Nucleotide Sequence Analysis of Hypervariable Junctions of Haemophilus influenzae Pilus Gene Clusters

Abstract

Haemophilus influenzae pili are surface structures that promote attachment to human epithelial cells. The five genes that encode pili, hifABCDE, are found inserted in genomes either between pmbA and hpt (hif-1) or between purE and pepN (hif-2). We determined the sequence between the ends of the pilus clusters and bordering genes in a number of H. influenzae strains. The junctions of the hif-1 cluster (limited to biogroup aegyptius isolates) are structurally simple. In contrast, hif-2 junctions are highly diverse, complex assemblies of conserved intergenic sequences (including genes hicA and hicB) with evidence of frequent recombination. Variation at hif-2 junctions seems to be tied to multiple copies of a 23-bp Haemophilus intergenic dyad sequence. The hif-1 cluster appears to have originated in biogroup aegyptius strains from invasion of the hpt-pmbA region by a DNA template containing the hif-2 genes with termini in the hairpin loop of flanking intergenic dyad sequences. The pilus gene clusters are an interesting model of a mobile "pathogenicity island" not associated with a phage, transposon, or insertion element.

Haemophilus influenzae : Genetic Variability and Natural Selection To Identify Virulence Factors

“…The role of insertion elements (IS) and phage elements in the horizontal transfer of virulence genes is shown by the 711-bp IS1016 direct repeats that flank the cap (polysaccharide) region (22), the 32-bp direct repeats flanking the hif-1 gene cluster present in certain H. influenzae biogroup aegyptius strains (36), the 59-bp direct repeats flanking the hif region (29), and the duplicated inverted repeats flanking the hif region (29,36). Furthermore, as described for Staphylococcus aureus (39), phage-and transposon-like elements may catalyze deletional events in H. influenzae.…”

“…The hif gene region encoding H. influenzae pili, for example, shows remarkable strain-to-strain heterogeneity (17,29,36), with insertions, deletions, and duplications of genes, open reading frames, and intergenic regions. Among 20 H. influenzae isolates, nine different gene arrangements were found in this region (29).…”

Prevalence of the hifBC , hmw1A , hmw2A , hmwC , and hia Genes in Haemophilus influenzae Isolates

“…Recent studies of many H. influenzae strains have documented dramatic genetic variation within the hif gene region, which is located between genes homologous to pepN and purE of Escherichia coli and is flanked by dyad repeat sequences (33) that may facilitate recombination. NTHi strains exhibit insertions, deletions, duplications, and rearrangements both within and flanking the hif cluster; in some strains the entire cluster is deleted (9,13,24,27,33,34).…”

“…NTHi strains exhibit insertions, deletions, duplications, and rearrangements both within and flanking the hif cluster; in some strains the entire cluster is deleted (9,13,24,27,33,34). A subset of NTHi strains asso-ciated with conjunctivitis, the so-called H. influenzae biogroup aegyptius strains, possess a second copy of the hif cluster, located between genes homologous to pmbA and hpt genes of E. coli.…”

Typing of Nonencapsulated Haemophilus Strains by Repetitive-Element Sequence-Based PCR Using Intergenic Dyad Sequences

“…Mrázek and Karlin (24) have described a short noncoding repeated sequence that is widely distributed throughout the H. influenzae Rd genome and is often found in pairs as inverted repeats (18,34). This 23-bp sequence, commonly called intergenic dyad sequence (IDS), has been found in several Haemophilus strains (3,9,22,35,43). A full and systematic BLAST search for IDSs in the combined EMBL and GenBank databases produced matches with sequences from only two other bacterial genera, Neisseria and Pseudomonas.…”