PXD014610

PXD014610 is an original dataset announced via ProteomeXchange.

Title	Proteomic Analysis of Affinity-Purified Proteasomes Identifies a Suite of Assembly Chaperones in Arabidopsis
Description	The 26S proteasome is an essential protease for the selective elimination of dysfunctional and short-lived regulatory proteins in eukaryotes. To define the composition of this multi-catalytic, ATP-dependent proteolytic machine in plants, we exploited Arabidopsis particles tagged at either the core protease (CP) or regulatory particle (RP) sub-complexes for rapid affinity purification followed by deep sequence analysis via mass spectrometry. Studies on proteasomes purified from whole seedlings via either a CP or RP subunit with or without ATP, which is needed to maintain the holo-proteasome complex, identified all known core subunits but failed to detect subunit isoform preferences, suggesting that Arabidopsis does not construct unique proteasomes sub-types. We also identified a suite of proteasome-interacting proteins, including likely orthologs of the yeast and mammalian chaperones Pba1, Pba2, Pba3, and Pba4 that assist in CP assembly; Ump1 that helps connect CP half-barrels; Nas2, Nas6, and Hsm3 that assist in RP assembly; and Ecm29 that promotes CP-RP association. Analysis of proteasomes enriched from seedlings exposed to the proteasome inhibitor MG132 revealed the accumulation of novel assembly intermediates, which reflect partially built proteasome sub-complexes associated with assembly chaperones, and the CP capped with the PA200/Blm10 regulator. Unlike in yeast, genetic analyses of Arabidopsis UMP1 showed that this chaperone is essential, with mutants missing the major UMP1a and UMP1b isoforms displaying a strong gametophytic defect. Single mutants impacting ump1a also accumulate a collection of proteasome assembly intermediates, consistent with its importance for CP construction. With this list of chaperones, it should now be possible to study the assembly events that generate the 26S holo-proteasome in Arabidopsis from the collection of 64 or more core subunits.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:04:59.087.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	David C Gemperline
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationList	ubiquitination signature dipeptidyl lysine; monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-07-15 02:45:37	ID requested
1	2019-09-25 15:22:28	announced
2	2019-11-08 00:40:58	announced	2019-11-08: Updated publication reference for PubMed record(s): 31562246.
⏵ 3	2024-10-22 04:05:07	announced	2024-10-22: Updated project metadata.

10.1074/jbc.ra119.010219;

Gemperline DC, Marshall RS, Lee KH, Zhao Q, Hu W, McLoughlin F, Scalf M, Smith LM, Vierstra RD, . J Biol Chem, 294(46):17570-17592(2019) [pubmed]

submitter keyword: chaperone

core protease

degradation

proteasome

proteolysis

regulatory particle

ubiquitin

Richard D Vierstra
contact affiliation	George & Charmaine Mallinckrodt Professor Department of Biology Washington University in St. Louis
contact email	rdvierstra@wustl.edu
lab head
David C Gemperline
contact affiliation	UW Madison
contact email	dcgemperline@gmail.com
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/2019/09/PXD014610

PRIDE project URI

• PRIDE
  1. PXD014610
     1. Label: PRIDE project
     2. Name: Proteomic Analysis of Affinity-Purified Proteasomes Identifies a Suite of Assembly Chaperones in Arabidopsis