Adaptive Evolution of RH5 in Ape Plasmodium species of the Laverania Subgenus

Abstract

Plasmodium falciparum, the major cause of malaria morbidity and mortality in humans, has been shown to have emerged after cross-species transmission of one of six host-specific parasites (subgenus Laverania) infecting wild chimpanzees (Pan troglodytes) and western gorillas (Gorilla gorilla). Binding of the parasite-encoded ligand RH5 to the host protein basigin is essential for erythrocyte invasion and has been implicated in host specificity. A recent study claimed to have found two amino acid changes in RH5 that "drove the host shift leading to the emergence of P. falciparum as a human pathogen." However, the ape Laverania data available at that time, which included only a single distantly related chimpanzee parasite sequence, were inadequate to justify any such conclusion. Here, we have investigated Laverania Rh5 gene evolution using sequences from all six ape parasite species. Searching for gene-wide episodic selection across the entire Laverania phylogeny, we found eight codons to be under positive selection, including three that correspond to contact residues known to form hydrogen bonds between P. falciparum RH5 and human basigin. One of these sites (residue 197) has changed subsequent to the transmission from apes to humans that gave rise to P. falciparum, suggesting a possible role in the adaptation of the gorilla parasite to the human host. We also found evidence that the patterns of nucleotide polymorphisms in P. falciparum are not typical of Laverania species and likely reflect the recent demographic history of the human parasite.IMPORTANCE A number of closely related, host-specific malaria parasites infecting wild chimpanzees and gorillas have recently been described. The most important cause of human malaria, Plasmodium falciparum, is now known to have resulted from a cross-species transmission of one of the gorilla parasites. Overcoming species-specific interactions between a parasite ligand, RH5, and its receptor on host cells, basigin, was likely an important step in the origin of the human parasite. We have investigated the evolution of the Rh5 gene and found evidence of adaptive changes during the diversification of the ape parasite species at sites that are known to form bonds with human basigin. One of these changes occurred at the origin of P. falciparum, implicating it as an important adaptation to the human host.

Keywords: Laverania; Plasmodium falciparum; RH5; basigin; chimpanzee; gorilla.

FIG 1

Relationships among RH5 sequences analyzed by Forni et al. (19). (A) Phylogeny as depicted in reference . (B) Maximum-likelihood analysis of the same protein sequences, with branch lengths drawn to scale; the bar indicates 0.2 amino acid replacements per site. In each panel, the top sequence (red) is P. falciparum RH2b, a paralogue of RH5, and the bottom sequence (blue) is P. reichenowi strain CDC RH5; the other sequences (black) are RH5 from various P. falciparum strains.

FIG 2

Evolution of codon 27 in the basigin (BSG) genes of hominids. The amino acids seen in these species require a minimum of two nonsynonymous substitutions; the most parsimonious locations of these changes in the phylogeny are shown. Colors indicate different codons. The TCC codon at the root of this tree is inferred by comparison with the BSG genes of Old World monkeys.

FIG 3

Evolutionary relationships among Rh5 genes from Laverania species. Species infecting gorillas are shown in red (each sequence is represented by a triangle), species infecting chimpanzees in blue (circles), and P. falciparum isolates from humans in black (squares). Internal branches between species are labeled to allow them to be identified in the text. The scale bar indicates 0.02 nucleotide substitutions per site.

FIG 4

Codons in Rh5 identified as candidate sites of episodic selection during the diversification of the Laverania. Eight codons (excluding codon 190, in square brackets) were identified in the current analysis, including three (underlined codons 197, 207, and 447) that are contact residues involved in the binding of P. falciparum to human BSG (see Fig. 5). One of these (codon 197) changed during the recent divergence of P. falciparum from P. praefalciparum. Nucleotides differing from the P. falciparum sequence are shown in red. Note that the P. blacklocki sequence only covers codons 106 to 381.

FIG 5

Cocrystal structure of P. falciparum RH5 (ribbons) in complex with human BSG (mesh), modified from reference . Eight amino acids in RH5 encoded by sites identified here as candidates contributing to the signal of episodic selection across the Laverania phylogeny are highlighted either in red (if they are known binding sites between P. falciparum and human BSG) or in blue; two (K76 and L122) are within the N-terminal region, whose structure is unknown.