Protein acetylation-directed metabolic reprogramming determines differential cold tolerance in C4 Pennisetum species

Low-temperature stress constrains the productivity of C4 crops, yet the underlying molecular mechanisms remain poorly understood. Here, we integrated transcriptomic, proteomic, acetylomic and metabolomic analyses to dissect the regulatory networks governing differential cold tolerance between two Pennisetum genotypes: cold‑sensitive 583800 ( Pennisetum americanum ) and cold‑tolerant LQ ( Pennisetum alopecuroides ). Transcript and protein abundances showed low correlation during early cold stress, a phenomenon observed across diverse biological contexts, suggesting that post‑transcriptional and post‑translational regulations may play important roles in modulating protein abundance and function during cold stress responses. Acetylome analysis suggested fundamentally distinct regulatory architectures: LQ exhibited a pattern consistent with an energy‑efficient strategy, in which proteins showed altered acetylation without changes in abundance, targeting core metabolic networks, whereas 583800 showed a pattern indicative of slower, less efficient alterations in the protein synthesis machinery. Metabolite and enzyme activity dynamics validated these contrasting modes, with LQ displaying temporally coordinated metabolic reprogramming and sequential activation of PEPC and PPDK, while 583800 exhibited dysregulated oscillation characterized by enzyme–product decoupling and delayed compensatory responses. Functional validation using the pan‑HAT inhibitor PU139 confirmed that acetylation contributes critically to cold tolerance. Collectively, our findings establish acetylation‑mediated metabolic reprogramming as a key determinant of cold tolerance in C4 plants and provide a mechanistic framework for acetylome‑targeted breeding strategies.