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Promoter recognition and discrimination by Eσ S RNA polymerase
Author(s) -
Gaal Tamas,
Ross Wilma,
Estrem Shawn T.,
Nguyen Lam H.,
Burgess Richard R.,
Gourse Richard L.
Publication year - 2001
Publication title -
molecular microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.857
H-Index - 247
eISSN - 1365-2958
pISSN - 0950-382X
DOI - 10.1046/j.1365-2958.2001.02703.x
Subject(s) - promoter , biology , rna polymerase , genetics , dna , transcription (linguistics) , recognition sequence , consensus sequence , rna polymerase ii , gene , rna , microbiology and biotechnology , gene expression , base sequence , restriction enzyme , philosophy , linguistics
Although more than 30 Escherichia coli promoters utilize the RNA polymerase holoenzyme containing σ S (Eσ S ), and it is known that there is some overlap between the promoters recognized by Eσ S and by the major E. coli holoenzyme (Eσ 70 ), the sequence elements responsible for promoter recognition by Eσ S are not well understood. To define the DNA sequences recognized best by Eσ S in vitro , we started with random DNA and enriched for Eσ S promoter sequences by multiple cycles of binding and selection. Surprisingly, the sequences selected by Eσ S contained the known consensus elements (−10 and −35 hexamers) for recognition by Eσ 70 . Using genetic and biochemical approaches, we show that Eσ S and Eσ 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 Eσ S ‐specific promoters have sequences that differ significantly from the consensus in at least one of the recognition hexamers, and that promoter discrimination against Eσ 70 is achieved, at least in part, by the two enzymes tolerating different deviations from consensus. DNA recognition by Eσ S versus Eσ 70 thus presents an alternative solution to the problem of promoter selectivity.