Molecular characterization of the enzymes involved in the degradation of a brominated aromatic herbicide

Chen, Kai; Huang, Linglong; Xu, Changfeng; Liu, Xiaomei; He, Jun; Zinder, Stephen H.; Li, Shunpeng; Jiang, Jiandong

doi:10.1111/mmi.12332

Cited by 85 publications

(72 citation statements)

References 74 publications

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“…Genes for RDases typically occur in an operon containing the gene for the catalytically active enzyme (rdhA) and an associated rdhB gene coding for a membrane anchor protein featuring two or sometimes three transmembrane helices (12)(13)(14)(15)(16). Reductive dehalogenase homologous proteins (RdhA) are identified on the basis of the presence of four motifs: a twin-arginine TAT membrane export sequence (RRXFXK), two iron-sulfur cluster binding motifs, and various modifications of a cobalamin binding motif (DXHXXGSXLGG) (3,13,(17)(18)(19)(20).…”

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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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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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“…strain 7D-2. This plasmid is involved in the mineralization of the herbicide bromoxynil (3,5-dibromo-4-hydroxybenzonitrile), which includes the reductive dehalogenation of the bromoxynil nitrile hydrolyte 3,5-dibromo-4-hydroxybenzoate (DBHB) (14).Plasmids are among the most important elements in the evolution of prokaryotes and their adaptation to changing environments (15). In addition to the conserved backbone, which is important for DNA replication and mobilization, plasmids usually carry highly variable regions of accessory genes that are responsible for the phenotypic diversity of their hosts, such as the capability to catabolize organic pollutants and to resist heavy metals (13,16).…”

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confidence: 99%

“…To study the specificity of the extracytoplasmic binding receptor (BhbB/BhbB2) and its effect on the degradation activity of reductive dehalogenase (BhbA/BhbA2), different combinations of the extracytoplasmic binding receptor gene and the reductive dehalogenase gene (specifically, bhbAB, bhbA2B2, bhbA2B, and This study bhbAB2) were constructed and ligated into pMCSQ2 (see Fig. 6) as described previously (14). These constructs were then transformed into strain 2B to generate strains 2B-bhbAB, 2B-bhbA2B2, 2B-bhbA2B, and 2B-bhbAB2, respectively.…”

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“…The inocula were incubated at 30°C on a shaker at 150 rpm. Samples were collected at 8 h, and the concentration of DBHB or BHB was detected by HPLC as described previously (14). The crude enzymatic activities of BhbA and BhbA2, which were coexpressed with their native extracytoplasmic binding receptors, were also assayed.…”

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Comparison of Four Comamonas Catabolic Plasmids Reveals the Evolution of pBHB To Catabolize Haloaromatics

Chen

Zhang

et al. 2016

Appl Environ Microbiol

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bComamonas plasmids play important roles in shaping the phenotypes of their hosts and the adaptation of these hosts to changing environments, and understanding the evolutionary strategy of these plasmids is thus of great concern. In this study, the sequence of the 119-kb 3,5-dibromo-4-hydroxybenzonitrile-catabolizing plasmid pBHB from Comamonas sp. strain 7D-2 was studied and compared with those of three other Comamonas haloaromatic catabolic plasmids. Incompatibility group determination based on a phylogenetic analysis of 24 backbone gene proteins, as well as TrfA, revealed that these four plasmids all belong to the IncP-1␤ subgroup. Comparison of the four plasmids revealed a conserved backbone region and diverse genetic-load regions. The four plasmids share a core genome consisting of 40 genes (>50% similarities) and contain 12 to 50 unique genes each, most of which are xenobiotic-catabolic genes. Two functional reductive dehalogenase gene clusters are specifically located on pBHB, showing distinctive evolution of pBHB for haloaromatics. The higher catabolic ability of the bhbA2B2 cluster than the bhbAB cluster may be due to the transcription levels and the character of the dehalogenase gene itself rather than that of its extracytoplasmic binding receptor gene. The plasmid pBHB is riddled with transposons and insertion sequence (IS) elements, and ISs play important roles in the evolution of pBHB. The analysis of the origin of the bhb genes on pBHB suggested that these accessory genes evolved independently. Our work provides insights into the evolutionary strategies of Comamonas plasmids, especially into the adaptation mechanism employed by pBHB for haloaromatics. Comamonas species are ubiquitous in the environment and have been isolated from soil, mud, water, activated sludge, clinical samples, and organic pollutant-and heavy metal-contaminated environments (1). Comamonas species play an important role in matter cycling in nature and have been noted for their capabilities to degrade various aromatics (1-5). Interestingly, many Comamonas strains have been found to harbor plasmids, most of which have been confirmed to be related to the catabolism of xenobiotic aromatics (4, 6-8). For example, the plasmid pI2, responsible for the degradation of aniline/3-chloroaniline, was isolated from Comamonas testosteroni I2 (4, 9, 10). Another transferable plasmid, pTB30, which is involved in the mineralization of 3-chloroaniline, was isolated from C. testosteroni TB30 (9, 11). In addition, the plasmid pCNB1, encoding the catabolic pathway to convert 4-chloronitrobenzene to 5-chloro-4-hydroxy-2-oxovalerate, was sequenced in Comamonas sp. strain CNB-1 (12, 13). Recently, the plasmid pBHB was characterized in Comamonas sp. strain 7D-2. This plasmid is involved in the mineralization of the herbicide bromoxynil (3,5-dibromo-4-hydroxybenzonitrile), which includes the reductive dehalogenation of the bromoxynil nitrile hydrolyte 3,5-dibromo-4-hydroxybenzoate (DBHB) (14).Plasmids are among the most important elements in the evolutio...

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Primers That Target Functional Genes of Organohalide-Respiring Bacteria

Lu¹,

Atashgahi²,

Hug³

et al. 2015

Springer Protocols Handbooks

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Molecular characterization of the enzymes involved in the degradation of a brominated aromatic herbicide

Cited by 85 publications

References 74 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

Comparison of Four Comamonas Catabolic Plasmids Reveals the Evolution of pBHB To Catabolize Haloaromatics

Primers That Target Functional Genes of Organohalide-Respiring Bacteria

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