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

Microbial Cell Factories

Research

Meiyappan Lakshmanan¹  Shilpi Aggarwal¹  Iftekhar A Karimi¹  Dong-Yup Lee²  Na-Rae Lee³  Ji-Won Song³  Jin-Byung Park⁴ 

[1] Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, 117585, Singapore, Singapore;Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, 117585, Singapore, Singapore;Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Centros, 138668, Singapore, Singapore;Department of Food Science & Engineering, Ewha Womans University, 11-1 Daehyun-dong, 120-750, Seodaemun-gu, Seoul, Korea;Department of Food Science & Engineering, Ewha Womans University, 11-1 Daehyun-dong, 120-750, Seodaemun-gu, Seoul, Korea;Global Top5 Research Program, Ewha Womans University, 11-1 Daehyeon-dong, 120750, Seodaemun-gu, Seoul, Korea;

关键词: Thermus thermophilus;    Thermophile;    Genome-scale metabolic model;    Constraints-based flux analysis;    Ethanol;   

DOI  :  10.1186/1475-2859-13-61

 received in 2014-02-14, accepted in 2014-04-17,  发布年份 2014

来源: Springer

【 摘 要 】

BackgroundThermus 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.ResultsWe reconstructed a genome-scale metabolic model of T. thermophilus, i TT548, 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.ConclusionsThe 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.

【 授权许可】

CC BY   
© Lee et al.; licensee BioMed Central Ltd. 2014