Genome-scale metabolic reconstruction and metabolic versatility of an obligate methanotroph Methylococcus capsulatus str. Bath

PeerJ

article

Ankit Gupta¹  Ahmad Ahmad²  Dipesh Chothwe¹  Midhun K. Madhu¹  Shireesh Srivastava²  Vineet K. Sharma¹ 

[1] Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal;Systems Biology for Biofuels Group, International Centre For Genetic Engineering And Biotechnology;Department of Biotechnology, Noida International University

关键词: Methanotrophs;    Methylococcus capsulatus;    Methane mitigation;    Constraint-based model;    Metabolic model;    Metabolic network;    Genome-scale;   

DOI  :  10.7717/peerj.6685

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

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.

【 授权许可】

CC BY