Chloroplast ATP-dependent metalloprotease FtsH5/VAR1 confers cold stress tolerance through singlet oxygen and salicylic acid signaling

Cold stress significantly affects plant growth and productivity. Chloroplasts are hotspots of reactive oxygen species (ROS) production and sites for biosynthesis of the defense hormone salicylic acid (SA) under environmental stress conditions. However, how plants integrate ROS and SA signaling to adapt to stress remains poorly understood. Here, we report that Arabidopsis FILAMENTOUS TEMPERATURE-SENSITIVE H5/YELLOW VARIEGATED1 (FtsH5/VAR1), a thylakoid ATP-dependent zinc metalloprotease, plays an essential role in plant cold stress tolerance. The var1-1 mutant exhibits a strong chlorosis/variegated phenotype and retarded growth under cold stress. We revealed a strong correlation between elevated SA biosynthesis/signaling and the cold-sensitive phenotype of var1. A reduction in SA accumulation, by either overexpression of the salicylate hydroxylase gene (NahG) or knockout of SA biosynthesis-related genes (ICS1, EDS1, or PAD4), partially suppressed the chlorosis phenotype of var1. Furthermore, we demonstrate that EXECUTOR1 (EX1)-mediated singlet oxygen (1O2) signaling acts upstream of EDS1 to regulate the expression of SA-responsive genes (SARGs) in var1 under cold stress. Notably, we revealed a critical role of EX2, in which the mutation strongly suppressed the cold-sensitive phenotype of var1, in activating the expressing of SARGs while repressing photosynthesis-associated nuclear genes (PhANGs). Collectively, these results suggest a vital role of VAR1 in plant cold tolerance and a tight link between 1O2 and SA signaling, corroborating an unheeded function of EX2 which likely operates independently of EX1-mediated 1O2 signaling.