PXD001414

PXD001414 is an original dataset announced via ProteomeXchange.

Title	Tomato nuclear proteome reveals the involvement of specific E2 ubiquitin-conjugating enzymes in fruit ripening
Description	Fruits are unique to flowering plants and play a central role in seed maturation and dispersal. Molecular dissection of fruit ripening has received considerable interest because of the biological and dietary significance of fruit. To better understand the regulatory mechanisms underlying fruit ripening, we report here the first comprehensive analysis of the nuclear proteome in tomato fruits. Nuclear proteins were isolated from tomatoes in different stages of ripening, and subjected to iTRAQ (isobaric tags for relative and absolute quantification) analysis. The proteins that changed abundance across ripening stages are involved in various cellular processes. We additionally evaluated the changes in the nuclear proteome in the ripening-deficient mutant ripening inhibitor (rin) carrying a mutation in the transcription factor RIN. A set of proteins were identified and particular attention was paid to SlUBC32 and PSMD2, the components of ubiquitin-proteasome pathway. Through chromatin immunoprecipitation and gel mobility shift assay, we provide evidence that RIN directly bound to the promoters of SlUBC32 and PSMD2. Moreover, loss of RIN function affected protein ubiquitination in nuclei. SlUBC32 encodes an E2 ubiquitin-conjugating enzyme and genome-wide survey of the E2 gene family in tomatoes identified five more E2s as the direct targets of RIN. Two E2s were demonstrated to be involved in the regulation of fruit ripening based on virus-induced gene silencing assays. Our results uncover the novel function of protein ubiquitination, identifying specific E2s as regulator in fruit ripening. These findings contribute to the unraveling of the gene regulatory networks that control fruit ripening.
HostingRepository	PRIDE
AnnounceDate	2014-12-01
AnnouncementXML	Submission_2015-06-01_06:06:43.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Guozheng Qin
SpeciesList	scientific name: Solanum lycopersicum; NCBI TaxID: 4081;
ModificationList	ubiquitinylated lysine
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2014-10-20 03:18:59	ID requested
1	2014-11-18 00:51:48	announced
2	2014-11-18 08:22:42	announced	Updated publication details.
3	2014-12-01 00:39:28	announced	Updated project metadata.
⏵ 4	2015-06-01 06:06:44	announced	Updated project metadata.

Wang Y, Wang W, Cai J, Zhang Y, Qin G, Tian S, Tomato nuclear proteome reveals the involvement of specific E2 ubiquitin-conjugating enzymes in fruit ripening. Genome Biol, 15(12):548(2014) [pubmed]

curator keyword: Biological

submitter keyword: Nucleus, proteomics, fruit ripening, MADS-RIN, ubiquitination, tomato

gzqin@ibcas.ac.cn
contact affiliation	Institute of Botany, Chinese Academy of Sciences
contact email	gzqin@ibcas.ac.cn
lab head
Guozheng Qin
contact affiliation	Institute of Botany, Chinese Academy of Sciences
contact email	gzqin@ibcas.ac.cn
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD001414
     1. Label: PRIDE project
     2. Name: Tomato nuclear proteome reveals the involvement of specific E2 ubiquitin-conjugating enzymes in fruit ripening