Plant Communications最新文献

In an era characterized by rapidly changing and less-predictable weather conditions fueled by the climate crisis, understanding the mechanisms underlying local adaptation in plants is of paramount importance for the conservation of species. As the frequency and intensity of extreme precipitation events increase, so are the flooding events resulting from soil water saturation. The subsequent onset of hypoxic stress is one of the leading causes of crop damage and yield loss. By combining genomics and remote sensing data, it is now possible to probe natural plant populations that have evolved in different rainfall regimes and look for molecular adaptation to hypoxia. Here, using an environmental genome-wide association study (eGWAS) of 934 non-redundant georeferenced Arabidopsis ecotypes, we have identified functional variants of the gene MED25 BINDING RING-H2 PROTEIN 1 (MBR1). This gene encodes a ubiquitin-protein ligase that regulates MEDIATOR25 (MED25), part of a multiprotein complex that interacts with transcription factors that act as key drivers of the hypoxic response in Arabidopsis, namely the RELATED TO AP2 proteins RAP2.2 and RAP2.12. Through experimental validation, we show that natural variants of MBR1 have different effects on the stability of MED25 and, in turn, on hypoxia tolerance. This study also highlights the pivotal role of the MBR1/MED25 module in establishing a comprehensive hypoxic response. Our findings show that molecular candidates for plant environmental adaptation can be effectively mined from large datasets. This thus supports the need for integration of forward and reverse genetics with robust molecular physiology validation of outcomes.

Cytokinins (CKs) are one of the important classes of plant hormones essential for plant growth and development. TATA-box binding protein-associated factor 12b (TAF12b) is involved in CK signaling, but its molecular and biochemical mechanisms are not fully understood. In this study, TAF12b of Nicotiana benthamiana (NbTAF12b) was found to mediate the CK response by directly interacting with type B response regulators (B-RRs), positive regulators of CK signaling, and inhibiting their transcriptional activities. As a transcriptional co-factor, TAF12b specifically facilitated the proteasomal degradation of non-phosphorylated B-RRs by recruiting the KISS ME DEADLY family of F-box proteins. Such interactions between TAF12b and B-RRs also occur in other plant species. Genetic transformation experiments showed that overexpression of NbTAF12b attenuates the CK-hypersensitive phenotype conferred by NbRR1 overexpression. Taken together, these results suggest a conserved mechanism in which TAF12b negatively regulates CK responses by promoting 26S proteasome-mediated B-RR degradation in multiple plant species, providing novel insights into the regulatory network of CK signaling in plants.

The widely recognized pleiotropic adult plant resistance gene Lr34 encodes an ATP-binding cassette transporter and plays an important role in breeding wheat for enhanced resistance to multiple fungal diseases. Despite its significance, the mechanisms underlying Lr34-mediated pathogen defense remain largely unknown. Our study demonstrates that wheat lines carrying the Lr34res allele exhibit thicker cell walls and enhanced resistance to fungal penetration compared to those without Lr34res. Transcriptome and metabolite profiling revealed that the lignin biosynthetic pathway is suppressed in lr34 mutants, indicating a disruption in cell wall lignification. Additionally, we discovered that lr34 mutant lines are hypersensitive to sinapyl alcohol, a major monolignol crucial for cell wall lignification. Yeast accumulation and efflux assays confirmed that the LR34 protein functions as a sinapyl alcohol transporter. Both genetic and virus-induced gene silencing experiments demonstrated that the disease resistance conferred by Lr34 can be enhanced by incorporating the TaCOMT-3B gene, which is responsible for the biosynthesis of sinapyl alcohol. Collectively, our findings provide novel insights into the role of Lr34 in disease resistance through mediating sinapyl alcohol transport and cell wall deposition, and highlight the synergistic effect of TaCOMT-3B and Lr34 against multiple fungal pathogens by mediating cell wall lignification in adult wheat plants.

As an important yield component, rice tiller number controls panicle number and determines grain yield. Regulation of rice tiller number by chloroplast pentatricopeptide repeat (PPR) proteins has not been reported previously. Here, we report the rice reduced culm number22 (rcn22) mutant, which produces few tillers owing to suppressed tiller bud elongation. Map-based cloning revealed that RCN22 encodes a chloroplast-localized P-type PPR protein. We found that RCN22 specifically binds to the 5' UTR of RbcL mRNA (encoding the large subunit of Rubisco) and enhances its stability. The reduced abundance of RbcL mRNA in rcn22 leads to a lower photosynthetic rate and decreased sugar levels. Consequently, transcript levels of DWARF3 (D3) and TEOSINTE BRANCHED1 (TB1) (which encode negative regulators of tiller bud elongation) are increased, whereas protein levels of the positive regulator DWARF53 (D53) are decreased. Furthermore, high concentrations of sucrose can rescue the tiller bud growth defect of the rcn22 mutant. On the other hand, TB1 directly binds to the RCN22 promoter and downregulates its expression. The tb1/rcn22 double mutant shows a tillering phenotype similar to that of rcn22. Our results suggest that the TB1-RCN22-RbcL module plays a vital role in rice tiller bud elongation by affecting sugar levels.

Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) is the central enzyme for conversion of atmospheric CO₂ into organic molecules, playing a crucial role in the global carbon cycle. In cyanobacteria and some chemoautotrophs, Rubisco complexes, together with carbonic anhydrase, are enclosed within specific proteinaceous microcompartments known as carboxysomes. The polyhedral carboxysome shell ensures the dense packaging of Rubisco and creates a high-CO₂ internal environment to facilitate CO₂ fixation. Rubisco and carboxysomes have been popular targets for bioengineering, with the intent of enhancing plant photosynthesis, crop yields, and biofuel production. However, efficient generation of Form 1B Rubisco and cyanobacterial β-carboxysomes in heterologous systems remains a challenge. Here, we developed genetic systems to efficiently engineer functional cyanobacterial Form 1B Rubisco in Escherichia coli by incorporating Rubisco assembly factor Raf1 and modulating the RbcL/S stoichiometry. We then reconstituted catalytically active β-carboxysomes in E. coli with cognate Form 1B Rubisco by fine-tuning the expression levels of individual β-carboxysome components. In addition, we investigated the mechanism of Rubisco encapsulation into carboxysomes by constructing hybrid carboxysomes; this was achieved by creating a chimeric encapsulation peptide incorporating small sub-unit-like domains, which enabled the encapsulation of Form 1B Rubisco into α-carboxysome shells. Our study provides insights into the assembly mechanisms of plant-like Form 1B Rubisco and the principles of its encapsulation in both β-carboxysomes and hybrid carboxysomes, highlighting the inherent modularity of carboxysome structures. These findings lay the framework for rational design and repurposing of CO₂-fixing modules in bioengineering applications, e.g., crop engineering, biocatalyst production, and molecule delivery.

Dissecting the mechanism of drought resistance (DR) and designing drought-resistant rice varieties are promising strategies to address the challenge of climate change. Here, we selected a typical drought-avoidant (DA) variety, IRAT109, and a drought-tolerant (DT) variety, Hanhui15, as parents to develop a stable recombinant inbred line (RIL) population (F₈, 1262 lines). The de novo assembled genomes of both parents were released. By resequencing of the RIL population, a set of 1 189 216 reliable SNPs were obtained and used to construct a dense genetic map. Using above- and belowground phenomic platforms and multimodal cameras, we captured 139 040 image-based traits (i-traits) of whole-plant phenotypes in response to drought stress throughout the entire rice growth period and identified 32 586 drought-responsive quantitative trait loci (QTLs), including 2097 unique QTLs. QTLs associated with panicle i-traits occurred more than 600 times on the middle of chromosome 8, and QTLs associated with leaf i-traits occurred more than 800 times on the 5' end of chromosome 3, indicating the potential effects of these QTLs on plant phenotypes. We selected three candidate genes (OsMADS50, OsGhd8, OsSAUR11) related to leaf, panicle, and root traits, respectively, and verified their functions in DR. OsMADS50 was found to negatively regulate DR by modulating leaf dehydration, grain size, and downward root growth. A total of 18 and 21 composite QTLs significantly related to grain weight and plant biomass were also screened from 597 lines in the RIL population under drought conditions in field experiments, and the composite QTL regions showed substantial overlap (76.9%) with known DR gene regions. Based on three candidate DR genes, we proposed a haplotype design suitable for different environments and breeding objectives. This study provides a valuable reference for multimodal and time-series phenomic analyses, deciphers the genetic mechanisms of DA and DT rice varieties, and offers a molecular navigation map for breeding of DR varieties.

Rice panicle architecture is a pivotal trait that strongly contributes to grain yield. Small peptide ligands from the OsEPF/EPFL family synergistically control panicle architecture by recognition of the OsER1 receptor and subsequent activation of the OsMKKK10-OsMKK4-OsMPK6 cascade, indicating that specific ligand-receptor pairs orchestrate rice panicle development. However, how small homologous peptides fine-tune organ morphogenesis by targeting a common receptor remains to be clarified. Here, we report that the small peptide OsEPFL5 acts as a ligand of the OsER1 receptor that inactivates the OsMKKK10-OsMKK4-OsMPK6 cascade, suggesting that OsEPFL5 plays a role opposite to that of the OsEPFL6/7/8/9 subfamily in regulating spikelet number per panicle and grain size. Notably, OsEPFL5 competitively replaces binding of OsEPFL6, OsEPFL7, OsEPFL8, or OsEPFL9 to the OsER1 receptor, revealing antagonistic competition between these small homologous peptides. Specifically enhancing the expression of OsEPFL5 can significantly improve grain yield by suppressing functions of the ligand-receptor pairs OsEPFL6-OsER1, OsEPFL7-OsER1, OsEPFL8-OsER1, and OsEPFL9-OsER1, suggesting that competitive binding to the OsER1 receptor by small antagonistic peptides can optimize rice panicle architecture. Our findings clarify how a receptor agonist and antagonist define inductive and inhibitory cues to shape rice panicle architecture, thus providing a new method for rationally breaking yield-trait coupling by manipulating small antagonistic peptides.

The light-driven water-splitting reaction of photosystem II exposes its key reaction center core protein subunits to irreversible oxidative photodamage. A rapid repair cycle replaces the photodamaged core subunits in plants, but how the large antenna-core supercomplex structures of plant photosystem II disassemble for repair is not currently understood. Here, we report the specific involvement of phosphorylation in removal of the peripheral antenna from the core and monomerization of the dimeric cores. However, monomeric cores disassemble further into smaller subcomplexes, even in the absence of phosphorylation, suggesting that there are other unknown mechanisms of disassembly. In this regard, we show that oxidative modifications of amino acids in core protein subunits of photosystem II are active mediators of monomeric core disassembly. Oxidative modifications thus likely disassemble only the damaged monomeric cores, ensuring an economical photosystem disassembly process. Taken together, our results suggest that phosphorylation and oxidative modification play distinct roles in photosystem II disassembly and repair.

Hybrid breeding is widely acknowledged as the most effective method for increasing crop yield, particularly in maize and rice. However, a major challenge in hybrid breeding is the selection of desirable combinations from the vast pool of potential crosses. Genomic selection (GS) has emerged as a powerful tool to tackle this challenge, but its success in practical breeding depends on prediction accuracy. Several strategies have been explored to enhance prediction accuracy for complex traits, such as the incorporation of functional markers and multi-omics data. Metabolome-wide association studies (MWAS) help to identify metabolites that are closely linked to phenotypes, known as metabolic markers. However, the use of preselected metabolic markers from parental lines to predict hybrid performance has not yet been explored. In this study, we developed a novel approach called metabolic marker-assisted genomic prediction (MM_GP), which incorporates significant metabolites identified from MWAS into GS models to improve the accuracy of genomic hybrid prediction. In maize and rice hybrid populations, MM_GP outperformed genomic prediction (GP) for all traits, regardless of the method used (genomic best linear unbiased prediction or eXtreme gradient boosting). On average, MM_GP demonstrated 4.6% and 13.6% higher predictive abilities than GP for maize and rice, respectively. MM_GP could also match or even surpass the predictive ability of M_GP (integrated genomic-metabolomic prediction) for most traits. In maize, the integration of only six metabolic markers significantly associated with multiple traits resulted in 5.0% and 3.1% higher average predictive ability compared with GP and M_GP, respectively. With advances in high-throughput metabolomics technologies and prediction models, this approach holds great promise for revolutionizing genomic hybrid breeding by enhancing its accuracy and efficiency.