Regulation of noise in the expression of a single gene

Abstract

Stochastic mechanisms are ubiquitous in biological systems. Biochemical reactions that involve small numbers of molecules are intrinsically noisy, being dominated by large concentration fluctuations 1-3 . This intrinsic noise has been implicated in the random lysis/lysogeny decision of bacteriophage-λ 4 , in the loss of synchrony of circadian clocks 5,6 and in the decrease of precision of cell signals 7 . We sought to quantitatively investigate the extent to which the occurrence of molecular fluctuations within single cells (biochemical noise) could explain the variation of gene expression levels between cells in a genetically identical population (phenotypic noise). We have isolated the biochemical contribution to phenotypic noise from that of other noise sources by carrying out a series of differential measurements. We varied independently the rates of transcription and translation of a single fluorescent reporter gene in the chromosome of Bacillus subtilis, and we quantitatively measured the resulting changes in the phenotypic noise characteristics. We report that of these two parameters, increased translational efficiency is the predominant source of increased phenotypic noise. This effect is consistent with a stochastic model of gene expression in which proteins are produced in random and sharp bursts. Our results thus provide the first direct experimental evidence of the biochemical origin of phenotypic noise, demonstrating that the level of phenotypic variation in an isogenic population can be regulated by genetic parameters.We selected as our reporter system a single-copy chromosomal gene with an inducible promoter. As an estimated 50-80% of bacterial genes are transcriptionally regulated 8 , this system typifies the majority of naturally occurring genes, allowing our results to be extended to natural systems. We incorporated a single copy of our reporter, the green fluorescent protein gene (gfp), into the chromosome of B. subtilis. We chose to integrate gfp into the chromosome itself, rather than in the form of plasmids, as variation in plasmid copy number 9,10 can act as an additional and unwanted source of noise. Transcriptional efficiency was regulated by using an isopropyl-β-D-thiogalactopyranoside (IPTG)-inducible promoter, P spac , upstream of gfp, and varying the concentration of IPTG in the growth medium. Translational efficiency was regulated by constructing a series of B. subtilis strains ( Table 1) that contained point mutations in the ribosome binding site (RBS) and initiation codon of gfp 11 . The use of two different strategies to regulate transcriptional and translational processes introduces a potential bias in the relative contributions of these processes to biochemical noise. As a control, we constructed four additional strains (Table 2) whose transcription rates were altered by mutations in the promoter region of the reporter gene. As described below, both strategies of transcriptional regulation produced similar results.We measured expression of green fluorescent protein (GFP) for si...

Multiparticle reaction noise characteristics

“…In general, living cells adopt two strategies of dealing with noise by either controlling it or using it. On one hand, transcriptional noise needs to be carefully controlled at the single gene level [6], as errors in expression of a gene could have fatal consequences for a cell function [7]. On the other hand, noise can be used to achieve or enhance some function.…”

Signatures of gene expression noise in cellular systems

“…Considerable confusion stems from diverging experimental results which have identified different origins for the main contribution to gene expression noise (19) such that a complete picture is still missing. For prokaryotes, translational efficiency was identified as the main source of variability of expression levels consistent with a stochastic model in which proteins are produced in sharp and random bursts (20). However, later experimental observations in individual living cells either by measuring mRNA levels or by real-time observations at single molecule level indicated that promoter activation predominantly causes gene expression noise (21; 22).…”

Distinct noise-controlling roles of multiple negative feedback mechanisms in a prokaryotic operon system

“…For examples, increasing gene copies number through events such as gene duplication or polyploidy could effectively reduce noise [31]. Inefficient translation coupled with fast transcription was also thought to be adopted by some bacteria to curb protein fluctuations [5]. Other mechanisms include integral feedback [35] and regulatory checkpoints [36].…”

“…fluorescent reporters and single-cell imaging techniques) in recently years have allowed stochastic gene expression to be quantified in vivo [1,[5][6][7]. These elegant experiments, along with theoretical studies [8],…”

“…Intrinsic noise originates from the randomness in the biochemical processes that take place in gene expression whereas extrinsic noise comes from fluctuations in other factors that influence gene expression. Effort has since been carried out by different groups aiming to separate one type of noise from another experimentally [5,6] and theoretically [8,9].…”