Simple sequence repeats in Haemophilus influenzae

Abstract

Simple sequence repeat (SSRs) of DNA are subject to high rates of mutation and are important mediators of adaptation in Haemophilus influenzae. Previous studies of the Rd KW20 genome identified the primacy of tetranucleotide SSRs in mediating phase variation (the rapid reversible switching of gene expression) of surface exposed structures such as lipopolysaccharide. The recent sequencing of the genomes of multiple strains of H. influenzae allowed the comparison of the SSRs (repeat units of one to nine nucleotides in length) in detail across four complete H. influenzae genomes and then comparison with a further 12 genomes when they became available. The SSR loci were broadly classified into three groups: (1) those that did not vary; (2) those for which some variation between strains was observed but this could not be linked to variation of gene expression; and (3) those that both varied and were located in regions consistent with mediating phase variable gene expression. Comparative analysis of 988 SSR associated loci confirmed that tetranucleotide repeats were the major mediators of phase variation and extended the repertoire of known tetranucleotide SSR loci by identifying ten previously uncharacterised tetranucleotide SSR loci with the potential to mediate phase variation which were unequally distributed across the H. influenzae pan-genome. Further, analysis of non-tetranucleotide SSR in the 16 strains revealed a number of mononucleotide, dinucleotide, pentanucleotide, heptanucleotide, and octanucleotide SSRs which were consistent with these tracts mediating phase variation. This study substantiates previous findings as to the important role that tetranucleotide SSRs play in H. influenzae biology. Two Brazilian isolates showed the most variation in their complement of SSRs suggesting the possibility of geographic and phenotypic influences on SSR distribution.

DNA sequence repeats identify numerous Type I restriction‐modification systems that are potential epigenetic regulators controlling phase‐variable regulons; phasevarions

“…52 We also identify a number of phase-variable hsdR genes in unusual or emerging pathogens such as EleORF768 from Eggerthella lenta, an anaerobic Gram-positive bacilli associated with abdominal sepsis, and Slu143ORF9045 from Staphylococcus lugdunensis, a member of the Staphylococci that has been known to cause septic arthritis. 59 However, our findings demonstrate a high abundance of trinucleotide repeat tracts in open reading frames. In addition, in examples where a single gene is present in multiple different strains, there is no variation in repeat number observed between all the examples present.…”

A Naturally Occurring Single Nucleotide Polymorphism in a Multicopy Plasmid Produces a Reversible Increase in Antibiotic Resistance

“…This reversion is achieved through plasmid loss, which occurs at a higher frequency than potential mutations that revert the plasmid to the original genotype or compensate the cost associated with the plasmids. Actually, the theoretical rate of plasmid loss per generation for the plasmid alleles is 10 2 -to 10 4 -fold higher than the mutation rate per generation in H. influenzae (16,19,20). Therefore, this is a highly plastic strategy to modulate plasmid-mediated antibiotic resistance levels, and we argue that it could be more common in nature than previously thought.…”

The role of variable DNA tandem repeats in bacterial adaptation

“…However, exceptions have been reported. For example, tetranucleotide SSRs of H. influenzae are exclusively found in ORFs, which is consistent with their role in phase variation (Power et al ., ). An interesting situation exists in the mycoplasmas, where long trinucleotide repeats are overrepresented in Mycoplasma genitalium , Mycoplasma gallisepticum , and Mycoplasma hyopneumoniae , but occur mainly in intergenic regions in the former two species, but in coding regions in the latter one (Mrázek, ).…”