Premium
Comparative genomics provides structural and functional insights into Bacteroides RNA biology
Author(s) -
Prezza Gianluca,
Ryan Daniel,
Mädler Gohar,
Reichardt Sarah,
Barquist Lars,
Westermann Alexander J.
Publication year - 2022
Publication title -
molecular microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.857
H-Index - 247
eISSN - 1365-2958
pISSN - 0950-382X
DOI - 10.1111/mmi.14793
Subject(s) - biology , bacteroides thetaiotaomicron , computational biology , rna , non coding rna , in silico , synteny , genomics , comparative genomics , bacteroides , proteomics , function (biology) , genome , functional genomics , genetics , gene , bacteria
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.