The Generation of Promoter-Mediated Transcriptional Noise in Bacteria

TL;DR

This paper models how promoter properties and transcription initiation steps influence gene expression noise in bacteria, highlighting mechanisms like supercoiling and dead-end complexes that can be tuned to regulate noise levels.

Contribution

It extends a 3-step transcription initiation model to predict how promoter features affect bacterial transcriptional noise, emphasizing tunable mechanisms like supercoiling and complex formation.

Findings

Transcriptional bursting can be explained by supercoiling effects.

Dead-end RNAP-promoter complexes contribute to noise.

Promoter kinetics can be tuned to optimize noise levels.

Abstract

Noise in the expression of a gene produces fluctuations in the concentration of the gene product. These fluctuations can interfere with optimal function or can be exploited to generate beneficial diversity between cells; gene expression noise is therefore expected to be subject to evolutionary pressure. Shifts between modes of high and low rates of transcription initiation at a promoter appear to contribute to this noise both in eukaryotes and prokaryotes. However, models invoked for eukaryotic promoter noise such as stable activation scaffolds or persistent nucleosome alterations seem unlikely to apply to prokaryotic promoters. We consider the relative importance of the steps required for transcription initiation. The 3-step transcription initiation model of McClure is extended into a mathematical model that can be used to predict consequences of additional promoter properties. We show in principle that the transcriptional bursting observed at an E. coli promoter by Golding et al. (2005) can be explained by stimulation of initiation by the negative supercoiling behind a transcribing RNA polymerase (RNAP) or by the formation of moribund or dead-end RNAP-promoter complexes. Both mechanisms are tunable by the alteration of promoter kinetics and therefore allow the optimization of promoter mediated noise.