PXD065121-1

PXD065121 is an original dataset announced via ProteomeXchange.

Title	Subcellular proteomics of model diplonemid, Paradiplonema papillatum
Description	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.
HostingRepository	PRIDE
AnnounceDate	2025-10-23
AnnouncementXML	Submission_2025-10-23_12:20:59.688.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yu-Ping Poh
SpeciesList	scientific name: Diplonema; NCBI TaxID: NEWT:91373; scientific name: Diplonema papillatum; NCBI TaxID: NEWT:91374;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2025-06-17 10:24:18	ID requested
⏵ 1	2025-10-23 12:21:00	announced

10.1101/2025.07.16.665091;

submitter keyword: Subcellular proteomics, diplonemid

Jeremy G. Wideman
contact affiliation	Center for Mechanisms of Evolution, Biodesign Institute, School of Life Sciences, Arizona State University, Tempe, Arizona, USA
contact email	Jeremy.Wideman@asu.edu
lab head
Yu-Ping Poh
contact affiliation	Center for Mechanisms of Evolution, Biodesign Institute, School of Life Sciences, Arizona State University
contact email	yuping.poh@asu.edu
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/10/PXD065121

PRIDE project URI

• PRIDE
  1. PXD065121
     1. Label: PRIDE project
     2. Name: Subcellular proteomics of model diplonemid, Paradiplonema papillatum