The role of Region II in the RNA polymerase sigma factor sigma(N) (sigma(54))

Bacterial RNA polymerase holoenzymes containing the sigma subunit sigma(N) (sigma(54)) can form a stable closed complex with promoter DNA but only und ergo transition to an open complex and transcription initiation when acted on by an activator protein. Proteins of the sigma(N) family have a conserve d N-terminal region of 50 amino acids (Region I) that is separated from a c onserved C-terminal region of around 360 amino acids (Region III) by a much more variable sequence of between 30 and 110 residues (Region II). We have investigated the role of Region II in Klebsiella pneumoniae sigma(N) by st udying the properties of deletions of all or part of the region both in viv o and in vitro. We found that whilst Region II is not essential, deletion o f all or part of it can significantly impair sigma(N) activity. Deletions h ave effects on DNA binding by the isolated sigma factor and on holoenzyme f ormation, but the most marked effects are on transition of the holoenzyme f rom the closed to the open complex in the presence of the activator protein .