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Nucleic Acids Research Advance Access published online on February 10, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp027
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Molecular Biology

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

Sean P. Riley1, Tomasz Bykowski1, Anne E. Cooley1, Logan H. Burns1, Kelly Babb1, Catherine A. Brissette1, Amy Bowman1, Matthew Rotondi2, M. Clarke Miller2, Edward DeMoll2,3, Kap Lim4, Michael G. Fried5 and Brian Stevenson1,*

1Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky College of Medicine, 2Department of Chemistry, 3Department of Biology, University of Kentucky, Lexington, KY 40536-0298, 4Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland, MD 20850 and 5Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY 40536-0509, USA

*To whom correspondence should be addressed. Tel: +1 859 257 9358; Fax: +1 859 257 8994; Email: brian.stevenson{at}uky.edu

Received October 2, 2008. Revised January 5, 2009. Accepted January 11, 2009.

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.

Present addresses: Sean P. Riley, Department of Microbiology, University of Chicago, Chicago, Illinois, IL 60637, USA

Tomasz Bykowski, Center for Medical Education, 04-041 Warsaw, Poland

Anne E. Cooley, Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, IL 60611, USA

Kelly Babb, BioVitesse, West Lafayette, Indina, IN 47906, USA

Matthew Rotondi, Department of Neurology, Weill Cornell Medical College, New York, NY 10065, USA

M. Clarke Miller, Brown Cancer Center, University of Louisville, Louisville, Kentucky, KY 40202, USA


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