Light quantity impacts early response to cold and cold acclimation in young leaves of Arabidopsis

Plant reactions to stress vary with development stage and fitness. This study assessed the relationship between light and chilling stress in Arabidopsis acclimation. By analyzing the transcriptome and proteome responses of expanding leaves subjected to varying light intensity and cold, 2251 and 2064 early response genes and proteins were identified, respectively. Many of these represent as yet unknown part of early response to cold, illustrating development-dependent response to stress and a duality in plant adaptations. While standard light promoted photosynthetic upregulation, plastid maintenance, and increased resilience, low light triggered a unique metabolic shift, prioritizing ribosome biogenesis and lipid metabolism and attenuating expression of genes associated with plant immunity. The comparison of early response in young leaves with that in expanded ones showed striking differences, suggesting a sacrifice of expanded leaves to support young ones. Validations of selected DEGs in mutant background confirmed a role of HSP90-1, transcription factor FLZ13, and Phospholipase A1 (PLIP) in response to cold, and the PLIP family emerged as crucial in promoting acclimation and freezing stress tolerance. The findings highlight the dynamic mechanisms that enable plants to adapt to challenging environments and pave the way for the development of genetically modified crops with enhanced freezing tolerance. Overall design: To examine the influence of low light intensity (20 µmol-2.s-1) on the chilling stress response, we utilized A. thaliana plants, which were grown under standard light conditions (100 µmol-2.s-1) until they obtained developmental stage L1.06, and subsequently subjected to the following conditions for 3 hours: (i) S-PPFD at 100 µmol.m-2.s-1, 21°C (S); (ii) low-PPFD at 20 µmol.m-2.s-1, 21°C (LL); (iii) S-PPFD at 4°C (C); and (iv) low-PPFD at 4°C (CLL). Next, we have performed RNA-seq analyses and comparative gene profiles of LL, C and CLL. For more details, see manuscript published in Plant Cell & Environment (Luklova et al., 2025).