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Chen G, Jiang N, Villalobos Solis MI, Kara Murdoch F, Murdoch RW, Xie Y, Swift CM, Hettich RL, Löffler FE. Anaerobic Microbial Metabolism of Dichloroacetate. mBio 2021; 12:e00537-21. [PMID: 33906923 PMCID: PMC8092247 DOI: 10.1128/mbio.00537-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 03/17/2021] [Indexed: 12/23/2022] Open
Abstract
Dichloroacetate (DCA) commonly occurs in the environment due to natural production and anthropogenic releases, but its fate under anoxic conditions is uncertain. Mixed culture RM comprising "Candidatus Dichloromethanomonas elyunquensis" strain RM utilizes DCA as an energy source, and the transient formation of formate, H2, and carbon monoxide (CO) was observed during growth. Only about half of the DCA was recovered as acetate, suggesting a fermentative catabolic route rather than a reductive dechlorination pathway. Sequencing of 16S rRNA gene amplicons and 16S rRNA gene-targeted quantitative real-time PCR (qPCR) implicated "Candidatus Dichloromethanomonas elyunquensis" strain RM in DCA degradation. An (S)-2-haloacid dehalogenase (HAD) encoded on the genome of strain RM was heterologously expressed, and the purified HAD demonstrated the cofactor-independent stoichiometric conversion of DCA to glyoxylate at a rate of 90 ± 4.6 nkat mg-1 protein. Differential protein expression analysis identified enzymes catalyzing the conversion of DCA to acetyl coenzyme A (acetyl-CoA) via glyoxylate as well as enzymes of the Wood-Ljungdahl pathway. Glyoxylate carboligase, which catalyzes the condensation of two molecules of glyoxylate to form tartronate semialdehyde, was highly abundant in DCA-grown cells. The physiological, biochemical, and proteogenomic data demonstrate the involvement of an HAD and the Wood-Ljungdahl pathway in the anaerobic fermentation of DCA, which has implications for DCA turnover in natural and engineered environments, as well as the metabolism of the cancer drug DCA by gut microbiota.IMPORTANCE Dichloroacetate (DCA) is ubiquitous in the environment due to natural formation via biological and abiotic chlorination processes and the turnover of chlorinated organic materials (e.g., humic substances). Additional sources include DCA usage as a chemical feedstock and cancer drug and its unintentional formation during drinking water disinfection by chlorination. Despite the ubiquitous presence of DCA, its fate under anoxic conditions has remained obscure. We discovered an anaerobic bacterium capable of metabolizing DCA, identified the enzyme responsible for DCA dehalogenation, and elucidated a novel DCA fermentation pathway. The findings have implications for the turnover of DCA and the carbon and electron flow in electron acceptor-depleted environments and the human gastrointestinal tract.
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Affiliation(s)
- Gao Chen
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Nannan Jiang
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee, USA
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | | | - Fadime Kara Murdoch
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Robert Waller Murdoch
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
| | - Yongchao Xie
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Cynthia M Swift
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Frank E Löffler
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Biosystems Engineering & Soil Science, University of Tennessee, Knoxville, Tennessee, USA
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee, USA
- Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, USA
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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Zhang J, Cao X, Xin Y, Xue S, Zhang W. Purification and characterization of a dehalogenase from Pseudomonas stutzeri DEH130 isolated from the marine sponge Hymeniacidon perlevis. World J Microbiol Biotechnol 2013; 29:1791-9. [PMID: 23543208 DOI: 10.1007/s11274-013-1340-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 03/25/2013] [Indexed: 11/24/2022]
Abstract
2-haloacid dehalogenases are enzymes that are capable of degrading 2-haloacid compounds. These enzymes are produced by bacteria, but so far they have only been purified and characterized from terrestrial bacteria. The present study describes the purification and characterization of 2-haloacid dehalogenase from the marine bacterium Pseudomonas stutzeri DEH130. P. Stutzeri DEH130 contained two kinds of 2-haloacid dehalogenase (designated as Dehalogenase I and Dehalogenase II) as detected in the crude cell extract after ammonium sulfate fractionation. Both enzymes appeared to exhibit stereo-specificity with respect to substrate. Dehalogenase I was a 109.9-kDa enzyme that preferentially utilized D-2-chloropropropionate and had optimum activity at pH 7.5. Dehalogenase II, which preferentially utilized L-2-chloropropionate, was further purified by ion-exchange chromatography and gel filtration. Purified Dehalogenase II appeared to be a dimeric enzyme with a subunit of 26.0-kDa. It had maximum activity at pH 10.0 and a temperature of 40 °C. Its activity was not inhibited by DTT and EDTA, but strongly inhibited by Cu²⁺, Zn²⁺, and Co²⁺. The K(m) and V(max) for L-2-chloropropionate were 0.3 mM and 23.8 μmol/min/mg, respectively. Its substrate specificity was limited to short chain mono-substituted 2-halocarboxylic acids, with no activity detected toward fluoropropionate and monoiodoacetate. This is the first report on the purification and characterization of 2-haloacid dehalogenase from a marine bacterium.
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Affiliation(s)
- Jinyou Zhang
- Marine Bioproducts Engineering Group, Dalian Institution of chemical physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian, 116023, People's Republic of China
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Abstract
In the recent past, the development of dehalogenating enzymes for industrial biocatalysis has been limited, but significant advances have been made. Three classes of enzymes have received attention and development: halalkanoic acid dehalogenases (EC 3.8.1.2), hydrogen-halide lyases (EC 4.5.1), and haloalkane dehalogenases (EC 3.8.1). Applications range from the manufacture of chiral intermediates, to recycling of chlorinated byproducts from chemical manufacturing, and selective treatment of process waste streams.
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Affiliation(s)
- P E Swanson
- The Dow Chemical Company, Corporate Research and Development, Building 1707, Midland, MI 48674, USA.
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