Sponsor
This work was supported by Portland State University and by grants from the National Institute of Health (GM74738) and the Templeton Foundation (23536).
Published In
Genome Biology and Evolution
Document Type
Article
Publication Date
12-2015
Subjects
Non-coding RNA, Bacterial genomes, Escherichia coli -- Genetics, Salmonella typhimurium -- Genetics, Genomics
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 σ70 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.
DOI
10.1093/gbe/evv009
Persistent Identifier
http://archives.pdx.edu/ds/psu/16536
Citation Details
Raghavan, R., Kacharia, F. R., Millar, J. A., Sislak, C. D., & Ochman, H. (2015). Genome rearrangements can make and break small RNA genes. Genome Biology and Evolution, 7(2), 557–66.
Description
Copyright The Author(s) 2015. Published by Oxford University Press on behalf the Society for Molecular Biology and Evolution.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited.