THE HELIX-TURN-HELIX MOTIF OF SIGMA-54 IS INVOLVED IN RECOGNITION OF THE -13 PROMOTER REGION

Residue Arg-383 in the proposed helix-turn-helix motif of the novel RNA polymerase sigma factor sigma54 has been changed by site-directed mutagenesis to all possible alternative amino acids. Only two mutants, RK383 and RH383, are active in promoting transcription from either the glnAp2 promoter or the nifL promoter. We constructed a set of mutant derivatives of glnAp2 such that each base in the conserved GG and GC doublets at -24 and -12 was changed to all possible alternatives. All 12 mutant glnAp2 promoters showed a marked promoter-down phenotype with wild-type sigma54, but RK383 suppressed changes of both G to C and G to T at -13. This result suggests that the sigma54 helix-turn-helix is involved in recognition of the -13 region of sigma54-dependent promoters.