Protein-based signatures of functional evolution in Plasmodium falciparum

Abstract

BackgroundIt has been known for over a decade that Plasmodium falciparum proteins are enriched in non-globular domains of unknown function. The potential for these regions of protein sequence to undergo high levels of genetic drift provides a fundamental challenge to attempts to identify the molecular basis of adaptive change in malaria parasites.ResultsEvolutionary comparisons were undertaken using a set of forty P. falciparum metabolic enzyme genes, both within the hominid malaria clade (P. reichenowi) and across the genus (P. chabaudi). All genes contained coding elements highly conserved across the genus, but there were also a large number of regions of weakly or non-aligning coding sequence. These displayed remarkable levels of non-synonymous fixed differences within the hominid malaria clade indicating near complete release from purifying selection (dN/dS ratio at residues non-aligning across genus: 0.64, dN/dS ratio at residues identical across genus: 0.03). Regions of low conservation also possessed high levels of hydrophilicity, a marker of non-globularity. The propensity for such regions to act as potent sources of non-synonymous genetic drift within extant P. falciparum isolates was confirmed at chromosomal regions containing genes known to mediate drug resistance in field isolates, where 150 of 153 amino acid variants were located in poorly conserved regions. In contrast, all 22 amino acid variants associated with drug resistance were restricted to highly conserved regions. Additional mutations associated with laboratory-selected drug resistance, such as those in PfATPase4 selected by spiroindolone, were similarly restricted while mutations in another calcium ATPase (PfSERCA, a gene proposed to mediate artemisinin resistance) that reach significant frequencies in field isolates were located exclusively in poorly conserved regions consistent with genetic drift.ConclusionCoding sequences of malaria parasites contain prospectively definable domains subject to neutral or nearly neutral evolution on a scale that appears unrivalled in biology. This distinct evolutionary landscape has potential to confound analytical methods developed for other genera. Against this tide of genetic drift, polymorphisms mediating functional change stand out to such an extent that evolutionary context provides a useful signal for identifying the molecular basis of drug resistance in malaria parasites, a finding that is of relevance to both genome-wide and candidate gene studies in this genus.

The malaria parasite cation ATPase PfATP4 and its role in the mechanism of action of a new arsenal of antimalarial drugs

“…PfATP4 mutations conferring spiroindolone-resistance occur in regions of the protein that are highly conserved between malaria parasite species, with an evolutionary analysis concluding that these mutations play a role in drug resistance and are not present due to genetic drift ( Gardner et al., 2011 ). Distinguishing resistance-associated mutations from non-adaptive polymorphisms will contribute to effective surveillance if the spiroindolones progress to the field.…”

Antimalarial screening via large‐scale purification of Plasmodium falciparum Ca2+‐ATPase 6 and in vitro studies

“…Tanabe et al [26] demonstrated a natural and random occurrence of numerous single nucleotide polymorphisms on PfATP6, showing that this gene is naturally very polymorphic [26]. Furthermore, the PfATP6 mutations were located in poorly conserved regions of the protein, consistent with simple genetic drift [27]. These findings indicated that the mutations found on PfATP6 of P. falciparum strains presenting a diminished sensitivity to artemisinin may not correspond to a selective pressure of this drug on PfATP6.…”

An evolutionary perspective on the kinome of malaria parasites

“…Furthermore, most individual plasmodial enzymes clustering within known ePK groups and families display peculiarities that distinguish them from their homologues in other eukaryotes. These include (sometimes very large) low complexity extensions and insertions in the catalytic domain, usually occurring at loops between secondary structure elements; this feature is not restricted to kinases, but occurs throughout the parasite's proteome, and its evolutionary function is still being debated [37][38][39][40][41]. Many protein kinases, called 'semi-orphans' in the initial kinome characterization [22], clearly belong to a specific kinase group or family, but do not have a clear orthologue in other organisms.…”