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New insights into Dehalococcoides mccartyi metabolism from a reconstructed metabolic network-based systems-level analysis of D. mccartyi transcriptomes

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posted on 07.11.2017, 10:56 authored by Ahsan IslamAhsan Islam, Alison S. Waller, Laura A. Hug, Nicholas A. Provart, Elizabeth A. Edwards, Radhakrishnan Mahadevan
Organohalide respiration, mediated by Dehalococcoides mccartyi, is a useful bioremediation process that transforms ground water pollutants and known human carcinogens such as trichloroethene and vinyl chloride into benign ethenes. Successful application of this process depends on the fundamental understanding of the respiration and metabolism of D. mccartyi. Reductive dehalogenases, encoded by rdhA genes of these anaerobic bacteria, exclusively catalyze organohalide respiration and drive metabolism. To better elucidate D. mccartyi metabolism and physiology, we analyzed available transcriptomic data for a pure isolate (Dehalococcoides mccartyi strain 195) and a mixed microbial consortium (KB-1) using the previously developed pan-genome-scale reconstructed metabolic network of D. mccartyi. The transcriptomic data, together with available proteomic data helped confirm transcription and expression of the majority genes in D. mccartyi genomes. A composite genome of two highly similar D. mccartyi strains (KB-1 Dhc) from the KB-1 metagenome sequence was constructed, and operon prediction was conducted for this composite genome and other single genomes. This operon analysis, together with the quality threshold clustering analysis of transcriptomic data helped generate experimentally testable hypotheses regarding the function of a number of hypothetical proteins and the poorly understood mechanism of energy conservation in D. mccartyi. We also identified functionally enriched important clusters (13 for strain 195 and 11 for KB-1 Dhc) of co-expressed metabolic genes using information from the reconstructed metabolic network. This analysis highlighted some metabolic genes and processes, including lipid metabolism, energy metabolism, and transport that potentially play important roles in organohalide respiration. Overall, this study shows the importance of an organism’s metabolic reconstruction in analyzing various ‘‘omics’’ data to obtain improved understanding of the metabolism and physiology of the organism.

Funding

This research was funded by the University of Toronto, the Natural Sciences and Engineering Research Council of Canada (NSERC), the Government of Canada through Genome Canada and the Ontario Genomics Institute (2009-OGI-ABC-1405) and the United States Department of Defense Strategic Environmental Research and Development Program (SERDP). MAI was funded by the Ontario Graduate Scholarship (OGS), the SERDP and Genome Canada funds to EAE and the departmental faculty start-up funds to RM. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

History

School

  • Aeronautical, Automotive, Chemical and Materials Engineering

Department

  • Chemical Engineering

Published in

PLoS ONE

Volume

9

Issue

4

Pages

e94808 - e94808

Citation

ISLAM, M. ... et al., 2014. New insights into Dehalococcoides mccartyi metabolism from a reconstructed metabolic network-based systems-level analysis of D. mccartyi transcriptomes. PLoS ONE, 9 (4), DOI: 10.1371/journal.pone.0094808.

Publisher

PLoS (© the authors)

Version

VoR (Version of Record)

Publisher statement

This work is made available according to the conditions of the Creative Commons Attribution 4.0 International (CC BY 4.0) licence. Full details of this licence are available at: http://creativecommons.org/licenses/ by/4.0/

Publication date

2014

eISSN

1932-6203

Language

en

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