Genome-scale metabolic network reconstruction and in silico flux analysis of the thermophilic bacterium Thermus thermophilus HB27

Na Rae Lee, Meiyappan Lakshmanan, Shilpi Aggarwal, Ji Won Song, Iftekhar A. Karimi, Dong Yup Lee, Jin Byung Park

Research output: Contribution to journalArticlepeer-review

17 Scopus citations

Abstract

Background: Thermus thermophilus, an extremely thermophilic bacterium, has been widely recognized as a model organism for studying how microbes can survive and adapt under high temperature environment. However, the thermotolerant mechanisms and cellular metabolism still remains mostly unravelled. Thus, it is highly required to consider systems biological approaches where T. thermophilus metabolic network model can be employed together with high throughput experimental data for elucidating its physiological characteristics under such harsh conditions.Results: We reconstructed a genome-scale metabolic model of T. thermophilus, iTT548, the first ever large-scale network of a thermophilic bacterium, accounting for 548 unique genes, 796 reactions and 635 unique metabolites. Our initial comparative analysis of the model with Escherichia coli has revealed several distinctive metabolic reactions, mainly in amino acid metabolism and carotenoid biosynthesis, producing relevant compounds to retain the cellular membrane for withstanding high temperature. Constraints-based flux analysis was, then, applied to simulate the metabolic state in glucose minimal and amino acid rich media. Remarkably, resulting growth predictions were highly consistent with the experimental observations. The subsequent comparative flux analysis under different environmental conditions highlighted that the cells consumed branched chain amino acids preferably and utilized them directly in the relevant anabolic pathways for the fatty acid synthesis. Finally, gene essentiality study was also conducted via single gene deletion analysis, to identify the conditional essential genes in glucose minimal and complex media.Conclusions: The reconstructed genome-scale metabolic model elucidates the phenotypes of T. thermophilus, thus allowing us to gain valuable insights into its cellular metabolism through in silico simulations. The information obtained from such analysis would not only shed light on the understanding of physiology of thermophiles but also helps us to devise metabolic engineering strategies to develop T. thermophilus as a thermostable microbial cell factory.

Original languageEnglish
Article number61
JournalMicrobial Cell Factories
Volume13
Issue number1
DOIs
StatePublished - 28 Apr 2014

Bibliographical note

Funding Information:
This work was supported by the National University of Singapore, Biomedical Research Council of A*STAR (Agency for Science, Technology and Research), Singapore, Korea Research Foundation (KRF-2010–0009169), Republic of Korea, and a grant from the Next-Generation BioGreen 21 Program (SSAC, No. PJ009520), Rural Development Administration, Republic of Korea.

Keywords

  • Constraints-based flux analysis
  • Ethanol
  • Genome-scale metabolic model
  • Thermophile
  • Thermus thermophilus

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