Phosphoproteomic analysis highlights phosphorylation of primary metabolism-related proteins in response to postharvest cold storage and subsequent shelf-life in tomato fruit

Tomato fruit are susceptible to postharvest chilling injuries when stored at low temperatures, resulting in quality deterioration and economic losses worldwide. Protein phosphorylation is an important post-translational modification that has been proven to be involved in plant cold tolerance. However, the changes of protein phosphorylation underlying cold stress responses in tomatoes remain poorly understood. In this study, microscopic analyses showed that endomembranes and intracellular organelles were broken down after cold storage, and the breakdown became more pronounced when the fruit was restored to room temperature. Primary metabolomic analysis revealed that large amounts of lipids, amino acids, sugars, and organic acids were altered following cold treatment. Additionally, we performed comparative phosphoproteomics and determined the overall phosphoprotein profile of tomato fruit after postharvest cold storage and subsequent shelf life. A total of 10260 phosphopeptides corresponding to 9640 phosphosites in 3740 phosphoproteins were identified. Differentially phosphorylated proteins were mainly involved in primary metabolism, such as glycerolipid metabolism, glycolysis/gluconeogenesis, and the tricarboxylic acid cycle. Correspondingly, the phosphorylation of large amounts of important primary metabolic enzymes, such as fatty acid desaturase, sucrose synthase, and alcohol dehydrogenase, was upregulated after cold treatment. The present study revealed the involvement of phosphorylation of primary metabolism-related proteins in the response to postharvest cold storage in tomato fruit.