Abstract
BackgroundVinyl 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.ResultsWe 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.ConclusionsThe 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.
Highlights
Vinyl chloride is a widespread groundwater pollutant and Group 1 carcinogen
Results the transfer messenger RNA (tmRNA) encoding gene (ssrA) Genomic Islands in Dehalococcoides The region downstream of ssrA in available Dehalococcoidesgenome sequences contains multiple tandem genomic islands that are primarily distinguished by their boundaries - ssrA or its 20 bp direct repeat - as well as disruption to local gene synteny and in many cases the presence of a characteristic cluster of integration-associated genes adjacent to the left edge (Figure 1)
From available Dehalococcoides genomic data we have detected a total of 31 ssrA-specific genomic island (ssrA-genomic island” (GI)) containing 47 reductive dehalogenase homologous genes (rdhA), 75 hypothetical protein encoding genes, 2 putative complete clustered regularly interspaced short palindromic repeats (CRISPR) modules and arrays [35], as well as other genes; most of which are not believed to encode a core function and are present in only a subset of Dehalococcoides strains
Summary
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. A previous comparative genomic analysis revealed that the vinyl chloride reductase operon, vcrABC, of Dehalococcoides sp. Growth-linked reductive dechlorination of vinyl chloride is critical to avoid its accumulation and achieve in situ remediation of chloroethenes [1], but vinyl chloride respiration has only been observed in certain strains of Dehalococcoides [4,5]. The only reductive dehalogenase shown to catabolically reduce vinyl chloride, VcrA, was purified from a highlyenriched vinyl chloride respiring culture dominated by Dehalococcoides strain VS [5]. The operon encoding VcrA, vcrABC, was identified by reverse genetics, and highlysimilar vcrA were detected in other vinyl chloride respiring Dehalococcoides cultures [5,17,18]. A putative VC reductase operon, bvcAB, shares only limited similarity with vcrAB and is present in a different VC respiring Dehalococcoides strain, BAV1, which does not contain vcrABC [19]
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