title: Genome rearrangements can make and break small RNA genes.
abstract: Small RNAs (sRNAs) are short, transcribed regulatory elements that are typically encoded in the intergenic regions (IGRs) of bacterial genomes. Several sRNAs, first recognized in Escherichia coli, are conserved among enteric bacteria, but because of the regulatory roles of sRNAs, differences in sRNA repertoires might be responsible for features that differentiate closely related species. We scanned the E. coli MG1655 and Salmonella enterica Typhimurium genomes for nonsyntenic IGRs as a potential source of uncharacterized, species-specific sRNAs and found that genome rearrangements have reconfigured several IGRs causing the disruption and formation of sRNAs. Within an IGR that is present in E. coli but was disrupted in Salmonella by a translocation event is an sRNA that is associated with the FNR/CRP global regulators and influences E. coli biofilm formation. A Salmonella-specific sRNA evolved de novo through point mutations that generated a σ(70) promoter sequence in an IGR that arose through genome rearrangement events. The differences in the sRNA pools among bacterial species have previously been ascribed to duplication, deletion, or horizontal acquisition. Here, we show that genomic rearrangements also contribute to this process by either disrupting sRNA-containing IGRs or creating IGRs in which novel sRNAs may evolve.
authors.affiliation: Department of Biology and Center for Life in Extreme Environments, Portland State University rahul.raghavan@pdx.edu.
authors.forename: Rahul
authors.initials: R
authors.lastname: Raghavan
authors.affiliation: Department of Biology and Center for Life in Extreme Environments, Portland State University.
authors.forename: Fenil R
authors.initials: FR
authors.lastname: Kacharia
authors.affiliation: Department of Biology and Center for Life in Extreme Environments, Portland State University.
authors.forename: Jess A
authors.initials: JA
authors.lastname: Millar
authors.affiliation: Department of Biology and Center for Life in Extreme Environments, Portland State University.
authors.forename: Christine D
authors.initials: CD
authors.lastname: Sislak
authors.affiliation: Department of Integrative Biology, The University of Texas at Austin.
authors.forename: Howard
authors.initials: H
authors.lastname: Ochman
mesh_terms: D001483:Base Sequence; D018441:Biofilms; D021901:DNA, Intergenic / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics* / Q000502:physiology; D029968:Escherichia coli Proteins / Q000378:metabolism; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D015321:Gene Rearrangement / Q000235:genetics*; D022761:Gene Transfer, Horizontal / Q000235:genetics; D005798:Genes, Bacterial; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic / Q000235:genetics; D012329:RNA, Bacterial / Q000235:genetics*; D019779:Salmonella enterica / Q000235:genetics* / Q000472:pathogenicity; D013045:Species Specificity; D026801:Synteny / Q000235:genetics
chemical_list: D021901:DNA, Intergenic; D029968:Escherichia coli Proteins; D012329:RNA, Bacterial
keywords: E. coli; Salmonella; gene origination; intergenic regions; sRNA