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Generic Gene Expression System for Modeling Complex Gene Regulation Network Using E-CELL System

We present a general framework for modeling gene expression using the E-CELL system, a general purpose cell simulator developed at Keio University. Using the framework, we modeled and simulated the following three gene regulation systems: the lac operon and the ara operon of E. coli, and the lytic-lysogenic switch network in bacteriophage λ. We have previously constructed a detailed model [1] of the gene expression system as a part of the “virtual” cell with 127 genes [2]. The previous model faithfully reflected the gene expression system of M. genitalium, involving more than 100 objects including various subunits, factors, amino acids, nucleotides, tRNAs and their ligases. However, in order to simulate complex gene regulation systems with a large number of genes, a more abstract and simpler model is desired for the sake of efficiency. The gene expression system used in this work consists of the following four basic elements. 1) Production of RNAs and proteins, 2) Regulation of expression by various factors, 3) Time delay between regulation and production, and 4) Sigmoidal curve of product increase over time. All gene expressions are reduced to these four elements.