Carotenoids are natural pigments that are indispensable to plants and humans, whereas the regulation of carotenoid biosynthesis by post-translational modification remains elusive. Here, we show that a tomato E3 ubiquitin ligase, Plastid Protein Sensing RING E3 ligase 1 (PPSR1), is responsible for the regulation of carotenoid biosynthesis. PPSR1 exhibits self-ubiquitination activity and loss of PPSR1 function leads to an increase in carotenoids in tomato fruit. PPSR1 affects the abundance of 288 proteins, including phytoene synthase 1 (PSY1), the key rate-limiting enzyme in the carotenoid biosynthetic pathway. PSY1 contains two ubiquitinated lysine residues (Lys380 and Lys406) as revealed by the global analysis and characterization of protein ubiquitination. We provide evidence that PPSR1 interacts with PSY1 precursor protein and mediates its degradation via ubiquitination, thereby affecting the steady-state level of PSY1 protein. Our findings not only uncover a regulatory mechanism for controlling carotenoid biosynthesis, but also provide a strategy for developing carotenoid-enriched horticultural crops.

类胡萝卜素是植物和人类不可缺少的天然色素，而通过翻译后修饰来调节类胡萝卜素生物合成的调控仍然难以实现。在这里，我们显示番茄E3泛素连接酶Plastid Protein Sensing RING E3连接酶1（PPSR1）负责类胡萝卜素的生物合成调控。PPSR1表现出自泛素化活性，PPSR1功能的丧失导致番茄果实中类胡萝卜素的增加。PPSR1影响288种蛋白质的含量，其中包括八氢番茄红素合酶1（PSY1），这是类胡萝卜素生物合成途径中的关键限速酶。PSY1包含两个泛素化的赖氨酸残基（Lys380和Lys406），这是通过蛋白质泛素化的整体分析和表征揭示的。我们提供的证据表明PPSR1与PSY1前体蛋白相互作用，并通过泛素化介导其降解，从而影响PSY1蛋白的稳态水平。我们的发现不仅揭示了控制类胡萝卜素生物合成的调控机制，而且为开发富含类胡萝卜素的园艺作物提供了策略。