A computational study of the gene expression in the tryptophan operon with two types of cooperativity

Abstract

Intrinsic noise is inherent to many biological processes and provokes variation in gene expression in a population of isogenic cells leading to phenotypic diversity. Intrinsic noise is generated by different sources of noise such as the number of molecules, the stochastic binding and unbinding of transcription factor and/or the number and strength of transcription factor binding sites. In this work, we use numerical simulations to study the effects of the number of operators and different types of cooperativity on the Fano factor of three different molecules of the tryptophan (trp) operon of E. Coli. We analyze the Fano factor for the mRNA, anthranilate synthase and tryptophan molecules, because it represents the effects of the noise in the variation or variability of the gene expression, a larger Fano factor implies a larger variation. Our model takes into consideration the presence of intrinsic noise and all the known mechanisms of regulation. In particular, we consider hypothetical promoters in the repression mechanism with different numbers of operators and three cases of cooperativity: positive, negative, and no-cooperativity.