Universal functions of the sigma finger in alternative sigma factors during transcription initiation by bacterial RNA polymerase

The bacterial sigma factor plays the central role in promoter recognition by RNA polymerase (RNAP). The primary sigma factor, involved in transcription of housekeeping genes, was also shown to participate in the initiation of RNA synthesis and promoter escape by RNAP. In the open promoter complex, the sigma finger formed by sigma region 3.2 directly interacts with the template DNA strand upstream of the transcription start site. Here, we analysed the role of the sigma finger in transcription initiation by four alternative sigma factors in Escherichia coli, sigma(38), sigma(32), sigma(28) and sigma(24). We found that deletions of the sigma finger to various extent compromise the activity of RNAP holoenzymes containing alternative sigma factors, especially at low NTP concentrations. All four sigma s are able to utilize NADH as a noncanonical priming substrate but it has only mild effects on the efficiency of transcription initiation. The mediators of the stringent response, transcription factor DksA and the alarmone ppGpp decrease RNAP activity and promoter complex stability for all four sigma factors on tested promoters. For all sigma s except sigma(38), deletions of the sigma finger conversely increase the stability of promoter complexes and decrease their sensitivity to DksA and ppGpp. The result suggests that the sigma finger plays a universal role in transcription initiation by alternative sigma factors and sensitizes promoter complexes to the action of global transcription regulators DksA and ppGpp by modulating promoter complex stability.