Genetic diversity and natural selection on the thrombospondin-related adhesive protein (TRAP) gene of Plasmodium falciparum on Bioko Island, Equatorial Guinea and global comparative analysis

Abstract

Background: Thrombospondin-related adhesive protein (TRAP) is a transmembrane protein that plays a crucial role during the invasion of Plasmodium falciparum into liver cells. As a potential malaria vaccine candidate, the genetic diversity and natural selection of PfTRAP was assessed and the global PfTRAP polymorphism pattern was described.

Methods: 153 blood spot samples from Bioko malaria patients were collected during 2016-2018 and the target TRAP gene was amplified. Together with the sequences from database, nucleotide diversity and natural selection analysis, and the structural prediction were preformed using bioinformatical tools.

Results: A total of 119 Bioko PfTRAP sequences were amplified successfully. On Bioko Island, PfTRAP shows its high degree of genetic diversity and heterogeneity, with π value for 0.01046 and Hd for 0.99. The value of dN-dS (6.2231, p < 0.05) hinted at natural selection of PfTRAP on Bioko Island. Globally, the African PfTRAPs showed more diverse than the Asian ones, and significant genetic differentiation was discovered by the fixation index between African and Asian countries (Fst > 0.15, p < 0.05). 667 Asian isolates clustered in 136 haplotypes and 739 African isolates clustered in 528 haplotypes by network analysis. The mutations I116T, L221I, Y128F, G228V and P299S were predicted as probably damaging by PolyPhen online service, while mutations L49V, R285G, R285S, P299S and K421N would lead to a significant increase of free energy difference (ΔΔG > 1) indicated a destabilization of protein structure.

Conclusions: Evidences in the present investigation supported that PfTRAP gene from Bioko Island and other malaria endemic countries is highly polymorphic (especially at T cell epitopes), which provided the genetic information background for developing an PfTRAP-based universal effective vaccine. Moreover, some mutations have been shown to be detrimental to the protein structure or function and deserve further study and continuous monitoring.

Keywords: Bioko Island; Genetic diversity; Malaria; Natural selection; Plasmodium falciparum thrombospondin-related adhesive protein (PfTRAP); Vaccine candidate.

Fig. 1

Trend chart of Tajima’s D value of PfTRAP from Africa, Asia and Bioko Island. Red dot indicated p value < 0.05; Yellow dot indicated p value < 0.1; Blue dot indicated p value > 0.1. DomainI to Domain VI were presented in different color

Fig. 2

Haplotype network of global PfTRAP sequences. Each circle stands for one haplotype. The size of circle indicated the sample size of the haplotype. The length of the line connecting two haplotypes indicated the genetic distance. Blue circles represent sequences from Asia; Orange circles represent sequences from Africa; Green circles represent sequences from Bioko Island

Fig. 3

CD8+ T cell and linear B cell Epitopes and amino acids substitution distribution of PfTRAP gene. The full-length TRAP sequences (1–559aa) was referred to the 3D7 isolates (NCBI Gene ID: 814170). Sequences with blue block above is linear B cell epitope; Sequences with orange block above is CD8+ T cell epitope (Detail information of CD8+ T cell epitopes was shown in Additional File 6); Numbers in the color blocks are the corresponding epitope ID of IEDB database. Sequences in gray block is the repeat region. Amino acid in red is for mutant

Fig. 4

Predicted 3-dimensional structure of TRAP protein. a Molecular surface of predicted TRAP structure. Yellow for DomainI (Signal sequences); Cyan for DomainII (A domain); Green for Domain III (TSR region); Blue for Domain IV (Proline-rich region, including repeat region); Red for Domain V (transmembrane domain); Orange for Domain VI (cytoplasmic tail domain). b Predicted secondary structure of TRAP protein. Helix, Strand and Coil were shown in different color and form

Fig. 5

Structure changes before and after relatively common (> 10% globally) mutations which located in the T cell epitopes. The primary structures of the target amino acids were marked as yellow. The green dotted line indicated hydrogen bonding