Genomic, transcriptomic and proteomic analyses of Dehalobacter UNSWDHB in response to chloroform

Abstract

Organohalide respiring bacteria (ORB) are capable of utilising organohalides as electron acceptors for the generation of cellular energy and consequently play an important role in the turnover of natural and anthropogenically-derived organohalides. In this study, the response of a Dehalobacter sp. strain UNSWDHB to the addition of trichloromethane (TCM) after a 50 h period of its absence (suffocation) was evaluated from a transcriptomic and proteomic perspective. The up-regulation of TCM reductive dehalogenase genes (tmrABC) and their gene products (TmrABC) was confirmed at both transcriptional and proteomic levels. Other findings include the upregulation of various hydrogenases (membrane-associated Ni-Fe hydrogenase complexes and soluble Fe-Fe hydrogenases), formate dehydrogenases, complex I and a pyrophosphate-energized proton pump. The elevated expression of enzymes associated with carbon metabolism, including complete Wood Ljungdahl pathway, during TCM respiration raises interesting questions on possible fates of intracellular formate and its potential role in the physiology of this bacterium. Overall, the findings presented here provide a broader view on the bioenergetics and general physiology of Dehalobacter UNSWDHB cells actively respiring with TCM.

A bacterial chloroform reductive dehalogenase: purification and biochemical characterization

“…During the final days prior to harvest, CF dechlorination rate was 6.5 × 10 ‐11 mol cell −1 day −1 and the cell density was (9.8 ± 4.3) × 10 7 cells ml −1 . Before harvesting, we examined the expression of tmrA gene, as it was previously shown that the same gene is expressed upon CF respiration (Jugder et al ., ). To confirm the induction of tmrA at the gene level, transcription of tmrA gene was investigated.…”

“…strain UNSWDHB is able to use CF as a terminal electron acceptor for growth. It has previously been demonstrated that the enzyme directly responsible for reductive dechlorination of CF is the membrane‐associated TmrA, which is specifically overproduced in response to CF (Jugder et al ., ; Wong et al ., ). In this study, we for the first time report the production, purification and biochemical characterization of a chloroform‐reducing enzyme.…”

“…The bacteria can also utilize 1,1,1‐trichloroethane (TCA), 1,1,2‐TCA and 1,1‐dichloroethane (DCA) as electron acceptors. Its genome harbours 20 putative RDase homology ( rdh ) genes, of which only one (TmrA, gi736352001) was reported to be responsible for CF dechlorination and is expressed in response to CF addition (Deshpande et al ., ; Jugder et al ., ; Wong et al ., ). The maximum likelihood based phylogenetic analysis on the amino acid sequence of the characterized RDases revealed that TmrA shares high sequence homology with both CtrA and CfrA (Jugder et al ., ).…”

Isolation and Characterization of Dehalobacter sp. Strain TeCB1 Including Identification of TcbA: A Novel Tetra- and Trichlorobenzene Reductive Dehalogenase

“…Complete or partial WLP encoding genes have been reported in other OHRB, including: Dehalobacter restrictus strains PER-K23 and UNSWDHB (Kruse et al, 2013; Rupakula et al, 2013; Jugder et al, 2016b; Wong et al, 2016) among others. The WLP pathway can function in either reductive or oxidative directions.…”

Interspecies malate-pyruvate shuttle drives amino acid exchange in organohalide-respiring microbial communities

“…In this study, we first explored the metabolic dependency of Dhb using its genome-scale metabolic model (Correia et al ., 2018), which was built based on a highly annotated and experimentally refined Dhb genome (Wang et al, 2016), along with shared expression patterns in proteomic datasets of Dhb strains PER-K23, UNSWDHB, DCA and CF (Jugder et al ., 2016, Rupakula et al ., 2013, Rupakula et al ., 2015, Tang and Edwards, 2013a). The model simulations consider cofactor availability, enzyme promiscuity, physiological redox conditions, and further model constraints based on experimental values obtained in this study.…”