Reconstruction of Plastid Proteomes of Apicomplexans and Close Relatives Reveals the Major Evolutionary Outcomes of Cryptic Plastids

Abstract

Apicomplexans and related lineages comprise many obligate symbionts of animals; some of which cause notorious diseases such as malaria. They evolved from photosynthetic ancestors and transitioned into a symbiotic lifestyle several times, giving rise to species with diverse non-photosynthetic plastids. Here we sought to reconstruct the evolution of the cryptic plastids in the Apicomplexa, Chrompodellids, and Squirmida (ACS clade) by generating five new single-cell transcriptomes from understudied gregarine lineages, constructing a robust phylogenomic tree incorporating all ACS clade sequencing datasets available, and using these to examine in detail the evolutionary distribution of all 162 proteins recently shown to be in the apicoplast by spatial proteomics in Toxoplasma. This expanded homology-based reconstruction of plastid proteins found in the ACS clade confirm earlier work showing convergence in the overall metabolic pathways retained once photosynthesis is lost, but also reveals differences in the degrees of plastid reduction in specific lineages. We show that the loss of the plastid genome is common and unexpectedly find many lineage- and species-specific plastid proteins, suggesting the presence of evolutionary innovations and neofunctionalizations that may confer new functional and metabolic capabilities that are yet to be discovered in these enigmatic organelles.

A new and widespread group of fish apicomplexan parasites

“…While a parsimonious interpretation of evolution (shown by H2 in figure 3D) would presume one gain of the chlorophyll biosynthesis pathway in the corallicolids after an initial loss of it in the last common ancestor of the Apicomplexa, the more plausible scenario is the one (shown by H1 in figure 3D) where the chlorophyll biosynthesis pathway is repeatedly lost throughout apicomplexan evolution. Our results contribute to this hypothesis with the 6th apparent loss of the pathway (based on the latest phylogenomic analysis 18 ) within apicomplexans occurring in the ichthyocolids (Figure 3D). The reduction of the apicoplast genome through evolution is marked by the loss of photosystem genes from the common ancestor with chromerids, followed by independent, repeated loss of the chlorophyll biosynthesis pathway 3 .…”

Multiple plastid losses within photosynthetic stramenopiles revealed by comprehensive phylogenomics

“…This finding alone does not rule out the possibility of P. flagellatus possessing a genome-lacking plastid, as is found in the colorless chrysophyte genus Paraphysomonas (Dorrell et al 2019) and various taxa outside ochrophytes (e.g., Smith and Lee 2014; Gawryluk et al 2019; Janouškovec et al 2019; Mathur et al 2023). However, our analysis of the P. flagellatus transcriptome and draft genome assembly did not reveal any homologs of the components of the plastid protein complexes that mediate translocation of imported proteins across different plastidial membranes (SELMA, TOC and TIC complexes; Maier et al 2015).…”

“…Despite an inability to synthesize heme, numerous homologs of heme-utilizing proteins were detected (table S4), suggesting that P. flagellatus acquires heme from food. Other hallmark plastidial metabolic pathways, retained in different combinations by non-photosynthetic plastids across eukaryotes (e.g., Salomaki et al 2015; Dorrell et al 2019; Salomaki and Kolisko 2019; Füssy et al 2020; Kayama et al 2020; Pánek et al 2022; Mathur et al 2023; Barcytė et al 2024), are likewise completely missing in P. flagellatus . These include the DOXP pathway for the biosynthesis of isoprenoid precursors, the type II fatty acid synthesis (FAS) pathway, the shikimate pathway and its downstream branches leading to aromatic amino acids or folate, enzymes for the synthesis of plastid-specific structural lipids (galactolipids, sulfoquinovosyldiacylglycerol), or pathways for the synthesis of plastidial terpenoid quinols and their derivatives (plastoquinol, phylloquinol, tocopherols/tocotrienols).…”

“…Despite an inability to synthesize heme, numerous homologs of heme-utilizing proteins were detected (table S4), suggesting that P. flagellatus acquires heme from food. Other hallmark plastidial metabolic pathways, retained in different combinations by non-photosynthetic plastids across eukaryotes (e.g., Salomaki et al 2015;Dorrell et al 2019;Salomaki and Kolisko 2019;Füssy et al 2020;Kayama et al 2020;Pánek et al 2022;Mathur et al 2023;Barcytė et al 2024), are likewise completely missing in P.…”

Morphological and Phylogenetic Study of Protococcidians Sheds Light on the Evolution of Epicellular Parasitism in Sporozoa (Apicomplexa), with the Description of Eleutheroschizon planoratum sp. nov

“…An exception is Eleutheroschizon duboscqi Brasil, 1906, whose phylogenetic position as a sister branch to "true" coccidians (Eimeria, Sarcocystis, and Toxoplasma) was demonstrated using multiprotein phylogeny [1]. This was later supported by other multimarker phylogenies [5][6][7]. E. duboscqi is characterized by cell polarity and epicellular development on the host intestinal epithelium.…”