Distribution of membrane trafficking system components across ciliate diversity highlights heterogenous organelle‐associatedmachinery

Abstract

The ciliate phylum is a group of protists noted for their unusual membrane trafficking system and apparent environmental ubiquity; as highly successful microbial predators, they are found in all manner of environments and the ability for specific species to adapt to extremely challenging conditions makes them valued as bioindicators. Ciliates have also been used for many years as cell biological models because of their large cell size and ease of culturing, and for many fundamental cell structures, particularly membrane‐bound organelles, ciliates were some of the earliest organisms in which these were observed via microscopy. In this study, we carried out a comparative genomic survey of selected membrane trafficking proteins in a pan‐ciliate transcriptome and genome dataset. We observed considerable loss of membrane trafficking system (MTS) proteins that would indicate a loss of machinery that is generally conserved across eukaryotic diversity, even after controlling for potentially incomplete genome representation. In particular, the complete DSL1 complex was missing in all surveyed ciliates. This protein complex has been shown as involved in peroxisome biogenesis in some model systems, and a paucity of DSL1 components has been indicative of degenerate peroxisome. However, Tetrahymena thermophila (formerly Tetrahymena pyroformis) was one of the original models for visualizing peroxisomes. Conversely, the AP3 complex essential for mucocyst maturation in T. thermophila, is poorly conserved despite the presence of secretory lysosome‐related organelles across ciliate diversity. We discuss potential resolutions for these apparent paradoxes in the context of the heterogenous distribution of MTS machinery across the diversity of ciliates.

Combined nanometric and phylogenetic analysis of unique endocytic compartments in Giardia lamblia sheds light on the evolution of endocytosis in Fornicata

“…By contrast, robust predictions for CLC homologues were made for members of the Preaxostyla, Discoba and Parabasalia lineages. Nonetheless, other lineages appear also to have lost a bona fide CLC, like C. parvum and T. thermophila (Woo et al 2015; Richardson and Dacks 2022), but perhaps similar investigations to ours of CHC may identify CLC analogues/divergent homologues. Taken together, this data suggests that the constraints on the CHC primary structure are higher than on CLC even after massive changes in clathrin coat function with demonstrated complete losses in some protists.…”

“…These observations are in line with the notion that, unlike CHC, CLC is dispensable. This is also supported by failures to identify bona fide CLC in chromerids such as Cryptosporidium parvum and Babesia bovis (Woo et al 2015) and in some ciliate lineages, such as Tetrahymena thermophila and Paramecium caudatum (Richardson and Dacks 2022).…”

“…(A) CHC and CLC homology searches demonstrate the conservation of CHC orthologs in all analysed lineages. However, several lineages appeared to have lost a readily-detectable bona fide CLC including all selected Fornicata, certain Chromerids (Woo et al 2015), some ciliates (Richardson and Dacks 2022) and members of the Hemimastigophora. (B) Ab initio in silico protein modelling of G. lamblia ACLC (formerly Gl CLC/Gl4529), T. brucei CLC, T. foetus CLC, M. exilis CLC, D. discoideum and H. sapiens CLC sequences using AlphaFold, the current standard in in silico protein structure modelling.…”

Molecular evolutionary analysis of the SM and SNARE vesicle fusion machinery in ciliates shows concurrent expansions in late secretory machinery

“…The duplications that we observe of Syntaxin PM and Sec1 in the oligohymenophorean taxa sampled lead to the tantalizing hypothesis that the concurrent expansions of these interacting partners may be associated with the evolution of specialized of machinery associated with CV in the Oligohymenophorea. We described the distribution of the heterotetrameric adaptor complex and MTC complement across a similar taxonomic sampling of ciliates (Richardson and Dacks, 2022). This paper reported a reduction in some of these systems and heterogeneity in the complements between the major ciliate orders, with the greatest reduction observed in the oligohymenophoreans.…”

“…We recently described the distribution of the heterotetrameric adaptor complex and MTC complement across a similar taxonomic sampling of ciliates (Richardson and Dacks, 2022). This paper reported a reduction in some of these systems and heterogeneity in the complements between the major ciliate orders, with the greatest reduction observed in the oligohymenophoreans.…”