Promoter recognition and discrimination by EσS RNA polymerase

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Abstract
Although more than 30 Escherichia coli promoters utilize the RNA polymerase holoenzyme containing σS (EσS), and it is known that there is some overlap between the promoters recognized by EσS and by the major E. coli holoenzyme (Eσ70), the sequence elements responsible for promoter recognition by EσS are not well understood. To define the DNA sequences recognized best by EσSin vitro, we started with random DNA and enriched for EσS promoter sequences by multiple cycles of binding and selection. Surprisingly, the sequences selected by EσS contained the known consensus elements (−10 and −35 hexamers) for recognition by Eσ70. Using genetic and biochemical approaches, we show that EσS and Eσ70 do not achieve specificity through ‘best fit’ to different consensus promoter hexamers, the way that other forms of holoenzyme limit transcription to discrete sets of promoters. Rather, we suggest that EσS-specific promoters have sequences that differ significantly from the consensus in at least one of the recognition hexamers, and that promoter discrimination against Eσ70 is achieved, at least in part, by the two enzymes tolerating different deviations from consensus. DNA recognition by EσS versus Eσ70 thus presents an alternative solution to the problem of promoter selectivity.