Loss of Mitochondrial FMT Restores Chloroplast Proteostasis via Inter-organelle Compensation

Chloroplast proteostasis is vital for plant development, yet whether cells can actively reprogram organelle communication to restore plastid function when essential protease components fail remains unclear. Using a forward genetic suppressor screen in Arabidopsis, we identify loss of the mitochondria-associated protein FRIENDLY MITOCHONDRIA (FMT) as a strong suppressor of the virescent and growth-retarded clpc1 mutant, which lacks the major chloroplast Clp chaperone ClpC1. Suppression is highly specific and occurs independently of GUN1-mediated retrograde signaling. Integrated multi-omics analyses reveal that clpc1 and fmtclpc1 represent two distinct organelle signaling states. In clpc1, loss of ClpC1 triggers a plastid stress state characterized by repression of photosynthesis-associated transcription factors, induction of plastid metabolic stress markers, and impaired proteolytic activity. By contrast, loss of FMT shifts the system into a recovery state despite persistent mitochondrial clustering. Mechanistically, FMT negatively regulates CLPC2, a ClpC1 paralog, and fmt-mediated rescue results from CLPC2 derepression. Moderately elevated ClpC2 restores in vivo proteolysis, as evidenced by recovery of PAA2 substrate turnover, normalization of chloroplast ultrastructure, and reactivation of photosynthesis-related gene expression. Transcriptomic and proteomic profiling further reveal coordinated remodeling of nuclear gene expression and chloroplast protein investment in the recovery state, including reduced cytosolic folding stress and selective induction of jasmonic acid- and salicylic acid-associated signaling networks. Genetic analyses establish that REC1 and REC2 are required for full CLPC2 induction and phenotypic recovery. Together, our findings uncover a latent inter-organelle compensatory mechanism in which mitochondrial perturbation reprograms nuclear gene expression to restore chloroplast proteostasis when ClpC1 function is compromised.