Properties of Bacillus subtilis σ A Factors with Region 1.1 and the Conserved Arg-103 at the N Terminus of Region 1.2 Deleted

Abstract

ABSTRACT σ factors in the σ 70 family can be classified into the primary and alternative σ factors according to their physiological functions and amino acid sequence similarities. The primary σ factors are composed of four conserved regions, with the conserved region 1 being divided into two subregions. Region 1.1, which is absent from the alternative σ factor, is poor in conservation; however, region 1.2 is well conserved. We investigated the importance of these two subregions to the function of Bacillus subtilis σ A , which belongs to a subgroup of the primary σ factor lacking a 254-amino-acid spacer between regions 1 and 2. We found that deletion of not more than 100 amino acid residues from the N terminus of σ A , which removed part or all region 1.1, did not affect the overall transcription activity of the truncated σ A -RNA polymerase in vitro, indicating that region 1.1 is not required for the functioning of σ A in RNA polymerase holoenzyme. This finding is consistent with the complementation data obtained in vivo. However, region 1.1 is able to negatively modulate the promoter DNA-binding activity of the σ A -RNA polymerase. Further deletion of the conserved Arg-103 at the N terminus of region 1.2 increased the content of stable secondary structures of the truncated σ A and greatly reduced the transcription activity of the truncated σ A -RNA polymerase by lowering the efficiency of transcription initiation after core binding of σ A . More importantly, the conserved Arg-103 was also demonstrated to be critical for the functioning of the full-length σ A in RNA polymerase.