title: Effects of gene length on the dynamics of gene expression.
abstract: In Escherichia coli, the nucleotide length of a gene is bound to affect its expression dynamics. From simulations of a stochastic model of gene expression at the nucleotide and codon levels we show that, within realistic parameter values, the nucleotide length affects RNA and protein mean levels, as well as the expected transient time for RNA and protein numbers to change, following a signal. Fluctuations in RNA and protein numbers are found to be minimized for a small range of lengths, which matches the means of the distributions of lengths found in E. coli of both essential and non-essential genes. The variance of the length distribution for essential genes is found to be smaller than for non-essential genes, implying that these distributions are far from random. Finally, gene lengths are shown to affect the kinetics of a genetic switch, namely, the correlation between temporal proteins numbers, the stability of the two noisy attractors of the switch, and how biased is the choice of noisy attractor. The stability increases with gene length due to increased 'memory' about the previous states of the switch. We argue that, by affecting the dynamics of gene expression and of genetic circuits, gene lengths are subject to selection.
authors.affiliation: Laboratory of Biosystem Dynamics, Computational Systems Biology Research Group, Department of Signal Processing, Tampere University of Technology, PO Box 553, 33101 Tampere, Finland. andre.ribeiro@tut.fi
authors.forename: Andre S
authors.initials: AS
authors.lastname: Ribeiro
authors.forename: Antti
authors.initials: A
authors.lastname: Häkkinen
authors.forename: Jason
authors.initials: J
authors.lastname: Lloyd-Price
mesh_terms: D000465:Algorithms; D001426:Bacterial Proteins / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics*; D015964:Gene Expression Regulation, Bacterial / Q000235:genetics*; D005798:Genes, Bacterial / Q000235:genetics*; D020043:Genes, Essential / Q000235:genetics; D012329:RNA, Bacterial / Q000235:genetics; D013269:Stochastic Processes
chemical_list: D001426:Bacterial Proteins; D012329:RNA, Bacterial