A Eukaryote-Wide Perspective on the Diversity and Evolution of the ARF GTPase Protein Family

The evolution of eukaryotic cellular complexity is interwoven with the extensive diversification of many protein families. One key family is the ARFGT Pases that act in eukaryote-specific processes, includingmembrane traffic, tubulin assembly, actin dynamics, and cilia-related functions. Unfortunately, our understanding of the evolution of this family is limited. Sampling an extensive set of available genome and transcriptome sequences, we have assembled a data set of over 2,000 manually curated ARF family genes from 114 eukaryotic species, including many deeply diverged protist lineages, and carried out comprehensive molecular phylogenetic analyses. These reconstructed as many as 16 ARF family members present in the last eukaryotic common ancestor, nearly doublingthe previously inferredancient systemcomplexity. Evidence for thewideoccurrence and ancestral origin ofArf6, Arl13, and Arl16 is presented for the first time. Moreover, Arl17, Arl18, and SarB, newly described here, are absent from well-studied model organisms and as a result their function(s) remain unknown. Analyses of our data set revealed a previously unsuspected diversity of membrane association modes and domain architectureswithin theARF family. Wedetail thestep-wise expansion of theARF family in the metazoan lineage, including discovery of several new animal-specific family members. Delving back to its earliest evolution in eukaryotes, the resolved relationship observed between the ARF family paralogs sets boundaries for scenarios of vesicle coat origins during eukaryogenesis. Altogether, ourwork fundamentally broadens the understanding of the diversity and evolution of a protein family underpinning the structural and functional complexity of the eukaryote cells.

Automated summary

This study delves into the evolution of the ARF family in eukaryotes by analyzing genome and transcriptome sequences from 114 species. It reveals the complex evolutionary history of the ARF family, uncovers new animal-specific family members, and highlights the diversity within the ARF family and its early evolution in eukaryotes. Altogether, the research broadens our understanding of the structural and functional complexity of eukaryotic cells.