PXD040778

PXD040778 is an original dataset announced via ProteomeXchange.

Title	CRISPR/Cas9-mediated knockout of the ubiquitin variant UbKEKS reveals a role in regulating nucleolar structures and composition
Description	Ubiquitination is a well-known post-translational modification responsible for one of the most powerful multi-layered communication and regulation system in the cell. Over the past decades, new ubiquitin variants and ubiquitin-like proteins arose to further enrich this mechanism. Among them, the recently discovered ubiquitin variant UbKEKS can specifically target many proteins and yet, functional consequences of this new modification remain unknown. The absence of UbKEKS induces accumulation of lamin A in the nucleoli, highlighting the need for deeper investigations about protein composition and functions regulation of this highly dynamic and membrane-less compartment. By using data independent acquisition mass spectrometry and microscopy, we show here that despite not impacting protein stability, UbKEKS is required for correct nucleolar organization. The absence of UbKEKS increases nucleoli’s size and accentuate their circularity while disrupting dense fibrillar component and fibrillar center structures. Moreover, depletion of UbKEKS leads to distinct changes in nucleolar composition. Notably, lack of UbKEKS favors nucleolar sequestration of known apoptotic regulators such as IFI16 or P14arf. Increase of apoptosis in UbKEKS knockout cells was later validated by flow cytometry and real-time cellular growth monitoring. In the end, this work identifies the first cellular functions of the UbKEKS variant and lay the foundation stone to establish UbKEKS as a new universal layer of regulation in the already complex ubiquitination system.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:05:44.134.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Dominique Levesque
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	carbamoylated residue; acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2023-03-10 12:25:02	ID requested
1	2023-10-11 17:24:11	announced
2	2023-11-14 07:52:30	announced	2023-11-14: Updated project metadata.
⏵ 3	2024-10-22 06:05:44	announced	2024-10-22: Updated project metadata.

10.1242/BIO.059984;

submitter keyword: Nucleolus, Apoptosis, Protein sequestration, Data-Independent Acquisition (DIA),UbKEKS, Ubiquitin variant, Post-Translational Modification (PTM)

Francois-Michel Boisvert
contact affiliation	Department of Immunology and Cell Biology, Sherbrooke, QC, Canada
contact email	francois.michel.boisvert@usherbrooke.ca
lab head
Dominique Levesque
contact affiliation	University of Sherbrooke, FM Boisvert lab
contact email	dominique.levesque@usherbrooke.ca
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD040778
     1. Label: PRIDE project
     2. Name: CRISPR/Cas9-mediated knockout of the ubiquitin variant UbKEKS reveals a role in regulating nucleolar structures and composition