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Subcellular proteomics of model diplonemid, Paradiplonema papillatum

ABSTRACT: The genome of diplonemid Paradiplonema papillatum, like many other protist organisms, encodes a vast swathe of hypothetical proteins, for which no annotation is currently available, and confounds interpretations that can be drawn from molecular analysis. As a result, many outstanding questions remain for this clade of heterotrophic unicellular flagellates, including their evolutionary divergence and modes of nutrition. To rectify this, we initiated subcellular proteomics on P. papillatum to resolve localization for approximately 5,000 proteins of this model diplonemid. We ultimately predict 2,435 proteins to 22 cellular compartments of this organism, for which we performed additional validation via a series of endogenous tagging procedures across new predictions. For the first time, we resolve the cell membrane of P. papillatum, showing an accumulation of previously identified carbohydrate active enzymes. Our topological reconstructions for these enzymes suggest exposure to extracellular space and supports recent proposals for the breakdown of plant and algal cell wall carbohydrates in the world’s oceans as a means of nutrition. In turn we localize various metabolic enzymes of the cell, demonstrating broad amino acid processing capabilities within the mitochondrion, along with new glycosomal-localized carbohydrate enzymes, which strengthen claims for ancestral compartmentalisation for certain steps within the modified peroxisomes shared between sister-clades kinetoplastids and diplonemids. This dataset constitutes a proteomic resource from which to explore the unique cell biology of diplonemids and clarify developmental trends throughout their evolutionary differentiation.

INSTRUMENT(S):

ORGANISM(S): Diplonema Diplonema Papillatum

TISSUE(S): Cell Culture

SUBMITTER: Yu-Ping Poh

LAB HEAD: Jeremy G. Wideman

PROVIDER: PXD065121 | Pride | 2025-10-23

REPOSITORIES: Pride

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Project description:Environmental risk assessment relies heavily on the use of bioassays to assess the environmental impact of chemicals. Gene expression is gaining acceptance as a valuable mechanistic endpoint in bioassays and effect-based screening. Data analysis and its results however, are often complex and not directly applicable in risk assessment. Classifier analysis is a promising method to turn complex gene expression analysis results into answers suitable for risk assessment. We have assembled a large gene expression dataset assembled from multiple studies and experiments in the springtail Folsomia candida, with the aim of selecting a set of genes that can be trained to classify general toxic stress. By performing differential expression analysis prior to classification we were able to select a set of 135 genes which was enriched in stress related processes. This set was then used to classify two test sets comprised of chemical spiked soils, polluted soils and clean soils and compared to another, more traditional feature selection for classification. The gene set presented here outperformed the more traditionally selected gene set. This gene set has the potential to be used as a biomarker to test for adverse effects caused by chemicals in springtails to provide endpoints in environmental risk assessment. The data presented in our manuscript is part of a larger experiment which was performed in single, large loop design. Only the samples used in the study presented here are named while the other samples will remain unnamed. All the data can still be used for normalization after which the analysis presented in the manuscript can be replicated. A single channel, interwoven loop design was used to test animals exposed to a control and to 5 concentrations of cadmium and phenanthrene (cadmium concentrations are: cad_1 till cad_5: 5.8, 14.5, 28.9, 57.9 and 115.8 mg/Kg respectively and phenanthrene concentrations are: phe_1 till Phe_5: 0, 4.6, 11.4, 22.9, 45.8 and 91.6 mg/Kg soil respectively). Exposures lasted for 2 days and used 4 biological replicates per condition each containing 30 grams soil and 30 individuals.

			Action	DRS
	Hammond_Ppap-all.xlsx	Xlsx
	Hammond_Ppap00.raw	Raw
	Hammond_Ppap01.raw	Raw
	Hammond_Ppap02.raw	Raw
	Hammond_Ppap03.raw	Raw

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Subcellular proteomics of model diplonemid, Paradiplonema papillatum

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