A genome-scale metabolic model of Methanococcus maripaludis S2 for CO₂capture and conversion to methane

Abstract

Methane is a major energy source for heating and electricity. Its production by methanogenic bacteria is widely known in nature. M. maripaludis S2 is a fully sequenced hydrogenotrophic methanogen and an excellent laboratory strain with robust genetic tools. However, a quantitative systems biology model to complement these tools is absent in the literature. To understand and enhance its methanogenesis from CO2, this work presents the first constraint-based genome-scale metabolic model (iMM518). It comprises 570 reactions, 556 distinct metabolites, and 518 genes along with gene-protein-reaction (GPR) associations, and covers 30% of open reading frames (ORFs). The model was validated using biomass growth data and experimental phenotypic studies from the literature. Its comparison with the in silico models of Methanosarcina barkeri, Methanosarcina acetivorans, and Sulfolobus solfataricus P2 shows M. maripaludis S2 to be a better organism for producing methane. Using the model, genes essential for growth were identified, and the efficacies of alternative carbon, hydrogen and nitrogen sources were studied. The model can predict the effects of reengineering M. maripaludis S2 to guide or expedite experimental efforts.

Acidogenic fermentation of food waste for volatile fatty acid production with co-generation of biohydrogen

“…H 2 gets consumed by hydrogenotrophic methanogenesis as low H 2 and CO 2 concentration which was specifically observed with pH 9 and 10 operations at the later hours. Hydrogenotrophic methanogenesis creates an electrochemical gradient across cell membrane, which, is used to generate ATP through chemiosmosis (Goyal et al, 2014). The inhibition of hydrogenotrophic methanogenesis leads to H 2 accumulation which in turn inhibits acetogenesis (Zaher et al, 2004).…”

Exploring Hydrogenotrophic Methanogenesis: a Genome Scale Metabolic Reconstruction of Methanococcus maripaludis

“…This is a rather high percentage, eclipsing that of the previous M. maripaludis reconstruction (81.4%) (27) and comparing favorably to reconstructions of fellow methanogens Methanosarcina barkeri and Methanosarcina acetivorans (85.7% and 85.1%, respectively) (55, 56). We suspect that a major reason for this high percentage of gene-associated reactions was our use of likelihood-based gap filling (29), which resulted in the automated addition of 66 genes to our reconstruction before manual curation.…”

“…The energetic coupling of heterodisulfide reduction to ferredoxin reduction for the first step of cyclical methanogenesis is in stark contrast to existing methanogen models that contain the linear one based on oxidative (electron transport) phosphorylation (27, 55, 56). While the linear model is correct for methanogens with cytochromes, it is not correct for methanogens without cytochromes, such as M.…”

“…Other groups have already created metabolic models of M. maripaludis as part of a mutualistic community model with Desulfovibrio vulgaris (26) and under axenic conditions (27). In the former case, the model of M.…”

“…The latter case was the first genome scale metabolic reconstruction of M. maripaludis (27), an important step toward understanding M. maripaludis metabolism.…”