Construction and Validation of a Genome-Scale Metabolic Network of Thermotoga sp. Strain RQ7
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Construction and Validation of a Genome-Scale Metabolic Network of Thermotoga sp. Strain RQ7 Jyotshana Gautam 1 & Zhaohui Xu 1 Received: 1 May 2020 / Accepted: 9 November 2020/ # Springer Science+Business Media, LLC, part of Springer Nature 2020
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. Keywords Thermotoga . Genome-scale metabolic modeling . Biomass objective function . Constraint-based reconstruction and analysis . Flux balance analysis 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 * Zhaohui Xu [email protected]
1
Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
Applied Biochemistry and Biotechnology
Introduction Since the isolation of the first Thermotoga strain, much research interest has been gathered around these bacteria due to their evolutionary significance and biotechnological potentials, such as the production of biohydrogen gas and thermostable enzymes [1, 2]. These bacteria are Gram-negative, rod-shaped, non-sporulating, and anaerobic and have an outer sheath-like covering called “toga” [3]. They carry a complement of carbohydrate-degrading genes and can grow with simple or complex sugars ranging from glucose, sucrose, starch, cellobiose, xylan, and pectin [4, 5]. Genetic engineering of Thermotoga has been achieved in recent years [6–10], and dozens of Thermotoga genomes are publicly available in GenBank. With the advent of DNA sequencing technologies, developing genome-scale metabolic models (GEMs) to guide metabolic engineering has become a popular trend in recent years, especially through the approach of constraint-based reconstruction and analysis (COBRA) [11]. GEMs have been widely used in optimizing growth media [12–14] and designing knockout strains [15]. The first GEM of Thermotoga
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