Dual repression of OsSnRK1β1A by the deubiquitinase OsOTUB1 orchestrates energy metabolism and grain yield in rice.

Abstract

Rice grain yield is largely determined by grain number per panicle; however, the molecular basis of this key trait remains largely unclear, particularly regarding how energy metabolism is coordinated with panicle development. To elucidate this, we performed ethylmethanesulfonate (EMS) mutagenesis in the OsOTUB1 loss-of-function mutant npt1 and isolated npt-s1, a suppressor reverting the high-grain-number phenotype of npt1. Map-based cloning identified that NPT-S1 encodes OsSnRK1β1A, a regulatory subunit of the sucrose non-fermenting 1-related protein kinase 1 (SnRK1) energy-sensing complex. Functional analyses showed that OsSnRK1β1A promotes grain number by suppressing energy catabolism. Mechanistically, OsSnRK1β1A binds OsSnRK1α1 and, through N-terminal myristoylation, restricts its nuclear localization, thereby linking energy status to developmental outputs. Furthermore, we discovered that OsOTUB1 directly interacts with OsSnRK1β1A, exerting both competitive inhibition and K63-linked deubiquitination, the latter of which triggers 26S proteasome-mediated degradation. Genetic and transcriptomic analyses suggested that this module determines grain number by reshaping global carbon, nitrogen, and lipid metabolism to prioritize reproductive allocation. Crucially, we demonstrated that engineered upregulation of OsSnRK1β1A via CRISPR/Cas9-mediated promoter editing of CAREOSREP1 and CCAAT box consistently increases grain yield without compromising plant architecture. Together, our findings reveal a layered signaling pathway refined by post-translational modification, in which the OsOTUB1-OsSnRK1β1A module couples energy status to panicle development, providing both a mechanistic framework and actionable targets for breeding high-yield rice.