DNA Sequence Elements Located Immediately Upstream of the -10 Hexamer in Escherichia Coli Promoters: A Systematic Study

Nucleic Acids Res. 2000 May 1;28(9):1864-70. doi: 10.1093/nar/28.9.1864.


We have made a systematic study of how the activity of an Escherichia coli promoter is affected by the base sequence immediately upstream of the -10 hexamer. Starting with an activator-independent promoter, with a 17 bp spacing between the -10 and -35 hexamer elements, we constructed derivatives with all possible combinations of bases at positions -15 and -14. Promoter activity is greatest when the 'non-template' strand carries T and G at positions -15 and -14, respectively. Promoter activity can be further enhanced by a second T and G at positions -17 and -16, respectively, immediately upstream of the first 'TG motif'. Our results show that the base sequence of the DNA segment upstream of the -10 hexamer can make a significant contribution to promoter strength. Using published collections of characterised E.coli promoters, we have studied the frequency of occurrence of 'TG motifs' upstream of the promoters' -10 elements. We conclude that correctly placed 'TG motifs' are found at over 20% of E.coli promoters.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • DNA, Bacterial / genetics
  • DNA, Bacterial / metabolism
  • DNA-Directed RNA Polymerases / metabolism
  • Data Interpretation, Statistical
  • Escherichia coli / genetics*
  • Molecular Sequence Data
  • Promoter Regions, Genetic / genetics*
  • Protein Binding
  • Recombinant Fusion Proteins / genetics
  • Recombinant Fusion Proteins / metabolism
  • Regulatory Sequences, Nucleic Acid*
  • Sequence Homology, Nucleic Acid
  • Transcription, Genetic
  • beta-Galactosidase / genetics
  • beta-Galactosidase / metabolism


  • DNA, Bacterial
  • Recombinant Fusion Proteins
  • DNA-Directed RNA Polymerases
  • beta-Galactosidase