In silico scrutiny of genes revealing phylogenetic congruence with clinical prevalence or tropism properties of Chlamydia trachomatis strains.
Bottom Line: Approximately 28% of the genes, which include the majority of the genes encoding putative type III secretion system effectors and Inc proteins, present a phylogenetic tree where only lymphogranuloma venereum strains form a clade.Some clade-specific pseudogenes were identified (novel findings include the conserved hypothetical protein CT037 and the predicted α-hemolysin CT473), suggesting their putative expendability for the infection of particular niches.Approximately 3.5% of the genes revealed a significant overrepresentation of nonsynonymous mutations, and the majority encode proteins that directly interact with the host.
Affiliation: Reference Laboratory of Sexually Transmitted Bacterial Infections, Department of Infectious Diseases, National Institute of Health, Av. Padre Cruz, 1649-016 Lisbon, Portugal.Show MeSH
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Mentions: To identify loci that phylogenetically contribute for the main branches of the species tree (Harris et al. 2012), we performed a detailed analysis of each gene phylogenetic tree. For clarification purposes, a gene/protein was considered to segregate a group of strains sharing a specific phenotype (ocular, prevalent genital, non-prevalent genital and LGV serovars) when the genetic differences among them are lower than the differences to any other strain. Overall, we found that 136, 14, 431, and 695 genes phylogenetically segregate the ocular, genital, prevalent genital and LGV groups, respectively (Figure 5A, Table 2, and Table S2). The low number of genes segregating the group of genital serovars reflects the high heterogeneity within this group as a direct consequence of the recombination background affecting mostly these strains (Harris et al. 2012) and the existence of distinct polymorphism signatures. An example of the latter stands for the F(s)/70 strain, which was isolated from the cervix and frequently showed a rather unusual polymorphism pattern that did not resemble any of the other 52 strains. Therefore, only 11 (1.3%) of nucleotide trees and 12 (1.4%) of protein trees were found to segregate strains by full-tropism (Figure 5A and Table 2), where ocular, LGV and all genital (prevalent and nonprevalent) serovar strains are segregated into three main clusters. In silico studies have already implicated some of these genes in the different cell-appetence of the strains, namely CT456/tarp, CT870/pmpF, CT872/pmpH, CT115/incD, CT116/incE, two PLD (CT156 and CT157), and one MACPF domain family protein (CT153) (Gomes et al. 2006; Thomson et al. 2008; Borges et al. 2012; Lutter et al. 2012). The remainders include three housekeeping genes (CT106/yceC, CT110/groEL1, and CT703/engA), and genes encoding one T3SS effector (CT161) (da Cunha et al. 2014) and one putative inclusion membrane protein (Inc) (CT383) (Dehoux et al. 2011) (Table S2).
Affiliation: Reference Laboratory of Sexually Transmitted Bacterial Infections, Department of Infectious Diseases, National Institute of Health, Av. Padre Cruz, 1649-016 Lisbon, Portugal.