Lineage-specific positive selection at the merozoite surface protein 1 (msp1) locus of Plasmodium vivax and related simian malaria parasites

Abstract

Background: The 200 kDa merozoite surface protein 1 (MSP-1) of malaria parasites, a strong vaccine candidate, plays a key role during erythrocyte invasion and is a target of host protective immune response. Plasmodium vivax, the most widespread human malaria parasite, is closely related to parasites that infect Asian Old World monkeys, and has been considered to have become a parasite of man by host switch from a macaque malaria parasite. Several Asian monkey parasites have a range of natural hosts. The same parasite species shows different disease manifestations among host species. This suggests that host immune responses to P. vivax-related malaria parasites greatly differ among host species (albeit other factors). It is thus tempting to invoke that a major immune target parasite protein such as MSP-1 underwent unique evolution, depending on parasite species that exhibit difference in host range and host specificity.

Results: We performed comparative phylogenetic and population genetic analyses of the gene encoding MSP-1 (msp1) from P. vivax and nine P. vivax-related simian malaria parasites. The inferred phylogenetic tree of msp1 significantly differed from that of the mitochondrial genome, with a striking displacement of P. vivax from a position close to P. cynomolgi in the mitochondrial genome tree to an outlier of Asian monkey parasites. Importantly, positive selection was inferred for two ancestral branches, one leading to P. inui and P. hylobati and the other leading to P. vivax, P. fieldi and P. cynomolgi. This ancestral positive selection was estimated to have occurred three to six million years ago, coinciding with the period of radiation of Asian macaques. Comparisons of msp1 polymorphisms between P. vivax, P. inui and P. cynomolgi revealed that while some positively selected amino acid sites or regions are shared by these parasites, amino acid changes greatly differ, suggesting that diversifying selection is acting species-specifically on msp1.

Conclusions: The present results indicate that the msp1 locus of P. vivax and related parasite species has lineage-specific unique evolutionary history with positive selection. P. vivax and related simian malaria parasites offer an interesting system toward understanding host species-dependent adaptive evolution of immune-target surface antigen genes such as msp1.

Figure 1

Phylogenetic trees of the mitochondrial genome and msp1 of P. vivax and P. vivax-related simian malaria parasite species. (a) The maximum-likelihood (ML) tree of the mitochondrial genome. Aligned sequences of the mitochondrial genome (5818 bp) from P. vivax and related simian malaria parasite species were used for constructing the tree with 100 heuristic replicates under the GTR + I + G model with an α = 0.812. (b) The ML tree of the msp1 gene. The aligned 4176 bp (Additional file 3) sequences were used for constructing the tree with 100 heuristic replicates under the GTR + I + G model with an α = 0.866. Abbreviations of species and strains are: Pgo = P. gonderi, Pfr = P. fragile, Pco = P. coatneyi, Pkn = P. knowlesi, Pfi = P. fieldi, Psi = P. simiovale, Pcy = P. cynomolgi, Pvi = P. vivax, Phy = P. hylobati, and Pin = P. inui; and Hack = Hackeri, Nilg = Nilgiri, Mala = Malayan, N3 = N-3, Abi = A.b.introlatus, Smi = Smithsonian, Cam = Cambodian, Ceyl = Ceylonensis, Lan = Langur, Gom = Gombak, SalI = Sal-I, Bel = Belem, Cel = Celebes, CelII = Celebes II, Hawk = Hawking, Leaf1 = Leaf monkey #1, Mul = Mulligan. In both (a) and (b), only bootstrap values = 60% are indicated at nodes.

Figure 2

Lineage-specific positive selection in the phylogeny of msp1 from P. vivax and P. vivax-related simian malaria parasite species. The maximum-likelihood (ML) tree topology was constructed using sequences of msp1 codon 3 for (a) the whole msp1 gene, (b) the 5' region, (c) the central region and (d) the 3' region. The estimates of kA and kS (×100) are shown above each branch. Branches showing ω (= kA/kS) >1 are bold-lined. A branch showing ω significantly greater than 1 (P < 0.05), when the free ratio model was compared with the constrained model that fixed ω of the branch of interest at 1, is double-asterisked; and that weakly higher than 1 (P < 0.1) is asterisked. Abbreviations are: Pfi, P. fieldi N-3; Pvi, P. vivax Sal-I; Pcy, P. cynomolgi Smithsonian; Phy, P. hylobati; Pin, P. inui Celebes; Pco, P. coatneyi; Pkn, P. knowlesi H; Pfr, P. fragile NIH; Pgo, P. gonderi.

Figure 3

Positively selected codon sites along the msp1 alignment of P. vivax and P. vivax-related simian malaria parasites. Positively selected sites with ω (= dN/dS) >1 were detected by (a) omegaMap [29] and (b) HyPhy/Datamonkey [30]. Boxes indicate positively selected regions shared by three parasite species. In (a), positions of codon showing ω > 1 with more than 95% posterior probability are denoted by half-tone bars. In (b), individual sites with ω significantly greater than 1 are mapped by vertical lines. In P. vivax, computations were repeated five times after random sampling from a pool of sequences, and sites detected at least once in the analyses; or those detected 3 times or more are shown as "sum" and "consensus", respectively. Refer to Additional file 3; figure S1 for individual amino acid replacements.