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PXD040778

PXD040778 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleCRISPR/Cas9-mediated knockout of the ubiquitin variant UbKEKS reveals a role in regulating nucleolar structures and composition
DescriptionUbiquitination 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.
HostingRepositoryPRIDE
AnnounceDate2024-10-22
AnnouncementXMLSubmission_2024-10-22_06:05:44.134.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterDominique Levesque
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListcarbamoylated residue; acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
InstrumenttimsTOF Pro
Dataset History
RevisionDatetimeStatusChangeLog Entry
02023-03-10 12:25:02ID requested
12023-10-11 17:24:11announced
22023-11-14 07:52:30announced2023-11-14: Updated project metadata.
32024-10-22 06:05:44announced2024-10-22: Updated project metadata.
Publication List
10.1242/BIO.059984;
Keyword List
submitter keyword: Nucleolus, Apoptosis, Protein sequestration, Data-Independent Acquisition (DIA),UbKEKS, Ubiquitin variant, Post-Translational Modification (PTM)
Contact List
Francois-Michel Boisvert
contact affiliationDepartment of Immunology and Cell Biology, Sherbrooke, QC, Canada
contact emailfrancois.michel.boisvert@usherbrooke.ca
lab head
Dominique Levesque
contact affiliationUniversity of Sherbrooke, FM Boisvert lab
contact emaildominique.levesque@usherbrooke.ca
dataset submitter
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Dataset FTP location
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