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

<p>Abstract</p> <p>Background</p> <p>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. <it>Plasmodium vivax</it>, 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 <it>P. vivax</it>-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.</p> <p>Results</p> <p>We performed comparative phylogenetic and population genetic analyses of the gene encoding MSP-1 (<it>msp1</it>) from <it>P. vivax </it>and nine <it>P. vivax</it>-related simian malaria parasites. The inferred phylogenetic tree of <it>msp1 </it>significantly differed from that of the mitochondrial genome, with a striking displacement of <it>P. vivax </it>from a position close to <it>P. cynomolgi </it>in the mitochondrial genome tree to an outlier of Asian monkey parasites. Importantly, positive selection was inferred for two ancestral branches, one leading to <it>P. inui </it>and <it>P. hylobati </it>and the other leading to <it>P. vivax</it>, <it>P. fieldi </it>and <it>P. cynomolgi</it>. 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 <it>msp1 </it>polymorphisms between <it>P. vivax</it>, <it>P. inui </it>and <it>P. cynomolgi </it>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 <it>msp1</it>.</p> <p>Conclusions</p> <p>The present results indicate that the <it>msp1 </it>locus of <it>P. vivax </it>and related parasite species has lineage-specific unique evolutionary history with positive selection. <it>P. vivax </it>and related simian malaria parasites offer an interesting system toward understanding host species-dependent adaptive evolution of immune-target surface antigen genes such as <it>msp1</it>.</p

Serologic Markers in Relation to Parasite Exposure History Help to Estimate Transmission Dynamics of Plasmodium vivax

Plasmodium vivax infection has been gaining attention because of its re-emergence in several parts of the world. Southeastern Turkey is one of the places in which persistent focal malaria caused exclusively by P. vivax parasites occurs. Although control and elimination studies have been underway for many years, no detailed study has been conducted to understand the mechanisms underlying the ineffective control of malaria in this region. Here, for the first time, using serologic markers we try to extract as much information as possible in this region to get a glimpse of P. vivax transmission. We conducted a sero-immunological study, evaluating antibody responses of individuals living in Sanliurfa to four different P. vivax antigens; three blood-stage antigens (PvMSP119, PvAMA1-ecto, and PvSERA4) and one pre-erythrocytic stage antigen (PvCSP). The results suggest that a prior history of malaria infection and age can be determining factors for the levels and sustainability of naturally acquired antibodies. Significantly higher antibody responses to all the studied antigens were observed in blood smear-negative individuals with a prior history of malaria infection. Moreover, these individuals were significantly older than blood smear-negative individuals with no prior history of infection. These data from an area of sole P. vivax-endemic region may have important implications for the global malaria control/elimination programs and vaccine design

Clues to Evolution of the SERA Multigene Family in 18 Plasmodium Species

SERA gene sequences were newly determined from 11 primate Plasmodium species including two human parasites, P. ovale and P. malariae, and the evolutionary history of SERA genes was analyzed together with 7 known species. All have one each of Group I to III cysteine-type SERA genes and varying number of Group IV serine-type SERA genes in tandem cluster. Notably, Group IV SERA genes were ascertained in all mammalian parasite lineages; and in two primate parasite lineages gene events such as duplication, truncation, fragmentation and gene loss occurred at high frequency in a manner that mimics the birth-and-death evolution model. Transcription profile of individual SERA genes varied greatly among rodent and monkey parasites. Results support the lineage-specific evolution of the Plasmodium SERA gene family. These findings provide further impetus for studies that could clarify/provide proof-of-concept that duplications of SERA genes were associated with the parasites' expansion of host range and the evolutionary conundrums of multigene families in Plasmodium

Molecular phylogeny and evolution of the amitochondriate protists

Amitochondoriate protists are unicellular eukaryotes that lack mitochondria. Diplomonadida(including Giardia), Palabasala (including Trichomonas), Entamoebidae （including Entamoeba), Pelobionta(including Mastigamoeba), and Microsporidia (including Encephalitozoon) are well known as major lineages.Morphological evidence and findings on the ribosomes showing \u27primitive eukaryotic\u27 features for these lineages led a proposal of the \u27Archezoa\u27 hypothesis that several amitochondriate protist lineages(Archezoa) diverged preceding the endosymbiotic origin of proto-mitochondria, and thus have been living relics of the early phase of eukaryotic evolution.Early studies on the eukaryotic phylogenies based on the small subunit (SSU) ribosomal RNA (rRNA) and on the translation elongation factors(EF) supported this hypothesis, placing three amitochondriate protists lineages, Microsporidia, Parabasala and Diplomonadida, at the basal position of the eukaryotic tree.However, phylogenies based on other genes, such as tubulins, mitochondorial-type heat shock protein 70 (HSP70mit) and the largest subunit of RNA polymeraseII(RpoII). suggested that Microsporidia are not deep branching eukaryotes but are closely related to Fungi, Furthermore, phylogenies of various genes based on the recent accumulation of many sequence data from various protist lineages sometimes gave conflicting results with each other, indicating that the phylogenetic relationships among major eukaryotic lineages have still been an open problem.On the other hand, mitochondrion-related genes that are coded in nuclear DNA and target for mitochondria were isolated from Entamoebidae, Microsporidia, Parabasala and Diplomonadida. The findings suggested that ancestors of these amitochondriate lineages once harbored mitochondria and lost them secondarily during their evolution.On these backgrounds of the studies on early eukaryotic evolution, this work was intended to elucidate an evolutionary status of the amitochondriate protists.First, in order to establish a robust placement of the amitochondriate protist lineages in the eukaryotic tree, phylogenetic relationships among major eukaryotic lineages including amitochondriate protists were statistically analyzed in detail by applying a combined maximum likelihood (ML) method to the sequence data of multiple genes. Next, in order to establish whether the ribosomal features of potentially early-branching lineages are\u27primitive eukaryotic\u27, the ribosomes of the amitochondriate protists, Giardia intestinalis (Diplomonadida) and Trichomonas vaginalis (Parabasala), were analyzed, and the components were compared to those of other eukaryotic organisms including amitochondriate protists.Chapter 1 of this article described the analyses of the phylogenetic relationships among major eukaryotic lineages including amitochondriate protists, with the reports on 27 original sequence data of various genes mostly derived from amitochondriate protists.At first, phylogenetic positions of Microsporidia and of stramenopiles were analyzed. In order to clearly settle a phylogenetic position of　Microsporidia among major eukaryotic lineages, a combined ML analysis was performed using 6,391 positions from 10 genes for which data from Microsporidia were available. These genes were EF-1α, EF-2, valyl- and isoleucy1- tRNA synthetases (ValRS, IleRS), RpoII, Actin, α-tubulin,β-tubulin, SSUrRNA， and large subunit(LSU) rRNA. Although several phylogenies based on individual genes, such as EF-1α, IleRS, and SSUrRNA, did not support a close relationship between Microsporidia and Fungi, the combined analysis clearly demonstrated a relationship,(Metazoa,(Fungi, Microsporidia)) with a very high statistical support. In addition, another combined ML analysis was performed to examine a relationship between stramenopiles and Alveolata, using 5,423 positions from eight genes for which data from stramenopiles were available (EF-1α, EF-2, cytosolic-type HSP70 (HSP70c), non-catalytic \u27B\u27 subunit of vacuolar ATPase, Actin, β-tubulin, SSUrRNA, and LSUrRNA). The analysis demonstrated also with a very high statistical support that stramenopiles and Alveolata were the closest relatives with each other.In the next, the phylogenetic position of the Pelobiont Mastigamoeba balamuthi was analyzed in relation to the position of E. histolytica. A combined ML analysis using 3,935 positions from four genes, SSUrRNA, LSUrRNA, EF-1α, and EF-2, suggested that M. balamuthi was the closest relative of E. histolytica and that Mycetozoa were placed at the sistergroup to the common ancester of M. balamuthi and E. histolytica. These findings supported the notion, which had previously been proposed primarily on cytological evidence, that both M. balamuthi and E.histolytica are closely related to the Mycetozoa and that these three together represent a major eukaryotic lineage (Conosa). Finally, on the basis of the findings as mentioned above and as currently reported in the literatures, 13 major eukaryotic lineages were divided into seven groups:1.(Metazoa,(Fungi, Microsporidia)), 2. (Mycetozoa,(Pelobionta, Entamoebidae)) [Conosa], 3. (Viridiplantae, Rhodophyta), 4.(stramenopiles, Alveolata), 5. Euglenozoa，6. Diplomonadida, and 7. Parabasala. Phylogenetic relationships among these groups with an outgroup were examined by a combined ML analysis of the genes, EF-1α, EF-2, ribosomal protein (Rp) S14, RpS15a, RpL5, RpL8, RpL10a, IleRS, ValRS, RpoII, chaperonin 60, HSP70mit, endoplasmic reticulum-type HSP70, HSP70c and cytosolic-type HSP90, chaperonin-containing testis complex polypeptide-1 subunit (CCT) α, CCTγ, CCTδ, CCTζ, Actin,α-tubulin,β-tubulin, SSUrRNA, and LSUrRNA. The combined ML analysis clearly supported with statistical confidence that Diplomonadida and Parabasala diverged earlier than other five groups in the eukaryotic tree, although the branching order between these two lineages were still open for further analysis. In addition, especially when among-site rate heterogeneity was taken into consideration, it was clearly supported that (Metazoa, (Fungi, Microsporidia)), Conosa, and (Viridiplantae, Rhodophyta) were the first, the second and the third earliest offshoots among the five groups excluding Diplomonadida and Parabasala. The analysis at the first time demonstrated robustly that Diplomonadida and Parabasala are the early branching eukaryotes, although presence of a potential artefact derived from a long branch attraction could not be ruled out entirely.Chapter 2 of this article described the analyses of the ribosomes of potentially early branching amitochondriate protists, G. intestinalis and T. vaginalis. Sedimentation analyses demonstrated that the sedimentation coefficients of these ribosomes were larger than that of Escherichia coli and smaller than that of Saccharomyces cerevisiae or Artemia salina. Based on the radical free and highly reduced two dimensional polyacrylamide gel electrophoresis analysis, N-terminal sequencing analysis, and/or similarity search on the public database, the number of ribosomal proteins were estimated to be at least 74 for G. intestinalis and approximately 80 for T. vaginalis. These numbers were comparable with that of a\u27typical\u27eukaryote (about 80) and larger than that of E. coli (about 55). The N-terminal sequences of the protein spots and alignment analyses of all the ribosomal proteins currently available revealed that the sequences of G. intestinalis and T. vaginalis are clearly of ‘typical\u27 eukayotic type with no exception.On the other hand, sequence comparison analyses of rRNAs revealed that the SSU and LSUrRNAs of G. intestinalis and T. vaginalis were remarkably shorter in length than those of ‘typical\u27eukaryotes. All the helices that belong to the universal core, however, were strictly conserved also in G. intestinalis and T. vaginalis. In contrast, variable regions of both rRNAs were reduced to be short in G. intestinalis and T. vaginalis.As far as these results are concerned, the protein components and the essential parts of the rRNAs of the G. intestinalis and T. vaginalis ribosomes are clearly of \u27typical\u27 eukaryotic type. No\u27primitive eukaryotic\u27 features are found in the ribosomes of these amitochondriate protists. The smaller sedimentation coefficients of the ribosomes of G. intestinalis and T. vaginalis than those of \u27typical\u27 eukaryotes are due to the smaller size of rRNAs with shortened variable regions. These findings give additional evidence for fully developed eukaryotic nature of G. intestinalis and T. vaginalis. Probably Diplomonadida and Parabasala already had obtained major eukaryotic properties commonly found in the\u27typical\u27eukaryotes