Nucleotides from -16 to -12 determine specific promoter recognition by bacterial σS-RNA polymerase

Abstract

The alternative sigma factor σS, mainly active in stationary phase of growth, recognizes in vitro a -10 promoter sequence almost identical to the one for the main sigma factor, σ70, thus raising the problem of how specific promoter recognition by σ S-RNA polymerase (EσS) is achieved in vivo. We investigated the promoter features involved in selective recognition by EσS at the strictly σS-dependent aidB promoter. We show that the presence of a C nucleotide as first residue of the aidB - 10 sequence (-12C), instead of the T nucleotide canonical for σ70-dependent promoters, is the major determinant for selective recognition by EσS. The presence of the -12C does not allow formation of an open complex fully proficient in transcription initiation by Eσ70. The role of - 12C as specific determinant for promoter recognition by EσS was confirmed by sequence analysis of known EσS-dependent promoters as well as site-directed mutagenesis at the promoters of the csgB and sprE genes. We propose that EσS, unlike Eσ70, can recognize both C and T as the first nucleotide in the -10 sequence. Additional promoter features such as the presence of a C nucleotide at position - 13, contributing to open complex formation by EσS, and a TG motif found at the unusual -16/-15 location, possibly contributing to initial binding to the promoter, also represent important factors for σS-dependent transcription. We propose a new sequence, TG(N)0-2CCATA(c/a)T, as consensus -10 sequence for promoters exclusively recognized by Eσ S.