CLPC2 plays specific roles in CLP complex-mediated regulation of growth, photosynthesis, embryogenesis and response to growth-promoting microbial compounds

In Arabidopsis, exposure to growth-promoting microbial volatile compounds (VCs) enhances CLPC2 levels. This chaperone forms part of the CLP protease complex, which ensures the correct functioning of essential processes in plastids. Previous studies indicated considerable functional redundancy of CLPC2 with its dominant paralogue CLPC1. However, the function and action mechanism of CLPC2 still remain unknown. Here we found that CLPC2-lacking clpc2-2 mutants were unresponsive to microbial VCs, whereas clpc1-1 knockout mutants exhibited a WT-like response to VCs when grown on sucrose-containing medium. Unlike clpc1-1, clpc2-2 plants presented a fully functional photosystem II and lower than WT stomatal conductance. Furthermore, clpc2-2 plants, but not clpc1-1 plants, produced wrinkled seeds with delayed embryonic development and reduced postgerminative establishment rates that resembled those of mutants lacking P and R components of the CLP proteolytic core. Proteomic analyses revealed that knocking out of CLPC2 enhanced the levels of chloroplastic proteins that are essential for growth, embryo development and seedling establishment. These changes differed from those promoted by the lack of CLPC1, but partially resembled those promoted by CLPPR core inactivation. Nearly 40% of the proteins differentially accumulated by the lack of CLPC2 were VC-responsive. Notably, 35S promoter-driven CLPC2 expression promoted changes in the proteome similar to those promoted by the lack of CLPC1. Collectively, our findings highlighted contrasting functional and molecular specificities for CLPC1 and CLPC2, and provided strong evidence that CLPC2 plays specific roles in CLP complex-mediated regulation of plant growth, photosynthesis, embryogenesis, postgerminative seedling establishment and microbial VC responsiveness.