Decoupling tillering and fertilization: For rice as an agricultural crop, more tillers, or branches that carry grains, are desired, as is less demand for nitrogen fertilization. Unfortunately, for many rice varieties, the number of tillers depends on the amount of nitrogen fertilization. Wu et al. now show that nitrogen status affects chromatin function through modification of histones, a process in which the transcription factor NGR5 recruits polycomb repressive complex 2 to target genes. Some of these genes regulate tillering, such that with more nitrogen, the plants develop more tillers. NGR5 is regulated by proteasomal destruction and mediates hormone signaling. An increase in NGR5 levels can drive increases in rice tillering and yield without requiring increases in nitrogen-rich fertilizer. Science , this issue p. eaaz2046

Linear (Met1-linked) ubiquitination is involved inflammatory and innate immune signaling. Previous studies have characterized enzymes regulating the addition and removal of this modification in mammalian systems. However, only a few plant-derived deubiquitinases targeting Met1-linked ubiquitin chains have been reported and their mechanism of action remains elusive. Here, using a dehydroalanine-bearing Met1-diubiquitin suicide probe, we discover OTUB1 from Oryza sativa (OsOTUB1) as a Met1-linked ubiquitin chain-targeting deubiquitinase. By solving crystal structures of apo OsOTUB1 and an OsOTUB1/Met1-diubiquitin complex, we find that Met1 activity is conferred by Met1-specific motifs in the S1’ pocket of OsOTUB1. Large-scale sequence alignments and hydrolysis experiments provide evidence that these motifs are a general determinant of Met1 activity in the OTUB subfamily across species. Analysis of the species distribution of OTUBs capable of hydrolysing Met1-linked ubiquitin chains shows that this activity is conserved in green plants (Viridiplantae) and does not exist in metazoans, providing insights into the evolutionary differentiation between primitive plants and animals.

Ubiquitination, an essential post-transcriptional modification (PTM), plays a vital role in nearly every biological process, including development and growth. Despite its functions in plant reproductive development, its targets in rice panicles remain unclear. In this study, we used proteome-wide profiling of lysine ubiquitination in rice (O. sativa ssp. indica) young panicles. We created the largest ubiquitinome dataset in rice to date, identifying 1638 lysine ubiquitination sites on 916 unique proteins. We detected three conserved ubiquitination motifs, noting that acidic glutamic acid (E) and aspartic acid (D) were most frequently present around ubiquitinated lysine. Enrichment analysis of Gene Ontology (GO) annotations and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of these ubiquitinated proteins revealed that ubiquitination plays an important role in fundamental cellular processes in rice young panicles. Interestingly, enrichment analysis of protein domains indicated that ubiquitination was enriched on a variety of receptor-like kinases and cytoplasmic tyrosine and serine-threonine kinases. Furthermore, we analyzed the crosstalk between ubiquitination, acetylation, and succinylation, and constructed a potential protein interaction network within our rice ubiquitinome. Moreover, we identified ubiquitinated proteins related to pollen and grain development, indicating that ubiquitination may play a critical role in the physiological functions in young panicles. Taken together, we reported the most comprehensive lysine ubiquitinome in rice so far, and used it to reveal the functional role of lysine ubiquitination in rice young panicles.

Rice (Oryza sativa) yield is a complex trait determined by multiple factors, including grain number per panicle (GPP), which is mainly genetically regulated. In this study, we identified the E3 RING DOMAIN LIGASE (RGLG) OsRGLG6 as a key regulator of GPP in rice. A yeast two-hybrid screen revealed that OsRGLG6 interacts with OsOTUB1, an ovarian tumor domain-containing ubiquitin-specific protease involved in panicle development. Further experiments confirmed the interaction between OsRGLG6 and OsOTUB1 in vitro and in vivo. OsRGLG6, which contains a vWA domain and a RING domain, is localized in the cytoplasm and endoplasmic reticulum and is highly expressed specifically in rice panicles. In vitro and in vivo ubiquitination assays demonstrated that OsRGLG6 ubiquitinates OsOTUB1 and promotes its degradation via the 26S proteasome pathway. CRISPR/Cas9-generated osrglg6 mutants exhibited significant reductions in GPP, indicating a crucial role for OsRGLG6 in the regulation of grain number. Transcriptome analysis revealed that OsRGLG6 regulates multiple downstream genes involved in plant hormone signaling, nitrogen utilization, and stress response, and the OsRGLG6–OsOTUB1 module specifically mediated drought-stress responses in a simulated drought experiment. This study provides insight into the molecular mechanisms that regulate rice GPP and yield, highlighting the potential of OsRGLG6 as a target for improvement of rice productivity.

Rice grain yield is largely determined by grain number per panicle, however,the molecular basis for this key trait remains elusive, particularly regarding how energy metabolism coordinates with panicle development. To elucidate this, we performed EMS mutagenesis of 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 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 uncover that OsOTUB1 directly interacts with OsSnRK1β1A, exerting both competitive inhibition and K63-linked deubiquitination, with the latter triggering 26S proteasome-mediated degradation. Genetic and transcriptomic analyses indicate that this module determines grain number by reshaping global carbon, nitrogen, and lipid metabolism to prioritize reproductive allocation. Crucially, we demonstrate 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.