Genetic mechanisms of opa gene variation in Neisseria gonorrhoeae

Abstract

To understand the rates and mechanisms of Neisseria gonorrhoeae opacity (opa) gene variation, the 11 opa genes were amplified independently so that an opa allelic profile could be defined for any isolate from the sequences at each locus. Initial examination of 14 unrelated gonococcal isolates showed that no opa alleles were shared. Analysis of closely related isolates showed these typically shared most opa alleles and so the mechanisms by which recent changes occurred at individual opa loci could be determined. The great majority of changes were due to recombination among existing alleles that either duplicated an opa allele present at another locus or resulted in a mosaic of existing opa alleles. Single nucleotide changes or the insertion/deletion of a single codon also occurred, but few of these events were assigned to mutation, the majority being assigned to localised recombination. Introduction of novel opa genes from co-infecting strains was rare and all but one occurred in the same sexual network. Changes at the eleventh opa locus (opa11) occurred much more rapidly than at other opa loci, almost always differing even between recent sexual contacts. Examination of the neighbouring pilE gene showed that changes at opa11 and pilE often occurred together, although this linkage may not be a causal one. The Opa protein sequences encoded by the opa genes were determined and the regions spanning the two hyper-variable regions (HVR1 and HVR2) were analysed. An almost equal number of Opa protein and opa nucleotide sequences were detected but there was a limited number of HVR combinations, indicating that a large proportion of differences are located elsewhere in the protein. Very few novel HVRs were generated by recombination, even at opa11 where the rate of variation was greatest. Most changes resulted in re-assortment of existing HVRs, most likely due to protein function restriction/benefits.