Two modes of transcription initiation in vitro at the rrnB P1 promoter of Escherichia coli

The rrnB P1 promoter of Escherichia coli (starting sequence C^-4-A^-3- C^-2-C^-1-A⁺¹-C⁺²-U⁺³-G⁺⁴) forms a binary complex with RNA polymerase that is highly unstable and requires the presence of transcription substrates ATP and CTP for stabilizing the enzyme-DNA association (Gourse, R. L. (1988) Nucleic Acids Res. 16, 9789-9809). We show that in the absence of UTP and GTP the stabilization is accomplished by short RNA oligomers synthesized in an unusual '-3→' mode whereby the primer initiated at the +1 site presumably slips back by three nucleotides into the -3 site and is then extended yielding stable ternary complexes. By contrast, short oligomers initiated in the conventional '+1→' mode without slippage do not exert the stabilization effect and are readily aborted from the promoter complex. The stable -3→ ternary complexes carry σ factor but otherwise resemble elongation complexes in their high salt stability and in the fact that they are formed with a mutant RNA polymerase deficient in promoter binding. A model is proposed explaining the stability of the -3→ ternary complexes by RNA slipping into a putative 'tight RNA binding site' in RNA polymerase which is normally occupied by RNA during elongation.