An IS-mediated, RecA-dependent, bet-hedging strategy in Burkholderia thailandensis

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Abstract

Adaptation to fluctuating environmental conditions is difficult to achieve. Phase variation mechanisms can overcome this difficulty by altering genomic architecture in a subset of individuals, creating a phenotypically heterogeneous population with subpopulations optimized to persist when conditions change, or are encountered, suddenly. We have identified a phase variation system in Burkholderia thailandensis that generates a genotypically and phenotypically heterogeneous population. Genetic analyses revealed that RecA-mediated homologous recombination between a pair of insertion sequence (IS) 2-like elements duplicates a 208.6 kb region that contains 157 coding sequences. RecA-mediated homologous recombination also resolves merodiploids, and hence copy number of the region is varied and dynamic within populations. We showed that the presence of two or more copies of the region is advantageous for growth in a biofilm, and a single copy is advantageous during planktonic growth. While IS elements are well-known to contribute to evolution through gene inactivation, polar effects on downstream genes, and altering genomic architecture, we believe that this system represents a rare example of IS element-mediated evolution in which the IS elements provide homologous sequences for amplification of a chromosomal region that provides a selective advantage under specific growth conditions, thereby expanding the lifestyle repertoire of the species.

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All data generated or analysed during this study are included in the manuscript and supporting file; Source Data files have been provided for all gels.

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Lillian C Lowrey

Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-7602-033X
Leslie A Kent

Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-3195-0247
Bridgett M Rios

Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, United States

Competing interests
The authors declare that no competing interests exist.
Angelica B Ocasio

Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, United States

Competing interests
The authors declare that no competing interests exist.
Peggy A Cotter

Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, United States

For correspondence
pcotter@med.unc.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-3726-3990

Funding

National Institutes of Health (R35 GM136533)

Peggy A Cotter

National Institutes of Health (R01 GM121110)

Peggy A Cotter

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

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This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.