The linker sequence, joining the DNA-binding domain of the homologous transcription factors, Mlc and NagC, to the rest of the protein, determines the specificity of their DNA target recognition in Escherichia coli

Mol Microbiol. 2012 Sep;85(5):1007-19. doi: 10.1111/j.1365-2958.2012.08158.x. Epub 2012 Jul 13.


Protein-DNA recognition is fundamental to transcriptional regulation. Transcription factors must be capable of locating their specific sites situated throughout the genome and distinguishing them from related sites. Mlc and NagC control uptake and use of the sugars, glucose and N-acetylglucosamine. Both their helix-turn-helix motifs and their consensus binding sites on DNA are very similar. One distinguishing feature is that most NagC sites have a C/G bp at positions -11 and +11 from the centre of symmetry of the operator, while all Mlc sites have A/T. By constructing Mlc and NagC chimeras, we show that the helix-turn-helix motif per se is not responsible for specific recognition of Mlc or NagC sites, but that a linker, joining the DNA-binding domain to the rest of the protein, is the major determinant. We show that a change of just two amino acids in the NagC linker is sufficient to allow NagC to recognize an A/T bp at positions +/-11 and repress Mlc targets. Modelling of the NagC linker suggests that it forms an extended structure containing two arginines and we suggest that these arginines interact differently with the minor groove at positions +/-11 depending upon the presence of a C/G or A/T bp.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • DNA, Bacterial / genetics
  • DNA, Bacterial / metabolism*
  • Escherichia coli / genetics
  • Escherichia coli / metabolism*
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / metabolism*
  • Helix-Turn-Helix Motifs / genetics
  • Helix-Turn-Helix Motifs / physiology
  • Protein Binding
  • Repressor Proteins / genetics
  • Repressor Proteins / metabolism*


  • DNA, Bacterial
  • Escherichia coli Proteins
  • Mlc protein, E coli
  • Repressor Proteins
  • nagC protein, E coli