Genome sequences of two dehalogenation specialists<i>- Dehalococcoides mccartyi</i>strains BTF08 and DCMB5 enriched from the highly polluted Bitterfeld region

Pöritz, Marlén; Goris, Tobias; Wubet, Tesfaye; Tarkka, Mika; Buscot, François; Nijenhuis, Ivonne; Lechner, Ute; Adrian, Lorenz

doi:10.1111/1574-6968.12160

Cited by 76 publications

(67 citation statements)

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“…Recently, the genome of strain DCMB5 was sequenced and revealed the presence of 23 rdhAB genes encoding the catalytic subunit A and the putative membrane anchor subunit B, respectively, of reductive dehalogenases (or reductive dehalogenase homologous proteins, Rdh proteins, if not yet biochemically characterized) (7). This finding suggests that the bacterium has a high capacity for organohalide respiration with a broad range of pollutants (8).…”

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confidence: 99%

Dehalococcoides mccartyi Strain DCMB5 Respires a Broad Spectrum of Chlorinated Aromatic Compounds

Pöritz

Schiffmann

Hause

et al. 2015

Appl Environ Microbiol

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f Polyhalogenated aromatic compounds are harmful environmental contaminants and tend to persist in anoxic soils and sediments. Dehalococcoides mccartyi strain DCMB5, a strain originating from dioxin-polluted river sediment, was examined for its capacity to dehalogenate diverse chloroaromatic compounds. Strain DCMB5 used hexachlorobenzenes, pentachlorobenzenes, all three tetrachlorobenzenes, and 1,2,3-trichlorobenzene as well as 1,2,3,4-tetra-and 1,2,4-trichlorodibenzo-p-dioxin as electron acceptors for organohalide respiration. In addition, 1,2,3-trichlorodibenzo-p-dioxin and 1,3-, 1,2-, and 1,4-dichlorodibenzo-p-dioxin were dechlorinated, the latter to the nonchlorinated congener with a remarkably short lag phase of 1 to 4 days following transfer. Strain DCMB5 also dechlorinated pentachlorophenol and almost all tetra-and trichlorophenols. Tetrachloroethene was dechlorinated to trichloroethene and served as an electron acceptor for growth. To relate selected dechlorination activities to the expression of specific reductive dehalogenase genes, the proteomes of 1,2,3-trichlorobenzene-, pentachlorobenzene-, and tetrachloroethene-dechlorinating cultures were analyzed. Dcmb_86, an ortholog of the chlorobenzene reductive dehalogenase CbrA, was the most abundant reductive dehalogenase during growth with each electron acceptor, suggesting its pivotal role in organohalide respiration of strain DCMB5. Dcmb_1041 was specifically induced, however, by both chlorobenzenes, whereas 3 putative reductive dehalogenases, Dcmb_1434, Dcmb_1339, and Dcmb_1383, were detected only in tetrachloroethene-grown cells. The proteomes also harbored a type IV pilus protein and the components for its assembly, disassembly, and secretion. In addition, transmission electron microscopy of DCMB5 revealed an irregular mode of cell division as well as the presence of pili, indicating that pilus formation is a feature of D. mccartyi during organohalide respiration.

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confidence: 99%

Dehalococcoides mccartyi Strain DCMB5 Respires a Broad Spectrum of Chlorinated Aromatic Compounds

Pöritz

Schiffmann

Hause

et al. 2015

Appl Environ Microbiol

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“…All known D. mccartyi strains are obligate hydrogenotrophs and organohalide respirers that reductively dehalogenate a wide spectrum of halogenated organics (3), suggesting broad applicability for the bioremediation of various contaminants. However, despite the isolation and genome sequencing of several strains (D. mccartyi strains 195 [4,5], CBDB1 [6,7], VS [8][9][10], GT [11], BAV1 [10,12,13], BTF08 [14], and DCMB5 [14]), the complete set of enzymes participating in the central electron transport chain (ETC) and the organization of the ETC remain unknown. Previous studies have identified two main classes of enzymes involved in the ETC: reductive dehalogenases (RDases) (5), which pass an electron to halogenated organics, and hydrogenases (H 2 ases), which oxidize the sole known electron donor of D. mccartyi, hydrogen (15,16).…”

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Meta-Analyses of Dehalococcoides mccartyi Strain 195 Transcriptomic Profiles Identify a Respiration Rate-Related Gene Expression Transition Point and Interoperon Recruitment of a Key Oxidoreductase Subunit

Mansfeldt

Rowe

Heavner

et al. 2014

Appl Environ Microbiol

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A cDNA-microarray was designed and used to monitor the transcriptomic profile of Dehalococcoides mccartyi strain 195 (in a mixed community) respiring various chlorinated organics, including chloroethenes and 2,3-dichlorophenol. The cultures were continuously fed in order to establish steady-state respiration rates and substrate levels. The organization of array data into a clustered heat map revealed two major experimental partitions. This partitioning in the data set was further explored through principal component analysis. The first two principal components separated the experiments into those with slow (1.6 ؎ 0.6 M Cl ؊ /h)-and fast (22.9 ؎ 9.6 M Cl ؊ /h)-respiring cultures. Additionally, the transcripts with the highest loadings in these principal components were identified, suggesting that those transcripts were responsible for the partitioning of the experiments. By analyzing the transcriptomes (n ‫؍‬ 53) across experiments, relationships among transcripts were identified, and hypotheses about the relationships between electron transport chain members were proposed. One hypothesis, that the hydrogenases Hup and Hym and the formate dehydrogenase-like oxidoreductase (DET0186-DET0187) form a complex (as displayed by their tight clustering in the heat map analysis), was explored using a nondenaturing protein separation technique combined with proteomic sequencing. Although these proteins did not migrate as a single complex, DET0112 (an FdhB-like protein encoded in the Hup operon) was found to comigrate with DET0187 rather than with the catalytic Hup subunit DET0110. On closer inspection of the genome annotations of all Dehalococcoides strains, the DET0185-to-DET0187 operon was found to lack a key subunit, an FdhB-like protein. Therefore, on the basis of the transcriptomic, genomic, and proteomic evidence, the place of the missing subunit in the DET0185-to-DET0187 operon is likely filled by recruiting a subunit expressed from the Hup operon (DET0112). 5), which pass an electron to halogenated organics, and hydrogenases (H 2 ases), which oxidize the sole known electron donor of D. mccartyi, hydrogen (15, 16). Although expression has been confirmed at both the mRNA and protein levels for RDases (differing with the strain), H 2 ases (Hup, Hym-1, Hym-2, Vhu, Ech, and Hyc [5,17,18]), and other putative membrane-bound oxidoreductase proteins, the interactions among these proteins are not well described (19). Three of the other notable putative oxidoreductases are DET0187, a predicted (but not biochemically confirmed) molybdopterin-containing protein annotated as a formate dehydrogenase that maintains an atypical serine in its active site rather than the typical cysteine or selenocysteine (15); Nuo, a NADH-ubiquinone oxidoreductase that lacks the NADH-receiving subunits (NuoEFG) in its predicted operon; and Mod, an additional predicted (but not biochemically confirmed) molybdopterin-containing oxidoreductase.The main goal of this study was to observe broad transcriptional expression patterns during the steady-state...

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“…None of the dehalogenase genes analyzed were detected in samples grouped in Cluster 5, which consisted of samples deposited at depths below those grouped in Cluster 1 and a surface sample (Aa1). Previous studies demonstrate that Dehalococcoides has multiple reductive dehalogenase genes in addition to tceA, bvcA, and vcrA (Pöritz et al, 2013;Wang, Chng, Chen, Bedard, & He, 2015). Therefore, the samples grouped in Cluster 5 may have contained dehalogenase genes other than the three genes tested in the present study.…”

Section: Spatial Distribution Of Reductive Dehalogenase Genesmentioning

confidence: 73%

Distribution of Dehalococcoides 16S rRNA and Dehalogenase Genes in Contaminated Sites

Yoshikawa¹,

Takeuchi²,

Zhang³

2017

ENRR

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Understanding the spatial distribution of Dehalococcoides and its reductive dehalogenase genes in sediment is important for bioremediation of sites contaminated with chlorinated ethylenes. A total of 56 sediment samples were collected from four contaminated sites in Japan, and quantified copies of Dehalococcoides 16S rRNA and reductive dehalogenase genes: tceA, bvcA, and vcrA, as well as chlorinated ethylenes. Dehalococcoides was detected from 22 sediment samples with various geological formations, textures and saturation conditions. The

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Genome sequences of two dehalogenation specialists- Dehalococcoides mccartyistrains BTF08 and DCMB5 enriched from the highly polluted Bitterfeld region

Cited by 76 publications

References 20 publications

Dehalococcoides mccartyi Strain DCMB5 Respires a Broad Spectrum of Chlorinated Aromatic Compounds

Dehalococcoides mccartyi Strain DCMB5 Respires a Broad Spectrum of Chlorinated Aromatic Compounds

Meta-Analyses of Dehalococcoides mccartyi Strain 195 Transcriptomic Profiles Identify a Respiration Rate-Related Gene Expression Transition Point and Interoperon Recruitment of a Key Oxidoreductase Subunit

Distribution of Dehalococcoides 16S rRNA and Dehalogenase Genes in Contaminated Sites

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