scholarly journals Phylogenetic and Transcriptional Analyses of a Tetrachloroethene-Dechlorinating "Dehalococcoides" Enrichment Culture TUT2264 and Its Reductive-Dehalogenase Genes

2009 ◽  
Vol 24 (4) ◽  
pp. 330-337 ◽  
Author(s):  
Hiroyuki Futamata ◽  
Shinichi Kaiya ◽  
Mariko Sugawara ◽  
Akira Hiraishi
Keyword(s):  
Enrichment Culture ◽  
Reductive Dehalogenase ◽  
Reductive Dehalogenase Genes

scholarly journals Extrachromosomal circular elements targeted by CRISPR-Cas in Dehalococcoides mccartyi are linked to mobilization of reductive dehalogenase genes

2018 ◽  
Vol 13 (1) ◽  
pp. 24-38 ◽  
Author(s):  
Olivia Molenda ◽  
Shuiquan Tang ◽  
Line Lomheim ◽  
Vasu K. Gautam ◽  
Sofia Lemak ◽  
...  
Keyword(s):  
Reductive Dehalogenase ◽  
Dehalococcoides Mccartyi ◽  
Reductive Dehalogenase Genes

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

2013 ◽  
Vol 368 (1616) ◽  
pp. 20120322 ◽  
Author(s):  
Laura A. Hug ◽  
Farai Maphosa ◽  
David Leys ◽  
Frank E. Löffler ◽  
Hauke Smidt ◽  
...  
Keyword(s):  
Classification System ◽  
Sequence Similarity ◽  
Halogenated Hydrocarbons ◽  
Sequence Information ◽  
Sequencing Data ◽  
Functional Prediction ◽  
Groundwater Contaminants ◽  
Reductive Dehalogenase ◽  
Bacterial Phyla ◽  
Reductive Dehalogenase Genes

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.

scholarly journals A Novel Reductive Dehalogenase, Identified in a Contaminated Groundwater Enrichment Culture and in Desulfitobacterium dichloroeliminans Strain DCA1, Is Linked to Dehalogenation of 1,2-Dichloroethane

2007 ◽  
Vol 73 (9) ◽  
pp. 2990-2999 ◽  
Author(s):  
Massimo Marzorati ◽  
Francesca de Ferra ◽  
Hilde Van Raemdonck ◽  
Sara Borin ◽  
Elena Allifranchini ◽  
...  
Keyword(s):  
Amino Acid ◽  
Gene Cluster ◽  
Enrichment Culture ◽  
Gene Copy Number ◽  
Gene Clusters ◽  
Amino Acid Identity ◽  
Chlorinated Ethenes ◽  
Gene Copy ◽  
Direct Pcr ◽  
Reductive Dehalogenase

ABSTRACT A mixed culture dechlorinating 1,2-dichloroethane (1,2-DCA) to ethene was enriched from groundwater that had been subjected to long-term contamination. In the metagenome of the enrichment, a 7-kb reductive dehalogenase (RD) gene cluster sequence was detected by inverse and direct PCR. The RD gene cluster had four open reading frames (ORF) showing 99% nucleotide identity with pceB, pceC, pceT, and orf1 of Dehalobacter restrictus strain DSMZ 9455T, a bacterium able to dechlorinate chlorinated ethenes. However, dcaA, the ORF encoding the catalytic subunit, showed only 94% nucleotide and 90% amino acid identity with pceA of strain DSMZ 9455T. Fifty-three percent of the amino acid differences were localized in two defined regions of the predicted protein. Exposure of the culture to 1,2-DCA and lactate increased the dcaA gene copy number by 2 log units, and under these conditions the dcaA and dcaB genes were actively transcribed. A very similar RD gene cluster with 98% identity in the dcaA gene sequence was identified in Desulfitobacterium dichloroeliminans strain DCA1, the only known isolate that selectively dechlorinates 1,2-DCA but not chlorinated ethenes. The dcaA gene of strain DCA1 possesses the same amino acid motifs as the new dcaA gene. Southern hybridization using total genomic DNA of strain DCA1 with dcaA gene-specific and dcaB- and pceB-targeting probes indicated the presence of two identical or highly similar dehalogenase gene clusters. In conclusion, these data suggest that the newly described RDs are specifically adapted to 1,2-DCA dechlorination.

Development and application of a rapid, user-friendly, and inexpensive method to detect Dehalococcoides sp. reductive dehalogenase genes from groundwater

2017 ◽  
Vol 101 (11) ◽  
pp. 4827-4835 ◽  
Author(s):  
Yogendra H. Kanitkar ◽  
Robert D. Stedtfeld ◽  
Paul B. Hatzinger ◽  
Syed A. Hashsham ◽  
Alison M. Cupples
Keyword(s):  
Inexpensive Method ◽  
Reductive Dehalogenase ◽  
Reductive Dehalogenase Genes ◽  
User Friendly

scholarly journals Grape pomace compost harbors organohalide-respiring Dehalogenimonas species with novel reductive dehalogenase genes

2017 ◽  
Vol 11 (12) ◽  
pp. 2767-2780 ◽  
Author(s):  
Yi Yang ◽  
Steven A Higgins ◽  
Jun Yan ◽  
Burcu Şimşir ◽  
Karuna Chourey ◽  
...  
Keyword(s):  
Grape Pomace ◽  
Reductive Dehalogenase ◽  
Reductive Dehalogenase Genes

scholarly journals Complete Genome Sequence of Dehalococcoides mccartyi Strain FL2, a Trichloroethene-Respiring Anaerobe Isolated from Pristine Freshwater Sediment

2019 ◽  
Vol 8 (33) ◽  
Author(s):  
Jun Yan ◽  
Yi Yang ◽  
Xiuying Li ◽  
Frank E. Löffler
Keyword(s):  
Complete Genome Sequence ◽  
Reductive Dechlorination ◽  
Complete Genome ◽  
Hydrogen Oxidation ◽  
Protein Coding ◽  
Coding Sequences ◽  
Content Type ◽  
Reductive Dehalogenase ◽  
Dehalococcoides Mccartyi ◽  
Reductive Dehalogenase Genes

Dehalococcoides mccartyi strain FL2 couples growth to hydrogen oxidation and reductive dechlorination of trichloroethene and cis- and trans-1,2-dichloroethenes. Strain FL2 has a 1.42-Mb genome with a G+C content of 47.0% and carries 1,465 protein-coding sequences, including 24 reductive dehalogenase genes.

scholarly journals Multiple Nonidentical Reductive-Dehalogenase-Homologous Genes Are Common in Dehalococcoides

2004 ◽  
Vol 70 (9) ◽  
pp. 5290-5297 ◽  
Author(s):  
Tina Hölscher ◽  
Rosa Krajmalnik-Brown ◽  
Kirsti M. Ritalahti ◽  
Friedrich von Wintzingerode ◽  
Helmut Görisch ◽  
...  
Keyword(s):  
Amino Acid ◽  
Restriction Analysis ◽  
Sequence Similarity ◽  
Comparative Sequence Analysis ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Degenerate Primers ◽  
Reductive Dehalogenase ◽  
Genes Encoding ◽  
Reductive Dehalogenase Genes

ABSTRACT Degenerate primers were used to amplify large fragments of reductive-dehalogenase-homologous (RDH) genes from genomic DNA of two Dehalococcoides populations, the chlorobenzene- and dioxin-dechlorinating strain CBDB1 and the trichloroethene-dechlorinating strain FL2. The amplicons (1,350 to 1,495 bp) corresponded to nearly complete open reading frames of known reductive dehalogenase genes and short fragments (approximately 90 bp) of genes encoding putative membrane-anchoring proteins. Cloning and restriction analysis revealed the presence of at least 14 different RDH genes in each strain. All amplified RDH genes showed sequence similarity with known reductive dehalogenase genes over the whole length of the sequence and shared all characteristics described for reductive dehalogenases. Deduced amino acid sequences of seven RDH genes from strain CBDB1 were 98.5 to 100% identical to seven different RDH genes from strain FL2, suggesting that both strains have an overlapping substrate range. All RDH genes identified in strains CBDB1 and FL2 were related to the RDH genes present in the genomes of Dehalococcoides ethenogenes strain 195 and Dehalococcoides sp. strain BAV1; however, sequence identity did not exceed 94.4 and 93.1%, respectively. The presence of RDH genes in strains CBDB1, FL2, and BAV1 that have no orthologs in strain 195 suggests that these strains possess dechlorination activities not present in strain 195. Comparative sequence analysis identified consensus sequences for cobalamin binding in deduced amino acid sequences of seven RDH genes. In conclusion, this study demonstrates that the presence of multiple nonidentical RDH genes is characteristic of Dehalococcoides strains.

scholarly journals Quantitative Analysis of the Relative Transcript Levels of Four Chlorophenol Reductive Dehalogenase Genes in Desulfitobacterium hafniense PCP-1 Exposed to Chlorophenols

2011 ◽  
Vol 77 (17) ◽  
pp. 6261-6264 ◽  
Author(s):  
Ariane Bisaillon ◽  
Réjean Beaudet ◽  
François Lépine ◽  
Richard Villemur
Keyword(s):  
Quantitative Analysis ◽  
Transcript Levels ◽  
Content Type ◽  
Reductive Dehalogenase ◽  
Reductive Dehalogenase Genes ◽  
Desulfitobacterium Hafniense

ABSTRACTRelative to those of unexposed cultures, the transcript levels of the four CprA-type reductive dehalogenase genes (cprA2,cprA3,cprA4, andcprA5) inDesulfitobacterium hafniensePCP-1 were measured in cultures exposed to chlorophenols. In 2,4,6-trichlorophenol-amended cultures,cprA2andcprA3were upregulated, as wascprA5, but concomitantly with the appearance of 2,4-dichlorophenol (DCP). In 3,5-DCP-amended cultures, onlycprA5was upregulated. In pentachlorophenol-amended cultures grown for 12 h,cprA2andcprA3were upregulated but notcprA5. cprA4was not upregulated significantly in cultures containing any tested chlorophenols.

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