Analysis of l-glutamic acid fermentation by using a dynamic metabolic simulation model of Escherichia coli

BMC Systems Biology

Hiroshi Tanaka⁵  Tadashi Masuda¹  Yoshihiro Usuda²  Yohei Yamada³  Masao Ichikawa⁵  Soichi Ogishima⁴  Yousuke Nishio⁶ 

[1]Faculty of Symbiotic Systems Science, Fukushima University, Kanayagawa 1, Fukushima City, Fukushima 960-1296, Japan

[2]Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co. Inc., Suzuki-cho 1-1, Kawasaki-ku, Kawasaki City, Kanagawa 210-8681, Japan

[3]Pharmaceutical Custom Manufacturing Department, Ajinomoto Co. Inc., Kyobashi 1-chome 15-1, Chuo-ku, Tokyo 104-8315, Japan

[4]Current address: Department of Health Record Informatics, Tohoku Medical Megabank Organization, Tohoku University, Seiryo-cho 4-1, Aoba-ku, Sendai-City, Miyagi 980-8575, Japan

[5]Department of Bioinformatics, Tokyo Medical and Dental University, Yushima 1-5-45, Bunkyo-ku, Tokyo 113-8510, Japan

[6]Institute for Innovation, Ajinomoto Co. Inc., Suzuki-cho 1-1, Kawasaki-ku, Kawasaki City, Kanagawa 210-8681, Japan

关键词: Escherichia coli;    Phosphoglycerate kinase;    Sensitivity analysis;    Dynamic metabolic simulation;    L-glutamic acid fermentation;   

Others  :  1142197
DOI  :  10.1186/1752-0509-7-92

 received in 2012-12-27, accepted in 2013-09-13,  发布年份 2013

【 摘 要 】

Background

Understanding the process of amino acid fermentation as a comprehensive system is a challenging task. Previously, we developed a literature-based dynamic simulation model, which included transcriptional regulation, transcription, translation, and enzymatic reactions related to glycolysis, the pentose phosphate pathway, the tricarboxylic acid (TCA) cycle, and the anaplerotic pathway of Escherichia coli. During simulation, cell growth was defined such as to reproduce the experimental cell growth profile of fed-batch cultivation in jar fermenters. However, to confirm the biological appropriateness of our model, sensitivity analysis and experimental validation were required.

Results

We constructed an L-glutamic acid fermentation simulation model by removing sucAB, a gene encoding α-ketoglutarate dehydrogenase. We then performed systematic sensitivity analysis for L-glutamic acid production; the results of this process corresponded with previous experimental data regarding L-glutamic acid fermentation. Furthermore, it allowed us to predicted the possibility that accumulation of 3-phosphoglycerate in the cell would regulate the carbon flux into the TCA cycle and lead to an increase in the yield of L-glutamic acid via fermentation. We validated this hypothesis through a fermentation experiment involving a model L-glutamic acid-production strain, E. coli MG1655 ΔsucA in which the phosphoglycerate kinase gene had been amplified to cause accumulation of 3-phosphoglycerate. The observed increase in L-glutamic acid production verified the biologically meaningful predictive power of our dynamic metabolic simulation model.

Conclusions

In this study, dynamic simulation using a literature-based model was shown to be useful for elucidating the precise mechanisms involved in fermentation processes inside the cell. Further exhaustive sensitivity analysis will facilitate identification of novel factors involved in the metabolic regulation of amino acid fermentation.

【 授权许可】

   
2013 Nishio et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

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