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

• DOI: 10.1093/nar/gkp027
• Publication Date: 2009-02-11T03:03:36Z
• Authors: S. P. Riley; T. Bykowski; A. E. Cooley; L. H. Burns; K. Babb; C. A. Brissette; A. Bowman; M. Rotondi; M. C. Miller; E. DeMoll; K. Lim; M. G. Fried; B. Stevenson
• Keywords: DNA, Bacterial; 0301 basic medicine; Binding Sites; Operator Regions, Genetic; Base Sequence; Molecular Sequence Data; Protein Structure, Tertiary; DNA-Binding Proteins; 03 medical and health sciences; Bacterial Proteins; Borrelia burgdorferi; Nucleic Acid Conformation; Amino Acid Sequence; Protein Multimerization; Molecular Biology; Conserved Sequence; Protein Binding

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.