Tomato SlNAC3 regulates proteostasis in response to early cold stress

Cold stress poses a significant challenge to tomato production. SlNAC3, an NAC (NAM, ATAF1/2, and CUC2) transcription factor in tomato, plays a critical role in the early response to cold stress. However, only a few genes involved in ethylene biosynthesis were identified as NAC3-targets negatively regulating cold tolerance. This study investigated the mechanisms by which SlNAC3 influenced cold tolerance. RNA-seq analyses of SlNAC3 transient silencing and overexpression lines subjected to 2-h cold stress revealed that SlNAC3 downregulated the ribosome pathway while upregulating the ubiquitin-proteasome system. Further analysis showed that SlNAC3 directly targeted genes involved in ubiquitin-proteasome system, leading to the accumulation of ubiquitinated proteins and free amino acids. Additionally, SlNAC3 negatively regulated ribosomal protein expression, reducing soluble protein accumulation and impairing C-repeat binding factor protein levels under cold stress. Our findings suggest that the early induction of SlNAC3 likely activates CBF transcription, while constant high levels of SlNAC3 activate ubiquitin-proteasome system, thus impaired C-repeat binding factor protein accumulation and tomato cold tolerance.