PXD032822

PXD032822 is an original dataset announced via ProteomeXchange.

Title	Deubiquitinases that digest Met1 chains in Rice
Description	Met1 type ubiquitination and deubiquitination are involved in the regulation of many fundamental processes such as inflammation and innate immunity, and their interference by pathogens can suppress immune responses in human cells. However, few plant-derived deubiquitinases (DUBs) against Met1 ubiquitin chains has been reported, and the selection mechanism for linkage-type of ubiquitin chains remains elusive, which greatly limits our understanding of the functions of plant-derived DUBs. Using a dehydroalanine (DHA)-bearing Met1 diubiquitin (Met1-diUb) suicide probe, synthesized in one-pot, we captured OTUB1 from Oryza sativa (OsOTUB1) and uncovered its ability to hydrolyze Met1 ubiquitin chains (Met1 activity). Further, by resolving the apo structure of OsOTUB1 and its complex with Met1-diUb, we found that Met1-specific motifs (N-handle motif and C-handle motif) in the S1’ pocket of OsOTUB1 confers its Met1 activity. Through large-scale sequence alignment and hydrolysis experiments, Met1-specific motifs in the S1' pocket of the OTUB subfamily (OTUBs) were found to determine the Met1 ability of OTUBs, regardless of species. Furthermore, by analyzing the species distribution of OTUBs capable of hydrolyzing Met1 ubiquitin chains, we found that whereas this activity does not exist in metazoans, it is conserved in green plants (Viridiplantae). This discovery may inform studies of the differentiation between primitive plants and animals.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:25:10.728.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD032822
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Li-Ning Lu
SpeciesList	scientific name: Oryza sativa (Rice); NCBI TaxID: 4530;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2022-03-26 14:16:09	ID requested
1	2022-10-14 19:36:06	announced
⏵ 2	2023-11-14 08:25:12	announced	2023-11-14: Updated project metadata.

Lu L, Zhai X, Li X, Wang S, Zhang L, Wang L, Jin X, Liang L, Deng Z, Li Z, Wang Y, Fu X, Hu H, Wang J, Mei Z, He Z, Wang F, Met1-specific motifs conserved in OTUB subfamily of green plants enable rice OTUB1 to hydrolyse Met1 ubiquitin chains. Nat Commun, 13(1):4672(2022) [pubmed]

10.6019/PXD032822;

submitter keyword: Deubiquitinase, Met1 chains,Rice

Lining Lu
contact affiliation	College of life sciences and technology,Guangxi University
contact email	thu20151@sina.com
lab head
Li-Ning Lu
contact affiliation	Guangxi University
contact email	thu20151@sina.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/2022/10/PXD032822

PRIDE project URI

• PRIDE
  1. PXD032822
     1. Label: PRIDE project
     2. Name: Deubiquitinases that digest Met1 chains in Rice