Promoter recognition by bacterial alternative σ factors: the price of high selectivity?

A key step in bacterial transcription initiation is melting of the double-stranded promoter DNA by the RNA polymerase holoenzyme. Primary sigma factors mediate the melting of thousands of promoters through a conserved set of aromatic amino acids. Alternative ss, which direct transcription of restricted regulons, lack the full set of melting residues. In this issue of Genes & Development, Koo and colleagues (pp. 2426-2436) show that introducing the primary s melting residues into alternative ss relaxes their promoter specificity, pointing to a trade-off of reduced promoter melting capacity for increased promoter stringency.