PXD039560

PXD039560 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Znf598-mediated Rps10/eS10 Ubiquitination contributes to the ribosome ubiquitination dynamics during zebrafish development
Description	The ribosome is a translational apparatus that comprises about 80 ribosomal proteins and four rRNAs. Recent studies reported that ubiquitination of the ribosomal proteins plays a pivotal role in translational control and ribosome-associated quality control (RQC). However, little is known about the dynamics of ribosome ubiquitination under complex biological processes of multicellular organisms. To study ribosome ubiquitination during animal development, we generated a zebrafish strain that expresses a FLAG-tagged ribosomal protein Rpl36/eL36 from its endogenous locus. Combining affinity purification of ribosomes from rpl36-FLAG zebrafish embryos with immunoblotting analysis, we analyzed ribosome ubiquitination during zebrafish development. Our data showed that ubiquitination of ribosomal proteins dynamically changed as development proceeded. We further revealed that Znf598, an E3 ubiquitin ligase that triggers RQC, contributed to the ribosome ubiquitination during zebrafish development. LC-MS/MS analysis and immunoblotting analysis identified lysines 139 of ribosomal protein Rps10/eS10 as pivotal ubiquitination sites on the ribosome during development. Finally, we demonstrated that an Rps10 K139/140R mutation reduced overall ribosome ubiquitination pattern. Collectively, these results reveal dynamics and complexity of ribosome ubiquitination in zebrafish development.
HostingRepository	jPOST
AnnounceDate	2023-10-11
AnnouncementXML	Submission_2023-10-27_06:03:06.709.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Koshi Imami
SpeciesList	scientific name: Danio rerio; NCBI TaxID: 7955;
ModificationList	S-carboxamidomethyl-L-cysteine; alpha-amino acetylated residue; L-methionine sulfoxide; deamidated L-glutamine; deamidated L-asparagine; ubiquitinylated lysine
Instrument	Orbitrap Exploris 480; instrument

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2023-01-19 18:08:02	ID requested
1	2023-10-10 20:45:01	announced
⏵ 2	2023-10-27 06:03:07	announced	2023-10-11: Updated PubMed.

Publication List

Ugajin N, Imami K, Takada H, Ishihama Y, Chiba S, Mishima Y, Znf598-mediated Rps10/eS10 ubiquitination contributes to the ribosome ubiquitination dynamics during zebrafish development. RNA, 29(12):1910-1927(2023) [pubmed]

Ugajin N, Imami K, Takada H, Ishihama Y, Chiba S, Mishima Y, Znf598-mediated Rps10/eS10 ubiquitination contributes to the ribosome ubiquitination dynamics during zebrafish development. RNA, 29(12):1910-1927(2023) [pubmed]

Keyword List

submitter keyword: zebrafish, ribosome, IP, ubiquitination

submitter keyword: zebrafish, ribosome, IP, ubiquitination

Contact List

Yuichiro Mishima
lab head
Koshi Imami
contact affiliation	Kyoto University
dataset submitter

Full Dataset Link List

jPOST dataset URI
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jPOST dataset URI

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.jpostdb.org/JPST002001/