Factors mediating plastid dependency and the origins of parasitism in apicomplexans and their close relatives

Abstract

Apicomplexans are a major lineage of parasites, including causative agents of malaria and toxoplasmosis. How such highly adapted parasites evolved from free-living ancestors is poorly understood, particularly because they contain nonphotosynthetic plastids with which they have a complex metabolic dependency. Here, we examine the origin of apicomplexan parasitism by resolving the evolutionary distribution of several key characteristics in their closest free-living relatives, photosynthetic chromerids and predatory colpodellids. Using environmental sequence data, we describe the diversity of these apicomplexan-related lineages and select five species that represent this diversity for transcriptome sequencing. Phylogenomic analysis recovered a monophyletic lineage of chromerids and colpodellids as the sister group to apicomplexans, and a complex distribution of retention versus loss for photosynthesis, plastid genomes, and plastid organelles. Reconstructing the evolution of all plastid and cytosolic metabolic pathways related to apicomplexan plastid function revealed an ancient dependency on plastid isoprenoid biosynthesis, predating the divergence of apicomplexan and dinoflagellates. Similarly, plastid genome retention is strongly linked to the retention of two genes in the plastid genome, sufB and clpC, altogether suggesting a relatively simple model for plastid retention and loss. Lastly, we examine the broader distribution of a suite of molecular characteristics previously linked to the origins of apicomplexan parasitism and find that virtually all are present in their free-living relatives. The emergence of parasitism may not be driven by acquisition of novel components, but rather by loss and modification of the existing, conserved traits.

Keywords: Apicomplexa; Chromera; Colpodella; parasitism origin; plastid organelle.

Fig. 1.

Unsuspected diversity and novel clades and habitats in apicomplexan relatives. Maximum likelihood phylogeny (RAxML) of 106 eukaryotic and 226 environmental 18S rDNA sequences, color-coded according to their environmental source (box). The first set of support values (300 nonparametric bootstraps) corresponds to the topology shown; the second set corresponds to the analysis of sequences longer than 1,000 nucleotides (“na” denotes support not applicable in the second set). Only values greater than 65% are shown for clarity; those over 95% are highlighted. Full black circles denote 100/100 support. New environmental clades (green) are followed by reference accessions. The cross indicates the position of ∼1,700 sequences from a hypersaline lake. Other large clades are indicated by triangles, with the number of sequences in square brackets. Note that Env. clade I was related to apicomplexans rather than dinoflagellates in the analysis of sequences >1,000 nucleotides.

Fig. 2.

Chrompodellids represent a large sister group of apicomplexans with a complex distribution of photosynthesis. Maximum likelihood and Bayesian analyses inferred from the concatenation of 85 proteins (23,111 amino acids) resolve the relationships among apicomplexans and their relatives and demonstrate that the photosynthetic chromerids and predatory colpodellids are paraphyletic. Best RAxML tree (LG+GAMMA model) is shown with nonparametric bootstraps/Phylobayes posterior probabilities at branches. Full black circles indicate 100/1.0 support. Two alternative placements for Vitrella (at positions marked a and b) were rejected by approximately unbiased (AU) test at P = 0.005 (box).

Fig. 3.

Mechanisms of dependency on plastids and plastid genomes in myzozoans. (A) A phylogeny of myzozoans with genomic (G) and/or transcriptomic (T) data are shown (Left), together with a reconstruction of plastid and nonplastid variants of core metabolic pathways (on Right with pathway above and individual enzymes below; see SI Appendix, Table S2 for abbreviations of enzyme names) color-coded as to presence/absences and source (Below). Proteins were assigned to compartment and pathways by phylogeny and similarity, and plastid copies have targeting extensions where available. Uptake of compounds was based on published reports where available. Perkinsus was based on an unpublished draft genome. Loss of cytosolic isoprenoid biosynthesis before the divergence of myzozoans established a unilateral metabolic dependency on the plastid, which was relieved by uptake of host compounds by parasites. (B) Diagram showing how unilateral dependency on the plastid may result from functional redundancy during endosymbiosis. Additional symbioses, including parasitism, may reestablish functional redundancy leading to plastid loss (or retention, which is not illustrated). Photosynthesis is ignored and may be lost at different stages of plastid endosymbiosis. (C) Dependency on plastid genomes in myzozoans. Photosynthetic species rely on plastid-encoded photosystem subunits (photo) whereas apicomplexans rely on plastid-encoded sufB, clpC, and, potentially, ycf93. The discovery of nuclear sufB and clpC provides a rationale for plastid genome loss in Perkinsus, nonphotosynthetic dinoflagellates, and, most likely, colpodellids. ClpC occurs in two forms in some species, but their relationships are not clear (SI Appendix, Fig. S4) (plastid-encoded clpC in Chromera is probably a pseudogene).

Fig. 4.

Summary of “apicomplexan-specific” characteristics in their free-living relatives. (A) Classification of four groups of apicomplexan proteins based on distribution: horizontal gene transfers (HGTs), unique protein clusters [OrthoMCL and Wasmuth et al. (14)], and proteins associated with infection (Apiloc). Categories a–e correspond to the phylogenetic distribution of these proteins when free-living relatives are considered, which is broken down by specific processes and proteins in B. Note that putative GAP45 in Cryptosporidium is highly divergent (indicated by “?” in category d).