Promoter recognition and discrimination by Eσs RNA polymerase

Although more than 30 Escherichia coli promoters utilize the RNA polymerase holoenzyme containing sigma (s) (E sigma (s)), and it is known that there is some overlap between the promoters recognized by E sigma (s) and by the major E. coli holoenzyme (E sigma (70)), the sequence elements responsible for promoter recognition by E sigma (s) are not well understood. To define the DNA sequences recognized best by E sigma (s) in vitro, we started with random DNA and enriched for E sigma (s) promoter sequences by multiple cycles of binding and selection. Surprisingly, the sequences selected by E sigma (s) contained the known consensus elements (-10 and -35 hexamers) for recognition by E sigma (70). Using genetic and biochemical approaches, we show that E sigma (s) and E sigma (70) 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 E sigma (s)-specific promoters have sequences that differ significantly from the consensus in at least one of the recognition hexamers, and that promoter discrimination against E sigma (70) is achieved, at least in part, by the two enzymes tolerating different deviations from consensus. DNA recognition by E sigma (s) versus E sigma (70) thus presents an alternative solution to the problem of promoter selectivity.