The E. coli and H. influenzae YbaB proteins both exhibited preferences for certain tested DNA sequences, but neither showed the same high affinity for GTnAC as did the spirochetal ortholog. Both YbaB proteins also showed a marked preference for DNA derived from the B. burgdorferi erpAB promoter Necrostatin-1 in vivo over poly(dI-dC). Such large differences in affinities for target and non-target sequences may account for the previous failure to detect DNA-binding by YbaBHi [3]. These results suggest that YbaBEc and YbaBHi have higher affinities for some DNA sequences than for others, but whether those preferences depend upon a specific nucleotide sequence(s), A+T content, and/or DNA topology remain to be determined. The three-dimensional
structure of dimeric YbaB resembles “”tweezers”", with α-helices 1 and 3 of each monomeric subunit protruding from the dimerization domains [3]. The spacing between the α-helical protrusions is Selleckchem VX-680 approximately 15 Å at the base of the dimerization domain and approximately 22 Å at the distal ends of the α-helices [3], similar to the diameter of B-form duplex DNA (~20Å [3]). Site-directed mutagenesis selleck inhibitor studies of the orthologous B. burgdorferi EbfC demonstrated that certain amino acid substitutions in either α-helix 1 or 3 of EbfC eliminate DNA-binding, without affecting dimerization [10]. It is noteworthy that many of the α-helix 1 and 3 residues of EbfC are
distinct from residues in both YbaBEc and YbaBHi (Fig. 1), consistent with the differences in DNA preferences between the E. coli and H. influenzae YbaB proteins and their spirochetal ortholog. YbaB/EbfC orthologs of other bacterial species likewise exhibit sequence variations in their α-helices 1 and 3, suggesting that they PJ34 HCl may also possess unique DNA-binding properties. The function(s) of YbaB/EbfC proteins remains to be determined. Many bacterial ybaB/ebfC orthologs are located between dnaX and recR, a synteny that has led to suggestions of roles in DNA replication or recombination [3, 5, 6, 15–18]. While the abilities of the examined orthologs to bind DNA may support those hypotheses, several lines
of evidence suggest that YbaB/EbfC proteins perform functions that are independent of DNA recombination or replication. Proteomic analyses of cultured H. influenzae detected production of YbaB without accompanying production of DNA repair proteins [19]. A ybaB recR double mutant of Streptomyces coelicolor exhibited recombination defects that could be complemented with recR alone [18]. The ybaB/ebfC orthologs of some bacterial species are not linked to recR or any other recombination-related gene and some, such as the B. burgdorferi, do not even encode RecR [8, 20]. Several bacteria, such as H. influenzae, have ybaB genes located distantly from their dnaX [2]. Moreover, some ybaB family genes can be transcribed independently of their upstream genes, using promoter elements within the 5′ gene [4, 6, 21–23].