Towards a Whole-Cell Model of Escherichia Coli

The ability to predict molecular phenotypes at the genome scale is crucial to understanding biological systems. In an effort to address this need we recently published a gene-complete whole-cell model of Mycoplasma genitalium that computationally represents all functions and interactions of every annotated gene [1]. We now aim to extend the whole-cell modeling methodology to the Gram-negative bacteria Escherichia coli. First we will model several core aspects of E. coli physiology including transcription, translation, RNA/protein decay, replication, and metabolism. We will accomplish this by adapting modules of our M. genitalium model [1] to E. coli physiology, and developing new modules to represent E. coli unique phenomena. Furthermore, we will continue to update and streamline the whole-cell modeling infrastructure, improving tools for whole-cell model data curation, construction, simulation, and exploratory analysis. Once finished, the model will enable researchers to investigate single-cell E. coli physiology.

[1] J.R. Karr*, J.C. Sanghvi*, D.N. Macklin, M.V. Gutschow, J.M. Jacobs, B. Bolival, N. Assad-Garcia, J.I. Glass, M.W. Covert. "A Whole-Cell Computational Model Predicts Phenotype from Genotype". Cell. 2012. 150(2): 389-401