5mC DNA methylation modification-mediated regulation in tissue functional differentiation and important flavor substance synthesis of tea plant (Camellia sinensis L.)

Divergent MYB paralogs determine spatial distribution of linalool mediated by JA and DNA demethylation participating in aroma formation and cold tolerance of tea plants

Linalool not only is one of characteristic flavour volatiles of tea, contributing to floral aroma, but also a kind of defensive compounds, playing essential roles in resistance against biotic/abiotic stresses. Although the linalool synthases have been identified, much is unknown about the regulation mechanism in tea plants. We identified two pairs of MYB paralogs as linalool biosynthesis activators, in which one pair (CsMYB148/CsMYB193) specifically expressed in flowers, and another (CsMYB68/CsMYB147) highly expressed in flowers, leaves, fruits and roots. These activators interacted with CsMYC2 to form MYC2-MYB complexes to regulate linalool synthase. While Jasmonate ZIM-domain (JAZ) proteins served as the linalool biosynthesis repressors by interfering MYC2-MYB complex. Further, we found that the transcripts of CsMYB68/CsMYB147 were significantly upregulated by jasmonic acid (JA) to improve linalool products during tea processing and that linalool pathway may as one of the downstream pathways of JA signalling and DNA methylation processes to participate in cold resistance. Under cold stress, JA signalling was activated to elevate the abundance of MYC-MYB complexes; meanwhile, DNA demethylation was also activated, leading to declining methylation levels and increasing transcripts of CsMYB68/CsMYB147. Our study provides a new insight into synergistically improving tea quality and tea plant resistance.

5-Methylcytosine Methylation-Linked Hippo Pathway Molecular Interactions Regulate Lipid Metabolism

5-methylcytosine (5mC) is a common form of DNA methylation, essentially acting as an epigenetic modification that regulates gene expression by affecting the binding of transcription factors to DNA or by recruiting proteins that make it difficult to recognize and transcribe genes. 5mC methylation is present in eukaryotes in a variety of places, such as in CpG islands, within gene bodies, and in regions of repetitive sequences, whereas in prokaryotic organisms, it is mainly present in genomic DNA. The Hippo pathway is a highly conserved signal transduction pathway, which is extremely important in cell proliferation and death, controlling the size of tissues and organs and regulating cell differentiation, in addition to its important regulatory roles in lipid synthesis, transport, and catabolism. Lipid metabolism is an important part of various metabolic pathways in the human body, and problems in lipid metabolism are related to abnormalities in key enzymes, related proteins, epigenetic inheritance, and certain specific amino acids, which are the key factors affecting its proper regulation. In this article, we will introduce the molecular mechanisms of 5mC methylation and the Hippo signaling pathway, and the possibility of their co-regulation of lipid metabolism, with the aim of providing new ideas for further research and novel therapeutic modalities for lipid metabolism and a reference for the development and exploration of related research.

Z/E configuration controlled by a Taxus sesquiterpene synthase facilitating the biosynthesis of (3Z,6E)-α-farnesene

Plant enzymes often present advantages in the synthesis of natural products with specific configurations. Farnesene is a pharmacologically active sesquiterpene with three natural Z/E configurations, among which the enzyme selectively responsible for the biosynthesis of (3Z,6E)-α-farnesene remains elusive. Herein, a sesquiterpene synthase TwSTPS1 biosynthesizing (3Z,6E)-α-farnesene as the major product was identified from Taxus wallichiana through genome mining. Utilizing molecular dynamics simulations and mutation analysis, the catalytic mechanism of TwSTPS1, especially Z/E configuration control, was explored. Moreover, the crucial residues associated with the specific catalytic activity of TwSTPS1 was elucidated through mutagenesis experiments. The findings contribute to our understanding of the Z/E configuration control by plant terpene synthases and also provide an alternative tool for manipulating (3Z,6E)-α-farnesene production using synthetic biology.

Acetylation participation in theanine biosynthesis: Insights from transcriptomics, proteomics, and acetylomics

Acetylation, a crucial post-translational modification, regulates transcriptional activation, enzymatic activity, and protein interactions, playing vital roles in plant physiology and metabolism. However, the regulatory mechanism of acetylation in the biosynthesis of theanine remains unexplored. This study aims to elucidate the regulatory role of acetylation on the biosynthesis of theanine using transcriptomics, proteomics, and acetylomics in tea leaves from three tea plant cultivars with markedly different theanine content. Nineteen theanine biosynthesis-related genes were identified in the transcriptome, with ten showing significant correlation with theanine content. Proteomic analysis revealed elevated expression levels of proteins associated with the biosynthesis of theanine precursor glutamate in leaves with high theanine content, such as GOGAT and GDH. Unexpectedly, the expression level of TS was inversely correlated with the theanine content in leaves. Several highly expressed acetylated proteins and sites, such as TS, GS, and GOGAT, were found in the acetylome of leaves with high theanine content. Acetylation at lysine 304 (K304) of the TS protein may significantly contribute to the abundant accumulation of theanine in leaves. Our findings indicate that acetylation modification may play a pivotal role in theanine biosynthesis, thereby offering novel insights into the development of high-theanine tea plant germplasm resources.

The tea cultivar 'Chungui' with jasmine-like aroma: From genome and epigenome to quality

'Chungui' is a newly promoted tea cultivar in China, renowned for producing oolong tea with a distinctive jasmine-like aroma. However, the genetic basis of this unique aroma remains unclear. In this study, the 'Chungui' genome, one of the most complete and well-annotated tea genomes, was assembled using PacBio HiFi reads and Hi-C sequencing. Through comparative analysis with typical jasmine flower volatiles, eight core compounds responsible for this aroma were identified. Further research revealed that the jasmine-like aroma in 'Chungui' is regulated by a coordinated mechanism involving a significant increase in chromatin accessibility and the demethylation of CHH and CHG in the promoter regions of key aroma-related genes during oolong tea processing. The study proposes that the formation of this unique aroma is driven by the synergistic effect of enhanced chromatin accessibility and reduced methylation, which together lead to the robust upregulation of genes involved in the biosynthesis of these core aroma components. These results provide a molecular foundation for understanding the unique jasmine-like aroma of 'Chungui' tea and sets the stage for future studies to explore the roles of these regulatory mechanisms in aroma formation.

Impact of Mild Field Drought on the Aroma Profile and Metabolic Pathways of Fresh Tea (Camellia sinensis) Leaves Using HS-GC-IMS and HS-SPME-GC-MS

Aroma plays a pivotal role in defining tea quality and distinctiveness, and tea producers have often observed that specific drought conditions are closely associated with the formation and accumulation of characteristic aroma compounds in tea leaves. However, there is still limited understanding of the differential strategies employed by various tea cultivars in response to drought stress for the accumulation of key volatile aroma compounds in fresh tea leaves, as well as the associated metabolic pathways involved in aroma formation. In this study, two widely cultivated tea cultivars in China, Fuding Dabai (FD) and Wuniuzao (WNZ), were examined to assess the impact of mild field drought stress on the composition and accumulation of key volatile aroma compounds in fresh leaves using headspace gas chromatography-ion mobility spectrometry (HS-GC-IMS) and headspace solid phase micro-extraction gas chromatography-mass spectrometry (HS-SPME-GC-MS) technologies. Results revealed that drought stress led to a substantial increase in the diversity of volatile compounds (VOCs) in FD, while WNZ exhibited a notable rise in low-threshold VOC concentrations, amplifying sweet, floral, fruity, and earthy aroma profiles in post-drought fresh leaves. Through partial least squares discriminant analysis (PLS-DA) of HS-GC-IMS and HS-SPME-GC-MS data, integrating variable importance projection (VIP) scores and odor activity values (OAVs) above 1, 9, and 13, key odor-active compounds were identified as potential markers distinguishing the drought responses in the two cultivars. These compounds serve as crucial indicators of the aromatic profile shifts induced by drought, providing insights into the differential metabolic strategies of the cultivars. Additionally, KEGG enrichment analysis revealed 12 metabolic pathways, such as terpenoid biosynthesis, fatty acid synthesis, cutin, suberine, and wax biosynthesis, and phenylalanine metabolism, which may play crucial roles in the formation and accumulation of VOCs in tea leaves under drought stress. These findings provide a comprehensive framework for understanding the cultivar-specific mechanisms of aroma formation and accumulation in tea leaves under mild drought conditions.

Root-specific theanine metabolism and regulation at the single-cell level in tea plants (Camellia sinensis)

Root-synthesized secondary metabolites are critical quality-conferring compounds of foods, plant-derived medicines, and beverages. However, information at a single-cell level on root-specific secondary metabolism remains largely unexplored. L-Theanine, an important quality component of tea, is primarily synthesized in roots, from which it is then transported to new shoots of tea plant. In this study, we present a single-cell RNA sequencing (scRNA-seq)-derived map for the tea plant root, which enabled cell-type-specific analysis of glutamate and ethylamine (two precursors of theanine biosynthesis) metabolism, and theanine biosynthesis, storage, and transport. Our findings support a model in which the theanine biosynthesis pathway occurs via multicellular compartmentation and does not require high co-expression levels of transcription factors and their target genes within the same cell cluster. This study provides novel insights into theanine metabolism and regulation, at the single-cell level, and offers an example for studying root-specific secondary metabolism in other plant systems.

Genome-wide epigenetic dynamics of tea leaves under mechanical wounding stress during oolong tea postharvest processing

Understanding the epigenetic responses to mechanical wounding stress during the postharvest processing of oolong tea provides insight into the reprogramming of the tea genome and its impact on tea quality. Here, we characterized the 5mC DNA methylation and chromatin accessibility landscapes of tea leaves subjected to mechanical wounding stress during the postharvest processing of oolong tea. Analysis of the differentially methylated regions and preferentially accessible promoters revealed many overrepresented TF-binding motifs, highlighting sets of TFs that are likely important for the quality of oolong tea. Within these sets, we constructed a chromatin accessibility-mediated gene regulatory network specific to mechanical wounding stress. In combination with the results of the TF-centred yeast one-hybrid assay, we identified potential binding sites of CsMYC2 and constructed a gene regulatory network centred on CsMYC2, clarifying the potential regulatory role of CsMYC2 in the postharvest processing of oolong tea. Interestingly, highly accessible chromatin and hypomethylated cytosine were found to coexist in the promoter region of the indole biosynthesis gene (tryptophan synthase β-subunit, CsTSB) under wounding stress, which indicates that these two important epigenetic regulatory mechanisms are jointly involved in regulating the synthesis of indole during the postharvest processing of oolong tea. These findings improve our understanding of the epigenetic regulatory mechanisms involved in quality formation during the postharvest processing of oolong tea.

The complex transcriptional regulation of heat stress response in maize

As one of the most important food and feed crops worldwide, maize suffers much more tremendous damages under heat stress compared to other plants, which seriously inhibits plant growth and reduces productivity. To mitigate the heat-induced damages and adapt to high temperature environment, plants have evolved a series of molecular mechanisms to sense, respond and adapt high temperatures and heat stress. In this review, we summarized recent advances in molecular regulations underlying high temperature sensing, heat stress response and memory in maize, especially focusing on several important pathways and signals in high temperature sensing, and the complex transcriptional regulation of ZmHSFs (Heat Shock Factors) in heat stress response. In addition, we highlighted interactions between ZmHSFs and several epigenetic regulation factors in coordinately regulating heat stress response and memory. Finally, we laid out strategies to systematically elucidate the regulatory network of maize heat stress response, and discussed approaches for breeding future heat-tolerance maize.

Integrated VIS/NIR Spectrum and Genome-Wide Association Study for Genetic Dissection of Cellulose Crystallinity in Wheat Stems

Cellulose crystallinity is a crucial factor influencing stem strength and, consequently, wheat lodging. However, the genetic dissection of cellulose crystallinity is less reported due to the difficulty of its measurement. In this study, VIS/NIR spectra and cellulose crystallinity were measured for a wheat accession panel with diverse genetic backgrounds. We developed a reliable VIS/NIR model for cellulose crystallinity with a high determination coefficient (R2) (0.95) and residual prediction deviation (RPD) (4.04), enabling the rapid screening of wheat samples. A GWAS of the cellulose crystallinity in 326 wheat accessions revealed 14 significant SNPs and 13 QTLs. Two candidate genes, TraesCS4B03G0029800 and TraesCS5B03G1085500, were identified. In summary, this study establishes an efficient method for the measurement of cellulose crystallinity in wheat stems and provides a genetic basis for enhancing lodging resistance in wheat.

Dynamic DNA Methylation Regulates Season-Dependent Secondary Metabolism in the New Shoots of Tea Plants

Plant secondary metabolites are critical quality-conferring compositions of plant-derived beverages, medicines, and industrial materials. The accumulations of secondary metabolites are highly variable among seasons; however, the underlying regulatory mechanism remains unclear, especially in epigenetic regulation. Here, we used tea plants to explore an important epigenetic mark DNA methylation (5mC)-mediated regulation of plant secondary metabolism in different seasons. Multiple omics analyses were performed on spring and summer new shoots. The results showed that flavonoids and theanine metabolism dominated in the metabolic response to seasons in the new shoots. In summer new shoots, the genes encoding DNA methyltransferases and demethylases were up-regulated, and the global CG and CHG methylation reduced and CHH methylation increased. 5mC methylation in promoter and gene body regions influenced the seasonal response of gene expression; the amplitude of 5mC methylation was highly correlated with that of gene transcriptions. These differentially methylated genes included those encoding enzymes and transcription factors which play important roles in flavonoid and theanine metabolic pathways. The regulatory role of 5mC methylation was further verified by applying a DNA methylation inhibitor. These findings highlight that dynamic DNA methylation plays an important role in seasonal-dependent secondary metabolism and provide new insights for improving tea quality.

Chromatin accessibility mediated transcriptome changes contribute to flavor substance alterations and jasmonic acid hyperaccumulation during oolong tea withering process

During the oolong tea withering process, abiotic stresses induce significant changes in the content of various flavor substances and jasmonic acid (JA). However, the changes in chromatin accessibility during withering and their potential impact remain poorly understood. By integrating ATAC-seq, RNA-seq, metabolite, and hormone assays, we characterized the withering treatment-induced changes in chromatin accessibility, gene expression levels, important metabolite contents, and JA and JA-ILE contents. Additionally, we analyzed the effects of chromatin accessibility alterations on gene expression changes, content changes of important flavor substances, and JA hyperaccumulation. Our analysis identified a total of 3451 open- and 13 426 close-differentially accessible chromatin regions (DACRs) under withering treatment. Our findings indicate that close-DACRs-mediated down-regulated differentially expressed genes (DEGs) resulted in the reduced accumulation of multiple catechins during withering, whereas open-DACRs-mediated up-regulated DEGs contributed to the increased accumulation of important terpenoids, JA, JA-ILE and short-chain C5/C6 volatiles. We further highlighted important DACRs-mediated DEGs associated with the synthesis of catechins, terpenoids, JA and JA and short-chain C5/C6 volatiles and confirmed the broad effect of close-DACRs on catechin synthesis involving almost all enzymes in the pathway during withering. Importantly, we identified a novel MYB transcription factor (CsMYB83) regulating catechin synthesis and verified the binding of CsMYB83 in the promoter-DACRs regions of key catechin synthesis genes using DAP-seq. Overall, our results not only revealed a landscape of chromatin alters-mediated transcription, flavor substance and hormone changes under oolong tea withering, but also provided target genes for flavor improvement breeding in tea plant.

Multiomics Analysis Reveals the Genetic Basis of Volatile Terpenoid Formation in Oolong Tea

Oolong tea has gained great popularity in China due to its pleasant floral and fruity aromas. Although numerous studies have investigated the aroma differences across various tea cultivars, the genetic mechanism is unclear. This study performed multiomics analysis of three varieties suitable for oolong tea and three others with different processing suitability. Our analysis revealed that oolong tea varieties contained higher levels of cadinane sesquiterpenoids. PanTFBS was developed to identify variants of transcription factor binding sites (TFBSs). We found that the CsDCS gene had two TFBS variants in the promoter sequence and a single nucleotide polymorphism (SNP) in the coding sequence. Integrating data on genetic variations, gene expression, and protein-binding sites indicated that CsDCS might be a pivotal gene involved in the biosynthesis of cadinane sesquiterpenoids. These findings advance our understanding of the genetic factors involved in the aroma formation of oolong tea and offer insights into the enhancement of tea aroma.