Tetranucleotide repeats identify novel virulence determinant homologues in Neisseria meningitidis

Numerous outer membrane components of Neisseria meningitidis and N. gonorrhoeae exhibit phase variable expression (the rapid, reversible on/off switching of phenotypic expression). Many of the genes encoding these outer membrane components contain simple repetitive DNA motifs (mononucleotides, dinucleotides, tetranucleotides and other repeats) which mediate this variation. One such repeat motif, the tetranucleotide 5;-(GCAA)n-3;, is associated with phase-variable LPS biosynthetic genes in the pathogen Haemophilus influenzae. We have previously shown that N. meningitidis strain MC58 contains this repeat motif in at least three distinct genetic loci. In this study all three of these loci were investigated: two were cloned and identified as novel loci and designated nmrep1 and nmrep2. The third locus was assigned to a previously cloned gene and here is designated nmrep3. The distribution of these loci, and the number of repeat units at each locus was investigated in a range of strains. This analysis revealed that the nmrep1 and nmrep2 loci are present in all 45 strains examined, with 41/45 containing nmrep3. Sequences associated with nmrep1 showed no homology with reported proteins, but amino acid sequences of open reading frames of nmrep2 and nmrep3 exhibited sequence homology to the adhesins Aida of Escherichia coli and Prn of Bordetella sppand IcsA of Shigella flexneri which is involved in intracellular spread.