Natural selection and population genetic structure of domain-I of Plasmodium falciparum apical membrane antigen-1 in India

Basu, Madhumita; Maji, Ardhendu Kumar; Mitra, Mitashree; Sengupta, Sanghamitra

doi:10.1016/j.meegid.2013.05.015

Cited by 13 publications

(13 citation statements)

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“…Meiotic recombination between the adjacent polymorphic sites is one of main forces that drive allelic diversity in Plasmodium parasites [ 40 ]. Substantial levels of recombination events in PfAMA-1 from different geographical isolates have been reported previously [ 40 , 43 , 45 – 49 ]. Recombination events within Myanmar PfAMA-1 and decline of LD index R 2 with the increase of nucleotide distance of the sequences evidenced meiotic recombination in Myanmar PfAMA-1, consistent with previous studies [ 40 , 43 , 45 – 49 ].…”

Section: Discussionmentioning

confidence: 80%

“…Substantial levels of recombination events in PfAMA-1 from different geographical isolates have been reported previously [ 40 , 43 , 45 – 49 ]. Recombination events within Myanmar PfAMA-1 and decline of LD index R 2 with the increase of nucleotide distance of the sequences evidenced meiotic recombination in Myanmar PfAMA-1, consistent with previous studies [ 40 , 43 , 45 – 49 ]. Higher values of recombination events were found in African PfAMA-1 sequences (Ghana and Tanzania) than those of PfAMA-1 from other geographical areas, suggesting that African PfAMA-1 might have more opportunity to have recombination events than other geographical PfAMA-1 probably due to high multiclonal infections, subsequent cross fertilization, and recombination in mosquitoes.…”

Section: Discussionmentioning

confidence: 80%

“…The significant ratio of dN/dS and evidence of positive natural selection identified in PfAMA-1 of Myanmar and the other seven P. falciparum populations suggest that amino acid replacements are generally favored in PfAMA-1 and this adaptive evolution is presumably due to host immune pressure. Previous studies have suggested that polymorphic amino acid residues identified in PfAMA-1 are located on one side of the molecule, thereby exposing them to the exterior environment more easily with more access to host immune responses [ 40 , 43 , 51 ]. A recent study has provided information on potential RBC-binding regions, B-cell epitopes, and IURs across the ectodomain of PfAMA-1 [ 40 ].…”

Section: Discussionmentioning

confidence: 99%

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Population genetic structure and natural selection of Plasmodium falciparum apical membrane antigen-1 in Myanmar isolates

Kang

Lee

Moe³

et al. 2018

Malar J

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BackgroundPlasmodium falciparum apical membrane antigen-1 (PfAMA-1) is one of leading blood stage malaria vaccine candidates. However, genetic variation and antigenic diversity identified in global PfAMA-1 are major hurdles in the development of an effective vaccine based on this antigen. In this study, genetic structure and the effect of natural selection of PfAMA-1 among Myanmar P. falciparum isolates were analysed.MethodsBlood samples were collected from 58 Myanmar patients with falciparum malaria. Full-length PfAMA-1 gene was amplified by polymerase chain reaction and cloned into a TA cloning vector. PfAMA-1 sequence of each isolate was sequenced. Polymorphic characteristics and effect of natural selection were analysed with using DNASTAR, MEGA4, and DnaSP programs. Polymorphic nature and natural selection in 459 global PfAMA-1 were also analysed.ResultsThirty-seven different haplotypes of PfAMA-1 were identified in 58 Myanmar P. falciparum isolates. Most amino acid changes identified in Myanmar PfAMA-1 were found in domains I and III. Overall patterns of amino acid changes in Myanmar PfAMA-1 were similar to those in global PfAMA-1. However, frequencies of amino acid changes differed by country. Novel amino acid changes in Myanmar PfAMA-1 were also identified. Evidences for natural selection and recombination event were observed in global PfAMA-1. Among 51 commonly identified amino acid changes in global PfAMA-1 sequences, 43 were found in predicted RBC-binding sites, B-cell epitopes, or IUR regions.ConclusionsMyanmar PfAMA-1 showed similar patterns of nucleotide diversity and amino acid polymorphisms compared to those of global PfAMA-1. Balancing natural selection and intragenic recombination across PfAMA-1 are likely to play major roles in generating genetic diversity in global PfAMA-1. Most common amino acid changes in global PfAMA-1 were located in predicted B-cell epitopes where high levels of nucleotide diversity and balancing natural selection were found. These results highlight the strong selective pressure of host immunity on the PfAMA-1 gene. These results have significant implications in understanding the nature of Myanmar PfAMA-1 along with global PfAMA-1. They also provide useful information for the development of effective malaria vaccine based on this antigen.

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Section: Discussionmentioning

confidence: 80%

Section: Discussionmentioning

confidence: 80%

Section: Discussionmentioning

confidence: 99%

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Population genetic structure and natural selection of Plasmodium falciparum apical membrane antigen-1 in Myanmar isolates

Kang

Lee

Moe³

et al. 2018

Malar J

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“…Tajima’s D and Fu & Li’s statistics were deployed using DnaSP to assess the neutral theory of evolution [ 24 – 26 ]. To gauge the impact of natural selection over gene sequences the ratio of non-synonymous to synonymous substitutions (dN/dS) is commonly used [ 27 ]. The method of Nei and Gojobori with the Jukes and Cantor correction was used to assess these rates of substitution within species as implemented in the MEGA7 [ 28 , 29 ].…”

Section: Methodsmentioning

confidence: 99%

“…To derive an estimate of how did parasite sequence data generated in this study differ from those available in global data, particularly those from sub-Saharan Africa, Pfrh sequences were retrieved from NCBI and diversity analysis was performed (Additional file 2 : Table S2). Further, the evolutionary connections among nucleotide haplotypes of each Pfrh family members were predicted using Network program [ 27 , 30 – 33 ].…”

Section: Methodsmentioning

confidence: 99%

Population genetic and biophysical evidences reveal that purifying selection shapes the genetic landscape of Plasmodium falciparum RH ligands in Chhattisgarh and West Bengal, India

Ghoshal

Chowdhury

Ray

et al. 2020

Malar J

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Background Reticulocyte binding protein-like homologs (RHs) are currently being evaluated as anti-erythrocytic stage vaccine targets against Plasmodium falciparum malaria. Present study explores the possible evolutionary drivers shaping the genetic organization of Pfrhs in Indian parasite population. It simultaneously evaluates a putative gain-of-function variant of PfRH5, a keystone member of PfRH family. Methods Receptor binding regions of Pfrh1, Pfrh2a/b, Pfrh4 and whole Pfrh5 were amplified using blood samples of P. falciparum malaria patients from Chhattisgarh and West Bengal and sequenced. Assembled sequences were analysed using MEGA7 and DnaSPv6. Binding affinities of recombinant PfRH5 proteins with basigin (BSG) were compared using in silico (CHARMM and AUTODOCK) and in vitro (Circular dichroism, fluorescence spectroscopy and isothermal titration calorimetry) methods. Results Pfrh1 (0.5), Pfrh2a/b (0.875), Pfrh4 (0.667) and Pfrh5 (0.778) sequence changes corresponded to low frequency (< 0.05) variants which resulted in an overall negative Tajima’s D. Since mismatch distribution of none of the Pfrh loci corroborated with the model of demographic expansion, a possible role of natural selection formulating Pfrh sequence diversity was investigated. Among the 5 members, Pfrh5 displayed very high dN/dS (5.7) ratio. Nevertheless, the model of selective sweep due to presence of any advantageous substitutions could not be invoked as polymorphic nonsynonymous sites (17/18) for Pfrh5 exceeded significantly over the divergent (62/86) ones (p = 0.0436). The majority of extant PfRH5 sequences (52/83) differed from the reference Pf3D7 allele by a single amino acid mismatch (C203Y). This non-conservative alteration was predicted to lower the total interaction energy of that PfRH5variant with BSG, compared to PfRH53D7. Biophysical evidences validated the proposition that PfRH5variant formed a more stable complex with BSG. Thermodynamic association constant for interaction of BSG with PfRH5variant was also found to be higher (Kavariant = 3.63E6 ± 2.02E6 M−1 and Ka3D7 = 1.31E6 ± 1.21E6 M−1). Conclusions Together, the study indicates that the genetic architecture of Pfrhs is principally shaped by purifying selection. The most abundant and ubiquitous PfRH5 variant harbouring 203Y, exhibits a greater affinity for BSG compared to PfRH53D7 possessing 203C allele. The study underscores the importance of selecting the functional allele that best represents circulating strains in natural parasite populations as vaccine targets.

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Genetic polymorphism in domain I of the apical membrane antigen-1 among Plasmodium knowlesi clinical isolates from Peninsular Malaysia

et al. 2015

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Natural selection and population genetic structure of domain-I of Plasmodium falciparum apical membrane antigen-1 in India

Cited by 13 publications

References 80 publications

Population genetic structure and natural selection of Plasmodium falciparum apical membrane antigen-1 in Myanmar isolates

Population genetic structure and natural selection of Plasmodium falciparum apical membrane antigen-1 in Myanmar isolates

Population genetic and biophysical evidences reveal that purifying selection shapes the genetic landscape of Plasmodium falciparum RH ligands in Chhattisgarh and West Bengal, India

Genetic polymorphism in domain I of the apical membrane antigen-1 among Plasmodium knowlesi clinical isolates from Peninsular Malaysia

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