Single-nucleotide polymorphism characterization of gametocyte development 1 gene in Plasmodium falciparum isolates from Baringo, Uasin Gishu, and Nandi Counties, Kenya

Abstract

Introduction: Plasmodium falciparum relies on gametocytogenesis to transmit from humans to mosquitoes. Gametocyte development 1 (Pfgdv1) is an upstream activator and epigenetic controller of gametocytogenesis. The emergence of drug resistance is a major public health concern and this requires the development of new strategies that target the transmission of malaria. As a putative drug target, Pfgdv1 has not been characterized to identify its polymorphisms and alleles under selection and how such polymorphisms influence protein structure. Methods: This study characterized single-nucleotide polymorphisms (SNPs) in primary sequences (n ¼ 30) of Pfgdv1 gene generated from thirty blood samples collected from patients infected with P. falciparum and secondary sequences (n ¼ 216) retrieved from PlasmoDB. ChromasPro, MUSCLE, Tajima's D statistic, SLAC, and STRUM were used in editing raw sequences, performing multiple sequence alignment (MSA), identifying signatures of selection, detecting codon sites under selection pressure, and determining the effect of SNPs, respectively. Results: MSA of primary and secondary sequences established the existence of five SNPs, consisting of four nonsynonymous substitutions (nsSNPs) (p.P217H, p.R398Q, p.H417N, and p.D497E), and a synonymous substitution (p.S514S). The analysis of amino acid changes reveals that p.P217H, p.R398Q, and p.H417N comprise nonconservative changes. Tajima's D statistic showed that these SNPs were under balancing selection, while SLAC analysis identified p.P217H to be under the strongest positive selection. . Further analysis based on thermodynamics indicated that p.P217H has a destabilizing effect, while p.R398Q and p.D497E have stabilizing effects on the protein structure. Conclusions: The existence of four nsSNPs implies that Pfgdv1 has a minimal diversity in the encoded protein. Selection analysis demonstrates that these nsSNPs are under balancing selection in both local and global populations. However, p.P217H exhibits positive directional selection consistent with previous reports where it showed differentiatial selection of P. falciparum in low and high transmission regions. Therefore, in-silico prediction and experimental determination of protein structure are necessary to evaluate Pfgdv1 as a target candidate for drug design and development.

Stressed Out About Plasmodium falciparum Gametocytogenesis

“…The loss of gametocyte production in lab strains is frequently associated with Gdv1 deletions ( Tiburcio et al., 2021 ), while GDV1 overexpression increases gametocyte production ( Eksi et al., 2012 ; Filarsky et al., 2018 ). Field populations also exhibit high gdv1 allelic divergence that has been suggested to vary with transmission patterns ( Mobegi et al., 2014 ; Bungei et al., 2020 ). Ap2-g was also identified as the target of mutations in gametocyte-deficient parasite lines in both P. falciparum ( Kafsack et al., 2014 ) and P. berghei ( Sinha et al., 2014 ).…”