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

  • José Roberto Cantú-GonzálezEmail author
  • O. Díaz-Hernández
  • Elizeth Ramírez-Álvarez
  • C. I. Enríquez Flores
  • A. Flores Rosas
  • Gerardo J. Escalera Santos
Article
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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.

Keywords

trp operon Cooperativity Stochastic dynamics Fano factor Gene regulatory network 

Mathematics Subject Classification (2010)

87.18.-h 87.18.Tt 87.18.Vf 

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© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Universidad Autónoma de CoahuilaEscuela de Sistemas PMRVAcuña, CoahuilaMexico
  2. 2.Universidad Autónoma de ChiapasFacultad de Ciencias en Física y MatemáticasTuxtla GutiérrezMexico
  3. 3.Conacyt-Universidad Autónoma de ChiapasFacultad de Ciencias en Física y MatemáticasTuxtla GutiérrezMexico

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