Genome-scale metabolic network reconstruction of the chloroform-respiring Dehalobacter restrictus strain CF

Abstract

12Background. 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. 13 14 15 16 17 18Method. 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. 19 20 21 22 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. 23 24 25 26 27 28 29 30 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.31 32 33 34 35 36 37 1 INTRODUCTION 38 Organohalide-respiring bacteria (OHRB) play an important role in the global halogen cycle and bioremedi-39 ation of industrial sites contaminated with chlorinated organics, such as chloroform, 1,1,1-trichloroethane 40 and 1,1-dichloroethane (Jugder et al., 2016). One notable OHRB is Dehalobacter restrictus strain CF, 41 which is capable of dechlorinating chloroform to dichloromethane (Grostern et al., 2010). Improved 42 bioremediation strategies could be employed with a greater understanding of D. restrictus' metabolism in 43 isolate and community cultures. We reconstructed the genome-scale metabolic network of D. restrictus 44 CF, with the aim to better unders...

Interspecies malate-pyruvate shuttle drives amino acid exchange in organohalide-respiring microbial communities

“…The experimentally refined genome of D. restrictus strain CF (accession no. NC_018866) (Wang et al, 2016) was used to reconstruct a draft Dhb genome-scale metabolic model (Correia et al ., 2018). Flux balance analysis and flux variability analysis simulations were conducted with COBRApy (Ebrahim et al ., 2013).…”

“…In this study, we first explored the metabolic dependency of Dhb using its genome-scale metabolic model (Correia et al ., 2018), which was built based on a highly annotated and experimentally refined Dhb genome (Wang et al, 2016), along with shared expression patterns in proteomic datasets of Dhb strains PER-K23, UNSWDHB, DCA and CF (Jugder et al ., 2016, Rupakula et al ., 2013, Rupakula et al ., 2015, Tang and Edwards, 2013a). The model simulations consider cofactor availability, enzyme promiscuity, physiological redox conditions, and further model constraints based on experimental values obtained in this study.…”

An interspecies malate–pyruvate shuttle reconciles redox imbalance in an anaerobic microbial community

“…The experimentally refined genome of D. restrictus strain CF (accession no. NC_018866) [30] was used to reconstruct a draft Dehalobacter genome-scale metabolic model [33]. Flux balance analysis and flux variability analysis simulations were conducted with COBRApy [38].…”

“…Common features among these Dehalobacter genomes are gaps in the TCA cycle and serine biosynthesis. We then built a genome-scale constraint-based Dehalobacter metabolic model based on the refined metabolic annotation [33]. To increase accuracy in model reconstruction, we analyzed the presence/absence of enzyme orthologs involved in these metabolic pathways in a range of OHRB species, Firmicutes species, Bacteroides species, and some well-characterized or widely studied model organisms in Bacteria (Fig.…”

“…In this study, we elucidated some metabolic interdependencies in D. restrictus-containing consortium ACT-3, which first required resolving the discrepancy between observed amino acid auxotrophy and the genome annotation of D. restrictus. We explored the metabolic potential of D. restrictus using a genome-scale, constraint-based metabolic model built on a highly annotated D. restrictus strain CF genome [33]. The metabolic annotation was systematically curated with: (a) genome analysis [25] and (b) shared protein expression data available for strains DCA, PER-K23, E1, and UNSWDHB [34][35][36][37].…”