Chlorophagy of photodamaged chloroplasts involves the degradation of disorganized nucleoids in Arabidopsis leaves

Autophagy is a “self-eating” process that transports cytoplasmic components into lytic organelles for degradation in eukaryotic cells. In animals and yeast, the autophagic degradation of mitochondria mediates the clearance of mitochondrial DNA. Autophagy also occurs in plants, involving the degradation of plastids (including chloroplasts). However, the roles of plant autophagy in plastid DNA (ptDNA) degradation remain poorly understood. In this study, we established in vivo imaging methods to visualize ptDNA–protein complexes known as plastid nucleoids, along with chloroplast stroma or autophagy-associated membranes, in Arabidopsis (Arabidopsis thaliana) leaves using fluorescent proteins and probes. These methods facilitated monitoring the behavior of plastid nucleoids during chloroplast autophagy. We observed the exclusion of nucleoids from the autophagic cargo during piecemeal chloroplast autophagy in sugar-starved leaves. Monitoring leaf cells exposed to photooxidative damage indicated that the autophagic elimination of photodamaged chloroplasts, a process termed chlorophagy, is accompanied by the degradation of interior disorganized nucleoids. The absence of chlorophagy due to the mutation of autophagy-related genes led to the cytoplasmic accumulation of chloroplasts lacking nucleoid signals after photodamage treatment. These findings suggest that chlorophagy contributes to maintaining a healthy population of plastid nucleoids in plants under photooxidative stress.