A conserved DNA sequence is required for efficient gonococcal pilin antigenic variation.

Antigenic variation of the Neisseria gonorrhoeae pilus occurs when a variant pilin sequence from a silent locus recombines into the expression locus by predominantly unidirectional, homologous recombination. At the 3' end of all pilin loci lies a conserved DNA sequence, called the Sma/Cla repeat, which has sequence similarity to several recombinase-binding sites, and therefore may be involved in pilin recombination. We have developed a novel reverse transcriptase/polymerase chain reaction (RT-PCR) assay for direct monitoring of pilin recombination, and both RT-PCR and phase variation were used to examine pilin recombination in a gonococcal strain that had had the pilE Sma/Cla repeat removed. Results from these experiments showed a decrease in pilin recombination when the Sma/Cla sequence was deleted from the expression locus, showing that a specialized site (Sma/Cla) is involved in efficient pilin recombination.