Dataset Information

Ripening stage-resolved proteome and phosphoproteome profiling of tomato fruits reveals the involvement of reduced chloroplast coverage protein REC1a in fruit ripening

ABSTRACT: 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.

ORGANISM(S): Solanum Lycopersicum

SUBMITTER: Zhiping Deng

PROVIDER: PXD051570 | iProX | Fri Apr 19 00:00:00 BST 2024

REPOSITORIES: iProX

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Publications

Proteome and Phosphoproteome of Tomato Fruit Identify REDUCED CHLOROPLAST COVERAGE 1a as A Ripening Regulator.

Tan Jinjuan J Zhou Zhongjing Z Feng Hanqian H Zhang Jiateng J Zhang Ruikai R Chen Zhongkai Z Niu Yujie Y Liu Fangyu F Deng Zhiping Z

Genomics, proteomics & bioinformatics 20250609

Fruit ripening in tomato (Solanum lycopersicum) has been extensively studied at the transcriptomics level. However, comprehensive profiling of the tomato fruit proteome and phosphoproteome remains limited. In this study, we performed large-scale proteome and phosphoproteome profiling of tomato (Ailsa Craig) fruits across five ripening stages using tandem mass tags (TMT)-based quantitative proteomics. Our analysis quantified over 8800 proteins and 20,000 high-confidence phosphorylation sites. Rip ...[more]

PMID: 40489665

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Project description:Tomato fruit ripening is under the control of ethylene as well as a group of ethylene-independent transcription factors, including NON-RIPENING (NOR) and RIPENING INHIBITOR (RIN). During ripening, the linear carotene lycopene accumulates at the expense of cyclic carotenoids. Fruit-specific overexpression of LYCOPENE β-CYCLASE (LCYb) under the control of the PHYTOENE DESATURASE (PDS) promoter resulted in increased levels of β-carotene and ABA and in decreased ethylene levels. Genes regulated by ABA, or involved in its synthesis and signaling, were overexpressed, while those associated with ethylene and cell wall remodeling were repressed. In agreement with the transcriptional data, LCYb-overexpressing fruits exhibited increased density of cell wall material containing linear, under-methylated pectins and displayed an array of additional ripening phenotypes, including delayed softening, increased turgor, enhanced shelf life and a thicker cuticle with a higher content of cutin monomers and triterpenoids. The levels of several primary metabolites and phenylpropanoids also changed in the transgenics, which could be attributed to delayed fruit ripening and to ABA respectively. Network correlation analysis suggests that ABA, acting through NOR and RIN, is responsible for many of the above phenotypes. These data reinforce suggestions that ABA plays an important role in tomato fruit ripening and provide clues that fruit b-carotene, acting as a precursor for ABA, actively participates in controlling the ripening process rather than merely being an output thereof. Overexpression of a LCYb gene from Arabidopsis under the control of the ripening-associated PDS promoter leads to ripe tomato fruits accumulating high β-carotene levels. Using several independent transgenic lines, we conducted a system-wide study of the effect of increased β-carotene levels on tomato fruit ripening and shelf life. Our data suggest that β-carotene, acting through ABA, is involved in a regulatory loop within the network controlling tomato fruit ripening.

Dataset Information

Ripening stage-resolved proteome and phosphoproteome profiling of tomato fruits reveals the involvement of reduced chloroplast coverage protein REC1a in fruit ripening

Publications

Proteome and Phosphoproteome of Tomato Fruit Identify REDUCED CHLOROPLAST COVERAGE 1a as A Ripening Regulator.

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