The guanosine tetraphosphate (ppGpp) alarmone, DksA and promoter affinity for RNA polymerase in regulation of σ54-dependent transcription

The RNA polymerase-binding protein DksA is a cofactor required for guanosine tetraphosphate (ppGpp)-responsive control of transcription from sigma(70) promoters. Here we present evidence: (i) that both DksA and ppGpp are required for in vivo sigma(54) transcription even though they do not have any major direct effects on sigma(54) transcription in reconstituted in vitro transcription and sigma-factor competition assays, (ii) that previously defined mutations rendering the housekeeping sigma(70) less effective at competing with sigma(54) for limiting amounts of core RNA polymerase similarly suppress the requirement for DksA and ppGpp in vivo and (iii) that the extent to which ppGpp and DksA affect transcription from sigma(54) promoters in vivo reflects the innate affinity of the promoters for sigma(54)-RNA polymerase holoenzyme in vitro. Based on these findings, we propose a passive model for ppGpp/DksA regulation of sigma(54)-dependent transcription that depends on the potent negative effects of these regulatory molecules on transcription from powerful stringently regulated sigma(70) promoters.