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dc.contributor.authorPrezza, Gianluca
dc.contributor.authorRyan, Daniel
dc.contributor.authorMädler, Gohar
dc.contributor.authorReichardt, Sarah
dc.contributor.authorBarquist, Lars
dc.contributor.authorWestermann, Alexander J
dc.date.accessioned2022-01-27T09:56:06Z
dc.date.available2022-01-27T09:56:06Z
dc.date.issued2021-08-28
dc.identifier.citationMol Microbiol. 2022 Jan;117(1):67-85. doi: 10.1111/mmi.14793. Epub 2021 Aug 28.en_US
dc.identifier.pmid34379855
dc.identifier.doi10.1111/mmi.14793
dc.identifier.urihttp://hdl.handle.net/10033/623153
dc.description.abstractBacteria 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.en_US
dc.language.isoenen_US
dc.publisherWiley & Sons Ltd.en_US
dc.rightsAttribution 4.0 International*
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/*
dc.subject6S RNAen_US
dc.subjectBT_1884en_US
dc.subjectGibSen_US
dc.subjectRNA-binding proteinsen_US
dc.subjectcold-shock proteinen_US
dc.subjectsecondary structureen_US
dc.titleComparative genomics provides structural and functional insights into Bacteroides RNA biology.en_US
dc.typeArticleen_US
dc.identifier.eissn1365-2958
dc.contributor.departmentHIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.en_US
dc.identifier.journalMolecular microbiologyen_US
dc.source.volume117
dc.source.issue1
dc.source.beginpage67
dc.source.endpage85
refterms.dateFOA2022-01-27T09:56:06Z
dc.source.journaltitleMolecular microbiology
dc.source.countryEngland


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Attribution 4.0 International
Except where otherwise noted, this item's license is described as Attribution 4.0 International