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

S. Borukhov, V. Sagitov, C. A. Josaitis, R. L. Gourse, A. Goldfarb

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Abstract

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.

Original languageEnglish (US)
Pages (from-to)23477-23482
Number of pages6
JournalJournal of Biological Chemistry
Volume268
Issue number31
StatePublished - Jan 1 1993

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All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

Borukhov, S., Sagitov, V., Josaitis, C. A., Gourse, R. L., & Goldfarb, A. (1993). Two modes of transcription initiation in vitro at the rrnB P1 promoter of Escherichia coli. Journal of Biological Chemistry, 268(31), 23477-23482.