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|Title: ||New insights into Dehalococcoides mccartyi metabolism from a reconstructed metabolic network-based systems-level analysis of D. mccartyi transcriptomes|
|Authors: ||Islam, M. Ahsanul|
Waller, Alison S.
Hug, Laura A.
Provart, Nicholas A.
Edwards, Elizabeth A.
|Issue Date: ||2014|
|Publisher: ||PLoS (© the authors)|
|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.|
|Abstract: ||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.|
|Sponsor: ||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
|Publisher Link: ||https://doi.org/10.1371/journal.pone.0094808|
|Appears in Collections:||Published Articles (Chemical Engineering)|
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