Genome-scale metabolic reconstruction and metabolic versatility of an obligate methanotrophMethylococcus capsulatusstr. Bath

Author:

Gupta Ankit1,Ahmad Ahmad23,Chothwe Dipesh1,Madhu Midhun K.1,Srivastava Shireesh2ORCID,Sharma Vineet K.1

Affiliation:

1. Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India

2. Systems Biology for Biofuels Group, International Centre For Genetic Engineering And Biotechnology, New Delhi, India

3. Department of Biotechnology, Noida International University, Noida, India

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 capsulatusstr. Bath was reconstructed. The model contains 535 genes, 899 reactions and 865 metabolites and is namediMC535. 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 thatM. capsulatuscan 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 methanotrophMethylococcus capsulatusstr. 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 ofM. capsulatusBath.

Funder

MHRD, Govt of India, funded Centre for Research on Environment and Sustainable Technologies (CREST) at IISER Bhopal

Ankit Gupta is a recipient of DST-INSPIRE Fellowship

Publisher

PeerJ

Subject

General Agricultural and Biological Sciences,General Biochemistry, Genetics and Molecular Biology,General Medicine,General Neuroscience

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