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Background  Genes orthologous to the  ybaB  loci of  Escherichia coli  and  Haemophilus influenzae  are widely distributed among eubacteria. Several years ago, the three-dimensional structures of the YbaB orthologs of both  E. coli  and  H. influenzae  were determined, revealing a novel "tweezer"-like structure. However, a function for YbaB had remained elusive, with an early study of the  H. influenzae  ortholog failing to detect DNA-binding activity. Our group recently determined that the  Borrelia burgdorferi  YbaB ortholog, EbfC, is a DNA-binding protein. To reconcile those results, we assessed the abilities of both the  H. influenzae  and  E. coli  YbaB proteins to bind DNA to which  B. burgdorferi  EbfC can bind.    Results  Both the  H. influenzae  and the  E. coli  YbaB proteins bound to tested DNAs. DNA-binding was not well competed with poly-dI-dC, indicating some sequence preferences for those two proteins. Analyses of binding characteristics determined that both YbaB orthologs bind as homodimers. Different DNA sequence preferences were observed between  H. influenzae  YbaB,  E. coli  YbaB and  B. burgdorferi  EbfC, consistent with amino acid differences in the putative DNA-binding domains of these proteins.    Conclusion  Three distinct members of the YbaB/EbfC bacterial protein family have now been demonstrated to bind DNA. Members of this protein family are encoded by a broad range of bacteria, including many pathogenic species, and results of our studies suggest that all such proteins have DNA-binding activities. The functions of YbaB/EbfC family members in each bacterial species are as-yet unknown, but given the ubiquity of these DNA-binding proteins among Eubacteria, further investigations are warranted.

DNA-binding by Haemophilus influenzae and Escherichia coli YbaB, members of a widely-distributed bacterial protein family