Mosaic structure of intragenic repetitive elements in histone H1-like protein Hc2 varies within serovars of Chlamydia trachomatis

Abstract

Background: The histone-like protein Hc2 binds DNA in Chlamydia trachomatis 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 hctB gene, which encodes Hc2, were compared.

Results: 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 Bordetella but was now also found in other genera, including Burkholderia, Herminiimonas, Minibacterium and Ralstonia.Sequence determination resulted in 41 hctB 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.

Conclusions: 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 Chlamydiacae. The high sequence variation in the corresponding hctB gene enables phylogenetic analysis and provides a suitable target for the genotyping of C. trachomatis.

Figure 1

Amino acid alignment of the 14 variants of repetitive elements (A-M) found in Hc2 of Chlamydia trachomatis among 378 specimens in the MLST database.

Figure 2

Charge distribution in Hc2, Hc2-like proteins and Hc1. Positively charged residues (blue bars) and negatively charged residues (red bars) in the protein sequence of Hc2 in Chlamydia trachomatis, Chlamydophila pneumoniae, Protochlamydia amoebophila, an Hc2-like protein in Herminiimonas arsenicoxydans and Hc1 in Chlamydia trachomatis.

Figure 3

Phylogenetic relationships of 41 variants of the MLST target that include hctB from Chlamydia trachomatis. (A) Phylogenetic tree based on the MLST target that includes the hctB gene. Each variant of the MLST target is indicated by the allele number and the serotypes in which that variant has been found. The phylogeny has been estimated using Bayesian inferences and rooted using paralog rooting based on the repetitive elements. The numbers on branches are posterior probabilities. The clades discussed in the text have been designated I-V. The repetitive elements found in each MLST variant are illustrated in an alignment to the right (B). The alignment of the repetitive elements is based on the neighbor-joining phylogeny of the element types (C) where the scale bar represents one nucleotide change.

Figure 4

Schematic overview of repetitive elements in Hc2 in the Chlamydiales order and in an Hc2-like protein in Herminiimonas arsenicoxydans. Repetitive elements of 20 amino acids or longer are shown in black.