Organohalide respiration of a sulfate-reducer, Desulforhopalus singaporensis
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PROVIDER: PRJEB61466 | ENA |
REPOSITORIES: ENA
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Project description:Desulforhopalus singaporensis DSM 12130
| PRJNA262255 | ENA
Project description:Organohalide respiration by a Desulforhopalus-dominated community
| PRJEB61380 | ENA
Project description:The organohalide-respiring Sulfurospirillum multivorans uses chlorinated ethenes as electron acceptors for growth under anoxic conditions. However, little is known about the interaction of these substrates with proteins. Here, we apply thermal proteome profiling (TPP) to analyze enzyme-trichloroethene interactions. TPP is commonly used to investigate protein-ligand binding through protein melting curve shifts. Several modifications in the protocol, e.g. performing the incubation under anaerobic conditions and increasing the temperature range up to 97°C, improved the detection range and allowed the investigation of oxygen-sensitive proteins. Enzymatic reductive dehalogenation was prevented by omitting the electron donor during incubations. This enabled detecting the interaction of the tetrachloroethene reductive dehalogenase PceA with trichloroethene and confirms the enzyme’s specificity for this substrate. Another 19 proteins showed significant melting curve shifts with trichloroethene, pointing to other proteins directly or indirectly interacting with trichloroethene. Interestingly, a putative response regulator reacted similarly towards trichloroethene, which is potentially in line with its proposed role in regulating trichloroethene respiration. The TPP approach is here proven to facilitate the identification of substrate-enzyme interactions of strictly anaerobic reductive dehalogenases and probably their regulators. This strategy can be used to identify yet unknown substrate specificities and potential signal-sensing proteins in other difficult to study bacteria.
2018-06-06 | PXD009308 | Pride
Project description:uncultured Desulforhopalus sp. overview
| PRJNA1043377 | ENA
Project description:Complete genome of Desulforhopalus glucosivorans strain 52FAK
| PRJDB37753 | ENA
Project description:The reductive dehalogenation of halogenated benzenes by anaerobic bacteria is of great environmental and biotechnological importance; however, the role of specific reductive dehalogenases in the (sequential) dehalogenation of different isomers has not been studied in detail. Here, we cultivated the obligate organohalide-respiring Dehalococcoides mccartyi strain CBDB1 with either 1,2,3- or 1,2,4-trichlorobenzene (TCB) as electron acceptor and investigated differences in the expression of its 32 reductive dehalogenase (rdhA) genes using RNA-sequencing. The gene of the known chlorobenzene reductive dehalogenase, cbrA, and rdhA cbdbA80 were the two most highly expressed rdhA genes with 1,2,3-TCB. In the presence of 1,2,4-TCB, cbrA was also the most highly expressed rdhA, whereas rdhA cbdbA80 was transcribed at a slightly lower level. Instead, a third rdhA gene, cbdbA1588, encoding an orthologue of the tetrachloroethene reductive dehalogenase PceA, was the second most highly expressed rdhA. The screening of the transcripts encoded in intergenic regions predicted three abundant sRNAs and a so far unannotated small protein. Proteome analyses of cultures respiring 1,2,3-TCB, 1,2,4-TCB, or hexachlorobenzene (HCB) confirmed the specific synthesis of the RdhA CbdbA1588 protein during respiration with 1,2,4-TCB. It was also up-regulated by HCB, suggesting its involvement in sequential dechlorination to dichlorobenzenes. Dehalogenase activity assays with cell extracts from 1,2,4-TCB-grown cultures indicated a higher activity towards 1,2,4-TCB and a ten-fold higher activity towards 2,3-dichlorophenol compared to that in extracts from 1,2,3-TCB-grown cultures. These findings demonstrate the functionality of RdhA CbdbA1588 and further support a role in 1,2,4-TCB dechlorination by strain CBDB1.
2026-02-11 | PXD069682 | Pride
Project description:Reductive Dehalogenation in Aarhus Bay
| PRJEB50583 | ENA
Project description:Organohalide respiration (OHR), catalysed by reductive dehalogenases (RDases), plays an important role in halogen cycling. Natural organohalides and putative RDase-encoding genes have been reported in Aarhus Bay sediments, however, OHR has not been experimentally verified. Here we show that sediments of Aarhus Bay can dehalogenate a range of organohalides, and different organohalides differentially affected microbial community compositions. PCE-dechlorinating cultures were further examined by 16S rRNA gene-targeted quantitative PCR and amplicon sequencing. Known organohalide-respiring bacteria (OHRB) including Dehalococcoides, Dehalobacter and Desulfitobacterium decreased in abundance during transfers and serial dilutions, suggesting the importance of yet uncharacterized OHRB in these cultures. Switching from PCE to 2,6-DBP led to its complete debromination to phenol in cultures with and without sulfate. 2,6-DBP debrominating cultures differed in microbial composition from PCE-dechlorinating cultures. Desulfobacterota genera recently verified to include OHRB, including Desulfovibrio and Desulfuromusa, were enriched in all microcosms, whereas Halodesulfovibrio was only enriched in cultures without sulfate. Hydrogen and methane were detected in cultures without sulfate. Hydrogen likely served as electron donor for OHR and methanogenesis. This study shows that OHR can occur in marine environments mediated by yet unknown OHRB, suggesting their role in natural halogen cycling.
| S-EPMC9303371 | biostudies-literature
Project description:Dehalococcoides mccartyi obligately depends on organohalide respiration for energy conservation and growth. The genome of strain CBDB1 encodes 32 reductive dehalogenases, which enable the reductive dehalogenation of a broad range of halogenated compounds. It is one of the few strains able to respire chlorinated benzenes. The differential transcriptional response of the dehalogenase-encoding and –associated genes to halogenated aromatic compounds has so far not been studied on a genome-wide level. To understand the global transcriptional response to specific halogenated aromatic compounds, we analyzed and compared the transcriptomes during growth with 1,2,3- and 1,2,4-trichlorobenzene (TCB).
2026-01-28 | GSE306994 | GEO
Project description:The strictly anaerobic bacterium Dehalococcoides mccartyi is obligatory dependent on organohalide respiration for energy conservation and growth. Due to its capability to reductively dehalogenate a multitude of toxic halogenated electron acceptors, it plays an important role in the attenuation of these compounds at respective contaminated sites. Here, D. mccartyi strain CBDB1, specialized on the dehalogenation of chloroaromatic compounds, was grown in a two-liquid phase system with 1,2,3-trichlorobenzene as electron acceptor, acetate plus CO2 as carbon source and hydrogen as electron donor. The proteome and Nε-lysine acetylome were analyzed in the lag, exponential and stationary phases. The high and almost invariable abundance of the membrane-localized organohalide respiration complex consisting of the reductive dehalogenases CbrA and CbdbA80, the uptake hydrogenase HupLS and the organohalide respiration molybdoenzyme OmeAB was shown throughout growth and also after a prolonged stationary phase. Quantification of transcripts of reductive dehalogenase genes revealed their major synthesis starting in the lag phase, which might be a prerequisite for balanced growth in the exponential phase. The analyses of the coverage of functional pathways as well as indicator analysis revealed the growth-phase specificity of the proteome, with regulatory proteins identified as important indicators for the stationary phase. The number of acetylated proteins increased from the lag to the stationary phase. We detected pronounced acetylation of key proteins of the acetate metabolism, i.e. the synthesis of acetyl-CoA and its processing via gluconeogenesis and the incomplete Wood-Ljungdahl pathway, as well as of proteins central for the biosynthesis of amino acids, co-factors and terpenoids. In addition, the partial acetylation of the reductive dehalogenases as well as of TatA, a component of the twin-arginine translocation machinery, suggests that acetylation might be directly involved in the maintenance of the organohalide respiration capacity of D. mccartyi over periods without access to halogenated electron acceptors.
2021-02-15 | PXD018912 | Pride