The length of a tetranucleotide repeat tract in Haemophilus influenzae determines the phase variation rate of a gene with homology to type III DNA methyltransferases

Haemophilus influenzae is an obligate commensal of the upper respiratory tr act of humans that uses simple repeats (microsatellites) to alter gene expr ession. The mod gene of H. influenzae strain Rd has homology to DNA methylt ransferases of type III restriction/modification systems and has 40 tetranu cleotide (5'-AGTC) repeats within its open reading frame. This gene was fou nd in 21 out of 23 genetically distinct H. influenzae strains, and in 13 of these strains the locus contained repeats. H. influenzae strains were cons tructed in which a lacZ reporter was fused to a chromosomal copy of mod dow nstream of the repeats. Phase variation occurred at a high frequency in str ains with the wild-type number of repeats. Mutation rates were derived for similarly engineered strains, containing different numbers of repeats. Rate s increased linearly with tract length over the range 17-38 repeat units. T he majority of tract alterations were insertions or deletions of one repeat unit with a 2:1 bias towards contractions of the tract. These results demo nstrate the number of repeats to be an important determinant of phase varia tion rate in H. influenzae for a gene containing a microsatellite.