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

• Published in: Nucleic acids research Vol. 37; no. 6; pp. 1973 - 1983
• Main Authors: Riley, Sean P, Bykowski, Tomasz, Cooley, Anne E, Burns, Logan H, Babb, Kelly, Brissette, Catherine A, Bowman, Amy, Rotondi, Matthew, Miller, M. Clarke, DeMoll, Edward, Lim, Kap, Fried, Michael G, Stevenson, Brian
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01-04-2009; Oxford Publishing Limited (England)
• Subjects: Amino Acid Sequence; Bacteria; Bacterial Proteins - chemistry; Bacterial Proteins - classification; Bacterial Proteins - metabolism; Base Sequence; Binding Sites; Borrelia burgdorferi; Borrelia burgdorferi - genetics; Conserved Sequence; DNA, Bacterial - chemistry; DNA, Bacterial - metabolism; DNA-Binding Proteins - chemistry; DNA-Binding Proteins - classification; DNA-Binding Proteins - metabolism; Molecular Biology; Molecular Sequence Data; Nucleic Acid Conformation; Operator Regions, Genetic; Protein Binding; Protein Multimerization; Protein Structure, Tertiary
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkp027

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 α-helical 'tweezer'-like structure.