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Diversity of T cell epitopes in Plasmodium falciparum circumsporozoite protein likely due to protein-protein interactions.

Aragam NR, Thayer KM, Nge N, Hoffman I, Martinson F, Kamwendo D, Lin FC, Sutherland C, Bailey JA, Juliano JJ - PLoS ONE (2013)

Bottom Line: Using the information from these parasite populations, structural analysis reveals that polymorphic amino acids within TH2 and TH3 colocalize to one side of the protein, surround, but do not involve, the hydrophobic pocket in CS, and predominately involve charge switches.In addition, free energy analysis shows polymorphic residues tend to be populated by energetically unfavorable amino acids.In combination, these findings suggest the diversity of T cell epitopes in CS may be primarily an evolutionary response to intermolecular interactions at the surface of the protein potentially counteracting antibody-mediated immune recognition or evolving host receptor diversity.

View Article: PubMed Central - PubMed

Affiliation: Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America.

ABSTRACT
Circumsporozoite protein (CS) is a leading vaccine antigen for falciparum malaria, but is highly polymorphic in natural parasite populations. The factors driving this diversity are unclear, but non-random assortment of the T cell epitopes TH2 and TH3 has been observed in a Kenyan parasite population. The recent publication of the crystal structure of the variable C terminal region of the protein allows the assessment of the impact of diversity on protein structure and T cell epitope assortment. Using data from the Gambia (55 isolates) and Malawi (235 isolates), we evaluated the patterns of diversity within and between epitopes in these two distantly-separated populations. Only non-synonymous mutations were observed with the vast majority in both populations at similar frequencies suggesting strong selection on this region. A non-random pattern of T cell epitope assortment was seen in Malawi and in the Gambia, but structural analysis indicates no intramolecular spatial interactions. Using the information from these parasite populations, structural analysis reveals that polymorphic amino acids within TH2 and TH3 colocalize to one side of the protein, surround, but do not involve, the hydrophobic pocket in CS, and predominately involve charge switches. In addition, free energy analysis suggests residues forming and behind the novel pocket within CS are tightly constrained and well conserved in all alleles. In addition, free energy analysis shows polymorphic residues tend to be populated by energetically unfavorable amino acids. In combination, these findings suggest the diversity of T cell epitopes in CS may be primarily an evolutionary response to intermolecular interactions at the surface of the protein potentially counteracting antibody-mediated immune recognition or evolving host receptor diversity.

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Nucleotide Diversity of pfcsp from Malawi and the Gambia.The nucleotide diversity (π) was determined for the sequenced region using a sliding window (size: 50 bp, slide: 25 bp). Two peaks in diversity are seen corresponding to the TH2 (bp 897–972) and TH3 (bp 1046–1091) epitopes. The peak level of diversity and pattern of diversity was similar between the two populations.
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pone-0062427-g002: Nucleotide Diversity of pfcsp from Malawi and the Gambia.The nucleotide diversity (π) was determined for the sequenced region using a sliding window (size: 50 bp, slide: 25 bp). Two peaks in diversity are seen corresponding to the TH2 (bp 897–972) and TH3 (bp 1046–1091) epitopes. The peak level of diversity and pattern of diversity was similar between the two populations.

Mentions: In order to assess the extent of genetic diversity and the extent of genetic similarity between populations, we investigated the nucleotide diversity of this 220 bp region of CS. In general, both populations had high levels of haplotype diversity (Hd: Malawi = 0.957 and Gambia = 0.953), which essentially is the measure of two random strains within the population having different haplotypes. The average number of pairwise nucleotide differences expected between two strains (K) was similar (6.00 vs. 6.68) with similar overall nucleotide diversity (π) diversity (0.023 vs 0.025), which is K normalized for the length of the sequence. Measures of nucleotide diversity are summarized in Table 3. The level of nucleotide diversity across this region is known to be uneven; therefore we re-evaluated nucleotide diversity (π) for each population using a sliding window approach (50 bp size, 25 bp slide) across the T cell epitopes using the program DnaSP (Figure 2). As expected, the regions of peak nucleotide diversity correspond to the TH2 and TH3 epitope regions, with the maximum diversity seen between positions 897 to 972 (corresponding to the TH2 epitope). Interestingly, in both populations, all polymorphisms were nonsynonymous indicating that this region of the pfcsp gene is likely to be under strong selection. Since diversification of haplotypes within this region may also occur due to recombination, we estimated the minimum number of recombination sites using DnaSP v5.10.01 [23]. A high number of recombination sites were predicted in both populations (8 in Malawi and 7 in the Gambia). In Malawi, the majority of these (6) were located within the TH2 (nucleotides 978–1029) and TH3 (nucleotides 1100–1135) epitopes themselves, suggesting recombination may be important for generation of diversity in these sites (Table 3). A single recombination event was detected between the two epitopes. Between the two populations, the fixation index (FST), a measure of the population differentiation due to genetic structure was 0.034 suggesting little genetic distance between the populations. We confirmed this using both phylogenetic and statistical methods. A Hudson’s Nearest Neighbor analysis, a test measuring how often the nearest neighbors are from the same population, showed no significant geographic separation of haplotypes (Snn = 0.440; ns). A neighbor joining network was constructed in MEGA and visually shows no evidence of geographic clustering (Figure S2). These data suggest that the levels and distribution of nucleotide diversity are similar in Malawi and the Gambia, and that these two populations, separated by an extended geographic distance, are remarkably genetically similar at the nucleotide level.


Diversity of T cell epitopes in Plasmodium falciparum circumsporozoite protein likely due to protein-protein interactions.

Aragam NR, Thayer KM, Nge N, Hoffman I, Martinson F, Kamwendo D, Lin FC, Sutherland C, Bailey JA, Juliano JJ - PLoS ONE (2013)

Nucleotide Diversity of pfcsp from Malawi and the Gambia.The nucleotide diversity (π) was determined for the sequenced region using a sliding window (size: 50 bp, slide: 25 bp). Two peaks in diversity are seen corresponding to the TH2 (bp 897–972) and TH3 (bp 1046–1091) epitopes. The peak level of diversity and pattern of diversity was similar between the two populations.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3646838&req=5

pone-0062427-g002: Nucleotide Diversity of pfcsp from Malawi and the Gambia.The nucleotide diversity (π) was determined for the sequenced region using a sliding window (size: 50 bp, slide: 25 bp). Two peaks in diversity are seen corresponding to the TH2 (bp 897–972) and TH3 (bp 1046–1091) epitopes. The peak level of diversity and pattern of diversity was similar between the two populations.
Mentions: In order to assess the extent of genetic diversity and the extent of genetic similarity between populations, we investigated the nucleotide diversity of this 220 bp region of CS. In general, both populations had high levels of haplotype diversity (Hd: Malawi = 0.957 and Gambia = 0.953), which essentially is the measure of two random strains within the population having different haplotypes. The average number of pairwise nucleotide differences expected between two strains (K) was similar (6.00 vs. 6.68) with similar overall nucleotide diversity (π) diversity (0.023 vs 0.025), which is K normalized for the length of the sequence. Measures of nucleotide diversity are summarized in Table 3. The level of nucleotide diversity across this region is known to be uneven; therefore we re-evaluated nucleotide diversity (π) for each population using a sliding window approach (50 bp size, 25 bp slide) across the T cell epitopes using the program DnaSP (Figure 2). As expected, the regions of peak nucleotide diversity correspond to the TH2 and TH3 epitope regions, with the maximum diversity seen between positions 897 to 972 (corresponding to the TH2 epitope). Interestingly, in both populations, all polymorphisms were nonsynonymous indicating that this region of the pfcsp gene is likely to be under strong selection. Since diversification of haplotypes within this region may also occur due to recombination, we estimated the minimum number of recombination sites using DnaSP v5.10.01 [23]. A high number of recombination sites were predicted in both populations (8 in Malawi and 7 in the Gambia). In Malawi, the majority of these (6) were located within the TH2 (nucleotides 978–1029) and TH3 (nucleotides 1100–1135) epitopes themselves, suggesting recombination may be important for generation of diversity in these sites (Table 3). A single recombination event was detected between the two epitopes. Between the two populations, the fixation index (FST), a measure of the population differentiation due to genetic structure was 0.034 suggesting little genetic distance between the populations. We confirmed this using both phylogenetic and statistical methods. A Hudson’s Nearest Neighbor analysis, a test measuring how often the nearest neighbors are from the same population, showed no significant geographic separation of haplotypes (Snn = 0.440; ns). A neighbor joining network was constructed in MEGA and visually shows no evidence of geographic clustering (Figure S2). These data suggest that the levels and distribution of nucleotide diversity are similar in Malawi and the Gambia, and that these two populations, separated by an extended geographic distance, are remarkably genetically similar at the nucleotide level.

Bottom Line: Using the information from these parasite populations, structural analysis reveals that polymorphic amino acids within TH2 and TH3 colocalize to one side of the protein, surround, but do not involve, the hydrophobic pocket in CS, and predominately involve charge switches.In addition, free energy analysis shows polymorphic residues tend to be populated by energetically unfavorable amino acids.In combination, these findings suggest the diversity of T cell epitopes in CS may be primarily an evolutionary response to intermolecular interactions at the surface of the protein potentially counteracting antibody-mediated immune recognition or evolving host receptor diversity.

View Article: PubMed Central - PubMed

Affiliation: Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America.

ABSTRACT
Circumsporozoite protein (CS) is a leading vaccine antigen for falciparum malaria, but is highly polymorphic in natural parasite populations. The factors driving this diversity are unclear, but non-random assortment of the T cell epitopes TH2 and TH3 has been observed in a Kenyan parasite population. The recent publication of the crystal structure of the variable C terminal region of the protein allows the assessment of the impact of diversity on protein structure and T cell epitope assortment. Using data from the Gambia (55 isolates) and Malawi (235 isolates), we evaluated the patterns of diversity within and between epitopes in these two distantly-separated populations. Only non-synonymous mutations were observed with the vast majority in both populations at similar frequencies suggesting strong selection on this region. A non-random pattern of T cell epitope assortment was seen in Malawi and in the Gambia, but structural analysis indicates no intramolecular spatial interactions. Using the information from these parasite populations, structural analysis reveals that polymorphic amino acids within TH2 and TH3 colocalize to one side of the protein, surround, but do not involve, the hydrophobic pocket in CS, and predominately involve charge switches. In addition, free energy analysis suggests residues forming and behind the novel pocket within CS are tightly constrained and well conserved in all alleles. In addition, free energy analysis shows polymorphic residues tend to be populated by energetically unfavorable amino acids. In combination, these findings suggest the diversity of T cell epitopes in CS may be primarily an evolutionary response to intermolecular interactions at the surface of the protein potentially counteracting antibody-mediated immune recognition or evolving host receptor diversity.

Show MeSH
Related in: MedlinePlus