skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

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]
  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.
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.
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.
@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}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 4 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

Acetogenesis and the Wood–Ljungdahl pathway of CO2 fixation
journal, December 2008

  • Ragsdale, Stephen W.; Pierce, Elizabeth
  • Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Vol. 1784, Issue 12, p. 1873-1898
  • DOI: 10.1016/j.bbapap.2008.08.012

PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization
journal, January 1999


Overview of organohalide-respiring bacteria and a proposal for a classification system for reductive dehalogenases
journal, April 2013

  • Hug, Laura A.; Maphosa, Farai; Leys, David
  • Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 368, Issue 1616
  • DOI: 10.1098/rstb.2012.0322

Functional characterization of the trigger factor protein PceT of tetrachloroethene-dechlorinating Desulfitobacterium hafniense Y51
journal, April 2009

  • Morita, Yasuyuki; Futagami, Taiki; Goto, Masatoshi
  • Applied Microbiology and Biotechnology, Vol. 83, Issue 4
  • DOI: 10.1007/s00253-009-1958-z

Genomic, transcriptomic and proteomic analyses of Dehalobacter UNSWDHB in response to chloroform
journal, August 2016

  • Jugder, Bat-Erdene; Ertan, Haluk; Wong, Yie Kuan
  • Environmental Microbiology Reports, Vol. 8, Issue 5
  • DOI: 10.1111/1758-2229.12444

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences
journal, November 2015

  • Huerta-Cepas, Jaime; Szklarczyk, Damian; Forslund, Kristoffer
  • Nucleic Acids Research, Vol. 44, Issue D1
  • DOI: 10.1093/nar/gkv1248

Microbial reductive dehalogenation of trihalomethanes by a Dehalobacter-containing co-culture
journal, April 2017

  • Zhao, Siyan; Rogers, Matthew J.; He, Jianzhong
  • Applied Microbiology and Biotechnology, Vol. 101, Issue 13
  • DOI: 10.1007/s00253-017-8236-2

A subset of bacterial inner membrane proteins integrated by the twin-arginine translocase: Tat-dependent integral membrane proteins
journal, August 2003


Incomplete Wood-Ljungdahl pathway facilitates one-carbon metabolism in organohalide-respiring Dehalococcoides mccartyi
journal, April 2014

  • Zhuang, W. -Q.; Yi, S.; Bill, M.
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 17
  • DOI: 10.1073/pnas.1321542111

Draft Genome Sequence of a Strictly Anaerobic Dichloromethane-Degrading Bacterium
journal, March 2016

  • Kleindienst, Sara; Higgins, Steven A.; Tsementzi, Despina
  • Genome Announcements, Vol. 4, Issue 2
  • DOI: 10.1128/genomeA.00037-16

Multiple Reductive-Dehalogenase-Homologous Genes Are Simultaneously Transcribed during Dechlorination by Dehalococcoides-Containing Cultures
journal, December 2005


Functional Genotyping of Sulfurospirillum spp. in Mixed Cultures Allowed the Identification of a New Tetrachloroethene Reductive Dehalogenase
journal, August 2013

  • Buttet, Géraldine F.; Holliger, Christof; Maillard, Julien
  • Applied and Environmental Microbiology, Vol. 79, Issue 22
  • DOI: 10.1128/AEM.02312-13

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
journal, January 1994

  • Thompson, Julie D.; Higgins, Desmond G.; Gibson, Toby J.
  • Nucleic Acids Research, Vol. 22, Issue 22, p. 4673-4680
  • DOI: 10.1093/nar/22.22.4673

The Autotrophic Pathway of Acetate Synthesis in Acetogenic Bacteria
journal, October 1986


TIGRFAMs: a protein family resource for the functional identification of proteins
journal, January 2001


SignalP 4.0: discriminating signal peptides from transmembrane regions
journal, September 2011

  • Petersen, Thomas Nordahl; Brunak, Søren; von Heijne, Gunnar
  • Nature Methods, Vol. 8, Issue 10
  • DOI: 10.1038/nmeth.1701

Experimental Evaluation and Mathematical Modeling of Microbially Enhanced Tetrachloroethene (PCE) Dissolution
journal, February 2007

  • Amos, Benjamin K.; Christ, John A.; Abriola, Linda M.
  • Environmental Science & Technology, Vol. 41, Issue 3
  • DOI: 10.1021/es061438n

Dual Carbon–Chlorine Isotope Analysis Indicates Distinct Anaerobic Dichloromethane Degradation Pathways in Two Members of Peptococcaceae
journal, June 2018

  • Chen, Gao; Shouakar-Stash, Orfan; Phillips, Elizabeth
  • Environmental Science & Technology, Vol. 52, Issue 15
  • DOI: 10.1021/acs.est.8b01583

Real-Time PCR Quantification of Nitrifying Bacteria in a Municipal Wastewater Treatment Plant
journal, January 2003

  • Harms, Gerda; Layton, Alice C.; Dionisi, Hebe M.
  • Environmental Science & Technology, Vol. 37, Issue 2, p. 343-351
  • DOI: 10.1021/es0257164

ChemInform Abstract: Naturally Occurring Organohalogen Compounds - A Comprehensive Update
journal, June 2010


IMG: the integrated microbial genomes database and comparative analysis system
journal, December 2011

  • Markowitz, V. M.; Chen, I. -M. A.; Palaniappan, K.
  • Nucleic Acids Research, Vol. 40, Issue D1
  • DOI: 10.1093/nar/gkr1044

Functional Heterologous Production of Reductive Dehalogenases from Desulfitobacterium hafniense Strains
journal, May 2014

  • Mac Nelly, Anita; Kai, Marco; Svatoš, Aleš
  • Applied and Environmental Microbiology, Vol. 80, Issue 14
  • DOI: 10.1128/AEM.00881-14

Novel Twin-Arginine Translocation Pathway-Dependent Phenotypes of Bacillus subtilis Unveiled by Quantitative Proteomics
journal, January 2013

  • Goosens, Vivianne J.; Otto, Andreas; Glasner, Corinna
  • Journal of Proteome Research, Vol. 12, Issue 2
  • DOI: 10.1021/pr300866f

Quantitative PCR Targeting 16S rRNA and Reductive Dehalogenase Genes Simultaneously Monitors Multiple Dehalococcoides Strains
journal, April 2006


Coupling a Detergent Lysis/Cleanup Methodology with Intact Protein Fractionation for Enhanced Proteome Characterization
journal, October 2012

  • Sharma, Ritin; Dill, Brian D.; Chourey, Karuna
  • Journal of Proteome Research, Vol. 11, Issue 12
  • DOI: 10.1021/pr300709k

Development of an Enhanced Metaproteomic Approach for Deepening the Microbiome Characterization of the Human Infant Gut
journal, October 2014

  • Xiong, Weili; Giannone, Richard J.; Morowitz, Michael J.
  • Journal of Proteome Research, Vol. 14, Issue 1
  • DOI: 10.1021/pr500936p

The COG database: a tool for genome-scale analysis of protein functions and evolution
journal, January 2000


Direct Cellular Lysis/Protein Extraction Protocol for Soil Metaproteomics
journal, December 2010

  • Chourey, Karuna; Jansson, Janet; VerBerkmoes, Nathan
  • Journal of Proteome Research, Vol. 9, Issue 12
  • DOI: 10.1021/pr100787q

‘ Candidatus Dichloromethanomonas elyunquensis’ gen. nov., sp. nov., a dichloromethane-degrading anaerobe of the Peptococcaceae family
journal, April 2017

  • Kleindienst, Sara; Higgins, Steven A.; Tsementzi, Despina
  • Systematic and Applied Microbiology, Vol. 40, Issue 3
  • DOI: 10.1016/j.syapm.2016.12.001

Quantitative proteomic analysis of distinct mammalian Mediator complexes using normalized spectral abundance factors
journal, November 2006

  • Paoletti, A. C.; Parmely, T. J.; Tomomori-Sato, C.
  • Proceedings of the National Academy of Sciences, Vol. 103, Issue 50
  • DOI: 10.1073/pnas.0606379103

KEGG as a reference resource for gene and protein annotation
journal, October 2015

  • Kanehisa, Minoru; Sato, Yoko; Kawashima, Masayuki
  • Nucleic Acids Research, Vol. 44, Issue D1
  • DOI: 10.1093/nar/gkv1070

Dosage-Dependent Proteome Response of Shewanella oneidensis MR-1 to Acute Chromate Challenge
journal, May 2007

  • Thompson, Melissa R.; VerBerkmoes, Nathan C.; Chourey, Karuna
  • Journal of Proteome Research, Vol. 6, Issue 5
  • DOI: 10.1021/pr060502x

Mutualistic interaction between dichloromethane- and chloromethane-degrading bacteria in an anaerobic mixed culture: Mutualistic degradation of chlorinated methanes
journal, October 2017

  • Chen, Gao; Kleindienst, Sara; Griffiths, Daniel R.
  • Environmental Microbiology, Vol. 19, Issue 11
  • DOI: 10.1111/1462-2920.13945

Stable Carbon Isotopic Fractionations Associated with Inorganic Carbon Fixation by Anaerobic Ammonium-Oxidizing Bacteria
journal, June 2004


Molecular characterization of dichloromethane-degrading Hyphomicrobium strains using 16S rDNA and DCM dehalogenase gene sequences
journal, August 2005

  • Nikolausz, Marcell; Kappelmeyer, Uwe; Nijenhuis, Ivonne
  • Systematic and Applied Microbiology, Vol. 28, Issue 7
  • DOI: 10.1016/j.syapm.2005.03.011

Dichloromethane-degrading bacteria in the genomic age
journal, November 2011

  • Muller, Emilie E. L.; Bringel, Françoise; Vuilleumier, Stéphane
  • Research in Microbiology, Vol. 162, Issue 9
  • DOI: 10.1016/j.resmic.2011.01.008

Genome sequence of the chlorinated compound–respiring bacterium Dehalococcoides species strain CBDB1
journal, August 2005

  • Kube, Michael; Beck, Alfred; Zinder, Stephen H.
  • Nature Biotechnology, Vol. 23, Issue 10
  • DOI: 10.1038/nbt1131

Reductive dehalogenase structure suggests a mechanism for B12-dependent dehalogenation
journal, October 2014

  • Payne, Karl A. P.; Quezada, Carolina P.; Fisher, Karl
  • Nature, Vol. 517, Issue 7535
  • DOI: 10.1038/nature13901

Method for isolation of auxotrophs in the methanogenic archaebacteria: role of the acetyl-CoA pathway of autotrophic CO2 fixation in Methanococcus maripaludis.
journal, August 1990

  • Ladapo, J.; Whitman, W. B.
  • Proceedings of the National Academy of Sciences, Vol. 87, Issue 15
  • DOI: 10.1073/pnas.87.15.5598

The increasing threat to stratospheric ozone from dichloromethane
journal, June 2017

  • Hossaini, Ryan; Chipperfield, Martyn P.; Montzka, Stephen A.
  • Nature Communications, Vol. 8, Issue 1
  • DOI: 10.1038/ncomms15962

Transcriptomic microarray analysis of corrinoid responsive genes in Dehalococcoides ethenogenes strain 195
journal, May 2009


ARB: a software environment for sequence data
journal, February 2004


Redundancy and specificity of multiple trigger factor chaperones in Desulfitobacteria
journal, May 2011


The Pfam protein families database: towards a more sustainable future
journal, December 2015

  • Finn, Robert D.; Coggill, Penelope; Eberhardt, Ruth Y.
  • Nucleic Acids Research, Vol. 44, Issue D1
  • DOI: 10.1093/nar/gkv1344

Temporal Transcriptomic Microarray Analysis of "Dehalococcoides ethenogenes" Strain 195 during the Transition into Stationary Phase
journal, February 2008

  • Johnson, D. R.; Brodie, E. L.; Hubbard, A. E.
  • Applied and Environmental Microbiology, Vol. 74, Issue 9
  • DOI: 10.1128/AEM.02208-07

Complete chloroform dechlorination by organochlorine respiration and fermentation: Microbial chloroform metabolism
journal, November 2011


Bacterial Growth with Chlorinated Methanes
journal, June 1995

  • Leisinger, Thomas; Braus-Stromeyer, Susanna A.
  • Environmental Health Perspectives, Vol. 103
  • DOI: 10.2307/3432475

A functional Ni-Ni-[4Fe-4S] cluster in the monomeric acetyl-CoA synthase from Carboxydothermus hydrogenoformans
journal, December 2003

  • Svetlitchnyi, V.; Dobbek, H.; Meyer-Klaucke, W.
  • Proceedings of the National Academy of Sciences, Vol. 101, Issue 2
  • DOI: 10.1073/pnas.0304262101

Basic local alignment search tool
journal, October 1990

  • Altschul, Stephen F.; Gish, Warren; Miller, Webb
  • Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410
  • DOI: 10.1016/S0022-2836(05)80360-2

Dichloromethane Fermentation by a Dehalobacter sp. in an Enrichment Culture Derived from Pristine River Sediment
journal, December 2011

  • Justicia-Leon, Shandra D.; Ritalahti, Kirsti M.; Mack, E. Erin
  • Applied and Environmental Microbiology, Vol. 78, Issue 4
  • DOI: 10.1128/AEM.07325-11

Molecular Dynamics of the Shewanella oneidensis Response to Chromate Stress
journal, March 2006

  • Brown, Steven D.; Thompson, Melissa R.; VerBerkmoes, Nathan C.
  • Molecular & Cellular Proteomics, Vol. 5, Issue 6
  • DOI: 10.1074/mcp.M500394-MCP200

Molecular and carbon isotopic characterization of an anaerobic stable enrichment culture containing Dehalobacterium sp. during dichloromethane fermentation
journal, March 2017


Isotope ratio-based profiling of microbial folates
journal, May 2007

  • Lu, Wenyun; Kwon, Yun Kyung; Rabinowitz, Joshua D.
  • Journal of the American Society for Mass Spectrometry, Vol. 18, Issue 5
  • DOI: 10.1016/j.jasms.2007.01.017

Chloroform respiration to dichloromethane by a Dehalobacter population: Growth-linked reductive dechlorination of chloroform
journal, January 2010


MyriMatch:  Highly Accurate Tandem Mass Spectral Peptide Identification by Multivariate Hypergeometric Analysis
journal, February 2007

  • Tabb, David L.; Fernando, Christopher G.; Chambers, Matthew C.
  • Journal of Proteome Research, Vol. 6, Issue 2
  • DOI: 10.1021/pr0604054

Complete Genome Sequence of Dehalobacterium formicoaceticum Strain DMC, a Strictly Anaerobic Dichloromethane-Degrading Bacterium
journal, September 2017


Genome Sequence of the PCE-Dechlorinating Bacterium Dehalococcoides ethenogenes
journal, January 2005


Localized Plasticity in the Streamlined Genomes of Vinyl Chloride Respiring Dehalococcoides
journal, November 2009


An LC-MS chemical derivatization method for the measurement of five different one-carbon states of cellular tetrahydrofolate
journal, August 2017

  • Chen, Li; Ducker, Gregory S.; Lu, Wenyun
  • Analytical and Bioanalytical Chemistry, Vol. 409, Issue 25
  • DOI: 10.1007/s00216-017-0514-4

Methylobacterium Genome Sequences: A Reference Blueprint to Investigate Microbial Metabolism of C1 Compounds from Natural and Industrial Sources
journal, May 2009


Novel mechanism of outer membrane targeting of proteins in Gram-negative bacteria
journal, September 2008