Identification and Environmental Distribution of<i>dcpA</i>, Which Encodes the Reductive Dehalogenase Catalyzing the Dichloroelimination of 1,2-Dichloropropane to Propene in Organohalide-Respiring Chloroflexi

Padilla-Crespo, Elizabeth; Yan, Jun; Swift, Cynthia M.; Wagner, Darlene; Chourey, Karuna; Hettich, Robert L.; Ritalahti, Kirsti M.; Löffler, Frank E.

doi:10.1128/aem.02927-13

Cited by 47 publications

(47 citation statements)

References 56 publications

(65 reference statements)

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“…S4 in the supplemental material). Padilla-Crespo et al (45) suggested that Dehalogenimonas RDases cluster separately from Dehalococcoides RDases, based on analysis of DcpA, a 1,2-DCA dehalogenase from Dehalogenimonas lykanthroporepellens; however, this was not the case here. TdrA had poor identity with other Dehalogenimonas RDases, sharing 31% pairwise identity with the closest Dehalogenimonas lykanthroporepellens dehalogenase (GenBank accession number WP013217644).…”

Section: Resultscontrasting

confidence: 44%

“…This type of domain has been observed in some but not all RdhA proteins. For example, DcpA contains DHXG-X 39 -S-X 32 -G (12,17,45,46). No such binding motif could be identified in TdrA.…”

Section: Resultsmentioning

confidence: 99%

“…With the characterization of additional Dehalogenimonas genomes, it now appears that RdhA homologs of the Dehalococcoidaceae separate into at least five different mixed clusters (Fig. 5) (45). Cluster 5 has no characterized representatives but has a concentration of Dehalogenimonas sp.…”

Section: Figmentioning

confidence: 99%

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Dehalogenimonas sp. Strain WBC-2 Genome and Identification of Its trans -Dichloroethene Reductive Dehalogenase, TdrA

Molenda

Quaile

Edwards

2016

Appl Environ Microbiol

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The Dehalogenimonas population in a dechlorinating enrichment culture referred to as WBC-2 was previously shown to be responsible for trans-dichloroethene (tDCE) hydrogenolysis to vinyl chloride (VC). In this study, blue native polyacrylamide gel electrophoresis (BN-PAGE) followed by enzymatic assays and protein identification using liquid chromatography coupled with mass spectrometry (LC-MS/MS) led to the functional characterization of a novel dehalogenase, TdrA. This new reductive dehalogenase (RDase) catalyzes the dechlorination of tDCE to VC. A metagenome of the WBC-2 culture was sequenced, and a complete Dehalogenimonas genome, only the second Dehalogenimonas genome to become publicly available, was closed. The tdrA dehalogenase found within the Dehalogenimonas genome appears to be on a genomic island similar to genomic islands found in Dehalococcoides. TdrA itself is most similar to TceA from Dehalococcoides sp. strain FL2 with 76.4% amino acid pairwise identity. It is likely that the horizontal transfer of rdhA genes is not only a feature of Dehalococcoides but also a feature of other Dehalococcoidia, including Dehalogenimonas. A set of primers was developed to track tdrA in WBC-2 subcultures maintained on different electron acceptors. This newest dehalogenase is an addition to the short list of functionally defined RDases sharing the usual characteristic motifs (including an AB operon, a TAT export sequence, two iron-sulfur clusters, and a corrinoid binding domain), substrate flexibility, and evidence for horizontal gene transfer within the Dehalococcoidia. Industrial, military, and agricultural practices have resulted in the release of a growing number of chemical compounds hazardous to human health and the environment. Contamination of soil and groundwater with chlorinated ethenes and ethanes is of concern due to their known toxicity and/or carcinogenicity. Although in situ bioremediation is already a well-established remediation approach, greater understanding of new microbial capabilities is important for optimization of this strategy (1, 2). Some of the most interesting dechlorinating organisms are organohalide-respiring bacteria (OHRB), which couple dehalogenation with a respiration process required for growth (3-5). The most studied genus of OHRB is Dehalococcoides because of the ability of members of this genus to respire the most common chlorinated solvent contaminants, trichloroethene (TCE) and perchloroethene (PCE). As recently as 2009, Dehalogenimonas was identified to be a new genus of OHRB most similar to Dehalococcoides. Dehalogenimonas lykanthroporepellens and Dehalogenimonas alkenigignens are the only two species of Dehalogenimonas described to date; they are capable of dihaloelimination of polychlorinated aliphatic alkanes (6-8), although Dehalogenimonas-like organisms are known to be widely distributed (9). The West Branch Canal Creek Consortium (WBC-2) culture was derived from sediments contaminated with 1,1,2,2-tetrachloroethane (1,1,2,2-TeCA) (10). In this consortium, 1,1,2,2-TeCA d...

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Section: Resultscontrasting

confidence: 44%

“…This type of domain has been observed in some but not all RdhA proteins. For example, DcpA contains DHXG-X 39 -S-X 32 -G (12,17,45,46). No such binding motif could be identified in TdrA.…”

Section: Resultsmentioning

confidence: 99%

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Dehalogenimonas sp. Strain WBC-2 Genome and Identification of Its trans -Dichloroethene Reductive Dehalogenase, TdrA

Molenda

Quaile

Edwards

2016

Appl Environ Microbiol

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“…In 2013, Tang et al (6) described a blue native polyacrylamide gel electrophoresis (BN-PAGE) method that significantly improved the recovery of dechlorinating activity in gel slices. Since then, several other reductive dehalogenases have been partially characterized with this approach, including chloroform and 1,1,1-trichlorethane and 1,1-dichloroethane RDases from Dehalobacter (26) and a chloroform and 1,1,1-trichloroethane RDase from Desulfitobacterium (27), 1,2-dichloropropane dehalogenases from Dehalococcoides and Dehalogenimonas (28), and a trans-DCE RDase from Dehalogenimonas (O. Molenda and E. A. Edwards, unpublished data). Very recently, the PCE RDase from Sulfurospirillum was successfully heterologously expressed in Shimwellia (29), and the VC RDase VcrA from Dehalococcoides was successfully expressed in E. coli (30), opening exciting new avenues for characterization of novel RDases.…”

mentioning

confidence: 99%

Identity and Substrate Specificity of Reductive Dehalogenases Expressed in Dehalococcoides-Containing Enrichment Cultures Maintained on Different Chlorinated Ethenes

Liang

Molenda

Tang

et al. 2015

Appl Environ Microbiol

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Many reductive dehalogenases (RDases) have been identified in organohalide-respiring microorganisms, and yet their substrates, specific activities, and conditions for expression are not well understood. We tested whether RDase expression varied depending on the substrate-exposure history of reductive dechlorinating communities. For this purpose, we used the enrichment culture KB-1 maintained on trichloroethene (TCE), as well as subcultures maintained on the intermediates cis-dichloroethene (cDCE) and vinyl chloride (VC). KB-1 contains a TCE-to-cDCE dechlorinating Geobacter and several Dehalococcoides strains that together harbor many of the known chloroethene reductases. Expressed RDases were identified using blue native polyacrylamide gel electrophoresis, enzyme assays in gel slices, and peptide sequencing. As anticipated but never previously quantified, the RDase from Geobacter was only detected transiently at the beginning of TCE dechlorination. The Dehalococcoides RDase VcrA and smaller amounts of TceA were expressed in the parent KB-1 culture during complete dechlorination of TCE to ethene regardless of time point or amended substrate. The Dehalococcoides RDase BvcA was only detected in enrichments maintained on cDCE as growth substrates, in roughly equal abundance to VcrA. Only VcrA was detected in subcultures enriched on VC. Enzyme assays revealed that 1,1-DCE, a substrate not used for culture enrichment, afforded the highest specific activity. trans-DCE was substantially dechlorinated only by extracts from cDCE enrichments expressing BvcA. RDase gene distribution indicated enrichment of different strains of Dehalococcoides as a function of electron acceptor TCE, cDCE, or VC. Each chloroethene reductase has distinct substrate preferences leading to strain selection in mixed communities. Microbial reductive dechlorination and organohalide respiration play a significant role in the natural and engineered attenuation of chlorinated ethenes, such as tetrachloroethene (PCE) and trichloroethene (TCE). However, microbial dechlorination via hydrogenolysis sometimes stalls at dichloroethene (DCE) and vinyl chloride (VC) which is problematic as these intermediates are more water-soluble and more toxic than PCE or TCE, particularly VC (1). Organisms that are known to be capable of respiring chlorinated ethenes to nontoxic ethene are restricted to some Dehalococcoides mccartyi strains (2-4). The genomes of two VC-respiring Dehalococcoides isolates were described previously (5), as well as the metagenome of the VC-respiring mixed culture KB-1 (6, 7). In addition to chlorinated ethenes, some D. mccartyi strains can also dechlorinate 1,2-dichloroethane (1,2-DCA) (8), 1,2-dichloropropane (9), and a variety of chlorinated and brominated aromatic contaminants (10-12).Membrane-bound reductive dehalogenases (RDases) are key enzymes that mediate dechlorination reactions in organohalide respiring microorganisms. Many RDases and putative RDase sequences have been identified in D. mccartyi strains (13-21). To date, only a few RD...

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“…Overview of known organohalide-respiring bacteria -phylogenetic diversity and environmental distribution mediating 1,2-dichloropropane dichloroelimination to propene [104]. The dcpA gene was detected in all aquifer samples that yielded 1,2-D-dechlorinating microcosms [104], and dcpA sequences retrieved from geographically distinct samples shared >98% sequence identity with dcpA sequences from D. mccartyi strains RC and KS [50,51] and D. lykanthroporepellens BL-DC-9 [105].…”

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confidence: 99%

Ecophysiology and environmental distribution of organohalide-respiring bacteria

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Identification and Environmental Distribution ofdcpA, Which Encodes the Reductive Dehalogenase Catalyzing the Dichloroelimination of 1,2-Dichloropropane to Propene in Organohalide-Respiring Chloroflexi

Cited by 47 publications

References 56 publications

Dehalogenimonas sp. Strain WBC-2 Genome and Identification of Its trans -Dichloroethene Reductive Dehalogenase, TdrA

Dehalogenimonas sp. Strain WBC-2 Genome and Identification of Its trans -Dichloroethene Reductive Dehalogenase, TdrA

Identity and Substrate Specificity of Reductive Dehalogenases Expressed in Dehalococcoides-Containing Enrichment Cultures Maintained on Different Chlorinated Ethenes

Ecophysiology and environmental distribution of organohalide-respiring bacteria

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