Global transcriptome analysis of the tetrachloroethene-dechlorinating bacterium Desulfitobacterium hafniense Y51 in the presence of various electron donors and terminal electron acceptors

Abstract

Desulfitobacterium hafniense Y51 is a dechlorinating bacterium that encodes an unusually large set of O-demethylase paralogs and specialized respiratory systems including specialized electron donors and acceptors. To use this organism in bioremediation of tetrachloroethene (PCE) or trichloroethene (TCE) pollution, expression patterns of its 5,060 genes were determined under different conditions using 60-mer probes in DNA microarrays. PCE, TCE, fumarate, nitrate, and dimethyl sulfoxide (DMSO) respiration all sustain the growth of strain Y51. Global transcriptome analyses were thus performed using various electron donor and acceptor couples (respectively, pyruvate and either fumarate, TCE, nitrate, or DMSO, and vanillate/fumarate). When TCE is used as terminal electron acceptor, resulting in its detoxification, a series of electron carriers comprising a cytochrome bd-type quinol oxidase (DSY4055-4056), a ferredoxin (DSY1451), and four Fe-S proteins (DSY1626, DSY1629, DSY0733, DSY3309) are upregulated, suggesting that the products of these genes are involved in PCE oxidoreduction. Interestingly, the PCE dehalogenase cluster (pceABCT) is constitutively expressed in the media tested, with pceT being upregulated and pceC downregulated in pyruvate/TCE-containing medium. In addition, another dehalogenation enzyme (DSY1155 coding for a putative chlorophenol reductive dehalogenase), is induced 225-fold in that medium, despite not being involved in PCE respiration. Remarkably since the reducing equivalents formed during pyruvate conversion to acetyl-CoA are channeled to electron acceptors including halogenated compounds, pyruvate induces expression of a pyruvate:ferredoxin oxidoreductase. This study paves the way to understanding the physiology of D. hafniense, optimizing this microbe as a bioremediation agent, and designing bioarray sensors to monitor the presence of dechlorinating organisms in the environment.

Genomic, Proteomic, and Biochemical Analysis of the Organohalide Respiratory Pathway in Desulfitobacterium dehalogenans

“…This is in line with previous findings of the involvement of hydrogenases in respiratory growth of D. dehalogenans (40). Interestingly, a similar increase in the expression of genes encoding an uptake hydrogenase corresponding to hydABC has been reported for Desulfitobacterium hafniense Y51 under respiratory growth compared to fermentative growth (65). This points toward a more general role in respiratory metabolism rather than a specific role in organohalide respiration, potentially as part of a hydrogen recycling mechanism as described elsewhere for diazotrophs and sulfate reducers (68)(69)(70).…”

“…As the genome of D. dehalogenans does not encode the minimum machinery necessary for nitrogen fixation (64), the Fix-ABCX complex most likely is linked to other cellular processes in this bacterium. Recently, comparative transcriptomics of D. hafniense Y51 (65) and proteomics of D. hafniense TCE1 (51) showed expression of fixABCX to be induced under organohaliderespiring conditions, leading to the speculation that the encoded complex may provide low-redox-potential electrons for organohalide respiration (51). In our proteomic data set, we saw no differences in the abundances of the fixABCX gene products between the tested growth conditions (P Ͻ 0.05) ( Fig.…”

The restricted metabolism of the obligate organohalide respiring bacterium Dehalobacter restrictus: lessons from tiered functional genomics

“…Recently, proteomics and transcriptomics studies were used to study the metabolism of two OHRB, Desulfitobacterium hafniense strain TCE1 [21] and Y51 [22], respectively, under different growth conditions, both confirming the apparent lack of regulation of the pceA gene that was postulated earlier [4]. Most omics studies involving OHRB have however focused on members of the Dehalococcoides genus.…”

Reductive Dehalogenases Come of Age in Biological Destruction of Organohalides

“…The function and control of transcription of pceT genes, which are remotely located from pceAB operons, remains largely unknown. Surprisingly, the constitutive expression of the pceABCT genes that form an operon in strain Y51 was observed [27]; however, in obligate ORB, such as Dehalococcoides mccartyi, the expression of rdhA genes is induced during reductive dechlorination of the electron acceptor [28,29].…”