Novel Translational and Phosphorylation Modification Regulation Mechanisms of Tomato (Solanum lycopersicum) Fruit Ripening Revealed by Integrative Proteomics and Phosphoproteomics

Abstract

The tomato is a research model for fruit-ripening, however, its fruit-ripening mechanism still needs more extensive and in-depth exploration. Here, using TMT and LC-MS, the proteome and phosphoproteome of AC++ (wild type) and rin (ripening-inhibitor) mutant fruits were studied to investigate the translation and post-translational regulation mechanisms of tomato fruit-ripening. A total of 6141 proteins and 4011 phosphorylation sites contained quantitative information. One-hundred proteins were identified in both omics’ profiles, which were mainly found in ethylene biosynthesis and signal transduction, photosynthesis regulation, carotenoid and flavonoid biosynthesis, chlorophyll degradation, ribosomal subunit expression changes, MAPK pathway, transcription factors and kinases. The affected protein levels were correlated with their corresponding gene transcript levels, such as NAC-NOR, MADS-RIN, IMA, TAGL1, MADS-MC and TDR4. Changes in the phosphorylation levels of NAC-NOR and IMA were involved in the regulation of tomato fruit-ripening. Although photosynthesis was inhibited, there were diverse primary and secondary metabolic pathways, such as glycolysis, fatty acid metabolism, vitamin metabolism and isoprenoid biosynthesis, regulated by phosphorylation. These data constitute a map of protein—protein phosphorylation in the regulation of tomato fruit-ripening, which lays the foundation for future in-depth study of the sophisticated molecular mechanisms of fruit-ripening and provide guidance for molecular breeding.

Proteomics of Reproductive Development, Fruit Ripening, and Stress Responses in Tomato

“…30 The fruits of wild-type (AC++) and mutant (rin) tomatoes have been reported to be heavily phosphorylated during the ripening stages of development, mostly at pSer (4017) and followed by pThr (592) and pTyr (233). 197 The phosphorylation of several signaling and transcription factors such as NAC-NOR, MADS-RIN, IMA, TAGL1, and TDR4 was involved in the ripening stages. Another assessment of Pseudomonas-infected PTI and ETI immunity function dissected the abundance of 225 proteins and 79 phosphopeptides that were related to cell signaling (Ca 2+ and MAPK), ROS homeostasis, transport, trafficking, and cell wallremodeling enzymes.…”

“…These phosphopeptides were linked to the phosphorylation cascade of the activation of proteins during infection by C. fulvum . The fruits of wild-type (AC++) and mutant ( rin ) tomatoes have been reported to be heavily phosphorylated during the ripening stages of development, mostly at pSer (4017) and followed by pThr (592) and pTyr (233) . The phosphorylation of several signaling and transcription factors such as NAC-NOR, MADS-RIN, IMA, TAGL1, and TDR4 was involved in the ripening stages.…”

Integrative Proteomics and Phosphoproteomics Analysis of the Rat Adenohypophysis after GnRH Treatment

“…Despite the complex structure of proteins, their functions are not only influenced by their structure. Various post-translational modifications (PTMs) also control the function of the protein, including phosphorylation, ubiquitination, glycosylation, and lactic acidation [ 19 ]. Among these, reversible protein phosphorylation is one of the most intensively studied PTMs [ 20 ].…”

Quantitative proteomic analysis of tomato fruit ripening behavior in response to exogenous abscisic acid

“…Wang et al 24 demonstrated that melatonin participated in cellular resistance to oxidative stress by upregulating polyamine metabolism in berries. Several researchers have also used it to investigate the protein responses during tomato fruit ripening, 25 tomato spotted wilt virus invasion, 26 and exogenous strigolactone and auxin treatment. 27 In this study, based on our previous research demonstrating that exogenous ABA induced tomato fruit ripening, 10,12,14 a quantitative proteomic analysis of tomato fruit treated with ABA or nordihydroguaiaretic acid (NDGA) was performed using TMT-labeled quantitative proteomics to measure the effect of ABA on the tomato fruit ripening process at the protein level and provide valuable insights and evidence for further research on the regulation of ABA on tomato fruit quality.…”

“…demonstrated that melatonin participated in cellular resistance to oxidative stress by upregulating polyamine metabolism in berries. Several researchers have also used it to investigate the protein responses during tomato fruit ripening, 25 tomato spotted wilt virus invasion, 26 and exogenous strigolactone and auxin treatment 27 …”