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Title: Proteogenomics reveals novel reductive dehalogenases and methyltransferases expressed during anaerobic dichloromethane metabolism

Abstract

Dichloromethane (DCM) is susceptible to microbial degradation under anoxic conditions and is metabolized via the Wood-Ljungdahl Pathway; however, mechanistic understanding of carbon-chlorine bond cleavage is lacking. The microbial consortium RM contains the DCM degrader Candidatus Dichloromethanomonas elyunquensis strain RM, which strictly requires DCM as a growth substrate. Proteomic workflows applied to DCM-grown consortium RM biomass revealed a total of 1,705 non-redundant proteins, of which 521 could be assigned to strain RM. In the presence of DCM, strain RM expressed a complete set of Wood-Ljungdahl Pathway enzymes, as well as proteins implicated in chemotaxis, motility, sporulation, and vitamin/co-factor synthesis. Four corrinoid-dependent methyltransferases were among the most abundant proteins. Notably, two of three putative reductive dehalogenases (RDases) encoded within strain RM's genome were also detected in high abundance. Expressed RDase 1 and RDase 2 shared 30% amino acid identity, and RDase 1 was most similar to an RDase of Dehalococcoides mccartyi strain WBC-2 (AOV99960, 52% amino acid identity), while RDase 2 was most similar to an RDase of Dehalobacter sp. strain UNSWDHB (EQB22800, 72% amino acid identity). Although the involvement of RDases in anaerobic DCM metabolism has yet to be experimentally verified, the proteome characterization results implicated the possible participation of onemore » or more reductive dechlorination steps and methyl group transfer reactions, leading to a revised proposal for an anaerobic DCM degradation pathway.« less

Authors:
ORCiD logo [1];  [2];  [3];  [3]; ORCiD logo [4];  [4];  [3];  [5];  [6];  [4];  [4]
+ Show Author Affiliations
  1. Eberhard-Karls-Univ. Tubingen, Tubingen (Germany); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)
  2. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  3. Univ. of Tennessee, Knoxville, TN (United States)
  4. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)
  5. E. I. DuPont de Nemours and Company, Wilmington, DE (United States)
  6. The Chemours Company, Wilmington, DE (United States)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1494871
Grant/Contract Number:  
AC05-00OR22725
Resource Type:
Accepted Manuscript
Journal Name:
Applied and Environmental Microbiology
Additional Journal Information:
Journal Volume: 85; Journal Issue: 6; Journal ID: ISSN 0099-2240
Publisher:
American Society for Microbiology
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Candidatus Dichloromethanomonas elyunquensis; anaerobic dichloromethane metabolism; reductive dehalogenases; methyltransferases; Wood-Ljungdahl pathway; proteomics; genomics

Citation Formats

Kleindienst, Sara, Chourey, Karuna, Chen, Gao, Murdoch, Robert W., Higgins, Steven A., Iyer, Ramsunder, Campagna, Shawn R., Mack, E. Erin, Seger, Edward S., Hettich, Robert L., and Löffler, Frank E. Proteogenomics reveals novel reductive dehalogenases and methyltransferases expressed during anaerobic dichloromethane metabolism. United States: N. p., 2019. Web. doi:10.1128/AEM.02768-18.
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Kleindienst, Sara, Chourey, Karuna, Chen, Gao, Murdoch, Robert W., Higgins, Steven A., Iyer, Ramsunder, Campagna, Shawn R., Mack, E. Erin, Seger, Edward S., Hettich, Robert L., & Löffler, Frank E. Proteogenomics reveals novel reductive dehalogenases and methyltransferases expressed during anaerobic dichloromethane metabolism. United States. doi:10.1128/AEM.02768-18.
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Kleindienst, Sara, Chourey, Karuna, Chen, Gao, Murdoch, Robert W., Higgins, Steven A., Iyer, Ramsunder, Campagna, Shawn R., Mack, E. Erin, Seger, Edward S., Hettich, Robert L., and Löffler, Frank E. Fri . "Proteogenomics reveals novel reductive dehalogenases and methyltransferases expressed during anaerobic dichloromethane metabolism". United States. doi:10.1128/AEM.02768-18. https://www.osti.gov/servlets/purl/1494871.
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@article{osti_1494871,
title = {Proteogenomics reveals novel reductive dehalogenases and methyltransferases expressed during anaerobic dichloromethane metabolism},
author = {Kleindienst, Sara and Chourey, Karuna and Chen, Gao and Murdoch, Robert W. and Higgins, Steven A. and Iyer, Ramsunder and Campagna, Shawn R. and Mack, E. Erin and Seger, Edward S. and Hettich, Robert L. and Löffler, Frank E.},
abstractNote = {Dichloromethane (DCM) is susceptible to microbial degradation under anoxic conditions and is metabolized via the Wood-Ljungdahl Pathway; however, mechanistic understanding of carbon-chlorine bond cleavage is lacking. The microbial consortium RM contains the DCM degrader Candidatus Dichloromethanomonas elyunquensis strain RM, which strictly requires DCM as a growth substrate. Proteomic workflows applied to DCM-grown consortium RM biomass revealed a total of 1,705 non-redundant proteins, of which 521 could be assigned to strain RM. In the presence of DCM, strain RM expressed a complete set of Wood-Ljungdahl Pathway enzymes, as well as proteins implicated in chemotaxis, motility, sporulation, and vitamin/co-factor synthesis. Four corrinoid-dependent methyltransferases were among the most abundant proteins. Notably, two of three putative reductive dehalogenases (RDases) encoded within strain RM's genome were also detected in high abundance. Expressed RDase 1 and RDase 2 shared 30% amino acid identity, and RDase 1 was most similar to an RDase of Dehalococcoides mccartyi strain WBC-2 (AOV99960, 52% amino acid identity), while RDase 2 was most similar to an RDase of Dehalobacter sp. strain UNSWDHB (EQB22800, 72% amino acid identity). Although the involvement of RDases in anaerobic DCM metabolism has yet to be experimentally verified, the proteome characterization results implicated the possible participation of one or more reductive dechlorination steps and methyl group transfer reactions, leading to a revised proposal for an anaerobic DCM degradation pathway.},
doi = {10.1128/AEM.02768-18},
journal = {Applied and Environmental Microbiology},
number = 6,
volume = 85,
place = {United States},
year = {2019},
month = {1}
}
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DOI:  10.1128/AEM.02768-18
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