CORE RNA-POLYMERASE ASSISTS BINDING OF THE TRANSCRIPTION FACTOR SIGMA(54) TO PROMOTER DNA

The sigma subunit of bacterial RNA polymerase is necessary for the spe cific binding of RNA polymerase holoenzyme to promoter DNA. Promoter c omplexes which form with holoenzyme containing sigma54 remain as close d complexes unless they are activated by one class of enhancer binding protein. The sigma54 transcription factor can bind specifically to ce rtain promoter sites in the absence of the core RNA polymerase subunit s. This property has allowed demonstration of a new role for core poly merase in transcription, namely that it assists the binding of sigma54 to promoter DNA. An altered form of sigma54 with a deletion within th e amino-terminal region showed increased affinity for specific DNA-bin ding sites. Although able to complex with core RNA polymerase the muta nt sigma54 failed to respond to core polymerase in the manner characte ristic of the wild-type sigma54 by altering its footprint. This result indicates that sigma54 has a latent DNA-binding activity which is rev ealed by core RNA polymerase, and possibly involves a change in sigma5 4 conformation. Promoter complexes which formed with sigma54 -holoenzy me appeared to be qualitatively different, depending upon the target p romoter sequence, suggesting that different activatable complexes form at different promoter sequences.