Factor independent activation of rrnB P1. An "extended" promoter with an upstream element that dramatically increases promoter strength

J Mol Biol. 1994 Feb 4;235(5):1421-35. doi: 10.1006/jmbi.1994.1098.


The extraordinary strength of the Escherichia coli rRNA promoter rrnB P1 derives primarily from sequences upstream of the core (-10, -35) region. We find that sequences between -40 and -60 increase the activity of this promoter at least 30-fold in vitro and in vivo. This region, which we refer to as the upstream (UP) element, is located between the -35 consensus hexamer and the previously characterized binding sites for the rRNA transcription factor Fis. The effect of the UP element is independent of Fis in vivo, and independent of any other proteins besides RNA polymerase (RNAP) in vitro. The UP element increases the overall second-order rate constant for association of RNAP with the promoter (ka) and probably the apparent overall first-order isomerization constant (ki). Together with the previously reported protection of the UP element region by RNAP in footprinting experiments, these results indicate that rrnB P1 has an "extended" promoter structure, consisting of the UP element and the core promoter region. We find that the UP element is a separable promoter module that can function to increase the activity of the lac core promoter in an rrnB P1-lac hybrid promoter construct. A functional UP element is not absolutely essential for stimulation of rrnB P1 by the Fis protein.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Base Sequence
  • DNA, Ribosomal / genetics*
  • DNA, Ribosomal / metabolism
  • DNA-Directed RNA Polymerases / metabolism
  • Escherichia coli / genetics*
  • Kinetics
  • Molecular Sequence Data
  • Mutagenesis, Insertional
  • Oligodeoxyribonucleotides
  • Plasmids
  • Promoter Regions, Genetic*
  • RNA, Ribosomal / biosynthesis*
  • RNA, Ribosomal / genetics
  • Restriction Mapping
  • Transcription, Genetic


  • DNA, Ribosomal
  • Oligodeoxyribonucleotides
  • RNA, Ribosomal
  • DNA-Directed RNA Polymerases