Simple sequence repeats in Haemophilus influenzae

E.R. Moxon,D.W. Hood,W.A. Sweetman,Peter M. Power,G.A. Kumar,N.J. Gallacher,M.R. Woodhall

doi:10.1016/j.meegid.2008.11.006

E.R. Moxon, D.W. Hood + Show 5 more

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https://doi.org/10.1016/j.meegid.2008.11.006

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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.

Highlights

Haemophilus influenzae (Hi), a common commensal bacterium of the upper respiratory tract of humans, is an important cause of diseases that include otitis media, pneumonia, meningitis, and septicaemia
Our aim was to extend the analysis of simple sequence repeats (SSRs) by comprehensively investigating the repertoire present in the four complete Hi genome sequences that were available for different strains of Hi at the commencement of this study (Four Genome Analysis; see Table 1)
The thresholds used in this study for all repeat unit lengths included at least all of the statistically unexpected SSRs determined by hidden Markov model analysis of the Hi genomes

Summary

Introduction

Haemophilus influenzae (Hi), a common commensal bacterium of the upper respiratory tract of humans, is an important cause of diseases that include otitis media, pneumonia, meningitis, and septicaemia. SSRs are hypermutable (e.g. tetranucleotide SSRs lose and gain units at a rate of 1 Â 10À4 per generation (De Bolle et al, 2000) compared with a basal mutation rate of approximately 1 Â 10À9) and, it has been suggested that their decreased prevalence reflects natural selection because the SSRs can be located in promoter regions or within open reading frames and changes in their length can result in the random, high frequency, reversible loss, gain or modulation of gene expression (phase variation) Since these regions of localised hypermutation, often termed ‘contingency loci’, can each independently result in altered gene expression, a repertoire of phenotypic variants is generated (Moxon et al, 2006). It has been suggested that this strategy has particular survival value when bacterial populations are subjected to periodic selection during transmission between genetically distinct hosts (Wolf et al, 2005)

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