Anatomy of Escherichia coli σ 70 promoters

Abstract

Information theory was used to build a promoter model that accounts for the −10, the −35 and the uncertainty of the gap between them on a common scale. Helical face assignment indicated that base −7, rather than −11, of the −10 may be flipping to initiate transcription. We found that the sequence conservation of σ70 binding sites is 6.5 ± 0.1 bits. Some promoters lack a −35 region, but have a 6.7 ± 0.2 bit extended −10, almost the same information as the bipartite promoter. These results and similarities between the contacts in the extended −10 binding and the −35 suggest that the flexible bipartite σ factor evolved from a simpler polymerase. Binding predicted by the bipartite model is enriched around 35 bases upstream of the translational start. This distance is the smallest 5′ mRNA leader necessary for ribosome binding, suggesting that selective pressure minimizes transcript length. The promoter model was combined with models of the transcription factors Fur and Lrp to locate new promoters, to quantify promoter strengths, and to predict activation and repression. Finally, the DNA-bending proteins Fis, H-NS and IHF frequently have sites within one DNA persistence length from the −35, so bending allows distal activators to reach the polymerase.

Reduced capacity of alternative σs to melt promoters ensures stringent promoter recognition

“…1B; Koo et al 2009a,b). Consistent with this, the information content of the core regions of s 32 promoters (18.3 bits) (Shultzaberger et al 2007). Requiring extensive recognition determinants would limit transcription to a relatively restricted set of promoters, making it important to understand how these ss maintain dependence on all three promoter motifs.…”

Regulation of the rplY gene encoding 5S rRNA binding protein L25 in Escherichia coli and related bacteria

“…The rplY promoter is negatively regulated by ppGpp and transcription factor DksA Analysis of the rplY upstream regions in sequenced genomes of E. coli and related bacteria (NCBI Gene database) revealed that the presumable rplY promoter possesses features typical of the σ 70 -dependent promoters (Harley and Reynolds 1987;Schultzaberger et al 2007), including a "good" putative −10 element (TAg/ tAAT) separated from a −35 hexamer (bearing a universally conserved TTG triplet) by an optimal spacer region of 17 bp (Fig. 1A).…”

Interactions between RNA polymerase and the core recognition element are a determinant of transcription start site selection

“…The results of this work, together with results of previous work, establish that TSS selection involves at least four promoter sequence determinants: (i) position relative to the −10 element (preference for the position 7-bp downstream of the −10 element) (5-11); (ii) sequence of TSS T and TSS-1 T (strong preference for pyrimidine at TSS T and preference for purine at TSS-1 T , which enable initiation with a purine NTP and maximize stacking between DNA bases and the initiating purine NTP) (11,(17)(18)(19)(20); (iii) sequence of the discriminator element (preference for TSS selection at upstream positions for discriminator sequences that disfavor scrunching and preference for TSS selection at downstream positions for discriminator sequences that favor scrunching) (13,14); and (iv) sequence of the CRE (preference for G at TSS+1 NT ). In addition to these sequence determinants, DNA topology and NTP concentrations also influence TSS selection (6,8,9,11,(21)(22)(23)(24)(25)(26).…”