Protein-based signatures of functional evolution in Plasmodium falciparum

Kate B Gardner,Ipsita Sinha,Nicholas J White,Leyla Y Bustamante,Nicholas Pj Day,Charles J Woodrow

doi:10.1186/1471-2148-11-257

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.

Highlights

It has been known for over a decade that Plasmodium falciparum proteins are enriched in nonglobular domains of unknown function
Polymorphism and divergence: whole-gene level In order to study short-term evolutionary processes within the hominid malaria clade a reference set of 40 P. falciparum genes (Table 1) was identified, consisting of sequences well covered by genome sequencing of the closely related primate parasite P. reichenowi [18]
Single-nucleotide changes in these genes associated with divergence and intra-species polymorphism were quantified

Summary

Introduction

It has been known for over a decade that Plasmodium falciparum proteins are enriched in nonglobular domains of unknown function. Identifying the molecular basis of disease-causing traits is one of the major justifications for the recent expansion in genomic data covering a wide range of taxa Nowhere is this goal more clearly defined than in the case of malaria, where adaptive evolution in the form of approaches currently represent a promising route forward allowing detection of signatures of selection associated with drug resistance [6], this approach relies on identification of linkage disequilibrium which is known to be of variable strength [7]. A specific phenomenon that may complicate studies in this genus relates to the remarkable degree to which Plasmodium proteins are enriched in non-globular domains [10] Since their first systematic description more than a decade ago, the function of these domains has remained unresolved [11,12,13] with one possibility being that they represent downstream consequences of events at the DNA level (i.e. broadly neutral in functional terms). Measurement of selective forces is still generally undertaken at a whole-gene level, an approach that falls down if pressures vary considerably within individual genes, preventing determination of the true baseline for variation which is neutral evolution within and between malaria species

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