PXD027037

PXD027037 is an original dataset announced via ProteomeXchange.

Title	Ubiquitome profiling reveals metabolism related cell senescence and protein translation modified by UPL3
Description	The HECT domain-containing UPL3 ligase plays critical roles in plant development and stress protection, but its mechanism of action remains unclear. To identify its targets in Arabidopsis thaliana, we conducted proteomic analyses of enriched ubiquitinated proteins in upl3 mutants via label-free mass spectrometry. In 6-week-old plants, a landscape of UPL3-dependent ubiquitinated proteins is constructed based on correlated datasets of ubiquitome, proteome, and transcriptome. Preferential ubiquitination of proteins related to carbon fixation and cell senescence represented the largest set of enriched ubiquitinated proteins that occurred in the upl3 plant, while a small set of reduced ubiquitinated proteins caused by the upl3 mutation were linked to cysteine/methionine synthesis and protein translational processes. Furthermore, the upl3 mutation led to an increase in ubiquitination of some of its targets including chromatin remodeling ATPase (BRM), histone proteins, and carbon metabolic enzymes, but decreased the ubiquitination of Hexokinase 1 (HXK1), Phosphoenolpyruvate carboxylase 2 (PPC2), ribosomal protein S5, and H1/H5 domain proteins. Notably, ubiquitin hydrolase 12 (UBP12), BRM, HXK1, and PPC2 were among the UPL3-interacting partners identified by both GFP-nanotrap-Mass-Spectroscopy analyses and yeast two-hybrid assay. Characterization of upl3, and brm-em, ubp12, ubp12ubp13 double mutant plants suggested that UPL3 fine-tuned carbon metabolism during cellular senescence by interacting, in the nucleus, with dually modified targets specific to histone variants, cell senescence, and the carbon metabolic pathway. Our results highlight an important function of UPL3 as a hub of regulated degradation.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_07:24:34.160.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Wei Lan
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationList	ubiquitinylated lysine
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2021-07-01 07:56:15	ID requested
1	2022-10-14 03:14:38	announced
⏵ 2	2023-11-14 07:24:51	announced	2023-11-14: Updated project metadata.

Lan W, Ma W, Zheng S, Qiu Y, Zhang H, Lu H, Zhang Y, Miao Y, Ubiquitome profiling reveals a regulatory pattern of UPL3 with UBP12 on metabolic-leaf senescence. Life Sci Alliance, 5(12):(2022) [pubmed]

submitter keyword: HECT-type ubiquitin ligase, histone, DUBs, carbon fixation, senescence

Ying Miao
contact affiliation	Fujian Provincial Key Laboratory of Plant Functional Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
contact email	ymiao@fafu.edu.cn
lab head
Wei Lan
contact affiliation	Fujian provincial key laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University
contact email	1150538001@fafu.edu.cn
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD027037
     1. Label: PRIDE project
     2. Name: Ubiquitome profiling reveals metabolism related cell senescence and protein translation modified by UPL3