The splicing factor UAP1 modulates cold-regulated growth and stress responses in tomato, soybean and Arabidopsis

Abstract

Cold stress is a major environmental factor limiting the productivity and geographical distribution of horticultural crops. Here, we investigated the role of the spliceosome U4/U6.U5 tri-snRNP-associated protein 1 (UAP1) in modulating low-temperature responses across three dicotyledonous species: tomato (Solanum lycopersicum), soybean (Glycine max), and Arabidopsis thaliana. Using CRISPR/Cas9-mediated gene editing, we generated UAP1 knockout orthologs in two dicotyledonous species: tomato and soybean. The sluap1 and gmuap1 mutants exhibited significantly enhanced cold resilience, characterized by reduced membrane damage, lower reactive oxygen species accumulation, and higher survival rates after cold stress. To elucidate the underlying molecular mechanism, we further characterized the uap1 mutants in Arabidopsis, which displayed alterations in cold-regulated hypocotyl elongation. Transcriptome-wide analysis revealed that the loss of AtUAP1 results in widespread differential alternative splicing under cold stress. Notably, we identified a critical intron retention event in the circadian clock gene AtPRR3, leading to a truncated, non-functional protein. Genetic evidence confirmed that atprr3 mutants mimic the low-temperature growth phenotype of atuap1, and heterologous expression of SlUAP1 or GmUAP1 effectively rescued the atuap1 mutant, demonstrating high functional conservation at the molecular level. Our findings establish the UAP1-mediated splicing module participates in cold-regulated growth and stress responses in dicotyledonous plants, providing insights into post-transcriptional regulation under low temperature.