Haemophilus influenzae phasevarions have evolved from type III DNA restriction systems into epigenetic regulators of gene expression

Abstract

Phase variably expressed (randomly switching) methyltransferases associated with type III restriction-modification (R-M) systems have been identified in a variety of pathogenic bacteria. We have previously shown that a phase variable methyltransferase (Mod) associated with a type III R-M system in Haemophilus influenzae strain Rd coordinates the random switching of expression of multiple genes, and constitutes a phase variable regulon--'phasevarion'. We have now identified the recognition site for the Mod methyltransferase in H. influenzae strain Rd as 5'-CGAAT-3'. This is the same recognition site as the previously described HinfIII system. A survey of 59 H. influenzae strains indicated significant sequence heterogeneity in the central, variable region of the mod gene associated with target site recognition. Intra- and inter-strain transformation experiments using Mod methylated or non-methylated plasmids, and a methylation site assay demonstrated that the sequence heterogeneity seen in the region encoding target site specificity does correlate to distinct target sites. Mutations were identified within the res gene in several strains surveyed indicating that Res is not functional. These data suggest that evolution of this type III R-M system into an epigenetic mechanism for controlling gene expression has, in some strains, resulted in loss of the DNA restriction function.

Figure 1.

Assessment of Mod methylation in H. influenzae strains Rd and R2866. (a) Schematic diagram showing the overlapping recognition sites for restriction endonucleases HinfIII, ApoI and TaqI. Plasmid pHStet contains one overlapping ApoI/HinfIII, located on a 1.3-kb fragment. (b) ApoI digest of plasmid pHStet isolated from Rd mod ON and mod::kan cells, or R2866 mod ON and mod::kan cells. Differential cleavage pattern of the 1.3-kb fragment evident with plasmid isolated from Rd mod ON and mod::kan cells. (c) TaqI digest of plasmid pHStet isolated from Rd mod ON and mod::kan cells. The recognition site for restriction endonuclease TaqI overlaps with the first A of the HinfIII recognition sequence [see schematic in part (a)]. No difference in the cleavage pattern evident between plasmid isolated from Rd mod ON and mod::kan cells. (d) DpnI digest of plasmid pHStet isolated from R2866 mod ON and R2866 mod::kan cells (first panel). Separated DNA fragments were transferred to nitrocellulose membrane and probed with anti-N6-methyladenosine antisera (second panel). Differential binding of the antisera to plasmid isolated from R2866 mod ON and R2866 mod::kan cells is indicated by an arrow. Increased background in the R2866 mod ON sample compared to the R2866 mod::kan sample is due to differential binding of the antisera to chromosomal DNA.

Figure 2.

Phylogenetic relatedness of 59 H. influenzae strains, based on MLST data, and the relationship to mod sequence group, mod repeat tract length and capsular serotype. The capsular serotype of each strain is indicated as a prefix to each strain name (nt, non-typeable). The ON/OFF expression status of the mod gene due to the number of repeats within the mod repeat tract is indicated within each box in the repeat number column. MLST type (ST) is indicated for each strain. Mod groups specific to pathogenic Neisseria are indicated at the bottom of the figure. Black dots next to the strain name indicate that the res gene in that strain has a frame shift mutation and is inactive.

Figure 3.

Schematic diagram of the region of the genome containing the mod and res genes of six H. influenzae strains. Block arrows represent genes. The white regions of the block arrow representing the mod gene indicate the conserved N- and C-terminal regions. The coloured boxed region indicates the variable central region encoding DNA sequence recognition. The black box represents the position of the mod repeat tract indicated by an arrow, the sequence of the repeated motif, number of repeats and expression state of the gene are indicated below the black box. The block arrow representing the res gene indicates that the gene sequence is full-length in each case, with the transition from black to grey representing the position of a frame shift mutation. An asterisk indicates the position of a stop codon brought in frame due to the frame shift mutation in res. Strain Rd has no frame shift mutation in res. The genome sequence of strain KW20 Rd does have a frame shift mutation in res. It is not known whether this difference represents a sequencing error in the genome sequence or a genuine strain difference. The positions of the conserved motifs that are important in Res function are indicated above Res. Triangles indicate the site of insertion of a kanamycin resistance cassette. The solid black line indicates the intergenic region and the dotted line indicates a deletion.