Background Simple sequence repeats (SSR) are repetitive sequences of 1–6 base pairs in DNA which account for genotypic switching (phenotypic variation) through mechanism of polymerase slippage. This mechanism is common in pathogenic bacteria with reduced genome.
Methods Msatfinder v2.0.9 was used to identify SSR sequences in the genomes of five strains of Treponema pallidum subsp. pallidum (agent of syphilis); three strains of T. p. subsp. pertenue (agent of yaws); the Bosnia A strain of T. p. subsp. endemicum(agent of endemic syphilis); the Cuniculi A strain of T. paraluiscuniculi (agent of rabbit syphilis); and the Fribourg-Blanc strain (simian isolate genetically close to agent of yaws). Analysis of Solexa data and subsequent cloning approach were used for determination of intrastrain variability.
Results Sequence data analysis of 11 treponemal genomes revealed high degree of variability in guanosine/cytosine homopolymeric tracts (G/C-regions) among pathogenic treponemal strains. Altogether, 120 G/C-regions (containing > 7 nucleotides) were found, from which 53 regions showed no variability, 26 represented nucleotide substitution differences, and 41 contained variable numbers of G/Cs. From these 41 regions, 25 were located in intergenic regions and 16 affected ORFs. Interestingly, variable regions were located upstream or within genes coding for Tpr proteins, potential virulence factors, and hypothetical proteins. Furthermore, 30 regions were specific for Cuniculi A strain, 5 regions differentiated pallidum strains from other strains, and 3 regions were specific for pertenue strains. Moreover, additional variability within treponemal strains was found in 54 G/C-regions.
Conclusions Inter- and intrastrain variability of G/C-regions may play a significant role in pathogenesis of treponemal diseases. Further experimental studies are needed to verify this hypothesis.
- single sequence repeats
- Treponema pallidum