Comparative genomics provides structural and functional insights into Bacteroides RNA biology

Please always quote using this URN: urn:nbn:de:bvb:20-opus-259594
  • 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 theBacteria 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.show moreshow less

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Metadaten
Author: Gianluca Prezza, Daniel Ryan, Gohar Mädler, Sarah Reichardt, Lars Barquist, Alexander J. WestermannORCiD
URN:urn:nbn:de:bvb:20-opus-259594
Document Type:Journal article
Faculties:Medizinische Fakultät / Institut für Molekulare Infektionsbiologie
Language:English
Parent Title (English):Molecular Microbiology
Year of Completion:2022
Volume:117
Issue:1
Pagenumber:67–85
Source:Molecular Microbiology 2022, 117(1):67–85. DOI: 10.1111/mmi.14793
DOI:https://doi.org/10.1111/mmi.14793
Dewey Decimal Classification:6 Technik, Medizin, angewandte Wissenschaften / 61 Medizin und Gesundheit / 610 Medizin und Gesundheit
Tag:6S RNA; BT_1884; GibS; RNA-binding proteins; cold-shock protein; secondary structure
Release Date:2022/03/28
Licence (German):License LogoCC BY: Creative-Commons-Lizenz: Namensnennung 4.0 International