Escherichia coli Promoters with UP Elements of Different Strengths: Modular Structure of Bacterial Promoters

Abstract

The α subunit of Escherichia coli RNA polymerase (RNAP) participates in promoter recognition through specific interactions with UP element DNA, a region upstream of the recognition hexamers for the ς subunit (the −10 and −35 hexamers). UP elements have been described in only a small number of promoters, including the rRNA promoter rrnB P1, where the sequence has a very large (30- to 70-fold) effect on promoter activity. Here, we analyzed the effects of upstream sequences from several additional E. coli promoters (rrnD P1, rrnB P2, λp R, lac, merT, and RNA II). The relative effects of different upstream sequences were compared in the context of their own core promoters or as hybrids to thelac core promoter. Different upstream sequences had different effects, increasing transcription from 1.5- to ∼90-fold, and several had the properties of UP elements: they increased transcription in vitro in the absence of accessory protein factors, and transcription stimulation required the C-terminal domain of the RNAP α subunit. The effects of the upstream sequences correlated generally with their degree of similarity to an UP element consensus sequence derived previously. Protection of upstream sequences by RNAP in footprinting experiments occurred in all cases and was thus not a reliable indicator of UP element strength. These data support a modular view of bacterial promoters in which activity reflects the composite effects of RNAP interactions with appropriately spaced recognition elements (−10, −35, and UP elements), each of which contributes to activity depending on its similarity to the consensus.

Systematic Dissection of Sequence Elements Controlling σ70 Promoters Using a Genomically-Encoded Multiplexed Reporter Assay inE. coli

“…In addition, we found several cases where promoters decreased in expression upon receiving the UP element, and a majority of these promoters contained the consensus -10 variant ( Figure S6). It has been proposed that a strong UP element may decrease transcription of some promoters by inhibiting promoter escape 13,44 ,which may explain our observation. Despite the clear trend we observed, the consensus UP element had highly variable effects when added to different combinations of -10 and -35 elements ( Figure 5D).…”

Analysis of cepA and other Bacteroides fragilis genes reveals a unique promoter structure

“…The B. fragilis promoters also had a conserved TTTG element centered around 333 but sequences out to 354 appeared to be required for optimal activity. This is not unusual as the recent discovery of UP elements has extended the promoter region out to about 360 [17]. Deletion of the 333 TTTG motif did not abolish activity as it did in the 37 element but there was a sharp reduction in activity of the reporter gene (Fig.…”

Growth rate regulation inEscherichia coli

“…The first is its exceptional strength potential, which means that the promoter has the potential to be the strongest promoter only in the cell grown in nutrient-rich media; the promoter strength weakens in the cell grown in nutrient-poor media. The first property is mainly attributed to the presence of the UP element, which enhances RNAP recruitment by providing additional interaction sites (Gourse et al, 1986;Ross et al, 1993Ross et al, , 1998, similar to the upstream region of the stringent promoter of tyrT, encoding a major tRNA Tyr species (Travers et al, 1983). The UP element enhances the activity of the P1 core promoter (defined as ' À 41 to 11') 4 30-fold, giving rrn P1 the potential to be the strongest promoter in fast-growing cells.…”