Selections, frameshift mutations, and copy number variation detected on the surf4.1 gene in the western Kenyan Plasmodium falciparum population

Jesse N Gitaka,Mika Takeda,Osamu Kaneko,James Kongere,Chim W Chan,Kazuhide Yahata,Francis W Muregi,Yoshio Ichinose,Masatsugu Kimura,Zulkarnain Md Idris,Akira Kaneko

doi:10.1186/s12936-017-1743-x

Abstract

BackgroundPlasmodium falciparum SURFIN4.1 is a putative ligand expressed on the merozoite and likely on the infected red blood cell, whose gene was suggested to be under directional selection in the eastern Kenyan population, but under balancing selection in the Thai population. To understand this difference, surf4.1 sequences of western Kenyan P. falciparum isolates were analysed. Frameshift mutations and copy number variation (CNV) were also examined for the parasites from western Kenya and Thailand.ResultsPositively significant departures from neutral expectations were detected on the surf4.1 region encoding C-terminus of the variable region 2 (Var2) by 3 population-based tests in the western Kenyan population as similar in the Thai population, which was not covered by the previous analysis for eastern Kenyan population. Significant excess of non-synonymous substitutions per nonsynonymous site over synonymous substitutions per synonymous site was also detected in the Var2 region. Negatively significant departures from neutral expectations was detected on the region encoding Var1 C-terminus consistent to the previous observation in the eastern Kenyan population. Parasites possessing a frameshift mutation resulting a product without intracellular Trp-rich (WR) domains were 22/23 in western Kenya and 22/36 in Thailand. More than one copy of surf4.1 gene was detected in western Kenya (4/24), but no CNV was found in Thailand (0/36).ConclusionsThe authors infer that the high polymorphism of SURFIN4.1 Var2 C-terminus in both Kenyan and Thai populations were shaped-up by diversifying selection and maintained by balancing selection. These phenomena were most likely driven by immunological pressure. Whereas the SURFIN4.1 Var1 C-terminus is suggested to be under directional selection consistent to the previous report for the eastern Kenyan population. Most western Kenyan isolates possess a frameshift mutation that would limit the expression of SURFIN4.1 on the merozoite, but only 60% of Thai isolates possess this frameshift, which would affect the level and type of the selection pressure against this protein as seen in the two extremities of Tajima’s D values for Var1 C-terminus between Kenyan and Thai populations. CNV observed in Kenyan isolates may be a consequence of this frameshift mutation to increase benefits on the merozoite surface.

Highlights

Plasmodium falciparum SURFIN4.1 is a putative ligand expressed on the merozoite and likely on the infected red blood cell, whose gene was suggested to be under directional selection in the eastern Kenyan population, but under balancing selection in the Thai population
A large type 1 transmembrane protein SURFIN encoded by a surface-associated interspersed gene family has a unique position in such proteins, because its extracellular Cys-rich domain (CRD) and intracellular Trp-rich (WR) domain have homology with a variety of adhesins expressed on the surface of the red blood cell (RBC) infected by P. falciparum and other Plasmodium species, for example, CRD with PIR proteins encoded by the Plasmodium interspersed repeats super multigene family in primate and rodent malaria parasites and without intracellular Trp-rich (WR) with P. falciparum PfEMP1 and Plasmodium knowlesi SICAvar [2], suggesting SURFIN components were utilized to generate lineage-specific adhesins expressed on the iRBC surface through domain shuffling with other proteins
To evaluate the regions accumulating the polymorphisms, the extracellular region of SURFIN4.1 was divided into 4 regions based on amino acid sequence conservation among SURFIN members: N-terminal segment (Nter; aa 1–50, nt 1–150), Cys-rich domain (CRD; aa 51–195, nt 151–585), a variable region 1 (Var1; aa 196–502, nt 586–1506), and −2 (Var2; aa 503–765, nt 1507–2289) as described previously [17]

Summary

Introduction

Plasmodium falciparum SURFIN4.1 is a putative ligand expressed on the merozoite and likely on the infected red blood cell, whose gene was suggested to be under directional selection in the eastern Kenyan population, but under balancing selection in the Thai population. A large type 1 transmembrane protein SURFIN encoded by a surface-associated interspersed gene (surf gene) family has a unique position in such proteins, because its extracellular Cys-rich domain (CRD) and intracellular Trp-rich (WR) domain have homology with a variety of adhesins expressed on the surface of the RBC infected by P. falciparum and other Plasmodium species, for example, CRD with PIR proteins encoded by the Plasmodium interspersed repeats (pir) super multigene family in primate and rodent malaria parasites and WR with P. falciparum PfEMP1 and Plasmodium knowlesi SICAvar [2], suggesting SURFIN components were utilized to generate lineage-specific adhesins expressed on the iRBC surface through domain shuffling with other proteins These shared structural components point to an evolutionary basal position and important roles of SURFIN in the parasite–host interaction. Copy number variation (CNV) was reported for surf4.1, but its biological significance is not known [2]

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