Contingency Loci in Haemophilus influenzae and Neisseria meningitidis

Haemophilus influenzae illustrates several well-studied mechanisms that have evolved to cause random changes in gene expression, which help the bacterium evade host defenses. This bacterium is often found as a benign infection in the nose and throat, but can invade cerebrospinal fluid, thus causing meningitis. Several molecules on the cell surface are involved in colonizing the host and are targets for the host immune system (Fig. WN23.2). Random changes in gene expression cause random variation in these surface molecules and so help the bacterium evade the host defenses.

Fimbriae are appendages that allow bacteria to bind to host cells. They are found on bacteria isolated from the nasopharynx, but not on those from the cerebrospinal fluid. Fimbriae consist of repeated protein subunits encoded by hifA; these require the chaperone hifB for proper transport to the cell surface. These two genes are transcribed in opposite directions, and their promoter sequences at positions –10 and –35 overlap (Fig. WN23.3). Gene expression requires that these sequences be separated by about 16 nucleotides. The intergenic region includes TATA repeats, whose number changes randomly as a result of strand slippage during replication, which causes random switching of gene expression.

The major component of the outer membrane is lipopolysaccharide (LPS). This is a key antigen and hence plays a large part in determining the virulence of the bacterium. Many genes are involved in synthesizing the various components of the saccharide that extend out from the cell surface. Thus, random changes in expression of these genes cause random variation in LPS composition. For example, the 5′ end of the lic2 gene includes CAAT repeats, whose number varies through strand slippage (Fig WN23.4). With 16 repeats, the ATG start codons 1 and 2 bring the rest of the long coding region into the correct reading frame, whereas with 17 copies, start codon 3 gives a long open reading frame. With 15 copies, the gene cannot be translated correctly.

Production of capsule polysaccharides helps the bacterium survive clearance by the host’s immune system. Capsule production depends on the cap locus, which includes several copies of the cap gene, as well as the bexA gene, which is required for export of the polysaccharide. The cap genes are flanked by copies of the insertion element IS1016. Intragenomic recombination between these elements leads to frequent changes in copy number, and hence in capsule production. With one copy, the bexA gene is lost, and capsule cannot be produced (Fig. WN23.5).

There may be random changes in protein sequences as well as in gene expression. Neisseria meningitidis has a life history similar to that of H. influenzae: It usually is found as a benign infection of the nasopharynx, but occasionally causes meningitis. Attachment to epithelial cells is aided by a protein pilus, similar to the fimbriae of H. influenzae. The exposed region of the pilus protein, which is encoded by the gene pilE, is highly variable. This variation is generated by gene conversion. There is a single functional copy of pilE, but there are also eight pseudogenes with highly variable sequence. Gene conversion transfers small segments of pseudogene sequences to the pilE gene, generating extreme variation in the expressed proteins. The hypervariable regions of both pilE and the pseudogenes have a high rate of amino acid sequence evolution, relative to rates of synonymous evolution (i.e., K_A > K_S; p. 532), showing that selection favors novel protein sequences. Presumably, this diversifying selection on the pilus has caused the evolution of (in effect) high mutation rates, generated by this unusual gene conversion mechanism.