Indications for Acquisition of Reductive Dehalogenase Genes through Horizontal Gene Transfer by
            <i>Dehalococcoides ethenogenes</i>
            Strain 195

Regeard, Christophe; Maillard, Julien; Dufraigne, Christine; Deschavanne, Patrick; Holliger, Christof

doi:10.1128/aem.71.6.2955-2961.2005

Cited by 37 publications

(33 citation statements)

References 61 publications

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“…Therefore, it is likely that the mRNA of dceA7 is either not translated into the functional RDase enzyme or the translated protein might not be directly involved in the generation of trans-DCE. Strain MB contains RDase genes that share high identity to genes in strains 195, VS and CBDB1, suggesting that these RDases might be acquired through the process of horizontal gene transfer (Regeard et al, 2005). Although the identified mbrA gene consists of the same characteristics of typical cis-DCE-producing RDases (twin arginine translocation peptide signal and the Fe 4 S 4 clusters), they differ functionally.…”

Section: Discussionmentioning

confidence: 99%

Identification and transcriptional analysis of trans-DCE-producing reductive dehalogenases in Dehalococcoides species

et al. 2010

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During microbial reductive dechlorination of tetrachloroethene (PCE) and trichloroethene (TCE), trans-1, 2-dichloroethene (trans-DCE) has been observed to be produced predominantly by certain mixed and pure cultures. However, the reductive dehalogenase (RDase) genes involved in trans-DCE generation remain elusive. In this study, identification and transcriptional analysis of RDases were conducted on trans-DCE-producing Dehalococcoides sp. strain MB. Two pairs of degenerate primers targeting the conserved regions of RDases in known Dehalococcoides species were applied to amplify the putative RDase genes of strain MB. Cloning and restriction analysis revealed the presence of seven unique RDase gene fragments (dceA1 to dceA7) that possess sequence identity to known RDase genes. Gene expression analysis of the PCE-grown culture MB exhibited 10-fold regulation of the RDase gene dceA6 (designated mbrA gene), suggesting that it is involved in the production of trans-DCE. This is in agreement with the molecular size of the most abundant protein that is resolved on the denaturing protein gel. Complete sequence of the mbrA gene was obtained by chromosome walking, and the upstream of it is a regulator of transcription, indicating that the expression of this functional gene is tightly controlled in the microbe. The mbrA gene was subsequently found to be present in other trans-DCE-producing cultures containing Dehalococcoides sp. The new mbrA gene identified in this study may serve as an important biomarker for evaluating, predicting and elucidating the biological production of trans-DCE in the chloroethene-contaminated sites.

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Section: Discussionmentioning

confidence: 99%

Identification and transcriptional analysis of trans-DCE-producing reductive dehalogenases in Dehalococcoides species

et al. 2010

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“…The finding that D. ethenogenes (phylum Chloroflexi) and E. harbinense (phylum Firmicutes), two species living in contaminated waters, also code for CW_7-containing proteins may be the result of horizontal gene transfer events. Interestingly, although the root of the tree of life (and the last universal common ancestor) has been suggested to be located within or next to the Chloroflexi (66), evidence suggesting that D. ethenogenes has experimented horizontal transfer events has been provided (67).…”

Section: Discussionmentioning

confidence: 99%

Cpl-7, a Lysozyme Encoded by a Pneumococcal Bacteriophage with a Novel Cell Wall-binding Motif*

Bustamante

Campillo

Garcı́a

et al. 2010

Journal of Biological Chemistry

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Bacteriophage endolysins include a group of new antibacterials reluctant to development of resistance. We present here the first structural study of the Cpl-7 endolysin, encoded by pneumococcal bacteriophage Cp-7. It contains an N-terminal catalytic module (CM) belonging to the GH25 family of glycosyl hydrolases and a C-terminal region encompassing three identical repeats of 42 amino acids (CW_7 repeats). These repeats are unrelated to choline-targeting motifs present in other cell wall hydrolases produced by Streptococcus pneumoniae and its bacteriophages, and are responsible for the protein attachment to the cell wall. By combining different biophysical techniques and molecular modeling, a three-dimensional model of the overall protein structure is proposed, consistent with circular dichroism and sequence-based secondary structure prediction, small angle x-ray scattering data, and Cpl-7 hydrodynamic behavior. Cpl-7 is an ϳ115-Å long molecule with two well differentiated regions, corresponding to the CM and the cell wall binding region (CWBR), arranged in a lateral disposition. The CM displays the (␤␣) 5 ␤ 3 barrel topology characteristic of the GH25 family, and the impact of sequence differences with the CM of the Cpl-1 lysozyme in substrate binding is discussed. The CWBR is organized in three tandemly assembled three-helical bundles whose dispositions remind us of a super-helical structure. Its approximate dimensions are 60 ؋ 20 ؋ 20 Å and presents a concave face that might constitute the functional region involved in bacterial surface recognition. The distribution of CW_7 repeats in the sequences deposited in the Entrez Database have been examined, and the results drastically expanded the antimicrobial potential of the Cpl-7 endolysin.Bacteria and bacteriophages produce a variety of enzymes that cleave the peptidoglycan, the cell wall hydrolases (CWHs), 3 either to lyse host cells or to re-model the cell wall during growth and division. Many of these enzymes have a modular structure and are composed of catalytic units linked to a number of other modules. The Cpl-7 lysozyme, the lytic enzyme (endolysin) encoded by the pneumococcal bacteriophage Cp-7, consists of a catalytic N-terminal domain fused to a C-terminal region containing three identical tandem repeats of 48 amino acids (the third motif has the last six residues missing), which is essential for activity and unique among CWHs encoded by the pneumococcus and its bacteriophages (1, 2). However, the same type of repeats (termed CW_7 hereafter) has been later identified in other proteins putatively associated with bacterial cell wall degradation activity (3). The catalytic module (CM) of Cpl-7 belongs to the GH25 family of glycosyl hydrolases and shows 85.6% sequence identity with the CM of the Cpl-1 lysozyme, the endolysin encoded by the pneumococcal bacteriophage Cp-1 (4). However, the cell wall binding region (CWBR) of Cpl-1, made of six tandem copies of ϳ20 amino acid residues plus a terminal tail, belongs to the family of pneumococcal choline-binding...

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“…This patchy distribution of rdhA genes points either to rapid gene loss within the Dehalococcoides, or to lateral acquisition of novel rdhA genes within subsets of Dehalococcoides mccartyi strains. Lateral gene transfer has been invoked for rdhA gene acquisition in several scenarios [95][96][97][98][99] and is potentially a factor in the RdhA family diversification. Sequence information from new strains and complete genome sequences from strains for which some rdhA genes have been identified will help clarify orthologue and paralogue relationships.…”

Section: (B) Sequence Analysis Of Reductive Dehalogenasesmentioning

confidence: 99%

Overview of organohalide-respiring bacteria and a proposal for a classification system for reductive dehalogenases

Hug

Maphosa

Leys

et al. 2013

Phil. Trans. R. Soc. B

268

277

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Organohalide respiration is an anaerobic bacterial respiratory process that uses halogenated hydrocarbons as terminal electron acceptors during electron transport-based energy conservation. This dechlorination process has triggered considerable interest for detoxification of anthropogenic groundwater contaminants. Organohalide-respiring bacteria have been identified from multiple bacterial phyla, and can be categorized as obligate and non-obligate organohalide respirers. The majority of the currently known organohalide-respiring bacteria carry multiple reductive dehalogenase genes. Analysis of a curated set of reductive dehalogenases reveals that sequence similarity and substrate specificity are generally not correlated, making functional prediction from sequence information difficult. In this article, an orthologue-based classification system for the reductive dehalogenases is proposed to aid integration of new sequencing data and to unify terminology.

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Indications for Acquisition of Reductive Dehalogenase Genes through Horizontal Gene Transfer by Dehalococcoides ethenogenes Strain 195

Cited by 37 publications

References 61 publications

Identification and transcriptional analysis of trans-DCE-producing reductive dehalogenases in Dehalococcoides species

Identification and transcriptional analysis of trans-DCE-producing reductive dehalogenases in Dehalococcoides species

Cpl-7, a Lysozyme Encoded by a Pneumococcal Bacteriophage with a Novel Cell Wall-binding Motif*

Overview of organohalide-respiring bacteria and a proposal for a classification system for reductive dehalogenases

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