ESCHERICHIA-COLI PROMOTERS WITH UP ELEMENTS OF DIFFERENT STRENGTHS - MODULAR STRUCTURE OF BACTERIAL PROMOTERS

The alpha subunit of Escherichia coli RNA polymerase (RNAP) participat es in promoter recognition through specific interactions with UP eleme nt DNA, a region upstream of the recognition hexamers for the sigma su bunit (the -10 and -35 hexamers). UP elements have been described in o nly a small number of promoters, including the rRNA promoter rrnB P1, where the sequence has a very large (30- to 70-fold) effect on promote r activity. Here, we analyzed the effects of upstream sequences from s everal additional E. coli promoters (rrnD PI, rrnB P2, lambda p(R), la c, merT, and RNA II). The relative effects of different upstream seque nces were compared in the context of their own core promoters or as hy brids to the lac core promoter. Different upstream sequences had diffe rent effects, increasing transcription from 1.5- to similar to 90-fold , and several had the properties of UP elements: they increased transc ription in vitro in the absence of accessory protein factors, and tran scription stimulation required the C-terminal domain of the RNAP alpha subunit. The effects of the upstream sequences correlated generally w ith their degree of similarity to an UP element consensus sequence der ived previously. Protection of upstream sequences by RNAP in footprint ing experiments occurred in all cases and was thus not a reliable indi cator of UP element strength. These data support a modular view of bac terial promoters in which activity reflects the composite effects of R NAP interactions with appropriately spaced recognition elements (-10, -35, and UP elements), each of which contributes to activity depending on its similarity to the consensus.