Genome-Scale Metabolic Model Reconstruction and in Silico Investigations of Methane Metabolism in Methylosinus trichosporium OB3b

Abstract

Methylosinus trichosporium OB3b is an obligate aerobic methane-utilizing alpha-proteobacterium. Since its isolation, M. trichosporium OB3b has been established as a model organism to study methane metabolism in type II methanotrophs. M. trichosporium OB3b utilizes soluble and particulate methane monooxygenase (sMMO and pMMO respectively) for methane oxidation. While the source of electrons is known for sMMO, there is less consensus regarding electron donor to pMMO. To investigate this and other questions regarding methane metabolism, the genome-scale metabolic model for M. trichosporium OB3b (model ID: iMsOB3b) was reconstructed. The model accurately predicted oxygen: methane molar uptake ratios and specific growth rates on nitrate-supplemented medium with methane as carbon and energy source. The redox-arm mechanism which links methane oxidation with complex I of electron transport chain has been found to be the most optimal mode of electron transfer. The model was also qualitatively validated on ammonium-supplemented medium indicating its potential to accurately predict methane metabolism in different environmental conditions. Finally, in silico investigations regarding flux distribution in central carbon metabolism of M. trichosporium OB3b were performed. Overall, iMsOB3b can be used as an organism-specific knowledgebase and a platform for hypothesis-driven theoretical investigations of methane metabolism.

Strategies for Enhancing in vitro Degradation of Linuron by Variovorax sp. Strain SRS 16 Under the Guidance of Metabolic Modeling

“…First, further adaptations are required for the current version of iRZ1425 to meet the requirements of gold standard models (Thiele and Palsson, 2010). Mainly, the biomass composition is an approximation that relies on automatic protocols and genomic information (Oh et al, 2007;Henry et al, 2010), similar to other recent works (Bordel et al, 2019;Naizabekov and Lee, 2020;Ofaim et al, 2020). The construction of a biomass reaction specific to the SRS 16 reaction requires layers of experimental data that are currently missing, including the precursors of general biomass constructions (for example, proteins, lipids, and species-specific components).…”

Integrative Genome-Scale Metabolic Modeling Reveals Versatile Metabolic Strategies for Methane Utilization in Methylomicrobium album BG8

“…strain SC2 [ 38 ], Methylocystis sp. strain SB2 [ 38 ], Methylocystis parvus OBBP [ 39 ], Methylocella silvestris [ 40 ], and Methylosinus trichosporium OB3b [ 41 ]). Although some of these GEMs have been validated using growth yields, methane- and oxygen-specific uptake rates ( 38 ), transcriptomics data ( 34 ), or enzyme kinetics ( 35 ), most do not contain other integrated experimental data.…”

Peer Review #1 of "Investigation of microbial community interactions between Lake Washington methanotrophs using ­­­­­­­genome-scale metabolic modeling (v0.1)"

“…Other novel methods were also proposed for modeling of such communities involving elementary mode analysis, evolutionary game theory, nonlinear dynamics, and stochastic processes (Vallino, 2003;Lehmann & Keller, 2006;Shou, Ram & Vilar, 2007;Borenstein & Feldman, 2009;Freilich et al, 2009;Frey, 2010;Nadell, Foster & Xavier, 2010;Magnúsdóttir, Heinken & Kutt, 2017). While there have been multiple studies in recent years involved in the model development of various methanotrophs (Akberdin et al 2018;Bordel et al 2019a;Bordel et al 2019b;de la Torre et al 2015;Lieven et al 2018;Naizabekov & Lee 2020), an integrated community level analysis of freshwater methane utilizing ecosystems have not been performed yet.…”