Adding an environment and motility in a Whole Cell Model of Escherichia Coli

项目总结

PROJECT SUMMARY This proposal focuses on extending a large-scale “whole-cell” model (WCM) of Escherichia coli (wcEcoli) to include a bacterial micro-environment and cell motility. wcEcoli is developed at the Covert lab at Stanford University, and was recently released to an international community of scientists. The specific aims of this application outline a plan to multi-scale the WCM, to introduce a simulated spatial environmentsthat can include other cells -- this will lead to the very first whole-colony simulations. A cell’s environment significantly impact its growth, division, and its overall phenotype throughout both a single cell cycle and evolutionary timescales. By accounting for these influences, the extensions proposed here will open up a new domain for whole-cell modeling that can examine cellular behavior in more natural environments. I worked with software engineers in the Covert lab to develop a preliminary multi-scale framework that integrates whole-cell modeling with agent-based modeling techniques -- the result is a simulation that can include multiple WCMs running in a spatial environment with molecular concentrations and physical forces. With the training plan proposed here, I will develop and test this framework using the same standards that went into the original WCM. This will lay a foundation for future extensions; the software will be built for scalable and incremental modeling of new cell-environment interactions. I will begin integrating cell-environment interactions by focusing on E. coli chemotaxis. First, a gene regulatory network will be implemented to control the expression of flagellar proteins; E. coli exhibit a “just-in-time” mechanism for flagella expression, with proteins synthesized roughly in the order they are needed. Monomers will be assembled into flagella complexes in the complexation module. A new flagella module will model the motor activity of individual flagella, this will track the energy expenditure and will generate motile forces that push the cell through its simulated environment. A sensory module will model the activity of chemoreceptors, and their adaptation to signals by methylation. A signaling module will connect sensory activity to the flagellar motor output with a protein network that controls the flagallas’ motor biases. Finally, a transport module will model the trans-membrane uptake of nutrients from the local environment. These transported nutrient fluxes will feed into the existing metabolism module and constrain its activity. The most exciting part of this project will be testing the wide-ranging consequences of E. coli’s chemotaxis behavior on cellular physiology. To survive in the wild, E. coli needs to process noisy information and make quick survival decisions. Information processing and motility require the necessary molecules and energy, and this cost needs to be offset by reliably securing key resources. Systematic analysis of wcEcoli will determine many of the trade-offs and how they are successfully navigated to a degree not previously possible.