Roles for DNA repeats in 'Neisseria gonorrhoeae', including protein sequence variation

There are many types of repeated DNA sequences in the genomes of the Neisseria spp., from homopolymeric tracts to tandem repeats of hundreds of bases to sequences scattered hundreds of times across the genome. These each play differing roles in the biology of these bacteria, including mediating antigenic variation, phase variation, and differential expression of genes. Here we present analysis of the repetitive sequences in the Neisseria gonorrhoeae strain NCCP11945 genome sequence and comparisons to other data. Evidence is presented for 34 phase variable genes in this strain and for 48 phase variable genes in this species, including a new class of phase variation that causes amino acid changes at the C-terminus of the protein, never before described in the Neisseria spp. Strain NCCP11945 also contains 29 coding repeat containing genes, one more than the repertoire identified in N. gonorrhoeae strain FA1090. Areas of the genome lacking common neisserial repeat elements were investigated as regions of potential horizontal transfer. In addition, inverted repeats of the neisserial uptake sequence predicted to act as transcriptional terminators were identified for approximately one-seventh of the annotated CDSs in the strain NCCP11945 genome. The various repetitive sequence elements are important to the biology, adaptation, and evolution of N. gonorrhoeae.