| Summary: | <p>Abstract</p> <p>Background</p> <p>The histone-like protein Hc2 binds DNA in <it>Chlamydia trachomatis </it>and is known to vary in size between 165 and 237 amino acids, which is caused by different numbers of lysine-rich pentamers. A more complex structure was seen in this study when sequences from 378 specimens covering the <it>hctB </it>gene, which encodes Hc2, were compared.</p> <p>Results</p> <p>This study shows that the size variation is due to different numbers of 36-amino acid long repetitive elements built up of five pentamers and one hexamer. Deletions and amino acid substitutions result in 14 variants of repetitive elements and these elements are combined into 22 configurations. A protein with similar structure has been described in <it>Bordetella </it>but was now also found in other genera, including <it>Burkholderia</it>, <it>Herminiimonas</it>, <it>Minibacterium </it>and <it>Ralstonia</it>.</p> <p>Sequence determination resulted in 41 <it>hctB </it>variants that formed four clades in phylogenetic analysis. Strains causing the eye disease trachoma and strains causing invasive lymphogranuloma venereum infections formed separate clades, while strains from urogenital infections were more heterogeneous. Three cases of recombination were identified. The size variation of Hc2 has previously been attributed to deletions of pentamers but we show that the structure is more complex with both duplication and deletions of 36-amino acid long elements.</p> <p>Conclusions</p> <p>The polymorphisms in Hc2 need to be further investigated in experimental studies since DNA binding is essential for the unique biphasic life cycle of the <it>Chlamydiacae</it>. The high sequence variation in the corresponding <it>hctB </it>gene enables phylogenetic analysis and provides a suitable target for the genotyping of <it>C. trachomatis</it>.</p>
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