PXD051570-1

PXD051570 is an original dataset announced via ProteomeXchange.

Title	Ripening stage-resolved proteome and phosphoproteome profiling of tomato fruits reveals the involvement of reduced chloroplast coverage protein REC1a in fruit ripening
Description	Fruit ripening in tomato (Solanum lycopersicum) has been extensively studied at the molecular, biochemical, physiological, and transcriptomic levels, but comprehensive profiling of tomato fruit proteome and phosphoproteome remain limited. Plastid development and differentiation are critical for tomato nutritional quality, but the modulators that regulate the transition from chloroplast to chromoplast in fruits remain poorly understood. Here we present large-scale proteome and phosphoproteome profiling of tomato (Ailsa Craig) fruits at five ripening stages with TMTpro-based quantitative proteomics. Over 8800 proteins and 20,000 high-confidence phosphorylation sites (p-sites) were quantified and approximately one third of them showed significant disturbance during ripening at either the global proteome or site-specific phosphorylation levels. Many critical ripening associated proteins contain differentially expressed p-sites upon ripening, including transcriptional factors like RIN, NOR, FUL1, BES1, AP2a and MYC2; ethylene biosynthesis and signaling proteins ACO1, NR, ETR4, CTR1 and EIN2; and ripening regulators involved in DNA/mRNA methylation or histone deacetylase like CMT3a, DML2, ALKBH2, HDA3 and HDT3. Based on the weighted gene co-expression network analysis (WGCNA) with relating modules to tomato fruit pigments, we characterized a tetratricopeptide repeat protein reduced chloroplast coverage 1a (REC1a) that participates in plastid development and chlorophyll and carotenoids accumulation, and interestingly functions in a tissue-specific manner. Quantitative proteome analysis between rec1a mutant and wild type (MicroTom) fruits at different ripening stages suggested potential mechanisms deciphering the mutant phenotype. Taken together, this study provided the most comprehensive quantitative proteome and phosphoproteome atlas of tomato fruits to date, and revealed a new ripening regulator that play roles in plastid development.
HostingRepository	iProX
AnnounceDate	2024-04-19
AnnouncementXML	Submission_2025-07-09_23:01:53.509.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Zhiping Deng
SpeciesList	scientific name: Solanum lycopersicum; NCBI TaxID: 4081;
ModificationList	phosphorylated residue
Instrument	Q Exactive HF; Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2024-04-18 20:55:51	ID requested
⏵ 1	2025-07-09 23:01:54	announced

Tan J, Zhou Z, Feng H, Zhang J, Zhang R, Chen Z, Niu Y, Liu F, Deng Z, Proteome and Phosphoproteome of Tomato Fruit Identify REDUCED CHLOROPLAST COVERAGE 1a as A Ripening Regulator. Genomics Proteomics Bioinformatics, ():(2025) [pubmed]

submitter keyword: tomato, proteome, phosphoproteome, ripening, REC1, fruit, plastid, chloroplast, chromoplast

Zhiping Deng
contact affiliation	Zhejiang Academy of Agricultural Sciences
contact email	zhipingdeng@126.com
lab head
Zhiping Deng
contact affiliation	Zhejiang Academy of Agricultural Sciences
contact email	zhipingdeng@126.com
dataset submitter

iProX dataset URI