E-CELL Project: Towards Whole Cell Simulation

Masaru Tomita

Institute for Advanced Biosciences,
Keio University
E-mail: mt@sfc.keio.ac.jp

Key Words: in silico biology, simulation, E-CELL, Mycoplasma genitalium, Metabolome research

E-CELL Project (http://www.e-cell.org) was launched in 1996 at Keio University in order to model and simulate various cellular processes with the ultimate goal of simulating the cell as a whole. E-CELL System, a generic software package we have developed, enables us to model not only metabolic pathways but also other higher-order cellular processes such as protein synthesis and signal transduction.

Using the system, we have successfully constructed a virtual cell with 127 genes sufficient for "self-support". The gene set was selected from the genome of Mycoplasma genitalium, and the metabolisms include transcription, translation, membrane transport, the glycolysis pathway for energy production, and the phospholipid biosynthesis pathway for membrane structure. Since all its proteins and membrane structure are modeled to degrade spontaneously over time, the virtual cell must keep synthesizing proteins and phospholipid bilayer to sustain its life. It thus uptakes glucose as its energy source, and emptying glucose in the environment would result in "cell death from hunger".

During the starvation simulation, we found an interesting and rather counter-intuitive phenomenon: The number of intracellular ATP molecules momentarily increases despite empty glucose. We predict that this phenomenon could actually take place in real cells.

Modeling Groups in our institute are now developing many different models of cellular processes, including bacterial chemotaxis [Matsuzaki et al.], circadian rhythms [Miyoshi et al.], photosynthesis [Wang et al.], as well as cell cycle and cell division. For gene expression, we are working on general quantitative models [Hashimoto et al.] and their application to gene regulation network of lactose open in E.coli [Seno et al.] and lambda phage genetic switch [Andrews et al.]. For organelles, a quantitative model of mitochondria [Yugi et al.] is nearly complete, and we will be soon developing chloroplasts in the context of e-Rice Project funded by Japanese ministry of agriculture. For human cells, we have already developed a quantitative model of erythrocytes [Nakayama et al.], and being used in pathological analyses of enzyme deficiencies causing anemia. Other human cells now being developed include myocardial cells [Naito et al.], neural cells [Kikuchi et al.], and pancreatic beta-cells [Naito et al.], with close collaboration with physiologists.

A major bottleneck in cell modeling is lack of quantitative data, such as kinetic parameters, dissociation constants, steady state concentration, and flux rates. We have set up Metabolome Group for mass-production of those quantitative metabolic data. We analyze metabolic flux distributions (MFDs) with different conditions such as dissolved oxygen (DO) concentration, pH, temperature, and media composition [Shimizu et al.]. We also label certain substrates with U-13C or 1-13C [Shimzu et al.] and measure isotope distribution of intercellular metabolites using NMR and GC-MS [Soga et al.]. Gene expression analyses will also be conducted using DNA microarray for the transcription level, and 2D electrophoresis with SWISS-2D PAGE and TOF-MS for the protein level. For high-throughput measurement of metabolites, we are developing a novel analytical device based on capillary electrophoresis, which can eventually up to 500 metabolites at the same time [Nishioka et al.].

E-CELL System is a useful tool to conduct quantitative simulation based on those data obtained by the Metabolome Group.