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Extensive Cotransformation of Natural Variation into Chromosomes of Naturally Competent Haemophilus influenzae
Journal article   Open access

Extensive Cotransformation of Natural Variation into Chromosomes of Naturally Competent Haemophilus influenzae

Joshua Chang Mell, Jae Yun Lee, Marlo Firme, Sunita Sinha and Rosemary J. Redfield
G3 : genes - genomes - genetics, v 4(4), pp 717-731
25 Feb 2014
DOI: https://doi.org/10.1534/g3.113.009597
PMID: 24569039
Featured in Collection :   UN Sustainable Development Goals @ Drexel
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https://doi.org/10.1534/g3.113.009597View
Published, Version of Record (VoR)CC BY-NC V4.0,  Open

Abstract

bacteria heteroduplex segregation horizontal gene transfer Investigations nearly isogenic lines recombination
Naturally competent bacterial species actively take up environmental DNA and can incorporate it into their chromosomes by homologous recombination. This can bring genetic variation from environmental DNA to recipient chromosomes, often in multiple long “donor” segments. Here, we report the results of genome sequencing 96 colonies of a laboratory Haemophilus influenzae strain, which had been experimentally transformed by DNA from a diverged clinical isolate. Donor segments averaged 6.9 kb (spanning several genes) and were clustered into recombination tracts of ~19.5 kb. Individual colonies had replaced from 0.1 to 3.2% of their chromosomes, and ~1/3 of all donor-specific single-nucleotide variants were present in at least one recombinant. We found that nucleotide divergence did not obviously limit the locations of recombination tracts, although there were small but significant reductions in divergence at recombination breakpoints. Although indels occasionally transformed as parts of longer recombination tracts, they were common at breakpoints, suggesting that indels typically block progression of strand exchange. Some colonies had recombination tracts in which variant positions contained mixtures of both donor and recipient alleles. These tracts were clustered around the origin of replication and were interpreted as the result of heteroduplex segregation in the original transformed cell. Finally, a pilot experiment demonstrated the utility of natural transformation for genetically dissecting natural phenotypic variation. We discuss our results in the context of the potential to merge experimental and population genetic approaches, giving a more holistic understanding of bacterial gene transfer.

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Genetics & Heredity
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