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

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.

2012 ◽  
Vol 78 (22) ◽  
pp. 8025-8032 ◽  
Author(s):  
Anika Reinhold ◽  
Martin Westermann ◽  
Jana Seifert ◽  
Martin von Bergen ◽  
Torsten Schubert ◽  
...  

ABSTRACTCorrinoids are essential cofactors of reductive dehalogenases in anaerobic bacteria. Microorganisms mediating reductive dechlorination as part of their energy metabolism are either capable ofde novocorrinoid biosynthesis (e.g.,Desulfitobacteriumspp.) or dependent on exogenous vitamin B12(e.g.,Dehalococcoidesspp.). In this study, the impact of exogenous vitamin B12(cyanocobalamin) and of tetrachloroethene (PCE) on the synthesis and the subcellular localization of the reductive PCE dehalogenase was investigated in the Gram-positiveDesulfitobacterium hafniensestrain Y51, a bacterium able to synthesize corrinoidsde novo. PCE-depleted cells grown for several subcultivation steps on fumarate as an alternative electron acceptor lost the tetrachloroethene-reductive dehalogenase (PceA) activity by the transposition of thepcegene cluster. In the absence of vitamin B12, a gradual decrease of the PceA activity and protein amount was observed; after 5 subcultivation steps with 10% inoculum, more than 90% of the enzyme activity and of the PceA protein was lost. In the presence of vitamin B12, a significant delay in the decrease of the PceA activity with an ∼90% loss after 20 subcultivation steps was observed. This corresponded to the decrease in thepceAgene level, indicating that exogenous vitamin B12hampered the transposition of thepcegene cluster. In the absence or presence of exogenous vitamin B12, the intracellular corrinoid level decreased in fumarate-grown cells and the PceA precursor formed catalytically inactive, corrinoid-free multiprotein aggregates. The data indicate that exogenous vitamin B12is not incorporated into the PceA precursor, even though it affects the transposition of thepcegene cluster.


2019 ◽  
Vol 8 (33) ◽  
Author(s):  
Jun Yan ◽  
Yi Yang ◽  
Xiuying Li ◽  
Frank E. Löffler

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.


2003 ◽  
Vol 69 (8) ◽  
pp. 4628-4638 ◽  
Author(s):  
Julien Maillard ◽  
Wolfram Schumacher ◽  
Francisco Vazquez ◽  
Christophe Regeard ◽  
Wilfred R. Hagen ◽  
...  

ABSTRACT The membrane-bound tetrachloroethene reductive dehalogenase (PCE-RDase) (PceA; EC 1.97.1.8), the terminal component of the respiratory chain of Dehalobacter restrictus, was purified 25-fold to apparent electrophoretic homogeneity. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed a single band with an apparent molecular mass of 60 ± 1 kDa, whereas the native molecular mass was 71± 8 kDa according to size exclusion chromatography in the presence of the detergent octyl-β-d-glucopyranoside. The monomeric enzyme contained (per mol of the 60-kDa subunit) 1.0± 0.1 mol of cobalamin, 0.6 ± 0.02 mol of cobalt, 7.1± 0.6 mol of iron, and 5.8 ± 0.5 mol of acid-labile sulfur. Purified PceA catalyzed the reductive dechlorination of tetrachloroethene and trichloroethene to cis-1,2-dichloroethene with a specific activity of 250 ± 12 nkat/mg of protein. In addition, several chloroethanes and tetrachloromethane caused methyl viologen oxidation in the presence of PceA. The Km values for tetrachloroethene, trichloroethene, and methyl viologen were 20.4± 3.2, 23.7 ± 5.2, and 47 ± 10 μM, respectively. The PceA exhibited the highest activity at pH 8.1 and was oxygen sensitive, with a half-life of activity of 280 min upon exposure to air. Based on the almost identical N-terminal amino acid sequences of PceA of Dehalobacter restrictus, Desulfitobacterium hafniense strain TCE1 (formerly Desulfitobacterium frappieri strain TCE1), and Desulfitobacterium hafniense strain PCE-S (formerly Desulfitobacterium frappieri strain PCE-S), the pceA genes of the first two organisms were cloned and sequenced. Together with the pceA genes of Desulfitobacterium hafniense strains PCE-S and Y51, the pceA genes of Desulfitobacterium hafniense strain TCE1 and Dehalobacter restrictus form a coherent group of reductive dehalogenases with almost 100% sequence identity. Also, the pceB genes, which may code for a membrane anchor protein of PceA, and the intergenic regions of Dehalobacter restrictus and the three desulfitobacteria had identical sequences. Whereas the cprB (chlorophenol reductive dehalogenase) genes of chlorophenol-dehalorespiring bacteria are always located upstream of cprA, all pceB genes known so far are located downstream of pceA. The possible consequences of this feature for the annotation of putative reductive dehalogenase genes are discussed, as are the sequence around the iron-sulfur cluster binding motifs and the type of iron-sulfur clusters of the reductive dehalogenases of Dehalobacter restrictus and Desulfitobacterium dehalogenans identified by electron paramagnetic resonance spectroscopy.


2007 ◽  
Vol 73 (14) ◽  
pp. 4439-4445 ◽  
Author(s):  
Jennifer M. Fung ◽  
Robert M. Morris ◽  
Lorenz Adrian ◽  
Stephen H. Zinder

ABSTRACT Reductive dehalogenase (RD) gene transcript levels in Dehalococcoides ethenogenes strain 195 were investigated using reverse transcriptase quantitative PCR during growth and reductive dechlorination of tetrachloroethene (PCE), trichloroethene (TCE), or 2,3-dichlorophenol (2,3-DCP). Cells grown with PCE or TCE had high transcript levels (greater than that for rpoB) for tceA, which encodes the TCE RD, pceA, which encodes the PCE RD, and DET0162, which contains a predicted stop codon and is considered nonfunctional. In cells grown with 2,3-DCP, tceA mRNA was less than 1% of that for rpoB, indicating that its transcription was regulated. pceA and DET0162 were the only RD genes with high transcript levels in cells grown with 2,3-DCP. Proteomic analysis of PCE-grown cells detected both PceA and TceA with high peptide coverage but not DET0162, and analysis of 2,3-DCP-grown cells detected PceA with high coverage but not TceA, DET0162, or any other potential RD. Cells grown with PCE or 2,3-DCP were tested for the ability to dechlorinate PCE, TCE, or 2,3-DCP with H2 as the electron donor. 2,3-DCP-grown cells were unable to dechlorinate TCE but dechlorinated PCE to TCE without a lag, and PCE-grown cells dechlorinated 2,3-DCP without a lag. These results show that 2,3-DCP-grown cells do not produce TceA and that DET0162 is transcribed but its translation product is not detectable in cells and are consistent with PceA's being bifunctional, also serving as the 2,3-DCP RD. Chlorophenols naturally occur in soils and are good candidates for the original substrates for PceA.


mBio ◽  
2018 ◽  
Vol 9 (6) ◽  
Author(s):  
Jie Liu ◽  
Max M. Häggblom

ABSTRACTOrganohalide compounds are widespread in the environment as a result of both anthropogenic activities and natural production. The marine environment, in particular, is a major reservoir of organohalides, and reductive dehalogenation is thought to be an important process in the overall cycling of these compounds.Deltaproteobacteriaare important members of the marine microbiota with diverse metabolic capacities, and reductive dehalogenation has been observed in someDeltaproteobacteria. In this study, a comprehensive survey ofDeltaproteobacteriagenomes revealed that approximately 10% contain reductive dehalogenase (RDase) genes, which are found within a common gene neighborhood. The dehalogenating potential of select RDase A-containingDeltaproteobacteriaand their gene expression were experimentally verified. ThreeDeltaproteobacteriastrains isolated from marine environments representing diverse species,Halodesulfovibrio marinisediminis,Desulfuromusa kysingii, andDesulfovibrio bizertensis, were shown to reductively dehalogenate bromophenols and utilize them as terminal electron acceptors in organohalide respiration. Their debrominating activity was not inhibited by sulfate or elemental sulfur, and these species are either sulfate- or sulfur-reducing bacteria. The analysis of RDase A gene transcripts indicated significant upregulation induced by 2,6-dibromophenol. This study extends our knowledge of the phylogenetic diversity of organohalide-respiring bacteria and their functional RDase A gene diversity. The identification of reductive dehalogenase genes in diverseDeltaproteobacteriaand confirmation of their organohalide-respiring capability suggest thatDeltaproteobacteriaplay an important role in natural organohalide cycling.IMPORTANCEThe marine environment is a major reservoir for both anthropogenic and natural organohalides, and reductive dehalogenation is thought to be an important process in the overall cycling of these compounds. Here we demonstrate that the capacity of organohalide respiration appears to be widely distributed in members of marineDeltaproteobacteria. The identification of reductive dehalogenase genes in diverseDeltaproteobacteriaand the confirmation of their dehalogenating activity through functional assays and transcript analysis in select isolates extend our knowledge of organohalide-respiringDeltaproteobacteriadiversity. The presence of functional reductive dehalogenase genes in diverseDeltaproteobacteriaimplies that they may play an important role in organohalide respiration in the environment.


2011 ◽  
Vol 78 (4) ◽  
pp. 1178-1186 ◽  
Author(s):  
Alison S. Waller ◽  
Laura A. Hug ◽  
Kaiguo Mo ◽  
Devon R. Radford ◽  
Karen L. Maxwell ◽  
...  

ABSTRACTChlorinated solvents are among the most prevalent groundwater contaminants in the industrialized world. Biodegradation withDehalococcoides-containing mixed cultures is an effective remediation technology. To elucidate transcribed genes in aDehalococcoides-containing mixed culture, a shotgun metagenome microarray was created and used to investigate gene transcription during vinyl chloride (VC) dechlorination and during starvation (no chlorinated compounds) by a microbial enrichment culture called KB-1. In both treatment conditions, methanol was amended as an electron donor. Subsequently, spots were sequenced that contained the genes most differentially transcribed between the VC-degrading and methanol-only conditions, as well as spots with the highest intensities. Sequencing revealed that during VC degradationDehalococcoidesgenes involved in transcription, translation, metabolic energy generation, and amino acid and lipid metabolism and transport were overrepresented in the transcripts compared to the averageDehalococcoidesgenome. KB-1rdhA14(vcrA) was the only reductive dehalogenase homologous (RDH) gene with higher transcript levels during VC degradation, while multiple RDH genes had higher transcript levels in the absence of VC. Numerous hypothetical genes fromDehalococcoidesalso had higher transcript levels in methanol-only treatments, indicating that many uncharacterized proteins are involved in cell maintenance in the absence of chlorinated substrates. In addition, microarray results prompted biological experiments confirming that electron acceptor limiting conditions activated aDehalococcoidesprophage. Transcripts fromSpirochaetes,Chloroflexi,Geobacter, and methanogens demonstrate the importance of non-Dehalococcoidesorganisms to the culture, and sequencing of identified shotgun clones of interest provided information for follow-on targeted studies.


2014 ◽  
Vol 80 (14) ◽  
pp. 4313-4322 ◽  
Author(s):  
Anita Mac Nelly ◽  
Marco Kai ◽  
Aleš Svatoš ◽  
Gabriele Diekert ◽  
Torsten Schubert

ABSTRACTThe anaerobic dehalogenation of organohalides is catalyzed by the reductive dehalogenase (RdhA) enzymes produced in phylogenetically diverse bacteria. These enzymes contain a cobamide cofactor at the active site and two iron-sulfur clusters. In this study, the tetrachloroethene (PCE) reductive dehalogenase (PceA) of the Gram-positiveDesulfitobacterium hafniensestrain Y51 was produced in a catalytically active form in the nondechlorinating, cobamide-producing bacteriumShimwellia blattae(ATCC 33430), a Gram-negative gammaproteobacterium. The formation of recombinant catalytically active PceA enzyme was significantly enhanced when its dedicated PceT chaperone was coproduced and when 5,6-dimethylbenzimidazole and hydroxocobalamin were added to theS. blattaecultures. The experiments were extended toD. hafnienseDCB-2, a reductively dehalogenating bacterium harboring multiplerdhAgenes. To elucidate the substrate spectrum of therdhA3gene product of this organism, the recombinant enzyme was tested for the conversion of different dichlorophenols (DCP) in crude extracts of an RdhA3-producingS. blattaestrain. 3,5-DCP, 2,3-DCP, and 2,4-DCP, but not 2,6-DCP and 3,4-DCP, were reductively dechlorinated by the recombinant RdhA3. In addition, this enzyme dechlorinated PCE to trichloroethene at low rates.


2013 ◽  
Vol 79 (22) ◽  
pp. 6941-6947 ◽  
Author(s):  
Géraldine F. Buttet ◽  
Christof Holliger ◽  
Julien Maillard

ABSTRACTReductive dehalogenases are the key enzymes involved in the anaerobic respiration of organohalides such as the widespread groundwater pollutant tetrachloroethene. The increasing number of available bacterial genomes and metagenomes gives access to hundreds of new putative reductive dehalogenase genes that display a high level of sequence diversity and for which substrate prediction remains very challenging. In this study, we present the development of a functional genotyping method targeting the diverse reductive dehalogenases present inSulfurospirillumspp., which allowed us to unambiguously identify a new reductive dehalogenase from our tetrachloroethene-dechlorinating SL2 bacterial consortia. The new enzyme, named PceATCE, shows 92% sequence identity with the well-characterized PceA enzyme ofSulfurospirillum multivorans, but in contrast to the latter, it is restricted to tetrachloroethene as a substrate. Its apparent higher dechlorinating activity with tetrachloroethene likely allowed its selection and maintenance in the bacterial consortia among other enzymes showing broader substrate ranges. The sequence-substrate relationships within tetrachloroethene reductive dehalogenases are also discussed.


2015 ◽  
Vol 197 (11) ◽  
pp. 1921-1930 ◽  
Author(s):  
Jennifer Tsang ◽  
Timothy R. Hoover

ABSTRACTFlagellar biogenesis inHelicobacter pyloriis regulated by a transcriptional hierarchy governed by three sigma factors, RpoD (σ80), RpoN (σ54), and FliA (σ28), that temporally coordinates gene expression with the assembly of the flagellum. Previous studies showed that loss of flagellar protein export apparatus components inhibits transcription of flagellar genes. The FlgS/FlgR two-component system activates transcription of RpoN-dependent genes though an unknown mechanism. To understand better the extent to which flagellar gene regulation is coupled to flagellar assembly, we disrupted flagellar biogenesis at various points and determined how these mutations affected transcription of RpoN-dependent (flaBandflgE) and FliA-dependent (flaA) genes. The MS ring (encoded byfliF) is one of the earliest flagellar structures assembled. Deletion offliFresulted in the elimination of RpoN-dependent transcripts and an ∼4-fold decrease inflaAtranscript levels. FliH is a cytoplasmic protein that functions with the C ring protein FliN to shuttle substrates to the export apparatus. Deletions offliHand genes encoding C ring components (fliMandfliY) decreased transcript levels offlaBandflgEbut had little or no effect on transcript levels offlaA. Transcript levels offlaBandflgEwere elevated in mutants where genes encoding rod proteins (fliEandflgBC) were deleted, while transcript levels offlaAwas reduced ∼2-fold in both mutants. We propose that FlgS responds to an assembly checkpoint associated with the export apparatus and that FliH and one or more C ring component assist FlgS in engaging this flagellar structure.IMPORTANCEThe mechanisms used by bacteria to couple transcription of flagellar genes with assembly of the flagellum are poorly understood. The results from this study identified components of theH. pyloriflagellar basal body that either positively or negatively affect expression of RpoN-dependent flagellar genes. Some of these basal body proteins may interact directly with regulatory proteins that control transcription of theH. pyloriRpoN regulon, a hypothesis that can be tested by examining protein-protein interactionsin vitro.


2018 ◽  
Vol 33 (7) ◽  
pp. 911-930 ◽  
Author(s):  
Dheeraj Sharma ◽  
Biswajita Parida

Purpose The advent of the internet, digitization and e-commerce has changed the definition of business territory, re-invented direct selling, eradicated middle men and brought the customers and sellers closer. These changes in the business scenario must have had an impact on the intensity and nature of channel conflict which needs to be inspected to structure better channel relationship strategies in the changing context. This paper aims to attempt a systematic investigation into the determinants of channel conflict in today’s context and proposes a composite model by reconciling the research so far in the domain of channel relationships. Design/methodology/approach An exhaustive search was carried for extant research finding in the channels resulting in the identification of 284 research papers beyond the meta-analysis by Geyskens et al. (1999). The next step was to manually scan through each of these papers to identify the studies which involved quantitative analysis including measures of association such as correlations related to conflict and the determinants of conflict. This led to the finalization of 36 research papers for the meta-analysis. Findings This study proffers a model that illustrates ranking of major determinants of channel conflict. The results of the study suggest that determinants can be categorized into three major domains: organizational, interpersonal (communication, cooperation, relationship activities and opportunistic behaviour) and environmental factors (environmental volatility, competitive intensity and product or market volatility). Research limitations/implications The analysis is based on static data in the sense that the correlations do not reflect supplier-channel member interactions in specific conflict situations. It may be argued that conflicts ultimately occur among firms/businesses run by individuals and individual traits may also impact the formation and resolution of conflict. Further, the quality of the measures capturing the constructs was not investigated in many studies. Final limitation pertains to the measurement of conflict. Conflict may not have been measured in a uniform manner in each of the studies analysed. As this study has evaluated extant research through a meta-analysis, it was not possible to identify the correlations between the determinant variables and the three factors (or constructs). Practical implications This study reconciles different research streams in this domain with the visualization of the composite model. It presents a quantitative analysis of the correlations of the determinants of conflict with channel conflict holistically. It creates a base through the composite model to carry forward the academic discussion in this domain holistically. It aims to be a ready reference for understanding the antecedents of conflict along with their significant correlations to enable prioritization of their channel strategies. Social implications This meta-analysis and the suggested model that may be of use to practitioners in terms of prioritizing their activities to reduce channel conflicts through pre-emption. It is hoped that this study enhances the extant understanding of the determinants of channel conflict considerably based on the presented composite model. The results may assist to resolve channel conflicts, create channel synergies, identify optimal channel mix, reduce channel costs, increase channel efficiency and build partnerships in the changing business scenario. Originality/value A holistic view of the determinants of conflict would be of enormous use to practitioners and academics alike. Hence, a detailed study is required to enlist and categorize the determinants causing conflict in channels so that an attempt can be made to resolve channel conflict for better performance of the firms. This meta-analysis study is an attempt to fill this major gap in research in this domain to quantitatively analyse the major determinants of channel conflict on the basis of analysis of research work over the past 15 years.


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