As a core Autophagy-related (Atg) protein during yeast autophagy, Atg1 interacts with numerous other proteins, and its kinase activity facilitates to phosphorylate various substrates. How Atg1-interacting partners and substrates synergistically orchestrate autophagy remains to be further dissected. In this study, we conducted a transcriptomic, proteomic and phosphoproteomic profiling of Atg1-dependent molecular landscapes during nitrogen starvation-triggered autophagy.