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Title: Metagenome-Guided Proteomic Quantification of Reductive Dehalogenases in the Dehalococcoides mccartyi-Containing Consortium SDC-9

Abstract

At groundwater sites contaminated with chlorinated ethenes, fermentable substrates are often added to promote reductive dehalogenation by indigenous or augmented microorganisms. Contemporary bioremediation performance monitoring relies on nucleic acid biomarkers of key organohalide-respiring bacteria, such as Dehalococcoides mccartyi (Dhc). In this work, metagenome sequencing of the commercial, Dhc-containing consortium, SDC-9, identified 12 reductive dehalogenase (RDase) genes, including pceA (two copies), vcrA, and tceA, and allowed for specific detection and quantification of RDase peptides using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Shotgun (i.e., untargeted) proteomics applied to the SDC-9 consortium grown with tetrachloroethene (PCE) and lactate identified 143 RDase peptides, and 36 distinct peptides that covered greater than 99% of the protein-coding sequences of the PceA, TceA, and VcrA RDases. Quantification of RDase peptides using multiple reaction monitoring (MRM) assays with 13C-/15N-labeled peptides determined 1.8 × 103 TceA and 1.2 × 102 VcrA RDase molecules per Dhc cell. Ultimately, the MRM mass spectrometry approach allowed for sensitive detection and accurate quantification of relevant Dhc RDases and has potential utility in bioremediation monitoring regimes.

Authors:
ORCiD logo [1];  [1];  [2];  [3];  [2];  [4];  [1];  [1];  [4]; ORCiD logo [5]
  1. Battelle Memorial Inst., Columbus, OH (United States)
  2. Univ. of Tennessee, Knoxville, TN (United States)
  3. Univ. of Tennessee, Knoxville, TN (United States). Center for Environmental Biotechnology
  4. APTIM, Lawrenceville, NJ (United States). Biotechnology Development and Applications Group
  5. Univ. of Tennessee, Knoxville, TN (United States); Univ. of Tennessee, Knoxville, TN (United States). Center for Environmental Biotechnology; Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE; USDOD
OSTI Identifier:
1651260
Grant/Contract Number:  
AC05-00OR22725; ER-201726
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Proteome Research
Additional Journal Information:
Journal Volume: 19; Journal Issue: 4; Journal ID: ISSN 1535-3893
Publisher:
American Chemical Society (ACS)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; bioremediation; chlorinated ethenes; reductive dehalogenation; proteomics; metagenomics; consortium SDC-9

Citation Formats

Kucharzyk, Katarzyna H., Meisel, Jayda E., Kara-Murdoch, Fadime, Murdoch, Robert W., Higgins, Steven A., Vainberg, Simon, Bartling, Craig M., Mullins, Larry, Hatzinger, Paul B., and Löffler, Frank E.. Metagenome-Guided Proteomic Quantification of Reductive Dehalogenases in the Dehalococcoides mccartyi-Containing Consortium SDC-9. United States: N. p., 2020. Web. https://doi.org/10.1021/acs.jproteome.0c00072.
Kucharzyk, Katarzyna H., Meisel, Jayda E., Kara-Murdoch, Fadime, Murdoch, Robert W., Higgins, Steven A., Vainberg, Simon, Bartling, Craig M., Mullins, Larry, Hatzinger, Paul B., & Löffler, Frank E.. Metagenome-Guided Proteomic Quantification of Reductive Dehalogenases in the Dehalococcoides mccartyi-Containing Consortium SDC-9. United States. https://doi.org/10.1021/acs.jproteome.0c00072
Kucharzyk, Katarzyna H., Meisel, Jayda E., Kara-Murdoch, Fadime, Murdoch, Robert W., Higgins, Steven A., Vainberg, Simon, Bartling, Craig M., Mullins, Larry, Hatzinger, Paul B., and Löffler, Frank E.. Thu . "Metagenome-Guided Proteomic Quantification of Reductive Dehalogenases in the Dehalococcoides mccartyi-Containing Consortium SDC-9". United States. https://doi.org/10.1021/acs.jproteome.0c00072. https://www.osti.gov/servlets/purl/1651260.
@article{osti_1651260,
title = {Metagenome-Guided Proteomic Quantification of Reductive Dehalogenases in the Dehalococcoides mccartyi-Containing Consortium SDC-9},
author = {Kucharzyk, Katarzyna H. and Meisel, Jayda E. and Kara-Murdoch, Fadime and Murdoch, Robert W. and Higgins, Steven A. and Vainberg, Simon and Bartling, Craig M. and Mullins, Larry and Hatzinger, Paul B. and Löffler, Frank E.},
abstractNote = {At groundwater sites contaminated with chlorinated ethenes, fermentable substrates are often added to promote reductive dehalogenation by indigenous or augmented microorganisms. Contemporary bioremediation performance monitoring relies on nucleic acid biomarkers of key organohalide-respiring bacteria, such as Dehalococcoides mccartyi (Dhc). In this work, metagenome sequencing of the commercial, Dhc-containing consortium, SDC-9, identified 12 reductive dehalogenase (RDase) genes, including pceA (two copies), vcrA, and tceA, and allowed for specific detection and quantification of RDase peptides using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Shotgun (i.e., untargeted) proteomics applied to the SDC-9 consortium grown with tetrachloroethene (PCE) and lactate identified 143 RDase peptides, and 36 distinct peptides that covered greater than 99% of the protein-coding sequences of the PceA, TceA, and VcrA RDases. Quantification of RDase peptides using multiple reaction monitoring (MRM) assays with 13C-/15N-labeled peptides determined 1.8 × 103 TceA and 1.2 × 102 VcrA RDase molecules per Dhc cell. Ultimately, the MRM mass spectrometry approach allowed for sensitive detection and accurate quantification of relevant Dhc RDases and has potential utility in bioremediation monitoring regimes.},
doi = {10.1021/acs.jproteome.0c00072},
journal = {Journal of Proteome Research},
number = 4,
volume = 19,
place = {United States},
year = {2020},
month = {3}
}

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