Borrelia burgdorferi EbfC defines a newly-identified, widespread family of bacterial DNA-binding proteins

Nucleic Acids Res. 2009 Apr;37(6):1973-83. doi: 10.1093/nar/gkp027. Epub 2009 Feb 10.


The Lyme disease spirochete, Borrelia burgdorferi, encodes a novel type of DNA-binding protein named EbfC. Orthologs of EbfC are encoded by a wide range of bacterial species, so characterization of the borrelial protein has implications that span the eubacterial kingdom. The present work defines the DNA sequence required for high-affinity binding by EbfC to be the 4 bp broken palindrome GTnAC, where 'n' can be any nucleotide. Two high-affinity EbfC-binding sites are located immediately 5' of B. burgdorferi erp transcriptional promoters, and binding of EbfC was found to alter the conformation of erp promoter DNA. Consensus EbfC-binding sites are abundantly distributed throughout the B. burgdorferi genome, occurring approximately once every 1 kb. These and other features of EbfC suggest that this small protein and its orthologs may represent a distinctive type of bacterial nucleoid-associated protein. EbfC was shown to bind DNA as a homodimer, and site-directed mutagenesis studies indicated that EbfC and its orthologs appear to bind DNA via a novel alpha-helical 'tweezer'-like structure.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / classification
  • Bacterial Proteins / metabolism
  • Base Sequence
  • Binding Sites
  • Borrelia burgdorferi / genetics*
  • Conserved Sequence
  • DNA, Bacterial / chemistry*
  • DNA, Bacterial / metabolism
  • DNA-Binding Proteins / chemistry*
  • DNA-Binding Proteins / classification
  • DNA-Binding Proteins / metabolism
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Operator Regions, Genetic
  • Protein Binding
  • Protein Multimerization
  • Protein Structure, Tertiary


  • Bacterial Proteins
  • DNA, Bacterial
  • DNA-Binding Proteins