Moraxella catarrhalis Restriction-Modification Systems are Associated with Phylogenetic Lineage and Disease

Abstract

Moraxella catarrhalis is a human-adapted pathogen, and a major cause of otitis media (OM) and exacerbations of chronic obstructive pulmonary disease. The species is comprised of two main phylogenetic lineages, RB1 and RB2/3. Restriction–modification (R-M) systems are among the few lineage-associated genes identified in other bacterial genera and have multiple functions including defense against foreign invading DNA, maintenance of speciation, and epigenetic regulation of gene expression. Here, we define the repertoire of R-M systems in 51 publicly available M. catarrhalis genomes and report their distribution among M. catarrhalis phylogenetic lineages. An association with phylogenetic lineage (RB1 or RB2/3) was observed for six R-M systems, which may contribute to the evolution of the lineages by restricting DNA transformation. In addition, we observed a relationship between a mutually exclusive Type I R-M system and a Type III R-M system at a single locus conserved throughout a geographically and clinically diverse set of M. catarrhalis isolates. The Type III R-M system at this locus contains the phase-variable Type III DNA methyltransferase, modM, which controls a phasevarion (phase-variable regulon). We observed an association between modM presence and OM-associated middle ear isolates, indicating a potential role for ModM-mediated epigenetic regulation in OM pathobiology.

Phasevarions of bacterial pathogens – phase-variable epigenetic regulators evolving from restriction–modification systems

“…An association of the modM3 allele with isolates causing middle ear infection has been demonstrated [37], which like modA2 in NTHi above, implies that certain genes in the modM3 phasevarion provide a selective advantage in the middle ear [37]. A survey of all R-M systems in M. catarrhalis demonstrated the presence of two further putatively phase-variable Type III mod genes, which have been named modN and modO [86]. The presence of multiple phasevariable mod genes in multiple human-adapted pathogens shows that high levels of phenotypic variation are selected for in these organisms, and that this plays a key role in virulence and pathobiology.…”

“…catarrhalis is a human respiratory tract pathogen. Individual strains can contain one of six different alleles of the modM gene [72,86]. An association of the modM3 allele with isolates causing middle ear infection has been demonstrated [37], which like modA2 in NTHi above, implies that certain genes in the modM3 phasevarion provide a selective advantage in the middle ear [37].…”

Moraxella catarrhalis phase-variable loci show differences in expression during conditions relevant to disease

“…Three loci (restriction endonuclease subunit M, glutathione disulphide reductase (gor), and a hypothetical permease MC25239_RS00020 (hyp)) contained upstream repeat tracts which we considered as highly likely to mediate phase variation, as repeat tract lengths varied substantially between the five genomes. However, the restriction endonuclease subunit M was previously found to be a truncated ORF located in a recombinational hotspot for DNA restriction-modification systems and was excluded from further analysis [29]. Although the Type III DNA methyltransferase gene, modO (Table 1), was not identified in our bioinformatic analyses as there are no closed RB2/3 lineage genomes, it was included based on our previous work [29].…”

“…However, the restriction endonuclease subunit M was previously found to be a truncated ORF located in a recombinational hotspot for DNA restriction-modification systems and was excluded from further analysis [29]. Although the Type III DNA methyltransferase gene, modO (Table 1), was not identified in our bioinformatic analyses as there are no closed RB2/3 lineage genomes, it was included based on our previous work [29].…”

“…We have previously shown that 5 0 -CAAC (n) -3 0 tetranucleotide SSRs are responsible for phase variation of both the modM and modN genes [26], and differential methylation of the genome caused by ModM phase variation epigenetically regulates the switching of expression of multiple genes in a phasevarion [27,28], further complicating the identification of stably expressed genes in M. catarrhalis. Further to this, we have also identified a third potentially phase variable Type III DNA methyltransferase, modO, which contains a 5 0 -CAACG (n) -3 0 pentanucleotide repeat tract upstream of its ORF [29]. However, analysis of modO expression has not been described.…”