An R2R3-MYB network modulates stem strength by regulating lignin biosynthesis and secondary cell wall thickening in herbaceous peony

Herbicidal Sorbicillinoid Analogs Cause Lignin Accumulation in Aspergillus aculeatus TE-65L

Five new sorbicillinoid derivatives, including (±)-aspersorbicillin A [(±)-1], a pair of enantiomers at C-9, and aspersorbicillins B-D (2-4), together with two known analogs (5 and 6) were isolated from the endophytic fungus Aspergillus aculeatus TE-65L. Their structures including absolute configurations were determined by detailed spectroscopic analyses and electronic circular dichroism calculations. The herbicidal activity of sorbicillinoids on the germ and radicle elongation of various weed types was reported for the first time. Compound 1 displayed significant herbicidal activity against Eleusine indica germ elongation (IC50 = 28.8 μg/mL), while compound 6 inhibited radicle elongation (IC50 = 25.6 μg/mL). Both were stronger than those of glyphosate (66.2 and 30.9 μg/mL, respectively). Further transcriptomic and LC-MS/MS metabolomic analysis indicated that 6 induced the transcriptional expressions of genes related to the lignin biosynthetic pathway, resulting in lignin accumulation. Transmission electron microscopy confirmed the cell wall thickening of seeds treated with 6, suggesting weed growth inhibition. This study reveals new lead compounds for fabricating natural herbicides and expands the agricultural use of sorbicillinoid analogs.

The MYB transcription factor PpMYB5 regulates Pp4CL1/Pp4CL2 expression to promote lignin biosynthesis of fruit russeting in the flat nectarine

KEY MESSAGE

Transcription factor PpMYB5 promotes lignin synthesis by directly binding to the Pp4CL1/Pp4CL2 promoter and affecting their expression, which may be related to nectarine russeting formation. Nectarine russeting is usually considered to be a non-invasive physiological disease that usually occurs on late-maturing cultivars and seriously affects their appearance quality and commercial value. The cause of nectarine fruit rust is currently unknown. In this study, we compared two flat nectarine cultivars, 'zhongyoupanweidi' (HD; russeting-free cultivar) and 'zhongyoupanweihou' (TH; russeting-prone cultivar), with respect to nectarine russeting by means of microscopy, transcriptomics, and hormone analysis. Compared to HD fruits, TH fruits had a broken cuticle, missing wax layer, and heavy lignin deposition. RNA sequencing (RNA-seq) revealed significant alternations in the expression of genes related to lignin synthesis. Moreover, structure genes Pp4CL1 and Pp4CL2, MYB transcription factor (TF) gene PpMYB5 were identified through weighted gene co-expression network analysis (WGCNA). Molecular experiments and transgenic evidence suggested that PpMYB5 regulates Pp4CL1/Pp4CL2 expression to promote lignin synthesis. Overall, in addition to providing new insights into the formation of mechanisms for nectarine russeting, our study also establishes a foundation for nectarine russeting prevention.

R2R3-MYB Gene Family in Coptis teeta Wall.: Genome-Wide Identification, Phylogeny, Evolutionary Expansion, and Expression Analyses during Floral Development

The R2R3-MYB gene family represents a widely distributed class of plant transcription factors. This gene family plays an important role in many aspects of plant growth and development. However, the characterization of R2R3-MYB genes present in the genome of Coptis teeta has not been reported. Here, we describe the bioinformatic identification and characterization of 88 R2R3-MYB genes in this species, and the identification of members of the R2R3-MYB gene family in species within the order Ranales most closely related to Coptis teeta. The CteR2R3-MYB genes were shown to exhibit a higher degree of conservation compared to those of A. thaliana, as evidenced by phylogeny, conserved motifs, gene structure, and replication event analyses. Cis-acting element analysis confirmed the involvement of CteR2R3-MYB genes in a variety of developmental processes, including growth, cell differentiation, and reproduction mediated by hormone synthesis. In addition, through homology comparisons with the equivalent gene family in A. thaliana, protein regulatory network prediction and transcriptome data analysis of floral organs across three time periods of flower development, 17 candidate genes were shown to exhibit biased expression in two floral phenotypes of C. teeta. This suggests their potential involvement in floral development (anther development) in this species.

Identification and Functional Studies on the Role of PlSPL14 in Herbaceous Peony Stem Development

Stem strength plays a crucial role in the growth and development of plants, as well as in their flowering and fruiting. It not only impacts the lodging resistance of crops, but also influences the ornamental value of ornamental plants. Stem development is closely linked to stem strength; however, the roles of the SPL transcription factors in the stem development of herbaceous peony (Paeonia lactiflora Pall.) are not yet fully elucidated. In this study, we obtained and cloned the full-length sequence of PlSPL14, encoding 1085 amino acids. Quantitative real-time PCR (qRT-PCR) analysis revealed that the expression level of PlSPL14 gradually increased with the stem development of P. lactiflora and was significantly expressed in vascular bundles. Subsequently, utilizing the techniques of virus-induced gene silencing (VIGS) and heterologous overexpression in tobacco (Nicotiana tabacum L.), it was determined that PlSPL14-silenced P. lactiflora had a thinner xylem thickness, a decreased stem diameter, and weakened stem strength, while PlSPL14-overexpressing tobacco resulted in a thicker xylem thickness, an increased stem diameter, and enhanced stem strength. Further screening of the interacting proteins of PlSPL14 using a yeast two-hybrid (Y2H) assay revealed an interactive relationship between PlSPL14 and PlSLR1 protein, which acts as a negative regulator of gibberellin (GA). Additionally, the expression level of PlSLR1 gradually decreased during the stem development of P. lactiflora. The above results suggest that PlSPL14 may play a positive regulatory role in stem development and act in the xylem, making it a potential candidate gene for enhancing stem straightness in plants.

PagMYB128 regulates secondary cell wall formation by direct activation of cell wall biosynthetic genes during wood formation in poplar

The biosynthesis of cellulose, lignin, and hemicelluloses in plant secondary cell walls (SCWs) is regulated by a hierarchical transcriptional regulatory network. This network features orthologous transcription factors shared between poplar and Arabidopsis, highlighting a foundational similarity in their genetic regulation. However, knowledge on the discrepant behavior of the transcriptional-level molecular regulatory mechanisms between poplar and Arabidopsis remains limited. In this study, we investigated the function of PagMYB128 during wood formation and found it had broader impacts on SCW formation compared to its Arabidopsis ortholog, AtMYB103. Transgenic poplar trees overexpressing PagMYB128 exhibited significantly enhanced xylem development, with fiber cells and vessels displaying thicker walls, and an increase in the levels of cellulose, lignin, and hemicelluloses in the wood. In contrast, plants with dominant repression of PagMYB128 demonstrated the opposite phenotypes. RNA sequencing and reverse transcription - quantitative polymerase chain reaction showed that PagMYB128 could activate SCW biosynthetic gene expression, and chromatin immunoprecipitation along with yeast one-hybrid, and effector-reporter assays showed this regulation was direct. Further analysis revealed that PagSND1 (SECONDARY WALL-ASSOCIATED NAC-DOMAIN PROTEIN1) directly regulates PagMYB128 but not cell wall metabolic genes, highlighting the pivotal role of PagMYB128 in the SND1-driven regulatory network for wood development, thereby creating a feedforward loop in SCW biosynthesis.

Identification of the function of a key gene NnHCT1 in lignin synthesis in petioles of Nelumbo nucifera

Leaf petiole or stem strength is an important agronomic trait affecting the growth of underground organs as a channel for material exchange and plays a vital role in the quality and yield of crops and vegetables. There are two different types of petioles in lotus, floating leaf petioles and vertical leaf petioles; however, the internal difference mechanism between these petioles is unclear. In this study, we investigated the differences between the initial vertical leaf petioles and the initial floating leaf petioles based on RNA sequencing (RNA-seq), and >2858 differentially expressed genes were annotated. These genes were chiefly enriched in phenylpropanoid biosynthesis, which is the source of the lignin and cellulose in petioles and stems. Lignin biology-related gene NnHCT1 was identified, and subsequent biological function validation demonstrated that the transient overexpression of NnHCT1 significantly increased the lignin and cellulose contents in lotus petioles and tobacco leaves. In contrast, silencing NnHCT1 through virus-induced gene silencing significantly reduced petiole lignin synthesis. Additionally, differentially up-regulated MYB family transcription factors were identified using RNA-seq. Yeast-one-hybrid and dual-luciferase reporter assays demonstrated that MYB4 could bind to the NnHCT1 promoter and up-regulate NnHCT1 expression. These findings demonstrate the significant potential of NnHCT1 to enhance lignin synthesis, thereby improving stem or petiole resistance to stunting and explaining the need for the study of differential petiole relationships in plants.

Genome-Wide Identification and Characterization of Lignin Synthesis Genes in Maize

Lignin is a crucial substance in the formation of the secondary cell wall in plants. It is widely distributed in various plant tissues and plays a significant role in various biological processes. However, the number of copies, characteristics, and expression patterns of genes involved in lignin biosynthesis in maize are not fully understood. In this study, bioinformatic analysis and gene expression analysis were used to discover the lignin synthetic genes, and two representative maize inbred lines were used for stem strength phenotypic analysis and gene identification. Finally, 10 gene families harboring 117 related genes involved in the lignin synthesis pathway were retrieved in the maize genome. These genes have a high number of copies and are typically clustered on chromosomes. By examining the lignin content of stems and the expression patterns of stem-specific genes in two representative maize inbred lines, we identified three potential stem lodging resistance genes and their interactions with transcription factors. This study provides a foundation for further research on the regulation of lignin biosynthesis and maize lodging resistance genes.

The CsmiR397a-CsLAC17 module regulates lignin biosynthesis to balance the tenderness and gray blight resistance in young tea shoots

Lignin accumulation can enhance the disease resistance of young tea shoots (Camellia sinensis). It also greatly reduces their tenderness, which indirectly affects the quality and yield of tea. Therefore, the regulation of lignin biosynthesis appears to be an effective way to balance tenderness and disease resistance in young tea shoots. In this study, we identified a laccase gene, CsLAC17, that is induced during tenderness reduction and gray blight infection in young tea shoots. Overexpression of CsLAC17 significantly increased the lignin content in transgenic Arabidopsis, enhancing their resistance to gray blight and decreasing stem tenderness. In addition, we found that CsLAC17 was negatively regulated by the upstream CsmiR397a by 5'-RLM-RACE, dual-luciferase assay, and transient expression in young tea shoots. Interestingly, the expression of CsmiR397a was inhibited during tenderness reduction and gray blight infection of young tea shoots. Overexpression of CsmiR397a reduced lignin accumulation, resulting in decreased resistance to gray blight and increased stem tenderness in transgenic Arabidopsis. Furthermore, the transient overexpression of CsmiR397a and CsLAC17 in tea leaves directly confirms the function of the CsmiR397a-CsLAC17 module in lignin biosynthesis and its effect on disease resistance. These results suggest that the CsmiR397a-CsLAC17 module is involved in balancing tenderness and gray blight resistance in young tea shoots by regulating lignin biosynthesis.

Side chain of confined xylan affects cellulose integrity leading to bending stem with reduced mechanical strength in ornamental plants

The stem support for fresh-cut flowers exerts a profound influence on the display of their blossoms. During vase insertion, bending stems significantly affect the ornamental value, but much remains unclear about the underlying reasons. In this study, six pairs of ornamental plants were screened for the contrast of bending and straight stems. The bending stems have weakened mechanical force and biomass recalcitrance compared with the straight ones. Meanwhile, cells in the bending stems became more loosely packed, along with a decrease in cell wall thickness and cellulose levels. Furthermore, wall properties characterizations show bending stems have decreased lignocellulosic CrI and cellulose DP, and enhanced the branching ratio of hemicellulose which is trapped in the cellulose. Given the distinct cell wall factors in different species, all data are grouped in standardized to eliminate the variations among plant species. The principal composition analysis and correlation analysis of the processed dataset strongly suggest that cellulose association factors determine the stem mechanical force and recalcitrance. Based on our results, we propose a model for how branches of confined hemicellulose interacted with cellulose to modulate stem strength support for the straight or bending phenotype in cut flowers.

Comparative transcriptome analysis of major lodging resistant factors in hulless barley

Hulless barley (Hordeum vulgare L. var. nudum Hook. f.), belonging to the genus Gramineae, has high and steady output and thus considered as a principal food crop by Tibetan people. Hulless barley grain can be used for food, brewing, and functional health product development, while its straw serves as an essential supplementary forage and is a crucial cereal crop. Lodging can reduce the yield and quality of barley grain and straw, and it hinders mechanical harvesting. It is a significant factor affecting high and stable yields of barley. Unlike other Poaceae plants (such as rice, wheat), hulless barley is mainly grown in high-altitude regions, where it is susceptible to low temperatures, strong winds, and heavy rainfall. As a result, its stem lodging resistance is relatively weak, making it prone to lodging during the growth period. In this study, we observed that the lignin concentration and the contents of lignin monomers (H, S, and G), and neutral detergent fibre of the lodging-resistant variety Kunlun14 were substantially greater than those of the lodging-sensitive variety Menyuanlianglan. We performed the weighted gene co-expression network analysis (WGCNA) and Short Time-series Expression Miner (STEM) analysis of both the lodging-resistant and lodging-sensitive varieties. Through transcriptome sequencing analysis at different developmental stages, combined with the previously annotated genes related to lodging resistance, a total of 72 DEGs were identified. Among these DEGs, 17 genes were related to lignin, cellulose, and hemicellulose synthesis or regulation, including five transcription factors about NAC, MYB and WRKY. Our results provide a basis for further exploring the molecular mechanism of stem lodging resistance in hulless barley and provide valuable gene resources for stem lodging resistance molecular breeding.

Transcriptome analysis reveals that PbMYB61 and PbMYB308 are involved in the regulation of lignin biosynthesis in pear fruit stone cells

Pear fruit stone cells have thick walls and are formed by the secondary deposition of lignin in the primary cell wall of thin-walled cells. Their content and size seriously affect fruit characteristics related to edibility. To reveal the regulatory mechanism underlying stone cell formation during pear fruit development and to identify hub genes, we examined the stone cell and lignin contents of 30 'Shannongsu' pear flesh samples and analyzed the transcriptomes of 15 pear flesh samples collected at five developmental stages. On the basis of the RNA-seq data, 35 874 differentially expressed genes were detected. Additionally, two stone cell-related modules were identified according to a WGCNA. A total of 42 lignin-related structural genes were subsequently obtained. Furthermore, nine hub structural genes were identified in the lignin regulatory network. We also identified PbMYB61 and PbMYB308 as candidate transcriptional regulators of stone cell formation after analyzing co-expression networks and phylogenetic relationships. Finally, we experimentally validated and characterized the candidate transcription factors and revealed that PbMYB61 regulates stone cell lignin formation by binding to the AC element in the PbLAC1 promoter to upregulate expression. However, PbMYB308 negatively regulates stone cell lignin synthesis by binding to PbMYB61 to form a dimer that cannot activate PbLAC1 expression. In this study, we explored the lignin synthesis-related functions of MYB family members. The results presented herein are useful for elucidating the complex mechanisms underlying lignin biosynthesis during pear fruit stone cell development.

Two R2R3-MYB transcription factors from Chinese cedar (Cryptomeria fortunei Hooibrenk) are involved in the regulation of secondary cell wall formation

As the most abundant renewable energy source, wood comprises the secondary cell wall (SCW). SCW biosynthesis involves lignin and cellulose deposition. Increasing studies have illustrated that R2R3-MYB transcription factors (TFs) play pivotal roles in affecting lignin accumulation and SCW formation. Nevertheless, the regulatory roles of R2R3-MYBs are still unresolved in Cryptomeria fortunei Hooibrenk cambium and wood formation. To dissect the potentials of CfMYBs, we successfully cloned and intensively studied the functions of CfMYB4 and CfMYB5 in SCW formation and abiotic stress response. They both contained the conserved MYB domain capable of forming a special structure that could bind to the core motifs of downstream genes. The phylogenetic tree implied that two CfMYBs clustered into different evolutionary branches. They were predominantly expressed in the stem and were localized to the nucleus. Furthermore, CfMYB4 functioned as an activator to enhance lignin and cellulose accumulation, and increase the SCW thickness by elevating the expression levels of SCW-related genes. By contrast, CfMYB5 negatively regulated lignin and cellulose biosynthesis, and decreased SCW formation by reducing the expression of SCW biosynthetic genes. Our data not only highlight the regulatory functions of CfMYBs in lignin deposition but also provide critical insights into the development of strategies for the genetic improvement of Cryptomeria fortunei wood biomass.

Comparison of two contrasting Leymus chinensis accessions reveals the roles of the cell wall and auxin in rhizome development

Leymus chinensis, a perennial native forage grass, is widely distributed in the steppes of Inner Mongolia as the dominant species. The main reproductive strategy of this grass is clonal propagation, which occurs via the proliferation of subterranean horizontal stems known as rhizomes. To elucidate the mechanism underlying rhizome development in this grass, we collected 60 accessions of L. chinensis and evaluated their rhizome development. One accession, which we named SR-74 (Strong Rhizomes), had significantly better rhizome development capacity than the accession WR-16 (Weak Rhizomes) in terms of rhizome number, total and primary rhizome length, and number of rhizome seedlings. Rhizome elongation was positively correlated with the number of internodes in the rhizome, which affected plant biomass. Compared to WR-16, SR-74 had higher rhizome tip hardness, higher abundance of transcripts participating in the biosynthesis of cell wall components, and higher levels of the metabolites L-phenylalanine, trans-cinnamic acid, 3-coumaric acid, ferulic acid, and coniferin. These metabolites in the phenylpropanoid biosynthesis pathway are precursors of lignin. In addition, SR-74 rhizomes contained higher amounts of auxin and auxin metabolites, including L-Trp, IPA, IBA, IAA and IAA-Asp, as well as upregulated expression of the auxin biosynthesis and signaling genes YUCCA6, YUCCA8, YUCCA10, YUCCA11, PIN1, PIN2, UGT1, UGT2, UGT4, UGT10, GH3, IAA7, IAA23, and IAA30. We propose a network between auxin signaling and the cell wall underlying rhizome development in L. chinensis.

Elucidating Biological Functions of 9-cis-Epoxycarotenoid Dioxygenase Genes Involved in Seed Dormancy in Paeonia lactiflora

Abscisic acid (ABA) is a major phytohormone affecting seed dormancy and germination in plants. ABA is synthesized mainly through the C40 carotenoid pathway. In the ABA biosynthesis pathway, 9-cis-epoxycarotenoid dioxygenase (NCED) is a key rate-limiting enzyme that regulates the accumulation and content of ABA. However, the role of the NCED gene in perennial plants with complex seed dormancy remains largely unknown. Here, we cloned two differentially expressed paralogs of herbaceous peony NCED genes, named PlNCED1 and PlNCED2, and further identified their involvement in seed dormancy from perennial herbaceous peony experiencing complex double seed dormancy. The deduced PlNCED amino acid sequences had high sequence homology with NCED sequences from other plants and contained the typical conserved RPE65 domain of the NCED family. Phylogenetic analysis showed that PlNCED1 and PlNCED2 have a close relationship with PoNCED in Paeonia ostii and VvNCED6 in Vitis vinifera, respectively. A subcellular localization assay demonstrated that the PlNCED1 protein resided within the nucleus, while the PlNCED2 protein was located in the cytoplasm, indicating their different roles in the biosynthesis of ABA. Furthermore, the content of endogenous ABA in transgenic calluses showed that PlNCEDs were positively correlated with ABA content. Both PlNCED transgenic Arabidopsis lines and the functional complementation of Arabidopsis NCED mutants found that PlNCEDs promoted seed dormancy and delayed seed germination. These results reveal that PlNCEDs participate in the seed dormancy of herbaceous peony by regulating the accumulation of endogenous ABA.