A mutation in region 1.1 of sigma(70) affects promoter DNA binding by Escherichia coli RNA polymerase holoenzyme

The sigma subunit of eubacterial RNA polymerase is essential for initiation of transcription at promoter sites, It directs recognition of DNA sequence s by holoenzyme (alpha(2)beta beta'sigma) and facilitates subsequent steps in the initiation pathway. The primary a factor from Escherichia coli, sigm a(70), has four regions that are conserved among members of the sigma(70) f amily. Previous work has shown that region 1.1 modulates DNA binding by reg ions 2 and 4 when sigma is separated from the core subunits, and is require d for efficient progression through the later steps of initiation in the co ntext of holoenzyme, In this report, we show that an amino acid substitutio n at position 53 in region 1.1, which converts isoleucine to alanine (I53A) , creates a sigma factor that associates with the core subunits to form hol oenzyme, but the holoenzyme is severely deficient for promoter binding, The I53A phenotype can be suppressed by truncation of five amino acids from th e C-terminus of sigma(70). We propose that the behavior of sigma(70)-I53A i s a consequence of impaired ability to undergo a critical conformational ch ange upon binding to the core subunits, which is needed to expose the DNA-b inding domains and confer promoter recognition capability upon holoenzyme.