title: New insights into Dehalococcoides mccartyi metabolism from a reconstructed metabolic network-based systems-level analysis of D. mccartyi transcriptomes.
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.
authors.affiliation: Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada.
authors.forename: M Ahsanul
authors.initials: MA
authors.lastname: Islam
authors.affiliation: European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
authors.forename: Alison S
authors.initials: AS
authors.lastname: Waller
authors.affiliation: Department of Earth and Planetary Science, University of California, Berkeley, California, United States of America.
authors.forename: Laura A
authors.initials: LA
authors.lastname: Hug
authors.affiliation: Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada.
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: Provart
authors.affiliation: Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada; Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada.
authors.forename: Elizabeth A
authors.initials: EA
authors.lastname: Edwards
authors.affiliation: Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada; Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada.
authors.forename: Radhakrishnan
authors.initials: R
authors.lastname: Mahadevan
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D041862:Chloroflexi / Q000235:genetics* / Q000378:metabolism*; D016000:Cluster Analysis; D004579:Electron Transport; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial; D006867:Hydrolases / Q000378:metabolism; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D058977:Molecular Sequence Annotation; D009876:Operon / Q000235:genetics; D025341:Principal Component Analysis; D040901:Proteomics; D015203:Reproducibility of Results; D049490:Systems Biology; D059467:Transcriptome / Q000235:genetics*
chemical_list: D001426:Bacterial Proteins; D006867:Hydrolases
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