Genetic diversity and natural selection of Plasmodium knowlesi merozoite surface protein 1 paralog gene in Malaysia

Abstract

BackgroundHuman infections due to the monkey malaria parasite Plasmodium knowlesi is on the rise in most Southeast Asian countries specifically Malaysia. The C-terminal 19 kDa domain of PvMSP1P is a potential vaccine candidate, however, no study has been conducted in the orthologous gene of P. knowlesi. This study investigates level of polymorphisms, haplotypes and natural selection of full-length pkmsp1p in clinical samples from Malaysia.MethodsA total of 36 full-length pkmsp1p sequences along with the reference H-strain and 40 C-terminal pkmsp1p sequences from clinical isolates of Malaysia were downloaded from published genomes. Genetic diversity, polymorphism, haplotype and natural selection were determined using DnaSP 5.10 and MEGA 5.0 software. Genealogical relationships were determined using haplotype network tree in NETWORK software v5.0. Population genetic differentiation index (FST) and population structure of parasite was determined using Arlequin v3.5 and STRUCTURE v2.3.4 software.ResultsComparison of 36 full-length pkmsp1p sequences along with the H-strain identified 339 SNPs (175 non-synonymous and 164 synonymous substitutions). The nucleotide diversity across the full-length gene was low compared to its ortholog pvmsp1p. The nucleotide diversity was higher toward the N-terminal domains (pkmsp1p-83 and 30) compared to the C-terminal domains (pkmsp1p-38, 33 and 19). Phylogenetic analysis of full-length genes identified 2 distinct clusters of P. knowlesi from Malaysian Borneo. The 40 pkmsp1p-19 sequences showed low polymorphisms with 16 polymorphisms leading to 18 haplotypes. In total there were 10 synonymous and 6 non-synonymous substitutions and 12 cysteine residues were intact within the two EGF domains. Evidence of strong purifying selection was observed within the full-length sequences as well in all the domains. Shared haplotypes of 40 pkmsp1p-19 were identified within Malaysian Borneo haplotypes.ConclusionsThis study is the first to report on the genetic diversity and natural selection of pkmsp1p. A low level of genetic diversity and strong evidence of negative selection was detected and observed in all the domains of pkmsp1p of P. knowlesi indicating functional constrains. Shared haplotypes were identified within pkmsp1p-19 highlighting further evaluation using larger number of clinical samples from Malaysia.Electronic supplementary materialThe online version of this article (10.1186/s12936-018-2256-y) contains supplementary material, which is available to authorized users.

Within-population genetic diversity and population structure of Plasmodium knowlesi merozoite surface protein 1 gene from geographically distinct regions of Malaysia and Thailand

“…2 ). It is interesting to note that the two distinct sub-populations of P. knowlesi reported in clinical samples from Sarawak in other MSP antigens [ 30 ] were not observed in the phylogenetic network analysis of the haplotypes in this study.

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“…Sequence alignment of 11 full-length sequences of pkmsp1 genes from Malaysia illustrated that it has extensive polymorphisms across the gene, mostly due to the variable regions II, IV, VI and VIII. Among the conserved domains, the C-terminal domain IX (42 kDa) had the lowest nucleotide diversity, a phenomenon observed in all MSPs specifically in the 19 kDa domain [ 27 , 30 , 39 ]. Interestingly, all of the conserved domains I, III, V, VII and IX exhibited high haplotype diversity and it is due to the presence of high number of singleton sites low frequency polymorphisms (Si = 107).…”

“…The median-joining based haplotype network analysis did not show separation of the P. knowlesi msp1 - 42 into two sub-populations as observed for other invasion genes such as nbpxa, msp1p, dbpII etc. where deep dimorphism was noted due to host associated factors [ 22 , 25 , 30 , 47 , 48 ]. Instead, the MSP1 haplotypes revealed geographical clustering, indicating an evolutionary conservation based on sample origin.…”

“…A recent genetic association study on P. knowlesi invasion genes nbpxa and nbpxb (normocyte binding protein xa and xb) showed that some SNPs were strongly associated with high parasitaemia and disease severity in human infections [ 25 ]. Plasmodium knowlesi orthologous antigens of known vaccine candidates such as Duffy binding protein (DBP), merozoite surface protein (MSP) 1, 1P and 3, normocyte binding protein xa have recently been studied from P. knowlesi clinical isolates [ 27 – 30 ]. Merozoite surface protein 1 (MSP1), a important blood stage antigen which is localized on the merozoite surface, and the C-terminus 19 kDa domain of the antigen has been found to adhere to host erythrocyte and antigenicity against the 19 kDa domain has been observed in patient serum [ 31 – 33 ].…”

Diversity and natural selection on the thrombospondin-related adhesive protein (TRAP) gene of Plasmodium knowlesi in Malaysia

“…A recent P. knowlesi study showed association of polymorphisms within the merozoite invasion genes (normocyte binding protein xa and xb , nbpxa and nbpxb ) with high parasite counts and disease severity in human infections [ 17 ]. A number of blood stage antigens like Duffy binding protein (DBP), merozoite surface protein 1 (MSP-1), MSP-1 paralog, MSP-3 and nbpxa have very recently been studied from P. knowlesi clinical isolates but none has been shown to be under positive natural selection [ 18 – 21 ].…”