Prof. Hiroyuki Kurata, PhD
Dept. of Bioscience and Bioinformatics, Kyushu Institute of Technology (KIT), JAPAN http://www.bio.kyutech.ac.jp/~kurata/index-e.html
Plenary Talk: Virtual cell metabolism for systems and synthetic biology
Abstract: In systems and synthetic biology, computer simulation of the metabolic networks of a cell is a powerful method to predict their function and phenotype under different culture conditions and genetic modifications. To analyze or design metabolic networks, it is critical to understand the relationship between network structure and function, the mechanism through which biological parts or biomolecules are assembled into building blocks or functional networks. Understanding the mechanism of assembling functional networks would help us develop a methodology for analyzing large-scale networks and design robust biochemical networks. Based on such bottom-up approach, we developed a detailed kinetic model for the central carbon metabolism of E. coli in a batch culture, which includes the glycolytic pathway, tricarboxylic acid cycle, pentose phosphate pathway, Entner-Doudoroff pathway, anaplerotic pathway, glyoxylate shunt, oxidative phosphorylation, phosphotransferase system (Pts), non-Pts, and metabolic gene regulations by four protein transcription factors: cAMP receptor, catabolite repressor/activator, pyruvate dehydrogenase complex repressor, and acetate operon repressor. It enables the rational design of a metabolic network, which contributes to enhanced production of useful metabolites and proteins.