Analysis of protein binding to the Sma/Cla DNA repeat in pathogenic Neisseriae

Antigenic variation of the pilus is an essential component of Neisseria gonorrhoeae pathogenesis. Unidirectional recombination of silent pilin DNA into an expressed pilin gene allows for substantial sequence variation of this highly immunogenic surface structure. While the RecA protein is required for pilin gene recombination, the factors which maintain the silent reservoir of pilin sequences and/or allow unidirectional recombination from silent to expression loci remain undefined. We have previously shown that a conserved sequence at the 3'end of all pilin loci (the Sma/Cla repeat) is required to be present at the expression locus for efficient recombination from the silent loci. In this study, the binding of gonococcal proteins to this DNA sequence was investigated. Gel mobility shift assays and competition experiments using deletion derivatives of the repeat, show that multiple activities bind to different regions of the Sma/Cla repeat and define the boundaries of the binding sequences. Moreover, only the pathogenic Neisseria harbor proteins which specifically bind to this repeat, suggesting a correlation between the expression of these DNA binding proteins and the potential to cause disease.