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

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.

doi:10.1021/acs.jproteome.0c00072

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

Journal Article · Thu Mar 05 00:00:00 EST 2020 · Journal of Proteome Research

DOI:https://doi.org/10.1021/acs.jproteome.0c00072· OSTI ID:1651260

^[1]; Meisel, Jayda E. ^[1]; Kara-Murdoch, Fadime ^[2]; Murdoch, Robert W. ^[3]; Higgins, Steven A. ^[2]; Vainberg, Simon ^[4]; Bartling, Craig M. ^[1]; Mullins, Larry ^[1]; Hatzinger, Paul B. ^[4];

^[5]

Battelle Memorial Inst., Columbus, OH (United States)
Univ. of Tennessee, Knoxville, TN (United States)
Univ. of Tennessee, Knoxville, TN (United States). Center for Environmental Biotechnology
APTIM, Lawrenceville, NJ (United States). Biotechnology Development and Applications Group
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)

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.

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Research Organization:: Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE; USDOD

Grant/Contract Number:: AC05-00OR22725; ER-201726

OSTI ID:: 1651260

Journal Information:: Journal of Proteome Research, Vol. 19, Issue 4; ISSN 1535-3893

Publisher:: American Chemical Society (ACS)Copyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 8 works

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59 BASIC BIOLOGICAL SCIENCES
bioremediation
chlorinated ethenes
reductive dehalogenation
proteomics
metagenomics
consortium SDC-9

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

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