Abstract

Growth is a fundamental process of life. Growth requirements are well-characterized experimentally for many microbes; however, we lack a unified model for cellular growth. Such a model must be predictive of events at the molecular scale and capable of explaining the high-level behavior of the cell as a whole. Here, we construct an ME-Model for Escherichia coli—a genome-scale model that seamlessly integrates metabolic and gene product expression pathways. The model computes ∼80% of the functional proteome (by mass), which is used by the cell to support growth under a given condition. Metabolism and gene expression are interdependent processes that affect and constrain each other. We formalize these constraints and apply the principle of growth optimization to enable the accurate prediction of multi-scale phenotypes, ranging from coarse-grained (growth rate, nutrient uptake, by-product secretion) to fine-grained (metabolic fluxes, gene expression levels). Our results unify many existing principles developed to describe bacterial growth.

Details

Title
Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction
Author
O'Brien, Edward J 1 ; Lerman, Joshua A 1 ; Chang, Roger L 1 ; Hyduke, Daniel R 1 ; Palsson, Bernhard Ø 1 

 Department of Bioengineering, University of California San Diego, La Jolla, CA, USA 
Section
Article
Publication year
2013
Publication date
2013
Publisher
EMBO Press
e-ISSN
17444292
Source type
Scholarly Journal
Language of publication
English
ProQuest document ID
2299147282
Copyright
© 2013. This work is published under http://creativecommons.org/licenses/by-nc-sa/3.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.