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. coil 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 Eas promoter sequences by multiple cycles of bi
nding and selection. Surprisingly, the sequences selected by E sigma (s) co
ntained 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 holoenz
yme limit transcription to discrete sets of promoters. Rather, we suggest t
hat E sigma (s)-specific promoters have sequences that differ significantly
from the consensus in at least one of the recognition hexamers, and that p
romoter discrimination against E sigma (70) is achieved, at least in part,
by the two enzymes tolerating different deviations from consensus. DNA reco
gnition by E sigma (s) versus E sigma (70) thus presents an alternative sol
ution to the problem of promoter selectivity.