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Low levels of polymorphisms and no evidence for diversifying selection on the Plasmodium knowlesi Apical Membrane Antigen 1 gene.

Faber BW, Abdul Kadir K, Rodriguez-Garcia R, Remarque EJ, Saul FA, Vulliez-Le Normand B, Bentley GA, Kocken CH, Singh B - PLoS ONE (2015)

Bottom Line: Statistically significant differences in the quantity of three of the six high frequency mutations were observed between the two regions.These analyses suggest that the pkama1 gene is not under balancing selection, as observed for pfama1 and pvama1, and that the PkAMA1 protein is not a primary target for protective humoral immune responses in their reservoir macaque hosts, unlike PfAMA1 and PvAMA1 in humans.The low level of polymorphism justifies the development of a single allele PkAMA1-based vaccine.

View Article: PubMed Central - PubMed

Affiliation: Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, The Netherlands.

ABSTRACT
Infection with Plasmodium knowlesi, a zoonotic primate malaria, is a growing human health problem in Southeast Asia. P. knowlesi is being used in malaria vaccine studies, and a number of proteins are being considered as candidate malaria vaccine antigens, including the Apical Membrane Antigen 1 (AMA1). In order to determine genetic diversity of the ama1 gene and to identify epitopes of AMA1 under strongest immune selection, the ama1 gene of 52 P. knowlesi isolates derived from human infections was sequenced. Sequence analysis of isolates from two geographically isolated regions in Sarawak showed that polymorphism in the protein is low compared to that of AMA1 of the major human malaria parasites, P. falciparum and P. vivax. Although the number of haplotypes was 27, the frequency of mutations at the majority of the polymorphic positions was low, and only six positions had a variance frequency higher than 10%. Only two positions had more than one alternative amino acid. Interestingly, three of the high-frequency polymorphic sites correspond to invariant sites in PfAMA1 or PvAMA1. Statistically significant differences in the quantity of three of the six high frequency mutations were observed between the two regions. These analyses suggest that the pkama1 gene is not under balancing selection, as observed for pfama1 and pvama1, and that the PkAMA1 protein is not a primary target for protective humoral immune responses in their reservoir macaque hosts, unlike PfAMA1 and PvAMA1 in humans. The low level of polymorphism justifies the development of a single allele PkAMA1-based vaccine.

No MeSH data available.


Related in: MedlinePlus

Analyses of the genes encoding the full length PkAMA1 protein.A) Schematic representation of the pkama1 gene, indicating the locations of all non-synonymous (NS, red lines), synonymous (SP, blue lines) and NS and SP singleton (black and grey lines, respectively) SNPs. B) Sliding window analysis showing the average pairwise nucleotide diversity (Pi) values in Pkama1 for the 52 sequences included in the analysis. A window size of 100 bp and a step size of 25 bp were used. C) Sliding window calculation of Tajima’s D. A window size of 100 and a step size of 25 were used. D) Sliding window calculation of Fu&Li’s D (red line) and F (blue line). A window size of 100 and a step size of 25 were used. E) Amino acid frequencies. The frequencies of 21 amino acid polymorphic positions are indicated by the proportion of each bar and its color. Light blue, most prominent amino acid; orange, second most prominent amino acid; dark blue, least prominent amino acid.
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pone.0124400.g002: Analyses of the genes encoding the full length PkAMA1 protein.A) Schematic representation of the pkama1 gene, indicating the locations of all non-synonymous (NS, red lines), synonymous (SP, blue lines) and NS and SP singleton (black and grey lines, respectively) SNPs. B) Sliding window analysis showing the average pairwise nucleotide diversity (Pi) values in Pkama1 for the 52 sequences included in the analysis. A window size of 100 bp and a step size of 25 bp were used. C) Sliding window calculation of Tajima’s D. A window size of 100 and a step size of 25 were used. D) Sliding window calculation of Fu&Li’s D (red line) and F (blue line). A window size of 100 and a step size of 25 were used. E) Amino acid frequencies. The frequencies of 21 amino acid polymorphic positions are indicated by the proportion of each bar and its color. Light blue, most prominent amino acid; orange, second most prominent amino acid; dark blue, least prominent amino acid.

Mentions: Six high frequency polymorphic sites (f >10%) were identified (Table 1, Fig 2E). Three of these are shared with PfAMA1 at the following positions: Pkaa188(KN)→Pfaa243(KNE), Pkaa228(KN)→Pfaa283(SL) and Pkaa277(RT)→Pfaa332(NI), the latter two also with PvAMA1 [17,18]. The three remaining high frequency polymorphisms occur neither in PfAMA1 nor in PvAMA1. Of these, residue aa481 and aa465 are very close to the membrane-spanning region. On basis of homology with PfAMA1, these sites are located outside the normal cleavage site of the shedding protease PfSUB1 (PfAMA1 T517, corresponding to K459 in PkAMA1 [19]). The third high-frequency polymorphic site in PkAMA1 that does not occur in PfAMA1 is R296. This residue is at a stem region of the flexible loop in domain II, and contributes a salt bridge. The implications of the PkAMA1 mutations for structure/function are discussed elsewhere [20].


Low levels of polymorphisms and no evidence for diversifying selection on the Plasmodium knowlesi Apical Membrane Antigen 1 gene.

Faber BW, Abdul Kadir K, Rodriguez-Garcia R, Remarque EJ, Saul FA, Vulliez-Le Normand B, Bentley GA, Kocken CH, Singh B - PLoS ONE (2015)

Analyses of the genes encoding the full length PkAMA1 protein.A) Schematic representation of the pkama1 gene, indicating the locations of all non-synonymous (NS, red lines), synonymous (SP, blue lines) and NS and SP singleton (black and grey lines, respectively) SNPs. B) Sliding window analysis showing the average pairwise nucleotide diversity (Pi) values in Pkama1 for the 52 sequences included in the analysis. A window size of 100 bp and a step size of 25 bp were used. C) Sliding window calculation of Tajima’s D. A window size of 100 and a step size of 25 were used. D) Sliding window calculation of Fu&Li’s D (red line) and F (blue line). A window size of 100 and a step size of 25 were used. E) Amino acid frequencies. The frequencies of 21 amino acid polymorphic positions are indicated by the proportion of each bar and its color. Light blue, most prominent amino acid; orange, second most prominent amino acid; dark blue, least prominent amino acid.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4400157&req=5

pone.0124400.g002: Analyses of the genes encoding the full length PkAMA1 protein.A) Schematic representation of the pkama1 gene, indicating the locations of all non-synonymous (NS, red lines), synonymous (SP, blue lines) and NS and SP singleton (black and grey lines, respectively) SNPs. B) Sliding window analysis showing the average pairwise nucleotide diversity (Pi) values in Pkama1 for the 52 sequences included in the analysis. A window size of 100 bp and a step size of 25 bp were used. C) Sliding window calculation of Tajima’s D. A window size of 100 and a step size of 25 were used. D) Sliding window calculation of Fu&Li’s D (red line) and F (blue line). A window size of 100 and a step size of 25 were used. E) Amino acid frequencies. The frequencies of 21 amino acid polymorphic positions are indicated by the proportion of each bar and its color. Light blue, most prominent amino acid; orange, second most prominent amino acid; dark blue, least prominent amino acid.
Mentions: Six high frequency polymorphic sites (f >10%) were identified (Table 1, Fig 2E). Three of these are shared with PfAMA1 at the following positions: Pkaa188(KN)→Pfaa243(KNE), Pkaa228(KN)→Pfaa283(SL) and Pkaa277(RT)→Pfaa332(NI), the latter two also with PvAMA1 [17,18]. The three remaining high frequency polymorphisms occur neither in PfAMA1 nor in PvAMA1. Of these, residue aa481 and aa465 are very close to the membrane-spanning region. On basis of homology with PfAMA1, these sites are located outside the normal cleavage site of the shedding protease PfSUB1 (PfAMA1 T517, corresponding to K459 in PkAMA1 [19]). The third high-frequency polymorphic site in PkAMA1 that does not occur in PfAMA1 is R296. This residue is at a stem region of the flexible loop in domain II, and contributes a salt bridge. The implications of the PkAMA1 mutations for structure/function are discussed elsewhere [20].

Bottom Line: Statistically significant differences in the quantity of three of the six high frequency mutations were observed between the two regions.These analyses suggest that the pkama1 gene is not under balancing selection, as observed for pfama1 and pvama1, and that the PkAMA1 protein is not a primary target for protective humoral immune responses in their reservoir macaque hosts, unlike PfAMA1 and PvAMA1 in humans.The low level of polymorphism justifies the development of a single allele PkAMA1-based vaccine.

View Article: PubMed Central - PubMed

Affiliation: Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, The Netherlands.

ABSTRACT
Infection with Plasmodium knowlesi, a zoonotic primate malaria, is a growing human health problem in Southeast Asia. P. knowlesi is being used in malaria vaccine studies, and a number of proteins are being considered as candidate malaria vaccine antigens, including the Apical Membrane Antigen 1 (AMA1). In order to determine genetic diversity of the ama1 gene and to identify epitopes of AMA1 under strongest immune selection, the ama1 gene of 52 P. knowlesi isolates derived from human infections was sequenced. Sequence analysis of isolates from two geographically isolated regions in Sarawak showed that polymorphism in the protein is low compared to that of AMA1 of the major human malaria parasites, P. falciparum and P. vivax. Although the number of haplotypes was 27, the frequency of mutations at the majority of the polymorphic positions was low, and only six positions had a variance frequency higher than 10%. Only two positions had more than one alternative amino acid. Interestingly, three of the high-frequency polymorphic sites correspond to invariant sites in PfAMA1 or PvAMA1. Statistically significant differences in the quantity of three of the six high frequency mutations were observed between the two regions. These analyses suggest that the pkama1 gene is not under balancing selection, as observed for pfama1 and pvama1, and that the PkAMA1 protein is not a primary target for protective humoral immune responses in their reservoir macaque hosts, unlike PfAMA1 and PvAMA1 in humans. The low level of polymorphism justifies the development of a single allele PkAMA1-based vaccine.

No MeSH data available.


Related in: MedlinePlus