biostudies-literatureHammond MJDirectorate for Biological SciencesWellcome TrustGrantová Agentura České RepublikyWellcome Discovery Awarde3003319https://www.ebi.ac.uk/biostudies/studies/S-EPMC12697944biostudies-literatureUnknown23(12)Diplonemids are among the most diverse and abundant protists in the deep ocean, have extremely complex and ancient cellular systems, and exhibit unique metabolic capacities. Despite this, we know very little about this major group of eukaryotes. To establish a model organism for comprehensive investigation, we performed subcellular proteomics on Paradiplonema papillatum and localized 4,870 proteins to 22 cellular compartments. We additionally confirmed the predicted location of several proteins by epitope tagging and fluorescence microscopy. To probe the metabolic capacities of P. papillatum, we explored the proteins predicted to the cell membrane compartment in our subcellular proteomics dataset. Our data revealed an accumulation of many carbohydrate-degrading enzymes (CDZymes). Our prediPLoS biologySubcellular proteomics of the protist Paradiplonema papillatum reveals the digestive capacity of the cell membrane and the plasticity of peroxisomes across euglenozoans.PMC12697944DBI-211996325-15298S23-06479X227243/Z/23/ZPoh YPHammond MJSvobodova MFaktorova DIorillo OLicknack TAkiyoshi BWideman JGLukes JfalseSubcellular proteomics of the protist Paradiplonema papillatum reveals the digestive capacity of the cell membrane and the plasticity of peroxisomes across euglenozoans.Diplonemids are among the most diverse and abundant protists in the deep ocean, have extremely complex and ancient cellular systems, and exhibit unique metabolic capacities. Despite this, we know very little about this major group of eukaryotes. To establish a model organism for comprehensive investigation, we performed subcellular proteomics on Paradiplonema papillatum and localized 4,870 proteins to 22 cellular compartments. We additionally confirmed the predicted location of several proteins by epitope tagging and fluorescence microscopy. To probe the metabolic capacities of P. papillatum, we explored the proteins predicted to the cell membrane compartment in our subcellular proteomics dataset. Our data revealed an accumulation of many carbohydrate-degrading enzymes (CDZymes). Our predi2025-01-01T00:00:00Z2025 Dec2026-07-15T07:47:39.913Z2026-07-01T03:08:06.427ZS-EPMC126979444133618010.1371/journal.pbio.3003319