MYB58 and MYB63 are transcriptional activators of the lignin biosynthetic pathway during secondary cell wall formation in Arabidopsis

Integration of comparative cytology, ionome, transcriptome and metabolome provide a basic framework for the response of foxtail millet to Cd stress

Apart from directly affecting the growth and development of crops, Cd in the soil can easily enter the human body through the food chain and pose a threat to human health. Therefore, understanding the toxicity of Cd to specific crops and the molecular mechanisms of their response to Cd is essential. In this study, hydroponic experiments were utilized to study the response of foxtail millet to Cd stress through phenotypic investigation, enzyme activity determination, ultrastructure, ionome, transcriptome and metabolome. With the increase in cadmium concentration, both the growth and photosynthetic capacity of foxtail millet seedlings are severely inhibited. The ultrastructure of cells is damaged, cells are deformed, chloroplasts swell and disappear, and cell walls thicken. Cd stress affects the absorption, transport, and redistribution of beneficial metal ions in the seedlings. Multi-omics analysis reveals the crucial roles of glycolysis, glutathione metabolism and phenylpropanoid and lignin biosynthesis pathways in Cd detoxification via energy metabolism, the antioxidant system and cell wall changes. Finally, a schematic diagram of foxtail millet in response to Cd stress was we preliminarily drew. This work provides a basic framework for further revealing the molecular mechanism of Cd tolerance in foxtail millet.

Duckweed genomes and epigenomes underlie triploid hybridization and clonal reproduction

The Lemnaceae (duckweeds) are the world's smallest but fastest-growing flowering plants. Prolific clonal propagation facilitates continuous micro-cropping for plant-based protein and starch production and holds tremendous promise for sequestration of atmospheric CO2. Here, we present chromosomal assemblies, annotations, and phylogenomic analysis of Lemna genomes that uncover candidate genes responsible for the unique metabolic and developmental traits of the family, such as anatomical reduction, adaxial stomata, lack of stomatal closure, and carbon sequestration via crystalline calcium oxalate. Lemnaceae have selectively lost genes required for RNA interference, including Argonaute genes required for reproductive isolation (the triploid block) and haploid gamete formation. Triploid hybrids arise commonly among Lemna, and we have found mutations in highly conserved meiotic crossover genes that could support polyploid meiosis. Further, mapping centromeres by chromatin immunoprecipitation suggests their epigenetic origin despite divergence of underlying tandem repeats and centromeric retrotransposons. Syntenic comparisons with Wolffia and Spirodela reveal that diversification of these genera coincided with the "Azolla event" in the mid-Eocene, during which aquatic macrophytes reduced high atmospheric CO2 levels to those of the current ice age. Facile regeneration of transgenic fronds from tissue culture, aided by reduced epigenetic silencing, makes Lemna a powerful biotechnological platform, as exemplified by recent engineering of high-oil Lemna that outperforms oil-seed crops.

Integrated metabolome and transcriptome analysis of maize roots response to different degrees of drought stress

BACKGROUND

Plants in arid environments can regulate the generation of specialized metabolites to enhance their adaptability. Roots serve as the first defense line, responding directly to drought situations; however, the knowledge regarding the molecular mechanisms of metabolite changes to drought in maize roots remain largely limited. Here, we employed RNA-seq and UPLC-MS/MS methods to examine changes in the root metabolome and transcriptome of maize seedlings subjected to moderate drought (MD) and severe drought (SD) conditions by controlling water supply.

RESULTS

Compared to the untreated control group, 460 differentially accumulated metabolites were detected in roots under MD and SD conditions. Among these metabolites, lignin compounds emerged as the primary response to drought. Most lignin metabolites, including caffealdehyde, sinapyl alcohol, coniferaldehyde, p-coumaryl alcohol, and p-coumaric acid, showed a significant increase under MD but decreased under SD. Transcriptional profiling identified 903 and 5306 differential genes in roots treated with MD and SD, respectively. The majority of these genes were associated with lignin biosynthesis, hormone synthesis and signal transduction, and defense response processes. These metabolites and genes play crucial roles in lignin biosynthesis, antioxidant capacity, hormone balance, and root growth, particularly under MD conditions, which aligns with the results from morpho-physiological studies. Further, a conjoint omics analysis highlighted the significant regulatory roles of hormone-associated genes in lignin formation.

CONCLUSION

Our results suggest that the co-regulation of the lignin biosynthesis pathway and hormone signals significantly enhances root performance, helping maize maintain growth under MD conditions. This study leads to a better understanding of the regulatory mechanisms involved in maize root adaptation to drought environments.

Physiological mechanism of lodging resistance of oat stalk and analysis of transcriptome differences

Introduction

Lodging has become an important factor limiting oats production.

Methods

To understand the relationship between oat lodging and stem growth, we selected three oat cultivars with different lodging resistance traits and conducted a detailed analysis of their stem physicochemical properties, and transcriptome sequencing on them at different growth stages were performed.

Results

Important plant characteristics like: length of the second stem internode, stem wall thickness, breaking force, mechanical strength, soluble sugar, starch, lignin, and silicon content were closely related to oat lodging performance. With the growth of the second stem internode at the base of oats, the number of coexpressed differentially expressed genes (DEGs) increased. And DEGs were specifically enriched in starch and sucrose metabolism, phenylpropanoidbiosynthesis, MAPK signaling pathway-plant and carbon metabolism. There were many TF family types among the different comparison groups, and p450, Myb_DNA-binding, WRKY, and AP2 families accounted for the most. Additionally, there was a specific high expression of genes related to the synthesis of cellulose(CesA9, CesA7, and CesA4) and lignin (CCR1, 4CL8, and 4CL3) in lodgingresistant cultivar and middle lodging-resistant cultivar. WGCNA analysis identified genes closely related to lodging resistance, namely MBF1c, SKP1, and CAND1, which were specifically up-regulated on the 35th day of growth in the second stem internode of the highly resistant 'LENA'. These genes can all serve as positive regulatory factors for oat lodging.

Discussion

Ultimately, our work analyzed the transcriptional network regulatory relationships, laying the foundation for elucidating the physiological and genetic mechanisms of oat lodging resistance, and providing excellent genetic resources for oat and other crop breeding.

Specificity landscapes of 40 R2R3-MYBs reveal how paralogs target different cis-elements by homodimeric binding

Paralogous transcription factors (TFs) frequently recognize highly similar DNA motifs. Homodimerization can help distinguish them according to their different dimeric configurations. Here, by studying R2R3-MYB TFs, we show that homodimerization can also directly change the recognized DNA motifs to distinguish between similar TFs. By high-throughput SELEX, we profiled the specificity landscape for 40 R2R3-MYBs of subfamily VIII and curated 833 motif models. The dimeric models show that homodimeric binding has evoked specificity changes for AtMYBs. Focusing on AtMYB2 as an example, we show that homodimerization has modified its specificity and allowed it to recognize additional cis-regulatory sequences that are different from the closely related CCWAA-box AtMYBs and are unique among all AtMYBs. Genomic sites described by the modified dimeric specificities of AtMYB2 are conserved in evolution and involved in AtMYB2-specific transcriptional activation. Collectively, this study provides rich data on sequence preferences of VIII R2R3-MYBs and suggests an alternative mechanism that guides closely related TFs to respective cis-regulatory sites.

Overexpression of the patatin-related phospholipase A gene, PgpPLAIIIβ, in ginseng adventitious roots reduces lignin and ginsenoside content while increasing fatty acid content

The patatin-related phospholipase AIII (pPLAIII) gene family plays a crucial role in regulating cell elongation, cell wall composition, and lipid metabolism in plants, making it a promising target for agricultural and commercial innovations. This study provides a comprehensive functional analysis of PgpPLAIIIβ in Panax ginseng, a medicinal plant of substantial economic importance. Overexpression of PgpPLAIIIβ led to significant morphological changes, including shorter, thicker roots, and an 8% reduction in lignin content, while cellulose levels remained unaffected. The reduced lignification was attributed to the downregulation of key lignin biosynthetic genes and decreased hydrogen peroxide accumulation. A yeast two-hybrid assay identified a CCCH-type zinc finger protein as a potential PgpPLAIIIβ interactor, pointing to a mechanism that may underlie the changes in root structure and lignin deposition. Metabolite analysis revealed a 7.6% increase in total free fatty acid content, with notable increases in palmitic and linoleic acids, alongside a 28% reduction in ginsenoside levels, linked to the downregulation of triterpenoid biosynthetic genes. These findings demonstrate that PgpPLAIIIβ is a key regulator of root architecture, lignin composition, and secondary metabolite balance in ginseng. The metabolic engineering of PgpPLAIIIβ could be a powerful strategy to improve root traits, optimize lignin deposition, and enhance metabolite profiles, ultimately boosting the commercial and medicinal value of ginseng.

MYB74 transcription factor guides de novo specification of epidermal cells in the abscission zone of Arabidopsis

The waxy cuticle layer is crucial for plant defence, growth and survival, and is produced by epidermal cells, which were thought to be specified only during embryogenesis. New surface cells are exposed during abscission, by which leaves, fruits, flowers and seeds are shed. Recent work has shown that nonepidermal residuum cells (RECs) can accumulate a protective cuticle layer after abscission, implying the potential de novo specification of epidermal cells by transdifferentiation. However, it remains unknown how this process occurs and what advantage this mechanism may offer over the other surface protection alternative, the wound healing pathways. Here we followed this transdifferentiation process with single-cell RNA sequencing analysis of RECs, showing that nonepidermal RECs transdifferentiate into epidermal cells through three distinct stages. During this vulnerable process, which involves a transient period when the protective layer is not yet formed, stress genes that protect the plant from environmental exposure are expressed before epidermis formation, ultimately facilitating cuticle development. We identify a central role for the transcription factor MYB74 in directing the transdifferentiation. In contrast to alternative protective mechanisms, our results suggest that de novo epidermal specification supports the subsequent growth of fruit at the abscission site. Altogether, we reveal a developmental programme by which plants use a transdifferentiation pathway to protect the plant while promoting growth.

The Good, the Bad, and the Epigenetic: Stress-Induced Metabolite Regulation and Transgenerational Effects

BACKGROUND

Plants face a wide range of environmental stresses that disrupt growth and productivity. To survive and adapt, they undergo complex metabolic reprogramming by redirecting carbon and nitrogen fluxes toward the biosynthesis of protective secondary metabolites such as phenylpropanoids, flavonoids, and lignin. Recent research has revealed that these stress-induced metabolic processes are tightly regulated by epigenetic mechanisms, including DNA methylation, histone modifications, chromatin remodeling, and non-coding RNAs.

METHODS

This review synthesizes current findings from studies on both model and crop plants, examining the roles of key epigenetic regulators in controlling secondary metabolism under stress. Special focus is placed on dynamic changes in DNA methylation, histone acetylation, and the action of small RNAs such as siRNAs and miRNAs in transcriptional and post-transcriptional regulation.

RESULTS

Evidence indicates that stress triggers rapid and reversible epigenetic modifications that modulate gene expression linked to secondary metabolic pathways. These modifications not only facilitate immediate metabolic responses but can also contribute to stress memory. In some cases, this memory is retained and transmitted to the next generation, influencing progeny stress responses. However, critical knowledge gaps remain, particularly concerning the temporal dynamics, tissue specificity, and long-term stability of these epigenetic marks in crops.

CONCLUSIONS

Understanding how epigenetic regulation governs secondary metabolite production offers promising avenues to enhance crop resilience and productivity in the context of climate change. Future research should prioritize dissecting the stability and heritability of these modifications to support the development of epigenetically informed breeding strategies.

SCPL48 regulates the vessel cell programmed cell death during xylem development in Arabidopsis thaliana

Secondary cell wall (SCW) deposition is tightly coordinated with programmed cell death (PCD) during xylem development and plays a crucial role in plant stress responses. In this study, we characterized a serine carboxypeptidase-like gene, SCPL48, which exhibits xylem cell-specific expression patterns in stem xylem during vascular development. The scpl48 plants exhibited reduced stem xylem cell numbers, particularly vessel cells, accompanied by delayed organelle degradation during PCD and increased secondary wall thickness in xylem vessel cells. In contrast, SCPL48 overexpression resulted in increased vessel cell abundance and accelerated degradation of vessel cell contents, suggesting its critical role in xylem vessel cell differentiation. Notably, SCPL48 expression was significantly up-regulated in response to ABA treatment and drought stress, with SCPL48 overexpression lines demonstrating enhanced drought resistance. Further molecular analyses revealed that SCPL48 was directly targeted and transcriptionally activated by key SCW regulators VND6, and MYB46. Furthermore, the expression of PCD-related protease genes, including XCP1, XSP1, RNS3, MC9, γVPE, and CEP1, showed compensatory changes in both scpl48 mutants and SCPL48 overexpression lines. Collectively, our findings demonstrate that SCPL48 functions as a key regulator in xylem vessel cell differentiation, PCD and drought stress responses.

Genome-wide study of the R2R3-MYB gene family and analysis of HhMYB111r-induced salt tolerance in Hibiscus hamabo Sieb. et Zucc

Hibiscus hamabo Sieb. et Zucc. (H. hamabo) is a semi-mangrove plant with excellent stress tolerance that plays a crucial role in the ecological restoration of saline and alkaline areas. It is an ideal candidate species for studying the mechanisms involved in stress tolerance. Although the MYB gene family has preliminarily been characterized in H. hamabo, the specific functions and action mechanisms of the R2R3-MYB genes in this species have not fully been elucidated. In this study, 190 R2R3-MYB genes were identified at the genomic level using bioinformatics methods. The genes were divided into 26 subgroups based on their evolutionary relationships and found to be distributed randomly on 46 chromosomes. RNA sequencing data and subsequent real-time quantitative PCR analysis of 12 differentially expressed R2R3-HhMYB genes showed HhMYB111r to be highly expressed under various abiotic stress conditions. Self-activation and subcellular localization results showed that the intact HhMYB111r had strong self-activation activity and located in both the nucleus and cytoplasm. Overexpression in Arabidopsis significantly improved salt tolerance, and silencing HhMYB111r reduced the tolerance of H. hamabo to salt stress, indicating that HhMYB111r positively regulates the salt stress response. In this first analysis of the R2R3-MYB gene family in H. hamabo, we identified a key salt stress response gene, HhMYB111r, enriching the understanding of MYB function and laying a foundation for exploring the abiotic stress response of plants.

Plant secondary metabolites against biotic stresses for sustainable crop protection

Sustainable agriculture practices are indispensable for achieving a hunger-free world, especially as the global population continues to expand. Biotic stresses, such as pathogens, insects, and pests, severely threaten global food security and crop productivity. Traditional chemical pesticides, while effective, can lead to environmental degradation and increase pest resistance over time. Plant-derived natural products such as secondary metabolites like alkaloids, terpenoids, phenolics, and phytoalexins offer promising alternatives due to their ability to enhance plant immunity and inhibit pest activity. Recent advances in molecular biology and biotechnology have improved our understanding of how these natural compounds function at the cellular level, activating specific plant defense through complex biochemical pathways regulated by various transcription factors (TFs) such as MYB, WRKY, bHLH, bZIP, NAC, and AP2/ERF. Advancements in multi-omics approaches, including genomics, transcriptomics, proteomics, and metabolomics, have significantly improved the understanding of the regulatory networks that govern PSM synthesis. These integrative approaches have led to the discovery of novel insights into plant responses to biotic stresses, identifying key regulatory genes and pathways involved in plant defense. Advanced technologies like CRISPR/Cas9-mediated gene editing allow precise manipulation of PSM pathways, further enhancing plant resistance. Understanding the complex interaction between PSMs, TFs, and biotic stress responses not only advances our knowledge of plant biology but also provides feasible strategies for developing crops with improved resistance to pests and diseases, contributing to sustainable agriculture and food security. This review emphasizes the crucial role of PSMs, their biosynthetic pathways, the regulatory influence of TFs, and their potential applications in enhancing plant defense and sustainability. It also highlights the astounding potential of multi-omics approaches to discover gene functions and the metabolic engineering of genes associated with secondary metabolite biosynthesis. Taken together, this review provides new insights into research opportunities for enhancing biotic stress tolerance in crops through utilizing plant secondary metabolites.

Multiple roles of NAC transcription factors in plant development and stress responses

NAC (NAM, ATAF1/2, and CUC2) transcription factors (TFs) are a family of plant-specific TFs that play crucial roles in various aspects of plant development and stress responses. Here, we provide an in-depth review of the structural characteristics, regulatory mechanisms, and functional roles of NACs in different plant species. One of the key features of NACs is their ability to regulate gene expression through a variety of mechanisms, including binding to DNA sequences in the promoter regions of target genes, interacting with other TFs, and modulating chromatin structure. We discuss these mechanisms in detail, providing insights into the complex regulatory networks that govern the activity of NACs. We explore the diverse functions of these TFs in plant growth and development processes, including embryogenesis, seed development, root and shoot development, floral development and fruit ripening, secondary cell wall formation, and senescence. We also discuss the diverse regulatory roles of NACs in response to various stresses, including drought, flooding, heat, cold, salinity, nutrient deficit, and diseases. Lastly, we emphasize the crosstalk role of NACs between developmental processes and stress responses. This integrated perspective highlights how NACs orchestrate plant growth and resilience. Overall, this review provides a comprehensive overview of the pivotal roles of NACs in plant development and stress responses, emphasizing their potential for engineering stress-resistant crops and enhancing agricultural productivity.

Integrated transcriptomic and metabolomic analyses uncover the key pathways of Limonium bicolor in response to salt stress

Salinity significantly inhibits plant growth and development. While the recretohalophyte Limonium bicolor can reduce its ion content by secreting salt, the metabolic pathways it employs to adapt to high salt stress remain unclear. This study aims to unravel this enigma through integrated transcriptomic and metabolomic analyses of L. bicolor under salt stress conditions. The results showed that compared to the control (S0), low salt treatment (S1) led to a significant increase in plant growth, photosynthesis efficiency and antioxidant enzyme activity but caused no significant changes in organic soluble substance and ROS contents. However, high salt treatments (S3 and S4) led to a significant decrease in plant growth, photosynthesis efficiency and antioxidant enzyme activity, accompanied by a significant increase in organic soluble substance and ROS contents. A significant increase in phenolic compounds, such as caffeoyl shikimic acid and coniferin, upon the treatments of S1, S3 and S4, and a decrease and increase in flavonoids upon the treatments of S1 and S3 were also observed, respectively. This study also demonstrated that the expression patterns of key genes responsible for the biosynthesis of these metabolites are consistent with the observed trends in their accumulation levels. These results suggest that under low salt stress conditions, the halophyte L. bicolor experiences minimal osmotic and oxidative stress. However, under high salt stress conditions, it suffers severe osmotic and oxidative stress, and the increase in organic soluble substances and flavonoids serves as a key response to these stresses and also represents a good strategy for the alleviation of them.

Transcriptome analysis of nitrate enhanced tobacco resistance to aphid infestation

Tobacco is an economic crop that primarily relies on nitrate (NO3-) as its nitrogen source, and tobacco aphid is one of the significant pests that harm its growth. However, the impact of NO3- supply on the resistance of tobacco to aphids remains unclear. Present study investigated the effects of different NO3- concentrations supply on the reproductive capacity of tobacco aphids, impact of aphid infestation on tobacco growth, secondary metabolic and transcription changes. Physiological experiments were performed to verity the transcription analysis. The results indicated that aphids preferred tobacco treated with higher concentration of nitrate, showing greater reproductive capacity under high nitrate supply. From the results of transcriptome analysis, it can be seen that the gene expression of the shoot changed significantly after aphid and NO3- treatment. GO analysis showed that the pathways associated with cell wall biosynthesis were enriched in different groups. At the same time, RNA-seq analysis revealed several genes related to the pathway of aphid damage in tobacco, as well as some transcription factors associated with insect resistance. Inoculating tobacco with aphids under different NO3- concentration increased the levels of soluble sugars, free amino acids, jasmonic acid, and salicylic acid in shoot of tobacco. Additionally, it was observed that the cell wall development of leaves from low NO3- supply was incomplete, and the cell wall from high NO3- supply concentration is notably thicker. The lignin content was lower under lower NO3- supply, regardless of aphid inoculation. The trends of transcription levels in genes related to cell wall and lignin biosynthesis were consistent with the lignin contents. Collectively, our findings not only shed light on the physiological and biochemical responses of tobacco plants to NO3- treatment, but also offer novel perspectives for optimizing tobacco cultivation practices and enhancing insect resistance.

Diverse roles of MYB transcription factors in plants

MYB transcription factors (TFs), one of the largest TF families in plants, are involved in various plant-specific processes as the central regulators, such as in phenylpropanoid metabolism, cell cycle, formation of root hair and trichome, phytohormones responses, reproductive growth and abiotic or biotic stress responses. Here we summarized multiple roles and explained the molecular mechanisms of MYB TFs in plant development and stress adaptation. The exploration of MYB TFs contributes to a better comprehension of molecular regulation in plant development and environmental adaptability.

Gibberellin promotes xylem expansion and cell lignification by regulating sugar accumulation and the expression of JcMYB43 and JcMYB63 in the woody plant Jatropha curcas

Gibberellins (GAs) are a group of diterpene plant hormones that regulate various plant developmental processes, including wood formation. Nevertheless, the regulatory pattern and the downstream targets of GA in the regulation of xylem expansion and cell lignification in woody plants remain unclear. In transgenic Jatropha curcas with significantly increased or decreased bioactive GA content via separate overexpression of JcGA20ox1 or JcGA2ox6, comparative transcriptomic, metabolomic and physiological investigations were conducted on the young stems. Lignin quantification and ultrastructural investigations of the young stems at different development stages revealed that JcGA20ox1 plants presented much faster lignin deposition and xylem expansion even at early development stages. The transcriptomic results revealed that the majority of the differentially expressed genes (DEGs) in the JcGA20ox1 and JcGA2ox6 plants were mainly related to metabolic pathways. Analysis of the DEGs and the gene regulatory network revealed that the increased lignification in JcGA20ox1 plants was due to the activated expression of several key transcription factors and the structural genes in the lignin biosynthesis pathway, which was confirmed by the significantly increased precursors of lignin identified via metabolomic analysis. Interestingly, a total of 15 sugar-related metabolites were differentially regulated, most of which were increased in the xylem of JcGA20ox1, but decreased in JcGA2ox6 plants. Importantly, two key GA-responsive transcription factors JcMYB43 and JcMYB63 were identified to play dual roles in promoting both xylem expansion and cell lignification. Conclusively, this study provides novel insights into the molecular mechanisms of GA-regulated xylem development in the woody plants.

Cell-Type Specific miRNA Regulatory Network Responses to ABA Stress Revealed by Time Series Transcriptional Atlases in Arabidopsis

In plants, microRNAs (miRNAs) participate in complex gene regulatory networks together with the transcription factors (TFs) in response to biotic and abiotic stresses. To date, analyses of miRNAs-induced transcriptome remodeling are at the whole plant or tissue levels. Here, Arabidopsis's ABA-induced single-cell RNA-seq (scRNA-seq) is performed at different stages of time points-early, middle, and late. Single-cell level primary miRNAs (pri-miRNAs) atlas supported the rapid, dynamic, and cell-type specific miRNA responses under ABA treatment. MiRNAs respond rapidly and prior to target gene expression dynamics, and these rapid response miRNAs are highly cell-type specific, especially in mesophyll and vascular cells. MiRNA-TF-mRNA regulation modules are identified by identifying miRNA-contained feed-forward loops (M-FFLs) in the regulatory network, and regulatory networks with M-FFLs have higher co-expression and clustering coefficient (CC) values than those without M-FFLs, suggesting the hub role of miRNAs in regulatory networks. The cell-type-specific M-FFLs are regulated by these hub miRNAs rather than TFs through sc-RNA-seq network analysis. MiR858a-FBH3-MYB module inhibited the expression of MYB63 and MYB20, which related to the formation of plant secondary wall and the production of lignin, through M-FFL specifically in vascular. These results can provide prominent insights into miRNAs' dynamic and cell-type-specific roles in plant development and stress responses.

ZINC FINGER PROTEIN2 suppresses funiculus lignification to ensure seed loading efficiency in Arabidopsis

The plant funiculus anchors the developing seed to the placenta within the inner dorsal pod strands of the silique wall and directly transports nutrients to the seeds. The lignified vasculature critically supports nutrient transport through the funiculus. However, molecular mechanisms underlying lignified secondary cell wall (SCW) biosynthesis in the funiculus remain elusive. Here, we show that the transcription factor ZINC FINGER PROTEIN2 (ZFP2) represses SCW formation in the cortex cells that surround the vasculature. This function is essential for efficient nutrient loading into the seeds. Notably, ZFP2 directly acts on the SCW transcription factor NAC SECONDARY WALL THICKENING PROMOTING FACTOR1 (NST1) to repress cortex cell lignification, providing a mechanism of how SCW biosynthesis is restricted to the vasculature of the funiculus to ensure proper seed loading in Arabidopsis.

Mitigating Response of SlCSE06 Induced by 2-Ethylfuran to Botrytis cinerea Infection

Tomato (Solanum lycopersicum L.) is a major economic vegetable crop globally, yet it is prone to gray mold disease caused by Botrytis cinerea infection during cultivation. Caffeoyl shikimate esterase (CSE) is a crucial component of the lignin biosynthesis pathway, which significantly contributes to plant stress resistance. Therefore, investigating the expression patterns of SlCSE after Botrytis cinerea infection may offer a theoretical foundation for breeding resistant tomato varieties. In this study, 11 SlCSE family members were identified from the tomato genome using bioinformatics analyses. Public transcriptome databases and RT-qPCR experiments were used to analyze gene expression in tomato tissues, responses to Botrytis cinerea infection, and the temporal characteristics of the response to 2-ethylfuran treatment during infection. These experiments resulted in the identification of the key gene SlCSE06. Transgenic tomato lines that overexpressed SlCSE06 were constructed to examine their resistance levels to gray mold disease. Many SlCSE genes were upregulated when tomato fruit were infected with Botrytis cinerea during the ripening stage. Furthermore, 24 h after treatment with 2-ethylfuran, most SlCSE genes exhibited increased expression levels compared with the control group, but they exhibited significantly lower levels at other time points. Thus, 2-ethylfuran treatment may enhance the responsiveness of SlCSEs. Based on this research, SlCSE06 was identified as the key gene involved in the response to Botrytis cinerea infection. The SlCSE06-overexpressing (OE6) tomato plants exhibited a 197.94% increase in expression levels compared to the wild type (WT). Furthermore, the lignin content in OE6 was significantly higher than in WT, suggesting that the overexpression of SlCSE06 enhanced lignin formation in tomato plants. At 5 days post-inoculation with Botrytis cinerea, the lesion diameter in OE6 decreased by 31.88% relative to the WT, whereas the lignin content increased by 370.90%. Furthermore, the expression level of SlCSE06 was significantly upregulated, showing a 17.08-fold increase compared with the WT. These findings suggest that 2-ethylfuran enhances the activation of the critical tomato disease resistance gene SlCSE06 in response to gray mold stress, thereby promoting lignin deposition to mitigate further infection by Botrytis cinerea.

Cbuhdz34, a Homeodomain Leucine Zipper Transcription Factor, Positively Regulates Tension Wood Formation and Xylem Fibre Cell Elongation in Catalpa bungei

Catalpa bungei is a highly valued timber species renowned for its superior wood properties. However, the development of tension wood (TW) induced by wind and other mechanical stresses during the growing season significantly reduces its economic value. Although Homeodomain Leucine Zipper (HD-Zip), a plant-specific transcription factor family, has been reported to play various roles in plant growth, development, and stress resistance, a systematic characterisation of the HD-Zip gene family in C. bungei, particularly regarding the regulatory mechanisms involved in TW formation, is still lacking. Here, we identified a total of 48 HD-Zip genes (Cbuhdzs) in C. bungei and analysed their phylogeny, structure, and expression profiles. In particular, Cbuhdz34, a member of the HD-Zip I subfamily, was specifically upregulated during TW formation. To further explore its function, we overexpressed Cbuhdz34 (OE-Cbuhdz34) in poplar '84 K', which led to noticeable changes in plant growth and fibre cell length. Moreover, compared with wild-type plants, the OE-Cbuhdz34 plants presented increased TW formation under bending stress, as indicated by increased TW width, gelatinous layer width, and eccentric growth rate, suggesting a positive regulatory role in TW formation. Additionally, hierarchical genetic regulatory network analysis revealed the direct targets of Cbuhdz34, including CbuMYB63 and three genes involved in cell wall synthesis (CbuGATL1, CbuFLA17, and CbuLRR14). Further, yeast one-hybrid and dual-luciferase reporter assays confirmed the activation of these targets by Cbuhdz34. In conclusion, our results provide insights into the molecular mechanisms by which Cbuhdz34 regulates TW formation and lay a genetic foundation for the potential improvement of wood quality in C. bungei.

Genome-wide identification of the MYB gene family and FfMYB13 regulation analysis in cell wall synthesis underlying tissue toughening process of yellow Flammulina filiformis stipes

MYB transcription factors (TFs) play important roles in fungal growth, development, stress response, and secondary metabolism. Cell wall glycan remodeling induced by oxidative damage levels is vital for stipe quality during mature stage of yellow Flammulina filiformis fruiting bodies. In this study, we identified 15 F. filiformis MYB (FfMYB) that are ranging from 28.43 kDa-172.3 kDa, with an average of 73.51 kDa. These FfMYB genes were unevenly distributed among six chromosomes. Phylogenetic analysis indicated that 15 FfMYBs were closely related to existing model fungi, while they were more distant from Arabidopsis thaliana. Based on expression analysis, a MYB TF termed FfMYB13 were isolated and identified as a potential regulator binding the promoter of Ff-FeSOD1, which was negatively correlated with tissue toughening of yellow F. filiformis stipes. The data of DAP-seq analysis suggested that the downstream target genes of FfMYB13 were significantly enriched in cell wall metabolism. The result of EMSA and dual luciferase report experiments demonstrated that FfMYB13 served as an upstream transcriptional regulatory factor that activates four cell wall synthesis metabolism related genes, FfKRE6, Ffgas1, FfHYD-1, and FfGFA1. Moreover, FfMYB13 might negatively influence tissue toughening in the inhibition of oxidative damage by activating Ff-FeSOD1.

Metabolic and physiological functions of Patatin-like phospholipase-A in plants

Patatin-like phospholipase-A (pPLA) is a class of lipid acyl hydrolase enzymes found in both, the animal and plant kingdoms. Plant pPLAs are related to the potato tuber storage protein patatin in solanaceous plants. Despite extensive investigation of pPLA functions in the animal system, the mechanistic functional details and regulatory roles of pPLA are poorly understood in plants. In recent years, research pertaining to pPLAs has gain some momentum as some of the key members of pPLA family have been characterized functionally. These findings have provided key insights into the structural features, biochemical activities, and functional roles of plant pPLAs. In this review, we are presenting a holistic overview of pPLAs in plants and providing the latest updates on pPLA research. We have highlighted the genomic diversity and structural features of pPLAs in plants. Importantly, we have discussed the role of pPLAs in lipid metabolism, including sphingolipid metabolism, lignin and cellulose accumulation, lipid breakdown and seed oil content enhancement. Moreover, regulatory roles of pPLAs in physiological processes, such as plant stress response, plant-pathogen interactions and plant development have been discussed. This information will be critical in the biotechnological programs for crop improvement.

Transcription factor PdMYB118 in poplar regulates lignin deposition and xylem differentiation in addition to anthocyanin synthesis through suppressing the expression of PagKNAT2/6b gene

R2R3-MYB transcription factors function as the master regulators of the phenylpropanoid pathway in which both lignin and anthocyanin are produced. In poplar, R2R3-MYB transcription factor PdMYB118 positively regulates anthocyanin production to change leaf color. However, the molecular mechanism by which it controls different branches of the phenylpropanoid pathway still remains poorly understood. Here, we reported that in addition to anthocyanin synthesis, lignin deposition and xylem differentiation were regulated by PdMYB118 through inhibiting PagKNAT2/6b gene expression. The transgenic poplar plants overexpressing PdMYB118 accumulated more xylem, lignin and anthocyanin. Transcriptome and reverse transcription quantitative PCR analyses revealed that the expression of PagKNAT2/6b gene which inhibited lignin deposition and xylem differentiation was significantly down-regulated in transgenic poplar plants. Subsequent dual-luciferase reporter and yeast-one-hybrid assays demonstrated that PdMYB118 directly inhibited the transcription of PagKNAT2/6b by binding to the AC elements in its promoter region. Further experiments with transgenic poplar plants overexpressing PagKNAT2/6b demonstrated that overexpression of PagKNAT2/6b in the PdMYB118 overexpression background rescued lignin accumulation and xylem width to the same level of wild type plants. The findings in this work suggest that PdMYB118 is involved in the lignin deposition and xylem differentiation via modulating the expression of PagKNAT2/6b, and the PdMYB118- PagKNAT2/6b model can be used for the genetic breeding of new woody tree with high lignin production.

The PtobZIP55-PtoMYB170 module regulates the wood anatomical and chemical properties of Populus tomentosa in acclimation to low nitrogen availability

Poplar plantations are often established on nitrogen-poor land, and poplar growth and wood formation are constrained by low nitrogen (LN) availability. However, the molecular mechanisms by which specific genes regulate wood formation in acclimation to LN availability remain unclear. Here, we report a previously unrecognized module, basic region/leucine zipper 55 (PtobZIP55)-PtoMYB170, which regulates the wood formation of Populus tomentosa in acclimation to LN availability. PtobZIP55 was highly expressed in poplar wood and induced by LN. Altered wood anatomical properties and increased lignification were detected in PtobZIP55-overexpressing poplars, whereas the opposite results were detected in PtobZIP55-knockout poplars. Molecular and transgenic analyses revealed that PtobZIP55 directly binds to the promoter sequence of PtoMYB170 to activate its transcription. The phenotypes of PtoMYB170 transgenic poplars were similar to those of PtobZIP55 transgenic poplars under LN conditions. Further molecular analyses revealed that PtoMYB170 directly bound the promoter sequences of lignin biosynthetic genes to activate their transcription to increase lignin concentrations in LN-treated poplar wood. These results suggest that PtobZIP55 activates PtoMYB170 transcription, which in turn positively regulates lignin biosynthetic genes, increasing lignin deposition in the wood of P. tomentosa in the context of acclimation to LN availability.

The first intron and promoter of Arabidopsis DIACYLGLYCEROL ACYLTRANSFERASE 1 exert synergistic effects on pollen and embryo lipid accumulation

Accumulation of triacylglycerols (TAGs) is crucial during various stages of plant development. In Arabidopsis, two enzymes share overlapping functions to produce TAGs, namely acyl-CoA:diacylglycerol acyltransferase 1 (DGAT1) and phospholipid:diacylglycerol acyltransferase 1 (PDAT1). Loss of function of both genes in a dgat1-1/pdat1-2 double mutant is gametophyte lethal. However, the key regulatory elements controlling tissue-specific expression of either gene has not yet been identified. We transformed a dgat1-1/dgat1-1//PDAT1/pdat1-2 parent with transgenic constructs containing the Arabidopsis DGAT1 promoter fused to the AtDGAT1 open reading frame either with or without the first intron. Triple homozygous plants were obtained, however, in the absence of the DGAT1 first intron anthers fail to fill with pollen, seed yield is c. 10% of wild-type, seed oil content remains reduced (similar to dgat1-1/dgat1-1), and non-Mendelian segregation of the PDAT1/pdat1-2 locus occurs. Whereas plants expressing the AtDGAT1pro:AtDGAT1 transgene containing the first intron mostly recover phenotypes to wild-type. This study establishes that a combination of the promoter and first intron of AtDGAT1 provides the proper context for temporal and tissue-specific expression of AtDGAT1 in pollen. Furthermore, we discuss possible mechanisms of intron mediated regulation and how regulatory elements can be used as genetic tools to functionally replace TAG biosynthetic enzymes in Arabidopsis.

The FERONIA-RESPONSIVE TO DESICCATION 26 module regulates vascular immunity to Ralstonia solanacearum

Some pathogens colonize plant leaves, but others invade the roots, including the vasculature, causing severe disease symptoms. Plant innate immunity has been extensively studied in leaf pathosystems; however, the precise regulation of immunity against vascular pathogens remains largely unexplored. We previously demonstrated that loss of function of the receptor kinase FERONIA (FER) increases plant resistance to the typical vascular bacterial pathogen Ralstonia solanacearum. Here, we show that upon infection with R. solanacearum, root xylem cell walls in Arabidopsis thaliana become highly lignified. FER is specifically upregulated in the root xylem in response to R. solanacearum infection, and inhibits lignin biosynthesis and resistance to this pathogen. We determined that FER interacts with and phosphorylates the transcription factor RESPONSIVE TO DESICCATION 26 (RD26), leading to its degradation. Overexpression and knockout of RD26 demonstrated that it positively regulates plant resistance to R. solanacearum by directly activating the expression of lignin-related genes. Tissue-specific expression of RD26 in the root xylem confirmed its role in vascular immunity. We confirmed that the FER-RD26 module regulates lignin biosynthesis and resistance against R. solanacearum in tomato (Solanum lycopersicum). Taken together, our findings unveil that the FER-RD26 cascade governs plant immunity against R. solanacearum in vascular tissues by regulating lignin deposition. This cascade may represent a key defense mechanism against vascular pathogens in plants.

Dynamic Chromatin Accessibility and Gene Expression Regulation During Maize Leaf Development

BACKGROUND/OBJECTIVES

Chromatin accessibility is closely associated with transcriptional regulation during maize (Zea mays) leaf development. However, its precise role in controlling gene expression at different developmental stages remains poorly understood. This study aimed to investigate the dynamics of chromatin accessibility and its influence on genome-wide gene expression during the BBCH_11, BBCH_13, and BBCH_17 stages of maize leaf development.

METHODS

Maize leaves were collected at the BBCH_11, BBCH_13, and BBCH_17 developmental stages, and chromatin accessibility was assessed using ATAC-seq. RNA-seq was performed to profile gene expression. Integrated analysis of ATAC-seq and RNA-seq data was conducted to elucidate the relationship between chromatin accessibility and transcriptional regulation.

RESULTS

A total of 46,808, 38,242, and 41,084 accessible chromatin regions (ACRs) were identified at the BBCH_11, BBCH_13, and BBCH_17 stages, respectively, with 23.4%, 12.2%, and 21.9% of these regions located near transcription start sites (TSSs). Integrated analyses revealed that both the number and intensity of ACRs significantly influence gene expression levels. Motif analysis identified key transcription factors associated with leaf development and potential transcriptional repressors among genes, showing divergent regulation patterns in ATAC-seq and RNA-seq datasets.

CONCLUSIONS

These findings demonstrate that chromatin accessibility plays a crucial role in regulating the spatial and temporal expression of key genes during maize leaf development by modulating transcription factor binding. This study provides novel insights into the regulatory mechanisms underlying maize leaf development, contributing to a deeper understanding of chromatin-mediated gene expression.

Multi Characteristic Analysis of Vascular Cambium Cells in Populus euphratica Reveals Its Anti-Aging Strategy

All multicellular organisms undergo senescence, but the continuous division of the vascular cambium in plants enables certain tree species to survive for hundreds or even thousands of years. Previous studies have focused on the development of the vascular cambium, but the mechanisms regulating age-related changes remain poorly understood. This study investigated age-related changes in the vascular cambium of P. euphratica trees aged 50 to 350 years. The number of cambium cells in the 50-year-old tree group was 10 ± 2, while the number of cambium cells in the 200-year-old and 350-year-old tree groups significantly decreased. The thickness of the cambium cells exhibited a similar trend. In addition, the net photosynthetic and transpiration rates continue to increase with age, but no notable differences were found in factors like average leaf area, palisade tissue thickness, and stomatal density. A total of 6491 differentially expressed genes (DEGs) were identified in the vascular cambium of P. euphratica at three distinct ages using RNA sequencing. The expression patterns of DEGs associated with cell division and differentiation, lignin biosynthesis, plant hormones, and transcription factors were analyzed. DEGs related to XTH, EXP, PAL, C4H, ABA, Br, GA, and others are highly expressed in older trees, whilst those encoding expansins, kinases, cyclins, 4CL, Auxin, Eth, SA, and others are more prevalent in younger trees. Gene family members, such as NAC, MYB, HD-ZIP III, WRKY, and GRF, have various regulatory functions in the vascular cambium. The findings offer insights into how ancient P. euphratica trees maintain vitality by balancing growth and aging, providing a foundation for future research on their longevity mechanisms.

Lignin lite: Boosting plant power through selective downregulation

This article explores the dual benefits of reducing lignin content in plants, which streamlines biofuel production while maintaining robust defence mechanisms. It discusses how plants compensate for lower lignin levels through alternative defence strategies, recent biotechnological advances in lignin modification, and the implications for agriculture and industry.

PbAGL7-PbNAC47-PbMYB73 complex coordinately regulates PbC3H1 and PbHCT17 to promote the lignin biosynthesis in stone cells of pear fruit

Lignification of the cell wall in pear (Pyrus) fruit results in the formation of stone cells, which affects the texture and quality of the fruit. However, it is still unclear that how different transcription factors (TFs) work together to coordinate the synthesis and deposition of lignin. Here, we examined the transcriptome of pear varieties with different stone cell contents and found a key TF (PbAGL7) that can promote the increase of stone cell contents and secondary cell wall thicknesses. In addition, PbAGL7 can facilitate the expression level of lignin biosynthesis-related genes and accelerate the lignin biosynthesis in pear fruit and Arabidopsis. However, PbAGL7 did not directly bind to the promoters of PbC3H1 and PbHCT17 which are crucial genes involved in lignin biosynthesis. On the other hand, yeast two-hybrid (Y2H) library showed that PbNAC47 and PbMYB73 interacted with PbAGL7 in the nucleus. PbNAC47 and PbMYB73 also increased the stone cell and lignin contents, and upregulated the expressions of PbC3H1 and PbHCT17 by binding to the SNBE and AC elements, respectively. Moreover, PbNAC47 also interacted with PbMYB73 to form PbAGL7-PbNAC47-PbMYB73 complex. This complex significantly activated the expression levels of PbC3H1 and PbHCT17 and promoted lignin biosynthesis to form stone cells in pear fruit. Overall, our study provides new insights into the molecular mechanism of TFs that coordinately regulate the stone cell formation in pear fruit and extend our knowledge to understand cell wall lignification in plants.

Functional analysis of two caffeoyl-coenzyme 3 a-o-methyltransferase involved in pear lignin metabolism

Caffeoyl-coenzyme 3 A-O-methyltransferase (CCoAOMT) plays a crucial role in the lignin synthesis in many higher plants. In this study, nine PbCCoAOMT genes in total were identified from pear, and classified into six categories. We treated pear fruits with hormones abscisic acid (ABA) and methyl jasmonate (MeJA) and salicylic acid (SA) and observed differential expression levels of these genes. Through qRT-PCR, we also preliminarily identified candidate PbCCoAOMT gene, potentially involved in lignin synthesis in pear fruits. Additionally, the overexpression of PbCCoAOMT1/2 in Arabidopsis and pear fruits increased in lignin content. Enzymatic assays showed that recombinant PbCCoAOMT1/2 proteins have similar enzymatic activity in vitro. The Y1H (Yeast one-hybrid) and dual luciferase (dual-LUC) experiments demonstrated that PbMYB25 can bind to the AC elements in the promoter region of the PbCCoAOMT1 gene. Our findings suggested that the PbCCoAOMT1 and PbCCoAOMT2 genes may contribute to the synthesis of lignin and provide insights into the mechanism of lignin biosynthesis and stone cell development in pear fruits.

Genome-Wide Identification and Characterization of the Laccase Gene Family in Fragaria vesca and Its Potential Roles in Response to Salt and Drought Stresses

Laccase (LAC, EC 1.10.3.2) is integral to the formation of lignin synthesis, flavonoid production, and responses to both biotic and abiotic stresses. While recent studies have characterized numerous LAC gene families and their functions across various plants, information regarding LAC genes in woodland strawberry (Fragaria vesca) remains limited. In this study, we identified a total of 57 FvLAC genes in the Fragaria vesca genome, which were phylogenetically categorized into five distinct groups. Analysis of the gene structures revealed a uniformity in the exon-intron structure among the subgroups, while conserved motifs identified unique motifs specific to certain subgroups, suggesting functional variations. Chromosomal localization studies indicated that FvLACs are distributed across seven chromosomes, and collinearity analysis demonstrated that FvLACs exhibit collinearity within the species. Additionally, cis-acting element analysis suggested that FvLAC genes are involved in stress responses, hormone responses, light responses, and the growth and development of plants. qRT-PCR demonstrated that FvLACs responded to salt, drought, and hormone stresses, with the expression levels of FvLAC24, FvLAC32, and FvLAC51 continuously increasing under these stress conditions. Furthermore, transgenic yeast experiments revealed that FvLAC51 enhanced yeast tolerance to both salt and drought stresses, while FvLAC24 and FvLAC32 negatively regulated yeast tolerance under these same conditions. These findings provide a theoretical foundation for further investigation into the functions of FvLAC genes in woodland strawberry.

MYB transcription factors in Peucedanum Praeruptorum Dunn: the diverse roles of the R2R3-MYB subfamily in mediating coumarin biosynthesis

BACKGROUND

The MYB superfamily (v-myb avian myeloblastosis viral oncogene homolog) plays a role in plant growth and development, environmental stress defense, and synthesis of secondary metabolites. Little is known about the regulatory function of MYB genes in Peucedanum praeruptorum Dunn, although many MYB family members, especially R2R3-MYB genes, have been extensively studied in model plants.

RESULTS

A total of 157 R2R3-MYB transcription factors from P. praeruptorum were identified using bioinformatics analysis. Comprehensive analyses including chromosome location, microsynteny, gene structure, conserved motif, phylogenetic tree, and conserved domain were further performed. The length of the 157 transcription factors ranged from 120 to 1,688 amino acids (molecular weight between 14.21 and 182.69 kDa). All proteins were hydrophilic. Subcellular localization predictions showed that 155 PpMYB proteins were localized in the nucleus, with PpMYB12 and PpMYB157 localized in the chloroplasts and mitochondria, respectively. Ten conserved motifs were identified in the PpMYBs, all of which contained typical MYB domains. Transcriptome analysis identified 47,902 unigenes. Kyoto Encyclopedia of Genes and Genomes analysis revealed 136 pathways, of which 524 genes were associated with the phenylpropanoid pathway. Differential expressed genes (DEGs) before and after bolting showed that 11 genes were enriched in the phenylpropanoid pathway. Moreover, the expression patterns of transcription genes were further verified by qRT-PCR. With high-performance liquid chromatography (HPLC), 8 coumarins were quantified from the root, stem, and leaf tissue samples of P. praeruptorum at different stages. Praeruptorin A was found in both roots and leaves before bolting, whereas praeruptorin B was mainly concentrated in the roots, and the content of both decreased in the roots and stems after bolting. Praeruptorin E content was highest in the leaves and increased with plant growth. The correlation analysis between transcription factors and coumarin content showed that the expression patterns of PpMYB3 and PpMYB103 in roots align with the accumulation trends of praeruptorin A, praeruptorin B, praeruptorin E, scopoletin, and isoscopoletin, which declined in content after bolting, suggesting that these genes may positively regulate the biosynthesis of coumarins. Eleven distinct metabolites and 48 DEGs were identified. Correlation analysis revealed that the expression of all DEGs were significantly related to the accumulation of coumarin metabolites, indicating that these genes are involved in the regulation of coumarin biosynthesis.

CONCLUSIONS

R2R3-MYB transcription factors may be involved in the synthesis of coumarin. Our findings provide basic data and a rationale for future an in-depth studies on the role of R2R3-MYB transcription factors in the growth and regulation of coumarin synthesis.

Synergistic actions of 3 MYB transcription factors underpin blotch formation in tree peony

Blotches in floral organs attract pollinators and promote pollination success. Tree peony (Paeonia suffruticosa Andr.) is an internationally renowned cut flower with extremely high ornamental and economic value. Blotch formation on P. suffruticosa petals is predominantly attributed to anthocyanin accumulation. However, the endogenous regulation of blotch formation in P. suffruticosa remains elusive. Here, we identified the regulatory modules governing anthocyanin-mediated blotch formation in P. suffruticosa petals, which involves the transcription factors PsMYB308, PsMYBPA2, and PsMYB21. PsMYBPA2 activated PsF3H expression to provide sufficient precursor substrate for anthocyanin biosynthesis. PsMYB21 activated both PsF3H and PsFLS expressions and promoted flavonol biosynthesis. The significantly high expression of PsMYB21 in nonblotch regions inhibited blotch formation by competing for anthocyanin biosynthesis substrates, while conversely, its low expression in the blotch region promoted blotch formation. PsMYB308 inhibited PsDFR and PsMYBPA2 expressions to directly prevent anthocyanin-mediated blotch formation. Notably, a smaller blotch area, decreased anthocyanin content, and inhibition of anthocyanin structural gene expression were observed in PsMYBPA2-silenced petals, while the opposite phenotypes were observed in PsMYB308-silenced and PsMYB21-silenced petals. Additionally, PsMYBPA2 and PsMYB308 interacted with PsbHLH1-3, and their regulatory intensity on target genes was synergistically regulated by the PsMYBPA2-PsbHLH1-3 and PsMYB308-PsbHLH1-3 complexes. PsMYB308 also competitively bound to PsbHLH1-3 with PsMYBPA2 to fine-tune the regulatory network to prevent overaccumulation of anthocyanin in blotch regions. Overall, our study uncovers a complex R2R3-MYB transcriptional regulatory network that governs anthocyanin-mediated blotch formation in P. suffruticosa petals, providing insights into the molecular mechanisms underlying blotch formation in P. suffruticosa.

The rice R2R3 MYB transcription factor FOUR LIPS connects brassinosteroid signaling to lignin deposition and leaf angle

Leaf angle is an important agronomic trait for crop architecture and yield. In rice (Oryza sativa), the lamina joint is a unique structure connecting the leaf blade and sheath that determines leaf angle. Brassinosteroid (BR) signaling involving GLYCOGEN SYNTHASE KINASE-3 (GSK3)/SHAGGY-like kinases and BRASSINAZOLE-RESISTANT1 (BZR1) has a central role in regulating leaf angle in rice. In this study, we identified the atypical R2R3-MYB transcription factor FOUR LIPS (OsFLP), the rice homolog of Arabidopsis (Arabidopsis thaliana) AtFLP, as a participant in BR-regulated leaf angle formation. The spatiotemporal specificity of OsFLP expression in the lamina joint was closely associated with lignin deposition in vascular bundles and sclerenchyma cells. OsFLP mutation caused loose plant architecture with droopy flag leaves and hypersensitivity to BRs. OsBZR1 directly targeted OsFLP, and OsFLP transduced BR signals to lignin deposition in the lamina joint. Moreover, OsFLP promoted the transcription of the phenylalanine ammonia-lyase family genes OsPAL4 and OsPAL6. Intriguingly, OsFLP feedback regulated OsGSK1 transcription and OsBZR1 phosphorylation status. In addition, an Ala-to-Thr substitution within the OsFLP R3 helix-turn-helix domain, an equivalent mutation to that in Osflp-1, affected the DNA-binding ability and transcriptional activity of OsFLP. Our results reveal that OsFLP functions with OsGSK1 and OsBZR1 in BR signaling to maintain optimal leaf angle by modulating the lignin deposition in mechanical tissues of the lamina joint.

Sweetpotato sucrose transporter IbSUT1 alters storage roots formation by regulating sucrose transport and lignin biosynthesis

The formation and development of storage roots is the most important physiological process in sweetpotato production. Sucrose transporters (SUTs) regulate sucrose transport from source to sink organs and play important roles in growth and development of plants. However, whether SUTs involved in sweetpotato storage roots formation is so far unknown. In this study, we show that IbSUT1, a SUT, is localized to the plasma membrane. Overexpression of IbSUT1 in sweetpotato promotes the sucrose efflux rate from leaves, leading to increased sucrose levels in roots, thus induces lignin deposition in the stele, which inhibits the storage roots formation and compromises the yield. Heterologous expression of IbSUT1 in Arabidopsis significantly increases the sucrose accumulation and promotes lignification in the inflorescence stems. RNA-seq and biochemical analysis further demonstrated that IbMYB1 negatively regulates the expression of IbSUT1. Overexpression of IbMYB1 in Arabidopsis reduces the sucrose accumulation and lignification degree in the inflorescence stems. Moreover, co-overexpression of IbMYB1 and IbSUT1 restores the phenotype of lignin over-deposition in Arabidopsis. Collectively, our results reveal that IbSUT1 regulates source-sink sucrose transport and participates in the formation of sweetpotato storage roots and highlight the potential application of IbSUT1 in improving sweetpotato yield in the future.

A GhLac1-centered transcriptional regulatory cascade mediates cotton resistance to Verticillium dahliae through the lignin biosynthesis pathway

The lignin biosynthesis pathway plays a crucial role in the defense response against V. dahliae in cotton, and it is essential to identify the key regulators in this pathway for disease-resistant breeding. In a previous study, the cotton laccase gene GhLac1 was identified as mediating plant broad-spectrum biotic stress tolerance by manipulating phenylpropanoid metabolism. However, the upstream master regulators and regulatory mechanism of lignin are still largely unknown. This study aims to identify the upstream regulators of GhLac1 and explore the molecular mechanism underlying cotton's disease resistance response to V. dahliae. Through the study, three WRKY, three MYB, and one APETALA2/ETHYLENE RESPONSIVE FACTOR (ERF) TFs were identified as differentially responding to V. dahliae infection in cotton. Among these TFs, GhWRKY30, GhWRKY41, GhMYB42, and GhTINY2 were found to directly bind to the GhLac1 promoter and activate its expression. Transient overexpression of these four TFs in cotton led to increased expression of GhLac1 and other the laccase family members, while knockdown of these TFs resulted in reduced lignin accumulation and increased susceptibility to V. dahliae. Additionally, GhWRKY30 and GhWRKY41 were observed to interact with themselves and with each other, synergistically transactivating the GhLac1 promoter. This study reveals a GhLac1-centered transcriptional regulatory cascade of lignin synthesis that contributes to cotton's defense response by modulating lignin metabolism.

Genome-wide computational analysis of the dirigent gene family in Solanum lycopersicum

BACKGROUND

Dirigent (DIR) genes play a key role in the development of organic products in plants. They confer conformational influence on processes that lack stereoselectivity and regioselectivity through processes that are mostly understood. They are required to produce lignans, which are a unique and widely distributed family of plant secondary metabolites with intriguing pharmacological characteristics and potential role in plant development. DIR genes are implicated in the process of lignification and protect plants from environmental stresses, including biotic and abiotic stresses. Nevertheless, no research has been performed on the DIR gene family in Solanum lycopersicum. This study provides detailed information on the DIR gene family in S. lycopersicum.

METHODS AND RESULTS

The conserved domain analysis, phylogenetic analysis, evolutionary adaptation, cis-acting elements, proteomic analysis, signal peptide detection, transmembrane potential analysis, sequence identity and similarity analysis, gene assembly, genomic localization, duplication of gene analysis, and evolutionary linkage of 31 potential DIR genes were studied. All these analyses provide a deep understanding of DIR genes in the S. lycopersicum genome that will provide a useful reference for further functional analysis of the DIR genes in S. lycopersicum.

CONCLUSION

This research provides an in-depth and comprehensive explanation of the detailed process and structural characterization of DIR genes in the genome of S. lycopersicum, laying the groundwork for future plant genetic engineering and crop development exploration. This work will provide valuable information for identifying DIR genes in higher plants and support future research on the DIR gene family.

Transcriptomic Remodeling Occurs During Cambium Activation and Xylem Cell Development in Taxodium ascendens

Taxodium ascendens has been extensively cultivated in the wetlands of the Yangtze River in south China and has significantly contributed to ecology and timber production. Until now, research on T. ascendens genomics has yet to be conducted due to its large and complex genome, which hinders the development of T. ascendens genomic resources. Combined with the microstructural changes during cambium cell differentiation across various growth periods, we investigate the transcriptome expression and regulatory mechanisms governing cambium activity in T. ascendens. Using RNA sequencing (RNA-Seq) technology, we identified the genes involved in the cambium development of cells at three stages (dormancy, reactivation, and activity). These genes encode the regulatory and control factors associated with the cambial activity, cell division, cell expansion, and biosynthesis of cell wall components. Blast comparison revealed that three genes (TR_DN69961_c0_g1, TRINITY_DN17100_c1_g1, TRINITY_DN111727_c0_g1) from the MYB and NAC families might regulate transcription during lignin formation in wood thickening. These results illustrate the dynamic changes in the transcriptional network during vascular cambium development. Additionally, they shed light on the genetic regulation mechanism of secondary growth in T. ascendens and guide further elucidation of the candidate genes involved in regulating cambium differentiation and wood formation.

How lignin biosynthesis responds to nitrogen in plants: a scoping review

Nitrogen (N) plays a critical role in the functioning of key amino acids and synthetic enzymes responsible for the various stages of lignin biosynthesis. However, the precise mechanisms through which N influences lignin biosynthesis have not been fully elucidated. This scoping review explores how lignin biosynthesis responds to N in plants. A systematic search of the literature in several databases was conducted using relevant keywords. Only 44 of the 1842 selected studies contained a range of plant species, experimental conditions, and research approaches. Lignin content, structure, and biosynthetic pathways in response to N are discussed, and possible response mechanisms of lignin under low N are proposed. Among the selected studies, 64.52% of the studies reter to lignin content found a negative correlation between N availability and lignin content. Usually, high N decreases the lignin content, delays cell lignification, increases p-hydroxyphenyl propane (H) monomer content, and regulates lignin synthesis through the expression of key genes (PAL, 4CL, CCR, CAD, COMT, LAC, and POD) encoding miRNAs and transcription factors (e.g., MYB, bHLH). N deficiency enhances lignin synthesis through the accumulation of phenylpropanoids, phenolics, and soluble carbohydrates, and indirect changes in phytohormones, secondary metabolites, etc. This review provides new insights and important references for future studies on the regulation of lignin biosynthesis.

Lignin biosynthesis pathway repressors in gymnosperms: differential repressor domains as compared to angiosperms

Lignin is a polyphenolic polymer present in the cell walls of specialized plant cell types in vascular plants that provides structural support and plays a major role in plant protection. The lignin biosynthesis pathway is regulated by transcription factors from the MYB (myeloblastosis) family. While several MYB members positively regulate lignin synthesis, only a few negatively regulate lignin synthesis. These lignin suppressors are well characterized in model plant species; however, their role has not been fully explored in gymnosperms. Lignin forms one of the major hurdles for the forest-based industry e.g. paper, pulp, and biofuel production. Therefore, the detailed mechanisms involved in the regulation of lignin synthesis are valuable, especially in conifers that form the major source of softwood for timber and paper production. In this review, the potential and differential domains present in the MYB suppressors in gymnosperms are discussed, along with their phylogenetic analysis. Sequence analysis revealed that the N-terminal regions of the MYB suppressor members were found to be conserved among the gymnosperms and angiosperms containing the R2, R3, and bHLH domains, while the C-terminal regions were found to be highly variable. The typical repressor motifs like the LxLxL-type EAR motif and the TLLLFR motif were absent from the C-terminal regions of MYB suppressors from most gymnosperms. However, although the gymnosperms lacked the characteristic repressor domains, a R2R3-type MYB member from Ginkgo was reported to repress the lignin biosynthetic pathway. It is proposed that gymnosperms possess unique kinds of repressors that need further functional validation.

NtMYB27 acts downstream of NtBES1 to modulate flavonoids accumulation in response to UV-B radiation in tobacco

UV-B radiation can induce the accumulation of many secondary metabolites, including flavonoids, in plants to protect them from oxidative damage. BRI1-EMS-SUPPRESSOR1 (BES1) has been shown to mediate the biosynthesis of flavonoids in response to UV-B. However, the detailed mechanism by which it acts still needs to be further elucidated. Here, we revealed that UV-B significantly inhibited the transcription of multiple transcription factor genes in tobacco, including NtMYB27, which was subsequently shown to be a repressor of flavonoids synthesis in tobacco. We further demonstrated that NtBES1 directly binds to the E-box motifs present in the promoter of NtMYB27 to mediate its transcriptional repression upon UV-B exposure. The UV-B-repressed NtMYB27 could bind to the ACCT-containing element (ACE) in the promoters of Nt4CL and NtCHS and served as a modulator that promoted the biosynthesis of lignin and chlorogenic acid (CGA) but inhibited the accumulation of flavonoids in tobacco. The expression of NtMYB27 was also significantly repressed by heat stress, suggesting its putative roles in regulating heat-induced flavonoids accumulation. Taken together, our results revealed the role of NtBES1 and NtMYB27 in regulating the synthesis of flavonoids during the plant response to UV-B radiation in tobacco.

Characterizing seed dormancy in Epimedium brevicornu Maxim.: Development of novel chill models and determination of dormancy release mechanisms by transcriptomics

PURPOSE

Epimedium brevicornu Maxim. is a perennial persistent C3 plant of the genus Epimedium Linn. in the family Berberaceae that exhibits severe physiological and morphological seed dormancy.We placed mature E. brevicornu seeds under nine stratification treatment conditions and explored the mechanisms of influence by combining seed embryo growth status assessment with related metabolic pathways and gene co-expression analysis.

RESULTS

We identified 3.9 °C as the optimum cold-stratification temperature of E. brevicornu seeds via a chilling unit (CU) model. The best treatment was variable-temperature stratification (10/20 °C, 12/12 h) for 4 months followed by low-temperature stratification (4 °C) for 3 months (4-3). A total of 63801 differentially expressed genes were annotated to 2587 transcription factors (TFs) in 17 clusters in nine treatments (0-0, 0-3, 1-3, 2-3, 3-3, 4-3, 4-2, 4-1, 4-0). Genes specifically highly expressed in the dormancy release treatment group were significantly enriched in embryo development ending in seed dormancy and fatty acid degradation, indicating the importance of these two processes. Coexpression analysis implied that the TF GRF had the most reciprocal relationships with genes, and multiple interactions centred on zf-HD and YABBY as well as on MYB, GRF, and TCP were observed.

CONCLUSION

In this study, analyses of plant hormone signal pathways and fatty acid degradation pathways revealed changes in key genes during the dormancy release of E. brevicornu seeds, providing evidence for the filtering of E. brevicornu seed dormancy-related genes.

The regulatory mechanism of rapid lignification for timely anther dehiscence

Anther dehiscence is a crucial event in plant reproduction, tightly regulated and dependent on the lignification of the anther endothecium. In this study, we investigated the rapid lignification process that ensures timely anther dehiscence in Arabidopsis. Our findings reveal that endothecium lignification can be divided into two distinct phases. During Phase I, lignin precursors are synthesized without polymerization, while Phase II involves simultaneous synthesis of lignin precursors and polymerization. The transcription factors MYB26, NST1/2, and ARF17 specifically regulate the pathway responsible for the synthesis and polymerization of lignin monomers in Phase II. MYB26-NST1/2 is the key regulatory pathway responsible for endothecium lignification, while ARF17 facilitates this process by interacting with MYB26. Interestingly, our results demonstrate that the lignification of the endothecium, which occurs within approximately 26 h, is much faster than that of the vascular tissue. These findings provide valuable insights into the regulation mechanism of rapid lignification in the endothecium, which enables timely anther dehiscence and successful pollen release during plant reproduction.

Stem lodging Resistance-1 controls stem strength by positively regulating the biosynthesis of cell wall components in Capsicum annuum L

Lodging presents a significant challenge in cultivating high-yield crops with extensive above-ground biomass, yet the molecular mechanisms underlying this phenomenon in the Solanaceae family remain largely unexplored. In this study, we identified a gene, CaSLR1 (Capsicum annuum Stem Lodging Resistance 1), which encodes a MYELOBLASTOSIS (MYB) family transcription factor, from a lodging-affected C. annuum EMS mutant. The suppression of CaSLR1 expression in pepper led to notable stem lodging, reduced thickness of the secondary cell wall, and decreased stem strength. A similar phenotype was observed in tomato with the knockdown of SlMYB61, the orthologous gene to CaSLR1. Further investigations demonstrated that CaNAC6, a gene involved in secondary cell wall (SCW) formation, is co-expressed with CaSLR1 and acts as a positive regulator of its expression, as confirmed through yeast one-hybrid, dual-luciferase reporter assays, and electrophoretic mobility shift assays. These findings elucidate the CaNAC6-CaSLR1 module that contributes to lodging resistance, emphasizing the critical role of CaSLR1 in the lodging resistance regulatory network.

OsMYB14, an R2R3-MYB transcription factor, regulates plant height through the control of hormone metabolism in rice

Plant growth must be regulated throughout the plant life cycle. The myeloblastosis (MYB) transcription factor (TF) family is one of the largest TF families and is involved in metabolism, lignin biosynthesis, and developmental processes. Here, we showed that OsMYB14, a rice R2R3-MYB TF, was expressed in leaves and roots, especially in rice culm and panicles, and that it localized to the nucleus. Overexpression of OsMYB14 (OsMYB14-ox) in rice resulted in a 30% reduction in plant height compared to that of the wild type (WT), while the height of the osmyb14-knockout (osmyb14-ko) mutant generated using the CRISPR/Cas9 system was not significantly different. Microscopic observations of the first internode revealed that the cell size did not differ significantly among the lines. RNA sequencing analysis revealed that genes associated with plant development, regulation, lipid metabolism, carbohydrate metabolism, and gibberellin (GA) and auxin metabolic processes were downregulated in the OsMYB14-ox line. Hormone quantitation revealed that inactive GA19 accumulated in OsMYB14-ox but not in the WT or knockout plants, suggesting that GA20 generation was repressed. Indole-3-acetic acid (IAA) and IAA-aspartate accumulated in OsMYB14-ox and osmyb14-ko, respectively. Indeed, real-time PCR analysis revealed that the expression of OsGA20ox1, encoding GA20 oxidase 1, and OsGH3-2, encoding IAA-amido synthetase, was downregulated in OsMYB14-ox and upregulated in osmyb14-ko. A protein-binding microarray revealed the presence of a consensus DNA-binding sequence, the ACCTACC-like motif, in the promoters of the OsGA20ox1 and GA20ox2 genes. These results suggest that OsMYB14 may act as a negative regulator of biological processes affecting plant height in rice by regulating GA biosynthesis and auxin metabolism.

The RALF2-FERONIA-MYB63 module orchestrates growth and defense in tomato roots

Plant secreted peptides RAPID ALKALINISATION FACTORs (RALFs), which act through the receptor FERONIA (FER), play important roles in plant growth. However, it remains unclear whether and how RALF-FER contributes to the trade-off of plant growth-defense. Here, we used a variety of techniques such as CRISPR/Cas9, protein-protein interaction and transcriptional regulation methods to investigate the role of RALF2 and its receptor FER in regulating lignin deposition, root growth, and defense against Fusarium oxysporum f. sp. lycopersici (Fol) in tomato (Solanum lycopersicum). The ralf2 and fer mutants show reduced primary root length, elevated lignin accumulation, and enhanced resistance against Fol than the wild-type. FER interacts with and phosphorylates MYB63 to promote its degradation. MYB63 serves as an activator of lignin deposition by regulating the transcription of dirigent protein gene DIR19. Mutation of DIR19 suppresses lignin accumulation, and reverses the short root phenotype and Fol resistance in ralf2 or fer mutant. Collectively, our results demonstrate that the RALF2-FER-MYB63 module fine-tunes root growth and resistance against Fol through regulating the deposition of lignin in tomato roots. The study sheds new light on how plants maintain the growth-defense balance via RALF-FER.

Genome-wide analysis of the common bean (Phaseolus vulgaris) laccase gene family and its functions in response to abiotic stress

BACKGROUND

Laccase (LAC) gene family plays a pivotal role in plant lignin biosynthesis and adaptation to various stresses. Limited research has been conducted on laccase genes in common beans.

RESULTS

29 LAC gene family members were identified within the common bean genome, distributed unevenly in 9 chromosomes. These members were divided into 6 distinct subclades by phylogenetic analysis. Further phylogenetic analyses and synteny analyses indicated that considerable gene duplication and loss presented throughout the evolution of the laccase gene family. Purified selection was shown to be the major evolutionary force through Ka / Ks. Transcriptional changes of PvLAC genes under low temperature and salt stress were observed, emphasizing the regulatory function of these genes in such conditions. Regulation by abscisic acid and gibberellins appears to be the case for PvLAC3, PvLAC4, PvLAC7, PvLAC13, PvLAC14, PvLAC18, PvLAC23, and PvLAC26, as indicated by hormone induction experiments. Additionally, the regulation of PvLAC3, PvLAC4, PvLAC7, and PvLAC14 in response to nicosulfuron and low-temperature stress were identified by virus-induced gene silence, which demonstrated inhibition on growth and development in common beans.

CONCLUSIONS

The research provides valuable genetic resources for improving the resistance of common beans to abiotic stresses and enhance the understanding of the functional roles of the LAC gene family.

Genome-Wide Identification, Evolution, and Expression Analysis of the DIR Gene Family in Schima superba

Schima superba, commonly known as the Chinese guger tree, is highly adaptable and tolerant of poor soil conditions. It is one of the primary species forming the evergreen broad-leaved forests in southern China. Dirigent proteins (DIRs) play crucial roles in the synthesis of plant lignin and lignans, secondary metabolism, and response to adversity stress. However, research on the DIR gene family in S. superba is currently limited. This study identified 24 SsDIR genes, categorizing them into three subfamilies. These genes are unevenly distributed across 13 chromosomes, with 83% being intronless. Collinearity analysis indicated that tandem duplication played a more significant role in the expansion of the gene family compared to segmental duplication. Additionally, we analyzed the expression patterns of SsDIRs in different tissues of S. superba. The SsDIR genes exhibited distinct expression patterns across various tissues, with most being specifically expressed in the roots. Further screening identified SsDIR genes that may regulate drought stress, with many showing differential expression under drought stress conditions. In the promoter regions of SsDIRs, various cis-regulatory elements involved in developmental regulation, hormone response, and stress response were identified, which may be closely related to their diverse regulatory functions. This study will contribute to the further functional identification of SsDIR genes, providing insights into the biosynthetic pathways of lignin and lignans and the mechanisms of plant stress resistance.

Physiological, cytological and multi-omics analysis revealed the molecular response of Fritillaria cirrhosa to Cd toxicity in Qinghai-Tibet Plateau

Fritillaria cirrhosa, an endangered plant endemic to plateau regions, faces escalating cadmium (Cd) stress due to pollution in the Qinghai-Tibet Plateau. This study employed physiological, cytological, and multi-omics techniques to investigate the toxic effects of Cd stress and detoxification mechanisms of F. cirrhosa. The results demonstrated that Cd caused severe damage to cell membranes and organelles, leading to significant oxidative damage and reducing photosynthesis, alkaloid and nucleoside contents, and biomass. Cd application increased cell wall thickness by 167.89% in leaves and 445.78% in bulbs, leading to weight percentage of Cd increases of 76.00% and 257.14%, respectively. PER, CESA, PME, and SUS, genes responsible for cell wall thickening, were significantly upregulated. Additionally, the levels of metabolites participating in the scavenging of reactive oxygen species, including oxidized glutathione, D-proline, L-citrulline, and putrescine, were significantly increased under Cd stress. Combined multi-omics analyses revealed that glutathione metabolism and cell wall biosynthesis pathways jointly constituted the detoxification mechanism of F. cirrhosa in response to Cd stress. This study provides a theoretical basis for further screening of new cultivars for Cd tolerance and developing appropriate cultivation strategies to alleviate Cd toxicity.