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In silico scrutiny of genes revealing phylogenetic congruence with clinical prevalence or tropism properties of Chlamydia trachomatis strains.

Ferreira R, Antelo M, Nunes A, Borges V, Damião V, Borrego MJ, Gomes JP - G3 (Bethesda) (2014)

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.Approximately 3.5% of the genes revealed a significant overrepresentation of nonsynonymous mutations, and the majority encode proteins that directly interact with the host.Overall, this in silico scrutiny of genes whose phylogeny is congruent with clinical prevalence or tissue specificity of C. trachomatis strains may constitute an important database of putative targets for future functional studies to evaluate their biological role in chlamydial infections.

View Article: PubMed Central - PubMed

Affiliation: Reference Laboratory of Sexually Transmitted Bacterial Infections, Department of Infectious Diseases, National Institute of Health, Av. Padre Cruz, 1649-016 Lisbon, Portugal.

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Genes that segregate strains according to their biological characteristics. The outer circle in both panels represents the genome of C. trachomatis D/UW-3/CX strain, where each bar represents a gene at its respective genomic position (light gray bars, forward strand; dark gray bars, reverse strand). (A) The tracks’ color scheme represent genes whose phylogeny segregates at least a group of strains according to their biological characteristics, i.e., each color illustrates a particular segregation (that may not be exclusive): full-tropism (purple), LGV strains (orange), strains from prevalent genital serovars (green), cosegregation of LGV and prevalent genital serovar strains (blue), genital strains (prevalent and nonprevalent serovars) (black), and ocular strains (red). (B) The tracks’ color scheme was maintained for the different groups of strains and represent genes that exclusively segregate a unique group of strains. For both panels, the outer and inner tracks of each color correspond to nucleotide and amino acid results, respectively.
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fig5: Genes that segregate strains according to their biological characteristics. The outer circle in both panels represents the genome of C. trachomatis D/UW-3/CX strain, where each bar represents a gene at its respective genomic position (light gray bars, forward strand; dark gray bars, reverse strand). (A) The tracks’ color scheme represent genes whose phylogeny segregates at least a group of strains according to their biological characteristics, i.e., each color illustrates a particular segregation (that may not be exclusive): full-tropism (purple), LGV strains (orange), strains from prevalent genital serovars (green), cosegregation of LGV and prevalent genital serovar strains (blue), genital strains (prevalent and nonprevalent serovars) (black), and ocular strains (red). (B) The tracks’ color scheme was maintained for the different groups of strains and represent genes that exclusively segregate a unique group of strains. For both panels, the outer and inner tracks of each color correspond to nucleotide and amino acid results, respectively.

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).


In silico scrutiny of genes revealing phylogenetic congruence with clinical prevalence or tropism properties of Chlamydia trachomatis strains.

Ferreira R, Antelo M, Nunes A, Borges V, Damião V, Borrego MJ, Gomes JP - G3 (Bethesda) (2014)

Genes that segregate strains according to their biological characteristics. The outer circle in both panels represents the genome of C. trachomatis D/UW-3/CX strain, where each bar represents a gene at its respective genomic position (light gray bars, forward strand; dark gray bars, reverse strand). (A) The tracks’ color scheme represent genes whose phylogeny segregates at least a group of strains according to their biological characteristics, i.e., each color illustrates a particular segregation (that may not be exclusive): full-tropism (purple), LGV strains (orange), strains from prevalent genital serovars (green), cosegregation of LGV and prevalent genital serovar strains (blue), genital strains (prevalent and nonprevalent serovars) (black), and ocular strains (red). (B) The tracks’ color scheme was maintained for the different groups of strains and represent genes that exclusively segregate a unique group of strains. For both panels, the outer and inner tracks of each color correspond to nucleotide and amino acid results, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4291473&req=5

fig5: Genes that segregate strains according to their biological characteristics. The outer circle in both panels represents the genome of C. trachomatis D/UW-3/CX strain, where each bar represents a gene at its respective genomic position (light gray bars, forward strand; dark gray bars, reverse strand). (A) The tracks’ color scheme represent genes whose phylogeny segregates at least a group of strains according to their biological characteristics, i.e., each color illustrates a particular segregation (that may not be exclusive): full-tropism (purple), LGV strains (orange), strains from prevalent genital serovars (green), cosegregation of LGV and prevalent genital serovar strains (blue), genital strains (prevalent and nonprevalent serovars) (black), and ocular strains (red). (B) The tracks’ color scheme was maintained for the different groups of strains and represent genes that exclusively segregate a unique group of strains. For both panels, the outer and inner tracks of each color correspond to nucleotide and amino acid results, respectively.
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).

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.Approximately 3.5% of the genes revealed a significant overrepresentation of nonsynonymous mutations, and the majority encode proteins that directly interact with the host.Overall, this in silico scrutiny of genes whose phylogeny is congruent with clinical prevalence or tissue specificity of C. trachomatis strains may constitute an important database of putative targets for future functional studies to evaluate their biological role in chlamydial infections.

View Article: PubMed Central - PubMed

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
Related in: MedlinePlus