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. 2015 Apr 16;10(4):e0124400.
doi: 10.1371/journal.pone.0124400. eCollection 2015.

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

Affiliations

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

Bart W Faber et al. PLoS One. .

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.

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Conflict of interest statement

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

Figures

Fig 1
Fig 1. Polymorphic residues in the PkAMA1 protein.
High frequency polymorphic sites in red, bold and highlighted in white; low frequency polymorphic sites in black.
Fig 2
Fig 2. 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.
Fig 3
Fig 3. Three-dimensional distribution of polymorphic amino acid residues of PkAMA1, PfAMA1 and PvAMA1.
Two views of a surface representation, rotated by 180° with respect to each other, are shown for the crystal structures of (A) PkAMA1 (PDB entry 4UV6), (B) PfAMA1 (PDB entry 2Z8V) and (C) PvAMA1 (PDB entry 1W8L), with each orthologue oriented at equivalent angles. PkAMA1 polymorphisms are from this study, PfAMA1 polymorphisms are from refs [23,24] and PvAMA1 polymorphisms are from ref [25]. Polymorphic residues are labeled and colored in red for high frequency polymorphisms (> 10%) and in blue for low frequency polymorphisms (< 10%). Domains 1 and 2 from crystal structures of all three orthologues are shown in white. Domain 3, shown in grey, was modeled for PkAMA1 and PfAMA1 from the crystal structure of PvAMA1 since the crystal structure of this domain has not been determined for these two orthologues. (PkAMA1 Domain 3 polymorphic residues 411 and 481 are not shown as these are disordered and thus not visible in the PvAMA1 structure).

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References

    1. Singh B, Daneshvar C (2013) Human infections and detection of Plasmodium knowlesi. Clin Microbiol Rev 26: 165–184. 10.1128/CMR.00079-12 - DOI - PMC - PubMed
    1. Lee KS, Cox-Singh J, Singh B (2009) Morphological features and differential counts of Plasmodium knowlesi parasites in naturally acquired human infections. Malar J 8: 73 10.1186/1475-2875-8-73 - DOI - PMC - PubMed
    1. William T, Jelip J, Menon J, Anderios F, Mohammad R, Awang Mohammad TA, et al. (2014) Changing epidemiology of malaria in Sabah, Malaysia: increasing incidence of Plasmodium knowlesi. Malar J 13: 390 10.1186/1475-2875-13-390 - DOI - PMC - PubMed
    1. Lee KS, Cox-Singh J, Brooke G, Matusop A, Singh B (2009) Plasmodium knowlesi from archival blood films: further evidence that human infections are widely distributed and not newly emergent in Malaysian Borneo. Int J Parasitol 39: 1125–1128. 10.1016/j.ijpara.2009.03.003 - DOI - PMC - PubMed
    1. Chin W, Contacos PG, Collins WE, Jeter MH, Alpert E (1968) Experimental mosquito-transmission of Plasmodium knowlesi to man and monkey. Am J Trop Med Hyg 17: 355–358. - PubMed

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Grants and funding

This work was supported by: European Commission EUROMALVAC2 (contract QLK2-CT-2002-01197), The Centre National de la Recherche Scientifique, The Universiti Malaysia Sarawak (grant number 01(TD03)/1003/2013(01)), European Commission EMVDA grant LSHP-CT-2007-037506, E(M)VI, The European (Malaria) Vaccine Initiative, and Universiti of Sarawak: Grant E14054/F05/54/PKI/09/2012(01); www.emvda.org; www.euvaccine.eu; www.evimalar.org; ec.europa.eu/research/health/infectious-diseases/poverty-diseases/projects/71_en.htm. The external funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.