A Genome-Scale Metabolic Model for Methylococcus capsulatus (Bath) Suggests Reduced Efficiency Electron Transfer to the Particulate Methane Monooxygenase

Christian Lieven*, Leander A. H. Petersen, Sten Bay Jørgensen, Krist V. Gernaey, Markus J. Herrgard, Nikolaus Sonnenschein

*Corresponding author for this work

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Abstract

Genome-scale metabolic models allow researchers to calculate yields, to predict consumption and production rates, and to study the effect of genetic modifications in silico, without running resource-intensive experiments. While these models have become an invaluable tool for optimizing industrial production hosts like E. coli and S. cerevisiae, few such models exist for one-carbon (C1) metabolizers. Here we present a genome-scale metabolic model for Methylococcus capsulatus (Bath), a well-studied obligate methanotroph, which has been used as a production strain of single cell protein (SCP). The model was manually curated, and spans a total of 879 metabolites connected via 913 reactions. The inclusion of 730 genes and comprehensive annotations, make this model not only a useful tool for modeling metabolic physiology, but also a centralized knowledge base for M. capsulatus (Bath). With it, we determined that oxidation of methane by the particulate methane monooxygenase could be driven both through direct coupling or uphill electron transfer, both operating at reduced efficiency, as either scenario matches well with experimental data and observations from literature. The metabolic model will serve the ongoing fundamental research of C1 metabolism, and pave the way for rational strain design strategies towards improved SCP production processes in M. capsulatus.
Original languageEnglish
Article number2947
JournalFrontiers in Microbiology
Volume9
Number of pages15
ISSN1664-302X
DOIs
Publication statusPublished - 2018

Keywords

  • COBRA
  • Genome-scale metabolic reconstruction
  • C1 metabolism
  • Single cell protein
  • Methanotrophy
  • Constraint-based reconstruction and analysis

Cite this

@article{a036953298e54c0ba399b06e4ebf379b,
title = "A Genome-Scale Metabolic Model for Methylococcus capsulatus (Bath) Suggests Reduced Efficiency Electron Transfer to the Particulate Methane Monooxygenase",
abstract = "Genome-scale metabolic models allow researchers to calculate yields, to predict consumption and production rates, and to study the effect of genetic modifications in silico, without running resource-intensive experiments. While these models have become an invaluable tool for optimizing industrial production hosts like E. coli and S. cerevisiae, few such models exist for one-carbon (C1) metabolizers. Here we present a genome-scale metabolic model for Methylococcus capsulatus (Bath), a well-studied obligate methanotroph, which has been used as a production strain of single cell protein (SCP). The model was manually curated, and spans a total of 879 metabolites connected via 913 reactions. The inclusion of 730 genes and comprehensive annotations, make this model not only a useful tool for modeling metabolic physiology, but also a centralized knowledge base for M. capsulatus (Bath). With it, we determined that oxidation of methane by the particulate methane monooxygenase could be driven both through direct coupling or uphill electron transfer, both operating at reduced efficiency, as either scenario matches well with experimental data and observations from literature. The metabolic model will serve the ongoing fundamental research of C1 metabolism, and pave the way for rational strain design strategies towards improved SCP production processes in M. capsulatus.",
keywords = "COBRA, Genome-scale metabolic reconstruction, C1 metabolism, Single cell protein, Methanotrophy, Constraint-based reconstruction and analysis",
author = "Christian Lieven and Petersen, {Leander A. H.} and J{\o}rgensen, {Sten Bay} and Gernaey, {Krist V.} and Herrgard, {Markus J.} and Nikolaus Sonnenschein",
year = "2018",
doi = "10.3389/fmicb.2018.02947",
language = "English",
volume = "9",
journal = "Frontiers in Microbiology",
issn = "1664-302X",
publisher = "Frontiers Media S.A.",

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TY - JOUR

T1 - A Genome-Scale Metabolic Model for Methylococcus capsulatus (Bath) Suggests Reduced Efficiency Electron Transfer to the Particulate Methane Monooxygenase

AU - Lieven, Christian

AU - Petersen, Leander A. H.

AU - Jørgensen, Sten Bay

AU - Gernaey, Krist V.

AU - Herrgard, Markus J.

AU - Sonnenschein, Nikolaus

PY - 2018

Y1 - 2018

N2 - Genome-scale metabolic models allow researchers to calculate yields, to predict consumption and production rates, and to study the effect of genetic modifications in silico, without running resource-intensive experiments. While these models have become an invaluable tool for optimizing industrial production hosts like E. coli and S. cerevisiae, few such models exist for one-carbon (C1) metabolizers. Here we present a genome-scale metabolic model for Methylococcus capsulatus (Bath), a well-studied obligate methanotroph, which has been used as a production strain of single cell protein (SCP). The model was manually curated, and spans a total of 879 metabolites connected via 913 reactions. The inclusion of 730 genes and comprehensive annotations, make this model not only a useful tool for modeling metabolic physiology, but also a centralized knowledge base for M. capsulatus (Bath). With it, we determined that oxidation of methane by the particulate methane monooxygenase could be driven both through direct coupling or uphill electron transfer, both operating at reduced efficiency, as either scenario matches well with experimental data and observations from literature. The metabolic model will serve the ongoing fundamental research of C1 metabolism, and pave the way for rational strain design strategies towards improved SCP production processes in M. capsulatus.

AB - Genome-scale metabolic models allow researchers to calculate yields, to predict consumption and production rates, and to study the effect of genetic modifications in silico, without running resource-intensive experiments. While these models have become an invaluable tool for optimizing industrial production hosts like E. coli and S. cerevisiae, few such models exist for one-carbon (C1) metabolizers. Here we present a genome-scale metabolic model for Methylococcus capsulatus (Bath), a well-studied obligate methanotroph, which has been used as a production strain of single cell protein (SCP). The model was manually curated, and spans a total of 879 metabolites connected via 913 reactions. The inclusion of 730 genes and comprehensive annotations, make this model not only a useful tool for modeling metabolic physiology, but also a centralized knowledge base for M. capsulatus (Bath). With it, we determined that oxidation of methane by the particulate methane monooxygenase could be driven both through direct coupling or uphill electron transfer, both operating at reduced efficiency, as either scenario matches well with experimental data and observations from literature. The metabolic model will serve the ongoing fundamental research of C1 metabolism, and pave the way for rational strain design strategies towards improved SCP production processes in M. capsulatus.

KW - COBRA

KW - Genome-scale metabolic reconstruction

KW - C1 metabolism

KW - Single cell protein

KW - Methanotrophy

KW - Constraint-based reconstruction and analysis

U2 - 10.3389/fmicb.2018.02947

DO - 10.3389/fmicb.2018.02947

M3 - Journal article

C2 - 30564208

VL - 9

JO - Frontiers in Microbiology

JF - Frontiers in Microbiology

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