Methylation is a common post-translational modification of arginine and lysine in eukaryotic proteins. Methylproteomes are best characterised for higher eukaryotes, where they are functionally expanded and evolved complex regulation. However, this is not the case for protist species evolved from the earliest eukaryotic lineages. Here, we integrated bioinformatic, proteomic and drug-screening datasets to comprehensively explore the methylproteome of Giardia duodenalis - a deeply-branching parasitic protist. We demonstrate Giardia and related diplomonads lack arginine-methyltransferases and have remodelled conserved RGG/RG motifs targeted by these enzymes. We also provide experimental evidence for methylarginine absence in proteomes of Giardia, but readily detect methyllysine. We bioinformatically infer 11 lysine-methyltransferases in Giardia, including highly-diverged SET-domain proteins with reduced domain architectures, and novel annotations demonstrating conserved methyllysine regulation of eukaryote Elongation Factor 1 alpha (eEF1a). Using mass spectrometry, we identify more than 200 methyllysine sites in Giardia, including in species-specific gene families involved in cytoskeletal regulation, enriched in coiled-coil features. Finally, we use known methylation-inhibitors to show that methylation plays key roles in replication and cyst formation in this parasite. This study highlights reduced methylation enzymes, sites and functions early in eukaryote evolution, including absent methylarginine networks in the Diplomonadida. These results challenge the view that arginine methylation is eukaryote-conserved, and demonstrates functional compensation of methylarginine was possible preceding expansion and diversification of these key networks in higher eukaryotes.
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