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Journal of Molecular Evolution

, Volume 84, Issue 4, pp 204–213 | Cite as

Emergence of New sRNAs in Enteric Bacteria is Associated with Low Expression and Rapid Evolution

  • Fenil R. Kacharia
  • Jess A. Millar
  • Rahul Raghavan
Original Research

Abstract

Non-coding small RNAs (sRNAs) are critical to post-transcriptional gene regulation in bacteria. However, unlike for protein-coding genes, the evolutionary forces that shape sRNAs are not understood. We investigated sRNAs in enteric bacteria and discovered that recently emerged sRNAs evolve at significantly faster rates than older sRNAs. Concomitantly, younger sRNAs are expressed at significantly lower levels than older sRNAs. This process could potentially facilitate the integration of newly emerged sRNAs into bacterial regulatory networks. Furthermore, it has previously been difficult to trace the evolutionary histories of sRNAs because rapid evolution obscures their original sources. We overcame this challenge by identifying a recently evolved sRNA in Escherichia coli, which allowed us to determine that novel sRNAs could emerge from vestigial bacteriophage genes, the first known source for sRNA origination.

Keywords

Small RNA sRNA evolution Bacteriophage Non-coding RNA ncRNA 

Notes

Acknowledgements

We thank Justin Merritt, Nan Liu, Abraham Moses, and Jim Archuleta for technical help. This work was supported in part by Portland State University. J.A.M. was supported by the Forbes-Lea Research Fund and by a Sigma Xi Grants-in-Aid of Research award (G201510151633590).

Supplementary material

239_2017_9793_MOESM1_ESM.pdf (1.5 mb)
Supplementary material 1 (PDF 1578 kb)
239_2017_9793_MOESM2_ESM.xls (102 kb)
Supplementary material 2 (XLS 101 kb)

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Copyright information

© Springer Science+Business Media New York 2017

Authors and Affiliations

  1. 1.Department of Biology and Center for Life in Extreme EnvironmentsPortland State UniversityPortlandUSA

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