Role of eukaryotic-type functional domains found in the prokaryotic enhancer receptor factor σ54

Abstract

E. coli σ 54 protein confers on promoters containing its recognition sequence the ability to be activated from distant DNA sites. Its functional domains include two leucine zipper motifs, an acidic region, and a glutamine-rich domain. Several domains were disrupted and the assembly of mutant transcription complexes was probed in vivo by footprinting. Promoter recognition was seen to depend on a C-terminal region containing a prokaryotic helix-turn-helix motif. Within the resulting stable closed complex, two leucine zipper motifs assist in positioning the σ 54 polymerase near the DNA region that must be meited upon activation. Finally, DNA opening depends on the σ 54 acid domain. The uncoupling of promoter recognition from DNA melting, mediated by the unusual domain structure of this prokaryotic protein, may be responsible for σ 54's ability to mediate activation from distant sites.