The guanosine tetraphosphate (ppGpp) alarmone, DksA and promoter affinity for RNA polymerase in regulation of σ 54 ‐dependent transcription

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