Phosphorylation-mediated rewiring of the plant ubiquitin system: from core machinery to ubiquitin-like modifications

Phosphorylation and ubiquitination are pivotal mechanisms that enable plants to coordinate development and environmental adaptation. These two post-translational modifications engage in multi-layered crosstalk with each other. While extensive research has elucidated ubiquitin-mediated control of kinase stability and substrate-level phosphorylation-ubiquitination interplay in plants, recent advances‌ now reveal that phosphorylation directly rewires the core machinery of the plant ubiquitin-proteasome system (UPS) and ubiquitin-like (UBL) pathways. This review focuses on emerging evidence demonstrating that phosphorylation serves as a molecular switch, targeting UPS/UBL components, including E1/E2 enzymes, E3 ligases, deubiquitinases (DUBs), ubiquitin, and UBL modifiers, to dynamically reconfigure plant protein homeostasis. We emphasize phosphorylation-mediated control over E3 ligases through four key mechanisms: substrate interaction modulation, subcellular relocalization, enzymatic activity tuning, and stability regulation. Furthermore, we discuss how phosphorylation extends beyond classical ubiquitination to regulate UBL pathways (SUMOylation, RUBylation, UFMylation, ATG8ylation). The integration of this regulatory layer provides a new framework for comprehending how phosphorylation globally regulates ubiquitin-dependent biological processes. We also highlight knowledge gaps in plant-specific mechanisms and propose phosphorylation site engineering as a strategy for designing climate-resilient crops through ubiquitination machinery optimization.