BIOPHYSICAL THEORY AND MODELING |
An algorithmic framework for genome-wide modeling and analysis of translation networks
Amit Mehra 1 and Vassily Hatzimanikatis 1*
1 Northwestern University
* To whom correspondence should be addressed. E-mail: vassily{at}northwestern.edu.
Submitted on May 30, 2005
Revised on July 13, 2005
Accepted on 31 August 2005
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Abstract |
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The sequencing of genomes of several organisms and advances in high throughput technologies for transcriptome and proteome analysis has allowed detailed mechanistic studies of transcription and translation using mathematical frameworks that allow integration of both sequence specific and kinetic properties of these fundamental cellular processes. In order to understand how perturbations in mRNA levels affect the synthesis of individual proteins within a large protein synthesis network, we consider here a genome-scale codon-wide model of the translation machinery with explicit description of the processes of initiation, elongation, and termination. The mechanistic codon-wide description of the translation process and the large number of mRNAs competing for resources, such as ribosomes, requires the use of novel efficient algorithmic approaches. We have developed such an efficient algorithmic framework for genome-scale models of protein synthesis. The mathematical and computational framework was applied to the analysis of the sensitivity of a translation network to perturbation in the rate constants and in the mRNA levels in the system. Our studies suggest that the highest specific protein synthesis rate (protein synthesis rate per mRNA molecule) is achieved when translation is elongation limited. We find that the mRNA species with the highest number of actively translating ribosomes exerts maximum control on the synthesis of every protein, and the response of protein synthesis rates to mRNA expression variation is a function of the strength of initiation of translation at different mRNA species. Such quantitative understanding of the sensitivity of protein synthesis to the variation of mRNA expression can provide insights into cellular robustness mechanisms and guide design of protein production systems.
Key Words:
complex systems, kinetics, protein expression, protein synthesis, ribosomes, sensitivity analysis
