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Phenylalanine ammonia-lyase (PAL) catalyzes the first rate-limiting step in the phenylpropanoid pathway, which controls carbon flux to a variety of bioactive small-molecule aromatic compounds, and to lignin, the structural component of the cell wall. PAL is regulated at both the transcriptional and translational levels. Our knowledge about the transcriptional regulation of PAL is relatively comprehensive, but our knowledge of the molecular basis of the posttranslational regulation of PAL remains limited. Here, we demonstrate that the Arabidopsis thaliana Kelch repeat F-box (KFB) proteins KFB01, KFB20, and KFB50 physically interact with four PAL isozymes and mediate their proteolytic turnover via the ubiquitination-26S proteasome pathway. The KFB genes are differentially expressed in Arabidopsis tissues and respond to developmental and environmental cues. Up- or downregulation of their expression reciprocally affects the stability of the PAL enzymes, consequently altering the levels of phenylpropanoids. These data suggest that the KFB-mediated protein ubiquitination and degradation regulates the proteolysis of PALs, thus posttranslationally regulating phenylpropanoid metabolism. Characterizing the KFB-mediated proteolysis of PAL enzymes may inform future strategies for manipulating the synthesis of bioactive phenolics.

Suberin, a lipophilic polymer deposited in the outer integument of the Arabidopsis (Arabidopsis thaliana) seed coat, represents an essential sealing component controlling water and solute movement and protecting seed from pathogenic infection. Although many genes responsible for suberin synthesis are identified, the regulatory components controlling its biosynthesis have not been definitively determined. Here, we show that the Arabidopsis MYB107 transcription factor acts as a positive regulator controlling suberin biosynthetic gene expression in the seed coat. MYB107 coexpresses with suberin biosynthetic genes in a temporal manner during seed development. Disrupting MYB107 particularly suppresses the expression of genes involved in suberin but not cutin biosynthesis, lowers seed coat suberin accumulation, alters suberin lamellar structure, and consequently renders higher seed coat permeability and susceptibility to abiotic stresses. Furthermore, MYB107 directly binds to the promoters of suberin biosynthetic genes, verifying its primary role in regulating their expression. Identifying MYB107 as a positive regulator for seed coat suberin synthesis offers a basis for discovering the potential transcriptional network behind one of the most abundant lipid-based polymers in nature.

Cytokinins are a major group of phytohormones regulating plant growth, development and stress responses. However, in contrast to the well-defined polar transport of auxins, the molecular basis of cytokinin transport is poorly understood. Here we show that an ATP-binding cassette transporter in Arabidopsis , AtABCG14, is essential for the acropetal (root to shoot) translocation of the root-synthesized cytokinins. AtABCG14 is expressed primarily in the pericycle and stelar cells of roots. Knocking out AtABCG14 strongly impairs the translocation of trans -zeatin ( t Z)-type cytokinins from roots to shoots, thereby affecting the plant’s growth and development. AtABCG14 localizes to the plasma membrane of transformed cells. In planta feeding of C 14 or C 13 -labelled t Z suggests that it acts as an efflux pump and its presence in the cells directly correlates with the transport of the fed cytokinin. Therefore, AtABCG14 is a transporter likely involved in the long-distance translocation of cytokinins in planta. Cytokinins are a major group of plant hormones that control plant development and some of these hormone species are translocated from roots to shoots, but how they are transported in planta is unknown. Here, ABCG14 is shown to transport cytokinins from the roots of Arabidopsis to the shoots.

Angiosperms have evolved the metabolic capacity to synthesize p-hydroxyphenyl, guaiacyl (G), and syringyl (S) lignin subunits in their cell walls to better adapt to the harsh terrestrial environment. The structural characteristics of lignin subunits are essentially determined by three cytochrome P450-catalzyed reactions. NADPH-dependent cytochrome P450 oxidoreductase (CPR) is commonly regarded as the electron carrier for P450-catalyzed reactions during monolignol biosynthesis. Here, we show that cytochrome b₅ isoform D (CB5D) is an indispensable electron shuttle protein specific for S-lignin biosynthesis. Arabidopsis (Arabidopsis thaliana) CB5D localizes to the endoplasmic reticulum membrane and physically associates with monolignol P450 enzymes. Disrupting CB5D in Arabidopsis resulted in a >60% reduction in S-lignin subunit levels but no impairment in G-lignin formation compared with the wild type, which sharply contrasts with the impaired G- and S-lignin synthesis observed after disrupting ATR2, encoding Arabidopsis CPR. The defective S-lignin synthesis in cb5d mutants was rescued by the expression of the gene encoding CB5D but not with mutant CB5D devoid of its electron shuttle properties. Disrupting ATR2 suppressed the catalytic activity of both cinnamic acid 4-hydroxylase and ferulate 5-hydroxylase (F5H), but eliminating CB5D specifically depleted the latter’s activity. Therefore, CB5D functions as an obligate electron shuttle intermediate that specifically augments F5H-catalyzed reactions, thereby controlling S-lignin biosynthesis.

Copine proteins are highly conserved and ubiquitously found in eukaryotes, and their indispensable roles in different species were proposed. However, their exact function remains unclear. The phytohormone brassinosteroids (BRs) play vital roles in plant growth, development and environmental responses. A key event in effective BR signaling is the formation of functional BRI1-SERK receptor complex and subsequent transphosphorylation upon ligand binding. Here, we demonstrate that BONZAI (BON) proteins, which are plasma membrane-associated copine proteins, are critical components of BR signaling in both the monocot maize and the dicot Arabidopsis. Biochemical and molecular analyses reveal that BON proteins directly interact with SERK kinases, thereby ensuring effective BRI1-SERK interaction and transphosphorylation. This study advances the knowledge on BR signaling and provides an important target for optimizing valuable agronomic traits, it also opens a way to study steroid hormone signaling and copine proteins of eukaryotes in a broader perspective. Brassinosteroids play vital role in plant growth and development. Here, the authors demonstrate that the plasma membrane-associated copine proteins are new components required for the receptor complex functioning in BR signaling in maize and Arabidopsis.

Calcium signaling is essential for environmental responses including immune responses. Here, we provide evidence that the evolutionarily conserved protein BONZAI1 (BON1) functions together with autoinhibited calcium ATPase10 (ACA10) and ACA8 to regulate calcium signals in Arabidopsis. BON1 is a plasma membrane localized protein that negatively regulates the expression of immune receptor genes and positively regulates stomatal closure. We found that BON1 interacts with the autoinhibitory domains of ACA10 and ACA8, and the aca10 loss-of-function (LOF) mutants have an autoimmune phenotype similar to that of the bon1 LOF mutants. Genetic evidences indicate that BON1 positively regulates the activities of ACA10 and ACA8. Consistent with this idea, the steady level of calcium concentration is increased in both aca10 and bon1 mutants. Most strikingly, cytosolic calcium oscillation imposed by external calcium treatment was altered in aca10, aca8, and bon1 mutants in guard cells. In addition, calcium- and pathogen-induced stomatal closure was compromised in the aca10 and bon1 mutants. Taken together, this study indicates that ACA10/8 and BON1 physically interact on plasma membrane and function in the generation of cytosol calcium signatures that are critical for stomatal movement and impact plant immunity.

Background The maize inbred line Chang7-2 and derived lines are important male donors for hybrid production, contributing significantly to the development of high-yield and stress-tolerant hybrids. Additionally, Chang7-2 serves as a valuable model inbred line for genetic and genomic studies, facilitating the discovery of genes underlying hybrid vigor and other agronomic traits. Results Here, a reference genome assembly and a chemical-induced mutant population ( N  = 1,716) through ethyl methyl sulfonate (EMS) treatments are generated using Chang7-2. Each EMS line is whole genome sequenced and compared to the Chang7-2 genome, identifying 2,586,769 mutations with 4,939 mutations causing premature stop codons or altered splicing sites. The effect estimation of mutations using two large language artificial intelligence (AI) models, namely the protein language model ESM1b and the DNA language model PlantCaduceus, reveals 15,264 and 18,326 deleterious mutations, respectively. Mutation effects estimated with AI models accelerate revelation of four causal mutations underlying phenotypes of albino leaf, reduced cuticular wax, altered seed color, and male sterility. In addition, allelic expression quantification of genic mutations in 13 EMS M1 lines and their M2 heterozygous progeny, which contain both wildtype and mutant alleles, shows that mutant alleles are overall accumulated at a lower level compared to wildtype. Such allelic disparity is observed for some synonymous mutations, indicating they may not be biologically inconsequential. Conclusions AI-based estimation of mutation effects offers cross-species evidence for functional impacts of mutations. Our study demonstrates its application in revealing deleterious EMS mutations and identifying causal mutations responsible for mutant phenotypes.

Background Lodging is one of the major factors that affect mechanical harvesting and decreases yield and quality of maize. Exploring quantitative trait loci (QTL) or genes underlying lodging resistance is vital for molecular breeding of lodging-resistant maize varieties. Specially, root lodging resistance (RLR) QTLs or genes are rarely reported. Results In this study, to explore the QTLs underlying root lodging resistance, we generated a F 2 population of CIMBL74 and CIMBL145 that have contrastive difference of root architecture and lodging resistance. We performed BSR-seq analysis of the populations and 8 QTLs were identified. Among them, qRLR1 , qRLR4 , qRLR5 and qRLR6 were further confirmed by chromosomal region-based association study (CRAS) and/or linkage mapping. Based on the integrated analysis, 40 and 266 candidate genes, including root development- and cell wall-related genes, were identified in qRLR4 and qRLR6 , respectively. Among them, the ZmNRT5 (encoding a nitrate transporter) located in qRLR6 was identified as a strong candidate gene based on candidate gene association analysis and haplotype analysis. Moreover, the expression level of ZmNRT5 in CIMBL74 was significantly lower than in CIMBL145. Conclusion This study provides valuable QTLs and candidate genes for maize improvement toward enhanced root lodging resistance.

Disease lesion mimic ( Les / les ) mutants display disease-like spontaneous lesions in the absence of pathogen infection, implying the constitutive activation of defense responses. However, the genetic and biochemical bases underlying the activated defense responses in those mutants remain largely unknown. Here, we performed integrated transcriptomics and metabolomics analysis on three typical maize Les mutants Les4 , Les10 , and Les17 with large, medium, and small lesion size, respectively, thereby dissecting the activated defense responses at the transcriptional and metabolomic level. A total of 1,714, 4,887, and 1,625 differentially expressed genes (DEGs) were identified in Les4 , Les10 , and Les17 , respectively. Among them, 570, 3,299, and 447 specific differentially expressed genes (SGs) were identified, implying a specific function of each LES gene. In addition, 480 common differentially expressed genes (CGs) and 42 common differentially accumulated metabolites (CMs) were identified in all Les mutants, suggesting the robust activation of shared signaling pathways. Intriguingly, substantial analysis of the CGs indicated that genes involved in the programmed cell death, defense responses, and phenylpropanoid and terpenoid biosynthesis were most commonly activated. Genes involved in photosynthetic biosynthesis, however, were generally repressed. Consistently, the dominant CMs identified were phenylpropanoids and flavonoids. In particular, lignin, the phenylpropanoid-based polymer, was significantly increased in all three mutants. These data collectively imply that transcriptional activation of defense-related gene expression; increase of phenylpropanoid, lignin, flavonoid, and terpenoid biosynthesis; and inhibition of photosynthesis are generalnatures associated with the lesion formation and constitutively activated defense responses in those mutants. Further studies on the identified SGs and CGs will shed new light on the function of each LES gene as well as the regulatory network of defense responses in maize.

Background The recalcitrance of lignin is a major bottleneck in the efficient conversion of lignocellulosic biomass to bioethanol. Genetic reduction of lignin content represents a key strategy to overcome this barrier. This study focuses on characterizing the brown midrib2 ( bm2 ) maize mutant to assess its potential for improving bioethanol production. Results Using a near-isogenic line (BC 4 F 5 ) harboring the bm2 mutation, an 8.01% reduction in acid-insoluble lignin content in stalks was observed, with no significant change in cellulose or hemicellulose. This lignin reduction led to a 25.17% increase in glucose release upon sulfuric acid pretreatment. Most importantly, the bm2 mutant showed significantly higher lignocellulosic bioethanol yields: 3.05 g/L Ethanol 1 from the pretreatment hydrolysate (fermentation via Pichia stipites ) and 25.88 g/L Ethanol 2 from the cellulose residue (fermentation via Saccharomyces cerevisiae ), corresponding to 59.07% and 38.58% increases over the wild-type control, respectively. Conclusions Our results provide direct evidence that the bm2 mutation enhances lignocellulosic ethanol production by reducing lignin content and improving saccharification efficiency. This work underscores the value of bm2 in breeding specialized corn varieties for sustainable biofuel feedstock.