Abstract
The increase in greenhouse gases with high global warming potential such as methane is a matter of concern and requires multifaceted efforts to reduce its emission and increase its mitigation from the environment. Microbes such as methanotrophs can assist in methane mitigation. To understand the metabolic capabilities of methanotrophs, a complete genome-scale metabolic model (GSMM) of an obligate methanotroph, Methylococcus capsulatus str. Bath was reconstructed. The model contains 535 genes, 899 reactions and 865 metabolites and is named iMC535. The predictive potential of the model was validated using previously-reported experimental data. The model predicted the Entner–Duodoroff pathway to be essential for the growth of this bacterium, whereas the Embden–Meyerhof–Parnas pathway was found non-essential. The performance of the model was simulated on various carbon and nitrogen sources and found that M. capsulatus can grow on amino acids. The analysis of network topology of the model identified that six amino acids were in the top-ranked metabolic hubs. Using flux balance analysis, 29% of the metabolic genes were predicted to be essential, and 76 double knockout combinations involving 92 unique genes were predicted to be lethal. In conclusion, we have reconstructed a GSMM of a methanotroph Methylococcus capsulatus str. Bath. This is the first high quality GSMM of a Methylococcus strain which can serve as an important resource for further strain-specific models of the Methylococcus genus, as well as identifying the biotechnological potential of M. capsulatus Bath.
Highlights
The problem of global warming needs urgent attention and requires a multifaceted approach including the control on the emission of greenhouse gases
We present a detailed genome-scale metabolic reconstruction “iMC535” for the type I methanotroph Methylococcus capsulatus Bath, constructed using a systematic standard approach (Ahmad et al, 2017; Shah et al, 2017; Thiele & Palsson, 2010) and was validated using flux balance analysis (FBA)
Model reconstruction The metabolic reconstruction of Methylococcus capsulatus Bath (Mcap) was carried out using its annotated genome sequence obtained from NCBI
Summary
The problem of global warming needs urgent attention and requires a multifaceted approach including the control on the emission of greenhouse gases. Methanotrophs can produce industrially important products and biopolymers such as polyhydroxybutarate, vitamins, carboxylic acids, single cell protein, and antibiotics using methane as the carbon source (Fei et al, 2014; Strong, Xie & Clarke, 2015). Despite these positives, bioconversion through methanotrophs faces multiple challenges of low energy and carbon efficiencies, and cultures with low productivity (Conrado & Gonzalez, 2014; Shima et al, 2012).
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