  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.
