The miR399-UBC24 module regulates starch metabolism through SlAGPS1 and SlBAM1 in tomato

Starch and its degradation products are essential sources of energy and carbon skeleton for plant growth and stress responses. In fruits, starch accumulation and its conversion to soluble sugars are critical determinants of yield, flavor, and nutritional quality. Despite their importance, the underlying mechanism of starch metabolism during fruit development remains largely unexplored. Our study uncovers previously unidentified roles of miR399 and its target gene UBC24, which have been known as important regulators of phosphate metabolism, in the regulation of starch metabolism in tomato fruits. We demonstrate by metabolome analysis that overexpression of Sly-miR399a affects carbohydrate metabolism, particularly leading to a substantial increase in starch and soluble sugar contents in tomato fruits. We further show that knockout of SlUBC24 also exerts a similar effect, promoting starch and sugar accumulation in fruits. We reveal through proteome and molecular studies that SlUBC24 exerts this regulatory role in starch metabolism by mediating the protein degradation of SlAGPS1 and SlBAM1. This process affects the enzyme activity of AGPase and BAM, which are essential for starch synthesis and breakdown, respectively. We propose that the miR399-UBC24 module could facilitate both starch turnover and phosphorus accumulation in tomato fruits, and could act to mitigate the adverse effects on fruit quality caused by phosphorus deficiency. Our study contributes substantially to the understanding of posttranscriptional mechanism in the regulation of fruit starch metabolism and highlights its potential applications in crop breeding.