Authors
Virgil A Rhodius, Vivek K Mutalik, Carol A Gross
Publication date
2012/4/1
Journal
Nucleic acids research
Volume
40
Issue
7
Pages
2907-2924
Publisher
Oxford University Press
Description
Predicting the location and strength of promoters from genomic sequence requires accurate sequenced-based promoter models. We present the first model of a full-length bacterial promoter, encompassing both upstream sequences (UP-elements) and core promoter modules, based on a set of 60 promoters dependent on σE, an alternative ECF-type σ factor. UP-element contribution, best described by the length and frequency of A- and T-tracts, in combination with a PWM-based core promoter model, accurately predicted promoter strength both in vivo and in vitro. This model also distinguished active from weak/inactive promoters. Systematic examination of promoter strength as a function of RNA polymerase (RNAP) concentration revealed that UP-element contribution varied with RNAP availability and that the σE regulon is comprised of two promoter types, one of which is active only at high concentrations of …
Scholar articles
VA Rhodius, VK Mutalik, CA Gross - Nucleic acids research, 2012