Proteome–Transcriptome Discordance in Rice Under Drought Is Modulated by Post-Translational Modifications with Functional Consequences for Photosynthesis and Energy Metabolism

Transcriptome profiling has been widely used to dissect the molecular mechanisms underlying plant responses to environmental stresses, yet the extent to which RNA changes reflect functional protein levels remains unclear. Here, we performed an integrated multi-omics analysis of the transcriptome, proteome, phosphoproteome, and acetylome in rice during a drought-rewatering cycle. We first identified 5449 differentially expressed genes (DEGs) and 525 differentially expressed proteins (DEPs) under drought stress, followed by 4340 DEGs and 328 DEPs upon rewatering, which underpinned an extensive remodeling of photosynthetic and metabolic pathways. Temporal clustering of transcriptomic and proteomic data then delineated five distinct expression patterns for both transcripts and proteins, uncovering transcriptional and translational strategies ranging from rapid reversal to persistent stress adaptation. Despite the observed coherence in some expression clusters, we nonetheless uncovered widespread transcriptome-proteome discordance, with a substantial fraction of gene-protein pairs exhibiting uncorrelated abundance changes. Remarkably, the observed discordance is quantitatively associated with the dynamic nature of post-translational modifications, including phosphorylation and acetylation, which act as key post-transcriptional tuners to independently regulate protein abundance-particularly for components of photosynthesis and energy metabolism-enabling plants to dynamically balance stress tolerance with the maintenance of core physiological functions. Our research delves into the intricate and often distinct regulatory networks that span transcriptional, translational, and post-translational levels, extending beyond a singular transcriptional focus.