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. 2013;8(3):e60116.
doi: 10.1371/journal.pone.0060116. Epub 2013 Mar 20.

Insight into the evolution of the histidine triad protein (HTP) family in Streptococcus

Zhu-Qing Shao  1 , Yan-Mei Zhang, Xiu-Zhen Pan, Bin Wang, Jian-Qun Chen
Affiliations

Insight into the evolution of the histidine triad protein (HTP) family in Streptococcus

Zhu-Qing Shao et al. PLoS One. 2013.

Abstract

The Histidine Triad Proteins (HTPs), also known as Pht proteins in Streptococcus pneumoniae, constitute a family of surface-exposed proteins that exist in many pathogenic streptococcal species. Although many studies have revealed the importance of HTPs in streptococcal physiology and pathogenicity, little is known about their origin and evolution. In this study, after identifying all htp homologs from 105 streptococcal genomes representing 38 different species/subspecies, we analyzed their domain structures, positions in genome, and most importantly, their evolutionary histories. By further projecting this information onto the streptococcal phylogeny, we made several major findings. First, htp genes originated earlier than the Streptococcus genus and gene-loss events have occurred among three streptococcal groups, resulting in the absence of the htp gene in the Bovis, Mutans and Salivarius groups. Second, the copy number of htp genes in other groups of Streptococcus is variable, ranging from one to four functional copies. Third, both phylogenetic evidence and domain structure analyses support the division of two htp subfamilies, designated as htp I and htp II. Although present mainly in the pyogenic group and in Streptococcus suis, htp II members are distinct from htp I due to the presence of an additional leucine-rich-repeat domain at the C-terminus. Finally, htp genes exhibit a faster nucleotide substitution rate than do housekeeping genes. Specifically, the regions outside the HTP domains are under strong positive selection. This distinct evolutionary pattern likely helped Streptococcus to easily escape from recognition by host immunity.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Distribution of all identified htp genes among 38 streptococci in a clear phylogenetic background.
A. Phylogenetic analysis of 38 streptococci based on 530 single-copy orthologous proteins. Node labels indicate aLRT SH-like branch support values. Twenty-six species have been used in the previous phylogeny analysis based on 16s rDNA, while 14 species or subspecies were newly added and labeled in bold. Group division was updated based on the phylogenetic relationship. B. Copy numbers of htp genes within each genome are indicated with complete genes plus pseudogenes.
Figure 2
Figure 2. The phylogenetic tree of htp genes based on CDS.
Node labels indicate aLRT SH-like branch support values. The htp genes found from non-streptococcal species are shaded. For each gene, the CDS number in its genome is found behind the species name. Arrows in different colors are used to represent htp I or htp II genes. Asterisks (*) are used to indicate the represented gene when a species has tandem duplicated htp genes.
Figure 3
Figure 3. Sliding-window analysis for Ka/Ks values of two subfamilies of htp genes.
Ka/Ks ratios were calculated for A) htp I subfamily and B) htp II subfamily using DnaSP with a sliding window of 60 bases and a 15-base step size.
See this image and copyright information in PMC

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Grants and funding

This work was supported by the National Natural Science Foundation of China (30930008, 31000105, 31170210 and 8117294), National Postdoctoral Science Foundation of China (20090461092, 201003570), Nanjing University Start Grant, the Natural Science Foundation of Jiangsu Province (BK2010113) and Postgraduate Students Innovation Project of Jiangsu Province (CXZZ11_0038). http://www.nsfc.gov.cn/; http://210.79.234.200/V1/Manage/Login.aspx; www.nju.edu.cn/. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.