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

摘要

Organohalide respiration, mediated by Dehalococcoides mccartyi, is a useful bioremediation process that transforms groundudwater pollutants and known human carcinogens such as trichloroethene and vinyl chloride into benign ethenes. Successfuludapplication of this process depends on the fundamental understanding of the respiration and metabolism of D. mccartyi.udReductive dehalogenases, encoded by rdhA genes of these anaerobic bacteria, exclusively catalyze organohalide respirationudand drive metabolism. To better elucidate D. mccartyi metabolism and physiology, we analyzed available transcriptomicuddata for a pure isolate (Dehalococcoides mccartyi strain 195) and a mixed microbial consortium (KB-1) using the previouslyuddeveloped pan-genome-scale reconstructed metabolic network of D. mccartyi. The transcriptomic data, together withudavailable proteomic data helped confirm transcription and expression of the majority genes in D. mccartyi genomes. Audcomposite genome of two highly similar D. mccartyi strains (KB-1 Dhc) from the KB-1 metagenome sequence wasudconstructed, and operon prediction was conducted for this composite genome and other single genomes. This operonudanalysis, together with the quality threshold clustering analysis of transcriptomic data helped generate experimentallyudtestable hypotheses regarding the function of a number of hypothetical proteins and the poorly understood mechanism ofudenergy conservation in D. mccartyi. We also identified functionally enriched important clusters (13 for strain 195 and 11 forudKB-1 Dhc) of co-expressed metabolic genes using information from the reconstructed metabolic network. This analysisudhighlighted some metabolic genes and processes, including lipid metabolism, energy metabolism, and transport thatudpotentially play important roles in organohalide respiration. Overall, this study shows the importance of an organism’sudmetabolic reconstruction in analyzing various ‘‘omics’’ data to obtain improved understanding of the metabolism andudphysiology of the organism.