Anaerobic Microbial Metabolism of Dichloroacetate

Gao

et al. 2022

Global Change Biology

Self Cite

Dichloromethane (DCM, methylene chloride) is a widely distributed halomethane, produced both naturally and industrially. While anthropogenic DCM has received attention due to widespread groundwater contamination and, more recently ozone destruction potential (Hossaini et al., 2017), analysis of Antarctic ice cores has demonstrated that DCM was present in the atmosphere prior to the industrial era at approximately 10% of modern levels (Trudinger et al., 2004). The natural sources of DCM are diverse, encompassing both abiotic (Isidorov

Section: Discussionmentioning

confidence: 98%

Identification and widespread environmental distribution of a gene cassette implicated in anaerobic dichloromethane degradation

Gao

et al. 2022

Global Change Biology

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“…MFA can be formed from MFA-CoA following thioester hydrolysis and converted by HAD-2 to the central metabolite glycolate and inorganic fluoride. HAD-2 affiliates with HADs that have demonstrated activity toward fluoroacetate and chloroacetate (Figure S5, Supporting Information), − however, functional prediction of HADs based on sequence analysis has limitations, and further studies are required to test if HAD-2 encoded on the strain 273 genome has defluorination activity. A prior study reported that strain 273 co-metabolizes MFA with decane as the primary substrate, supporting a role of had -2 in defluorination.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Expression Analysis Unravels Fluoroalkane Metabolism in Pseudomonas sp. Strain 273

Xie,

Ramirez,

Chen

et al. 2023

Environ. Sci. Technol.

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Pseudomonas sp. strain 273 grows with medium-chain terminally fluorinated alkanes under oxic conditions, releases fluoride, and synthesizes long-chain fluorofatty acids. To shed light on the genes involved in fluoroalkane metabolism, genome, and transcriptome sequencing of strain 273 grown with 1,10-difluorodecane (DFD), decane, and acetate were performed. Strain 273 harbors three genes encoding putative alkane monooxygenases (AlkB), key enzymes for initiating alkane degradation. Transcripts of alkB-2 were significantly more abundant in both decane- and DFD-grown cells compared to acetate-grown cells, suggesting AlkB-2 catalyzes the attack on terminal CH3 and CH2F groups. Coordinately expressed with alkB-2 was an adjacent gene encoding a fused ferredoxin–ferredoxin reductase (Fd–Fdr). Phylogenetic analysis distinguished AlkB that couples with fused Fd–Fdr reductases from AlkB with alternate architectures. A gene cluster containing an (S)-2-haloacid dehalogenase (had) gene was up-regulated in cells grown with DFD, suggesting a possible role in the removal of the ω-fluorine. Genes involved in long-chain fatty acid biosynthesis were not differentially expressed during growth with acetate, decane, or DFD, suggesting the bacterium’s biosynthetic machinery does not discriminate against monofluoro-fatty acid intermediates. The analysis sheds first light on genes and catalysts involved in the microbial metabolism of fluoroalkanes.

“…Focusing exclusively on OHRB belonging to the Firmicutes, proteomic analyses of Rdh proteins were reported in twelve studies (Prat et al, 2011 ; Rupakula et al, 2013 , 2015 ; Tang and Edwards, 2013 ; Kruse et al, 2015 ; Jugder et al, 2016 ; Alfán-Guzmán et al, 2017 ; Kleindienst et al, 2019 ; Liu et al, 2019 ; Low et al, 2019 ; Peng et al, 2020 ; Chen et al, 2021 ). The different methodologies that were applied in those studies (1 or 2D native or denaturing gels, and in-solution LC-MS/MS analyses) render their comparison very difficult.…”

Section: Discussionmentioning

confidence: 99%

Stoichiometry of the Gene Products From the Tetrachloroethene Reductive Dehalogenase Operon pceABCT

et al. 2022

Organohalide respiration (OHR) is a bacterial anaerobic process that uses halogenated compounds, e.g., tetrachloroethene (PCE), as terminal electron acceptors. Our model organisms are Dehalobacter restrictus strain PER-K23, an obligate OHR bacterium (OHRB), and Desulfitobacterium hafniense strain TCE1, a bacterium with a versatile metabolism. The key enzyme is the PCE reductive dehalogenase (PceA) that is encoded in the highly conserved gene cluster (pceABCT) in both above-mentioned strains, and in other Firmicutes OHRB. To date, the functions of PceA and PceT, a dedicated molecular chaperone for the maturation of PceA, are well defined. However, the role of PceB and PceC are still not elucidated. We present a multilevel study aiming at deciphering the stoichiometry of pceABCT individual gene products. The investigation was assessed at RNA level by reverse transcription and (quantitative) polymerase chain reaction, while at protein level, proteomic analyses based on parallel reaction monitoring were performed to quantify the Pce proteins in cell-free extracts as well as in soluble and membrane fractions of both strains using heavy-labeled reference peptides. At RNA level, our results confirmed the co-transcription of all pce genes, while the quantitative analysis revealed a relative stoichiometry of the gene transcripts of pceA, pceB, pceC, and pceT at ~ 1.0:3.0:0.1:0.1 in D. restrictus. This trend was not observed in D. hafniense strain TCE1, where no substantial difference was measured for the four genes. At proteomic level, an apparent 2:1 stoichiometry of PceA and PceB was obtained in the membrane fraction, and a low abundance of PceC in comparison to the other two proteins. In the soluble fraction, a 1:1 stoichiometry of PceA and PceT was identified. In summary, we show that the pce gene cluster is transcribed as an operon with, however, a level of transcription that differs for individual genes, an observation that could be explained by post-transcriptional events. Despite challenges in the quantification of integral membrane proteins such as PceB and PceC, the similar abundance of PceA and PceB invites to consider them as forming a membrane-bound PceA2B protein complex, which, in contrast to the proposed model, seems to be devoid of PceC.