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Open Access Research article

Site-Specific Mobilization of Vinyl Chloride Respiration Islands by a Mechanism Common in Dehalococcoides

Paul J McMurdie1, Laura A Hug2, Elizabeth A Edwards23, Susan Holmes4 and Alfred M Spormann15*

Author affiliations

1 Department of Civil and Environmental Engineering, Stanford University, Stanford, California, USA

2 Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada

3 Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada

4 Department of Statistics, Stanford University, Stanford, California, USA

5 Department of Chemical Engineering, Stanford University, Stanford, California, USA

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Citation and License

BMC Genomics 2011, 12:287  doi:10.1186/1471-2164-12-287

Published: 2 June 2011

Abstract

Background

Vinyl chloride is a widespread groundwater pollutant and Group 1 carcinogen. A previous comparative genomic analysis revealed that the vinyl chloride reductase operon, vcrABC, of Dehalococcoides sp. strain VS is embedded in a horizontally-acquired genomic island that integrated at the single-copy tmRNA gene, ssrA.

Results

We targeted conserved positions in available genomic islands to amplify and sequence four additional vcrABC -containing genomic islands from previously-unsequenced vinyl chloride respiring Dehalococcoides enrichments. We identified a total of 31 ssrA-specific genomic islands from Dehalococcoides genomic data, accounting for 47 reductive dehalogenase homologous genes and many other non-core genes. Sixteen of these genomic islands contain a syntenic module of integration-associated genes located adjacent to the predicted site of integration, and among these islands, eight contain vcrABC as genetic 'cargo'. These eight vcrABC -containing genomic islands are syntenic across their ~12 kbp length, but have two phylogenetically discordant segments that unambiguously differentiate the integration module from the vcrABC cargo. Using available Dehalococcoides phylogenomic data we estimate that these ssrA-specific genomic islands are at least as old as the Dehalococcoides group itself, which in turn is much older than human civilization.

Conclusions

The vcrABC -containing genomic islands are a recently-acquired subset of a diverse collection of ssrA-specific mobile elements that are a major contributor to strain-level diversity in Dehalococcoides, and may have been throughout its evolution. The high similarity between vcrABC sequences is quantitatively consistent with recent horizontal acquisition driven by ~100 years of industrial pollution with chlorinated ethenes.