A comparative genomics and reductive dehalogenase gene transcription study of two chloroethene-respiring bacteria, Dehalococcoides mccartyi strains MB and 11a.

Adrian Low,Patrick K. H. Lee,Matthew J. Rogers,Dan Cheng,Jianzhong He,Zhiyong Shen

doi:10.1038/srep15204

Adrian Low, Patrick K. H. Lee + Show 4 more

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https://doi.org/10.1038/srep15204

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Abstract

Genomes of two trichloroethene (TCE)-respiring Dehalococcoides (Dhc) mccartyi, strains MB and 11a, were sequenced to identify reductive dehalogenases (RDase) responsible for oraganohalide respiration. Transcription analyses were conducted to verify the roles of RDase subunit A genes (rdhA) in chloroethene respiration. Some interesting features of the strain MB draft genome include a large genome size, two CRISPR-cas type I systems, and 38 rdhA genes. Strain 11a has a stream-lined genome with 11 rdhA genes, of which nine are distinct. Quantitative real-time PCR transcription analysis of RDase gene transcripts showed that a single RDase gene, designated mbrA, was up-regulated upon exposure to TCE and no other RDase genes were considerably expressed in strain MB. A single RDase gene, designated vcrA, was up-regulated upon exposure to TCE and expressed at a steady level until all chloroethenes were completely dechlorinated to ethene at 147 h in strain 11a. Overall, this study reports the genomes of two distinct Dhc strains; both contain numerous uncharacterized RDase genes, but in each strain only one such gene was expressed highly during organohalide respiration.

Highlights

Organohalide-respiring Dehalococcoides (Dhc) mccartyi strains inhabit anaerobic environments and have environmentally relevant applications in remediating aquifers contaminated by organohalide compounds[1]
The mbrA gene was identified to be responsible for dechlorination of TCE to trans-DCE in strain MB based on a transcription study using quantitative real-time PCR23
A previous study using whole-genome microarray based on the genomes of four D. mccartyi strains, 195, BAV1, CBDB1, and VS17, showed that strain 11a was most similar to strains BAV1 (89.5%) and CBDB1 (85.4%) at the genomic level

Summary

Introduction

Organohalide-respiring Dehalococcoides (Dhc) mccartyi strains inhabit anaerobic environments and have environmentally relevant applications in remediating aquifers contaminated by organohalide compounds[1]. The mbrA gene was identified to be responsible for dechlorination of TCE to trans-DCE in strain MB based on a transcription study using quantitative real-time PCR (qPCR)[23]. From the same microarray study, 11 putative rdhA genes were identified in strain 11a including the vcrA gene, which was expressed more than tenfold upon exposure to TCE, trans-DCE or VC, implicating its involvement in all steps of dechlorination[6]. While previous studies have identified some rdhA genes in strains MB and 11a using microarray and PCR6,20, these methods were unable to detect novel sequences because of poor probe or primer specificity. Based on the rdhA sequences identified in the two strains, transcript expression studies were performed to determine the possible involvement of other RDase in the chloroethene dechlorination process

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