ABSTRACT
Background Organohalide-respiring bacteria (OHRB) play an important role in the global halogen cycle and bioremediation of industrial sites contaminated with chlorinated organics. One notable OHRB is Dehalobacter restrictus strain CF, which is capable of respiring chloroform to dichloromethane. Improved bioremediation strategies could be employed with a greater understanding of D. restrictus’ metabolism in isolate and community cultures. To this end, we reconstructed the genome-scale metabolic network of D. restrictus to study its metabolism in future studies using flux balance analysis.
Method The RAST annotation server and Model SEED framework were used to obtain a draft metabolic network reconstruction. Additional curation was required for its acetyl-CoA sources, the Wood-Ljungdahl pathway, TCA cycle, electron transport chain, hydrogenase complexes, and formate dehydrogenase complexes.
Results iHH623 is the first curated genome-scale metabolic model in the Peptococcaceae family. It spans 1087 reactions and 983 metabolites, covering 623 genes (21% of all ORF’s). Its potential sources of acetyl-CoA are pyruvate ferredoxin oxidoreductase, pyruvate formate lyase, acetyl-CoA synthetase, phosphate acetyltransferase, and CO-methylating acetyl-CoA synthase. NADPH may be regenerated by isocitrate dehydrogenase, malic enzyme, NADP-reducing hydrogenase, cytosolic formate dehydrogenase, ferredoxin-dependent bifurcating transhydrogenase, 5-methyltetrahydrofolate dehydrogenase, and 5-10-methylenetetrahydrofolate. Additional reactions that were added or removed to the D. restrictus reconstruction are discussed.
Conclusions We reconstructed the genome-scale metabolic network of D. restricus by obtaining an initial draft with the RAST server and Model SEED framework. Curation was required for D. restricus’ acetyl-CoA sources, TCA cycle, electron transport chain, hydrogenase complexes, and formate dehydrogenase complexes. This metabolic model can be used to decipher D. restrictus’ metabolism in isolate and community cultures in future studies, or as a template to reconstruct the metabolic network of other Peptococcaceae species. The extensive curation of the draft metabolic network reconstruction highlights the need to be cautious of automated metabolic network reconstruction.