Promoter melting by alternative sigma factors

Alternative sigma factors direct transcription to a specific subset of regulons in response to environmental signals and exhibit stringent promoter specificity. A crucial step in transcription initiation is the melting of the double-stranded promoter DNA by the bound RNA polymerase holoenzyme. Conserved amino acids in primary sigma factors initiate strand separation within the –10 region in target promoters; however, alternative sigma factors do not contain these key residues. The authors of this study investigated the mechanism of promoter melting by the Escherichia coli alternative sigma factor σ^E and solved the structure of the complex that is formed between σ^E and its cognate –10 promoter. They identified specific intramolecular contacts and found that σ^E induced strand separation by flipping out a single nucleotide from the non-template strand. Sequence-specific recognition of this nucleotide was mediated by a variable loop, which might explain the increased promoter stringency.