A PROMOTER MELTING REGION IN THE PRIMARY SIGMA-FACTOR OF BACILLUS-SUBTILIS - IDENTIFICATION OF FUNCTIONALLY IMPORTANT AROMATIC-AMINO-ACIDS

Sigma factor (σ) is a dissociable subunit of bacterial RNA polymerase that determines promoter recognition. It has been proposed that a cluster of highly conserved aromatic amino acids in bacterial a factors (region 2.3) defines a melting motif that functions in strand-separation during open complex formation. We demonstrate that many alterations in region 2.3 of the Bacillus subtilis σA protein specifically impair open complex formation. The region 2.3 mutations can be grouped in three classes: (1) mutations that do not significantly affect promoter recognition or melting; (2) mutations that lead to cold-sensitive transcription of linear templates; and (3) mutations that lead to little activity on linear templates but retain activity at high temperatures on supercoiled templates. RNA polymerase holoenzymes containing σ factor melting mutants (classes 2 and 3) form predominantly closed complexes at 40°C and are defective for RNA synthesis when initiation is rate-limiting. The melting defect of these mutant σ factors is suppressed by template supercoiling, but further enhanced by inclusion of the auxiliary RNA polymerase subunit δ. Consequently, in the presence of the δ polypeptide, the mutant holoenzymes display cold-sensitive transcription on supercoiled templates: conditions which mimic the in vivo situation. A subset of these mutations also affects promoter selectivity, suggesting that region 2.3 may participate in both -10 recognition and DNA melting. © 1994 Academic Press Limited.