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Construction and Validation of a Genome-Scale Metabolic Network of Thermotoga sp. Strain RQ7

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Abstract

Thermotoga are anaerobic hyperthermophiles that have a deep lineage to the last universal ancestor and produce biological hydrogen gas accompanying cell growth. In recent years, systems-level approaches have been used to elucidate their metabolic capacities, by integrating mathematical modeling and experimental results. To assist biochemical engineering studies of T. sp. strain RQ7, this work aims at building a metabolic model of the bacterium that quantitatively simulates its metabolism at the genome scale. The constructed model, RQ7_iJG408, consists of 408 genes, 692 reactions, and 538 metabolites. Constraint-based flux balance analyses were used to simulate cell growth in both the complex and defined media. Quantitative comparison of the predicted and measured growth rates resulted in good agreements. This model serves as a foundation for an integrated biochemical description of T. sp. strain RQ7. It is a useful tool in designing growth media, identifying metabolic engineering strategies, and exploiting the physiological potentials of this biotechnologically significant organism.

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Abbreviations

ATPM:

ATP maintenance

BOF:

Biomass objective function

COBRA:

Constraint-based reconstruction and analysis

GEM:

Genome-scale metabolic model

GPR:

Gene-protein association

LPS:

Lipopolysaccharides

SBML:

Systems Biology Markup Language

RQ7:

Thermotoga sp. strain RQ7

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  1. Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA

    Jyotshana Gautam & Zhaohui Xu

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  1. Jyotshana Gautam
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ZX conceived and coordinated the study. JG conducted growth experiments. Both authors contributed to model building, data analyzing, and manuscript writing.

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Correspondence to Zhaohui Xu.

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Supplementary Information

ESM 1.

Biomass objective function (.docx) (DOCX 56 kb)

ESM 2

Lists of reactions, metabolites, genes, and unique proteins (.xlsx) (XLSX 108 kb)

ESM 3

Model RQ7_iJG408 in SBML format (.xml) (XML 3262 kb)

ESM 4

MEMOTE analysis report of iJG408 (HTML 3714 kb)

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Gautam, J., Xu, Z. Construction and Validation of a Genome-Scale Metabolic Network of Thermotoga sp. Strain RQ7. Appl Biochem Biotechnol 193, 896–911 (2021). https://doi.org/10.1007/s12010-020-03470-z

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