Comparative genomics provides structural and functional insights into Bacteroides RNA biology
Gianluca Prezza,Daniel Ryan,Gohar Mädler,Sarah Reichardt,Lars Barquist,Alexander J. Westermann +5 more
TLDR
In this paper, a comparative genomics approach was used to investigate RNA biology in an understudied gut bacterium, using Bacteroides thetaiotaomicron as a representative microbiota member.Abstract:
Bacteria employ noncoding RNA molecules for a wide range of biological processes, including scaffolding large molecular complexes, catalyzing chemical reactions, defending against phages, and controlling gene expression. Secondary structures, binding partners, and molecular mechanisms have been determined for numerous small noncoding RNAs (sRNAs) in model aerobic bacteria. However, technical hurdles have largely prevented analogous analyses in the anaerobic gut microbiota. While experimental techniques are being developed to investigate the sRNAs of gut commensals, computational tools and comparative genomics can provide immediate functional insight. Here, using Bacteroides thetaiotaomicron as a representative microbiota member, we illustrate how comparative genomics improves our understanding of RNA biology in an understudied gut bacterium. We investigate putative RNA-binding proteins and predict a Bacteroides cold-shock protein homolog to have an RNA-related function. We apply an in silico protocol incorporating both sequence and structural analysis to determine the consensus structures and conservation of nine Bacteroides noncoding RNA families. Using structure probing, we validate and refine these predictions and deposit them in the Rfam database. Through synteny analyses, we illustrate how genomic coconservation can serve as a predictor of sRNA function. Altogether, this work showcases the power of RNA informatics for investigating the RNA biology of anaerobic microbiota members.read more
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An integrated transcriptomics–functional genomics approach reveals a small RNA that modulates Bacteroides thetaiotaomicron sensitivity to tetracyclines
Daniel Ryan,Elise Bornet,Gianluca Prezza,Shuba Varshini Alampalli,Taís Franco de Carvalho,Hannah Felchle,Titus Ebbecke,Regan J. Hayward,Adam M. Deutschbauer,Lars Barquist,Alexander J. Westermann +10 more
TL;DR: In this paper , the authors map transcriptional units and profile their expression levels in Bacteroides thetaiotaomicron over a suite of 15 defined experimental conditions that are relevant in vivo, such as variation of temperature, pH, and oxygen tension, exposure to antibiotic stress, and growth on simple carbohydrates or on host mucin derived glycans.
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