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PXD034491

PXD034491 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleTurboID identification of evolutionarily divergent components of the nuclear pore complex in the malaria model Plasmodium berghei
DescriptionTwenty 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.
HostingRepositoryPRIDE
AnnounceDate2022-08-21
AnnouncementXMLSubmission_2022-08-21_09:51:12.929.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterSushma Ambekar
SpeciesList scientific name: Plasmodium; NCBI TaxID: NCBITaxon:5820;
ModificationListNo PTMs are included in the dataset
InstrumentOrbitrap Fusion Lumos; LTQ Orbitrap
Dataset History
RevisionDatetimeStatusChangeLog Entry
02022-06-13 02:08:36ID requested
12022-08-21 09:51:13announced
Publication List
Dataset with its publication pending
Keyword List
submitter keyword: Plasmodium, malaria, proximity-labeling, BioID, TurboID, nuclear pore complex, nucleoporins, Nup
Contact List
Gunnar Mair
contact affiliationIowa State University
contact emailmair@iastate.edu
lab head
Sushma Ambekar
contact affiliationIowa State University
contact emailsushma@iastate.edu
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
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