PXD014318

PXD014318 is an original dataset announced via ProteomeXchange.

Title	UBB Pseudogene 4 encodes novel ubiquitin variants
Description	Post-translational modification by ubiquitin and ubiquitin-like modifiers proteins regulate cellular processes at almost every levels. Ubiquitin itself is encoded by four different genes, either as single copy of ubiquitin fused to ribosomal proteins, or by polyubiquitin precursors3. Early studies identified several additional genes potentially coding for ubiquitin, but they were considered as pseudogenes due to differences in amino acids, or lack of apparent transcription4-6. Through analysis of large-scale proteomics and RNA sequencing experiments, we found evidence for expression at the mRNA and protein levels of several ubiquitin pseudogenes. Our results show that UBBP4, a pseudogene of the UBB subfamily, produces functional ubiquitin proteins with different amino acids composition compared to the canonical sequence. These ubiquitins variants are covalently conjugated to proteins that are different from ubiquitin, and proteins modified by UBBP4 are not targeted for proteasomal degradation. Furthermore, invalidation of UBBP4 results in slower cell division, and accumulation of lamin A within the nucleolus. This implies that a subset of proteins reported as ubiquitin targets could rather be through these variants arising from wrongly annotated pseudogenes, and that there is a specificity in the modification and differences in the functional consequence of proteins modified by these new ubiquitin variants. The identification of additional ubiquitins thus entails a new layer of complexity in protein ubiquitylation that has been unnoticed until now.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:01:02.908.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Anonym Anonym
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	carbamoylated residue; ubiquitinylated lysine; 6x(13)C labeled residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-06-20 02:50:14	ID requested
1	2020-03-19 05:41:57	announced
⏵ 2	2024-10-22 05:01:03	announced	2024-10-22: Updated project metadata.

Dubois ML, Meller A, Samandi S, Brunelle M, Frion J, Brunet MA, Toupin A, Beaudoin MC, Jacques JF, L, é, vesque D, Scott MS, Lavigne P, Roucou X, Boisvert FM, UBB pseudogene 4 encodes functional ubiquitin variants. Nat Commun, 11(1):1306(2020) [pubmed]

10.1038/s41467-020-15090-6;

submitter keyword: Ubiquitin, Lamin A, Nucleolus, Pseudogene

Anonym Ous
contact affiliation	Anonymous for double-blind review.
contact email	Mikgree@Hotmail.com
lab head
Anonym Anonym
contact affiliation	Anony
contact email	mikgree@hotmail.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/2020/03/PXD014318

PRIDE project URI

• PRIDE
  1. PXD014318
     1. Label: PRIDE project
     2. Name: UBB Pseudogene 4 encodes novel ubiquitin variants