PXD022812

PXD022812 is an original dataset announced via ProteomeXchange.

Title	Proteome-wide identification of NEDD8 modification sites reveals distinct proteomes for canonical and atypical NEDDylation
Description	The Ubiquitin-like molecule NEDD8 controls several biological processes and is a promising target for therapeutic intervention. NEDDylation occurs through specific NEDD8 enzymes (canonical) or enzymes of the Ubiquitin system (atypical). Identification of NEDD8 sites on substrates is critical for delineating the processes controlled by NEDDylation. By combining the use of the NEDD8 R74K mutant with anti-diGly antibodies we identified 1101 unique NEDDylation sites in 620 proteins. Bioinformatics analysis reveals that canonical and atypical NEDDylation have distinct proteomes; the spliceosome/mRNA surveillance/DNA replication and ribosome/proteasome respectively. The data also reveal the formation of poly-NEDD8, hybrid NEDD8-Ubiquitin and NEDD8-SUMO-2 chains as potential molecular signals. In particular, NEDD8-SUMO-2 chains are induced upon proteotoxic stress (atypical) through NEDDylation of K11 in SUMO-2 and conjugates accumulate in previously described nucleolus-related inclusions. The study uncovers a diverse proteome for NEDDylation, and is consistent with the concept of extensive cross-talk between Ubiquitin and Ubls under proteotoxic stress conditions.
HostingRepository	PRIDE
AnnounceDate	2021-02-10
AnnouncementXML	Submission_2021-02-10_07:46:23.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Petra Beli
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	neddylated lysine
Instrument	Q Exactive Plus

Revision	Datetime	Status	ChangeLog Entry
0	2020-11-30 03:58:38	ID requested
⏵ 1	2021-02-10 07:46:23	announced

Lobato-Gil S, Heidelberger JB, Maghames C, Bailly A, Brunello L, Rodriguez MS, Beli P, Xirodimas DP, Proteome-wide identification of NEDD8 modification sites reveals distinct proteomes for canonical and atypical NEDDylation. Cell Rep, 34(3):108635(2021) [pubmed]

submitter keyword: NEDD8, proteomics, diGly remnants, NEDD8 polymers, SUMO-2, nucleolus-related inclusions

Petra Beli
contact affiliation	Institute of Molecular Biology (IMB), Mainz, Germany
contact email	p.beli@imb-mainz.de
lab head
Petra Beli
contact affiliation	Institute of Molecular Biology (IMB), Mainz, Germany
contact email	p.beli@imb-mainz.de
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/2021/02/PXD022812

PRIDE project URI

• PRIDE
  1. PXD022812
     1. Label: PRIDE project
     2. Name: Proteome-wide identification of NEDD8 modification sites reveals distinct proteomes for canonical and atypical NEDDylation