Fruit ripening is a tightly regulated developmental process, in which nuclear gene transcription represents a crucial component of the mechanisms1. Chloroplast-associated protein degradation, a recently discovered pathway for chloroplast protein degradation, has also been reported to control fruit ripening2. Here we report a negative regulator of tomato ripening, termed SlSAD8, which disturbs both nuclear gene transcription and chloroplast-associated protein degradation. As an atypical stearoyl-ACP desaturase (SAD) protein exhibiting dual localization in plastids and the nucleus, SlSAD8 negatively regulates ripening initiation and chloroplast-to-chromoplast transition during fruit ripening. In the nucleus, SlSAD8 interacts with ripening-initiation-associated transcription factor SlNAM1, thereby disturbing the transcriptional activation of ethylene biosynthesis genes. Additionally, SlSAD8 interacts with plastid-transition-associated E3 ligase SlSP1 in the plastid, disturbing the chloroplast-associated protein degradation pathway to elevate chloroplast protein levels. Our findings uncover an unusual ripening regulator that targets distinct subcellular compartments to manipulate gene expression, providing insights into the intricate regulatory networks of fruit ripening.
