PXD034491

PXD034491 is an original dataset announced via ProteomeXchange.

Title	TurboID identification of evolutionarily divergent components of the nuclear pore complex in the malaria model Plasmodium berghei
Description	Twenty years since publication of the Plasmodium falciparum and P. berghei genomes one-third of their protein-coding genes lack functional annotation. In the absence of sequence and structural homology, protein-protein interactions can facilitate functional prediction of such orphan genes by mapping protein complexes in their natural cellular environment. The Plasmodium NPC (nuclear pore complex) is a case in point: it remains poorly defined; its constituents lack conservation with the 30+ proteins described in the NPC of many opisthokonts, a clade of eukaryotes that includes fungi and animals, but not Plasmodium. Here we developed a labeling methodology based on TurboID fusion proteins, which allows visualization of the berghei NPC and facilitates the identification of its components. Following affinity purification and mass spectrometry we identify four known Nups (138, 205, 221, and the bait 313) and verify interaction with the putative FG Nup637; we assign five proteins lacking annotation (and therefore meaningful homology with proteins outside the genus) to the NPC, which is confirmed by GFP tagging. Based on gene deletion attempts, all new Nups  Nup176, 269, 335, 390, and 434  are essential to parasite survival. They lack primary sequence homology with proteins outside the Plasmodium genus; albeit two incorporate short domains with structural homology to human Nup155 and yeast Nup157, and the condensin SMC4. The protocols developed here showcase the power of proximity-labeling for elucidating protein complex composition and annotation in Plasmodium. It opens the door to exploring the function of the Plasmodium NPC and understanding its evolutionary position.
HostingRepository	PRIDE
AnnounceDate	2022-08-21
AnnouncementXML	Submission_2022-08-21_09:51:12.929.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sushma Ambekar
SpeciesList	scientific name: Plasmodium; NCBI TaxID: NCBITaxon:5820;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos; LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2022-06-13 02:08:36	ID requested
⏵ 1	2022-08-21 09:51:13	announced

Dataset with its publication pending

submitter keyword: Plasmodium, malaria, proximity-labeling, BioID, TurboID, nuclear pore complex, nucleoporins, Nup

Gunnar Mair
contact affiliation	Iowa State University
contact email	mair@iastate.edu
lab head
Sushma Ambekar
contact affiliation	Iowa State University
contact email	sushma@iastate.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/2022/08/PXD034491

PRIDE project URI

• PRIDE
  1. PXD034491
     1. Label: PRIDE project
     2. Name: TurboID identification of evolutionarily divergent components of the nuclear pore complex in the malaria model Plasmodium berghei