Chloroplasts are plant organelles responsible for photosynthesis and environmental sensing. Most chloroplast proteins are imported from the cytosol through the translocon at the outer envelope membrane of chloroplasts (TOC). Previous work showed that TOC components are regulated by the ubiquitin-proteasome system (UPS) to control the chloroplast proteome, which is crucial for organellar functions and plant development. Here, we demonstrate that the TOC apparatus is also subject to K63- type polyubiquitination and regulation by selective autophagy, potentially to promote plant stress tolerance. We identify NBR1 as a selective autophagy adaptor targeting TOC components, and mediating their relocation into vacuoles for autophagic degradation. Such selective autophagy is shown to control TOC protein levels, and chloroplast protein import, and to influence photosynthetic activity and UVB and heat stress tolerance in Arabidopsis plants. The work first time reveals the vital role of selective autophage in the proteolytic regulation of specific chloroplast proteins, and how dynamic control of chloroplast protein import is critically important for plants to cope with challenging environments.
