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

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.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.Genome sequencing of diverse bacterial species has revealed widespread distribution of conserved gene products with as-yet unknown functions. Among these are a family of small proteins with approximate molecular masses of 12 kDa, which have been variously classed as "domain of unknown function" (DUF) 149, Pfam 2575 and COG-0718 [1]. Such genes have been identified in a wide variety of bacterial phyla, a list that includes many significant pathogens of humans, domestic animals and plants (Fig. 1).After the genome sequence of H. influenzae strain KW20 rd (also known as H. influenzae Rd) was determined in 1995 [2], the "Structure 2 Function Project" was established to crystallize recombinant proteins from H. influenzae genes of unknown function http://s2f.umbi.umd.edu/ webcite. Among these orphan gene products was the H. influenzae DUF 149 group member annotated as open reading frame (ORF) HI0442, and tentatively named "YbaB" [3]. H. influenzae YbaB (YbaBHi) crystallized as a homodimer, with the central p