Multiomics analysis revealed the temporally common and specific molecular changes in Arabidopsis thaliana (L.) under salt stress

Salt stress is a major abiotic constraint that limits plant growth and productivity worldwide. In this study, we performed a comprehensive temporal analysis using transcriptomics (6 h), ribosome profiling (12 h), proteomics and phytohormone quantification (24 h), and metabolomics (48 h) to uncover the regulatory mechanisms in Arabidopsis thaliana underlying salt stress adaptation. Novel transcriptional regulators, including JAZ7, CBF4, bHLH92, and NAC041 that responded rapidly to early salt stress, were identified. At the post-transcriptional level, TAS1C and TAS2, along with chloroplast tRNAs (AtTRNR.1, AtTRNC, AtTRNV.1), were found to be translationally upregulated, suggesting a previously unrecognized role of organellar translation in stress response. At the protein level, chloroplast functional proteins, AtPSBA, AtRBCL, AtPSAA, AtPSAB, were revealed to respond to salt stress. Some functional proteins, including AtCER1, AtGGL19, and AtLEA14, with opposite trends between transcription and translation, highlighting the complexity of salt stress adaptation. Abscisic acid (ABA) was significantly upregulated, while jasmonic acid (JA) was dramatically suppressed, with AtOPR3 and JAZ7 identified as key regulatory nodes. Metabolomics analysis further showed that d-proline and 1-pyrroline-2-carboxylate accumulated at later stages, potentially contributing to increased salt stress resistance. Overall, these findings provide new insights into the temporal regulation of stress adaptation and identify candidate genes and metabolites that may serve as targets for improving salt tolerance in crops. A multiomics analysis revealed both common and specific regulatory responses to salt in A. thaliana. The results of this study can improve our understanding of the interconnected signaling networks in plants, linking transcriptional, post-transcriptional, proteomics, phytohormonal, and metabolic pathways.