Characterization of a Citrus R2R3-MYB Transcription Factor that Regulates the Flavonol and Hydroxycinnamic Acid Biosynthesis

A R2R3-MYB transcription factor LmMYB111 positively regulates chlorogenic acid and luteoloside biosynthesis in Lonicera macranthoides

Lonicera macranthoides is a vital medicinal herb frequently used in Chinese traditional medicine. Chlorogenic acid (CGA) and luteoloside are the most crucial bioactive pharmaceutical ingredients in L. macranthoides. Although CGA and luteoloside biosynthetic pathway and structural genes appeared to be extensively elucidated, the transcriptional regulation has yet to be unveiled. Here, integration of transcriptome and metabolome revealed a R2R3-MYB transcription factor LmMYB111 positively correlated with CGA concentration, which shares close homology with AtMYB111 and acts as a transcriptional activator. Overexpressing LmMYB111 in tobacco and Lonicera resulted in enhanced production of CGA and luteoloside. RNA-Seq demonstrated that overexpression of LmMYB111 dramatically upregulated CGA and luteoloside biosynthetic genes, including 10 PALs, 3 C4Hs, 7 4CLs, 4 HCT/HQTs, 3 CHSs and 5 CHIs. DNA Affinity Purification sequencing (DAP-Seq) revealed the binding motifs of LmMYB111 and 1135 downstream targets, including structural genes e.g. PAL1/PAL4s, C4H, 4CL2, CHI, and DFR as well as several transcription factors (TFs), e.g. MYB3/MYB4, bHLH62/TT8, BEL1, SCL15/SCL32 and ERF3.The electrophoretic mobility shift assay (EMSA) together with dual-luciferase reporter system (DLR) further proved that LmMYB111 bound to and activated proLmMYB4, proLmPAL1, proLm4CL2, proLmCHI and proLmDFR, therefore facilitating hyperaccumulation of CGA, luteoloside and other phenolics. These findings shed light on the participation of LmMYB111 in CGA and luteoloside biosynthetic regulatory networks in L. macranthoides mediated by controlling the expression of structural genes and TFs, which will contribute to elevate phenolics production by genetic engineering.

Copper Sulfate Elicitation Effect on Biomass Production, Phenolic Compounds Accumulation, and Antioxidant Activity of Morus nigra L. Stem Node Culture

Phenolic compounds are strong antioxidant and antibacterial agents with great pharmacological, medicinal, nutritional, and industrial value. The potential of Morus nigra in stem node culture was investigated for the production of phenolic compounds and their elicitation with CuSO4. Individual phenolic compounds in the samples were identified and quantified by using HPLC-PDA and HPLC-MS methods, while the content of total phenolic compounds, the content of total flavonoids, and the antioxidant activity of methanolic extracts were evaluated spectrophotometrically. The highest fresh and dry weights were obtained in plantlets treated with 0.5 mM CuSO4 for 42 days. The highest total phenolic content, total flavonoid content, and antioxidant activity of the extracts were determined in stem node cultures treated with 3 mM CuSO4 for 42 days. Under the latter conditions, the predominant representatives of the caffeoylquinic acids, p-coumaric acid derivatives, kaempferol derivatives, and quercetin derivatives also achieved the highest content. The most abundant phenolic compound in all samples was the chlorogenic acid. The nodal culture of M. nigra elicited with CuSO4 could potentially be used for the industrial production of phenolic compounds, especially caffeoylquinic acids. Moreover, considering the biochemical response to CuSO4 treatment and the ability to tolerate and accumulate copper, the potential application of M. nigra in phytoremediation is also highlighted.

MYB proteins: Versatile regulators of plant development, stress responses, and secondary metabolite biosynthetic pathways

MYB proteins are ubiquitous in nature, regulating key aspects of plant growth and development. Although MYB proteins are known for regulating genes involved in secondary metabolite biosynthesis, particularly phenylpropanoids, their roles in terpenoid, glucosinolate, and alkaloid biosynthesis remain less understood. This review explores the structural and functional differences between activator and repressor MYB proteins along with their roles in plant growth, development, stress responses, and secondary metabolite production. MYB proteins serve as central hubs in protein-protein interaction networks that regulate expression of numerous genes involved in the adaptation of plants to varying environmental conditions. Thus, we also highlight key interacting partners of MYB proteins and their roles in these adaptation mechanisms. We further discuss the mechanisms regulating MYB proteins, including autoregulation, epigenetics, and post-transcriptional and post-translational modifications. Overall, we propose MYB proteins as versatile regulators for improving plant traits, stress responses, and secondary metabolite production.

A novel transcription factor CsSNACA2 plays a pivotal role within nitrogen assimilation in tea plants

Tea (Camellia sinensis) is a globally renowned economic crop, with organs such as leaves and buds utilized for consumption. As a perennial foliage crop, tea plants have high-nitrogen consumption and demand but exhibit relatively low nitrogen use efficiency. Exploring the genetic factors involved in nitrogen assimilation in tea plants could lead to improvements in both tea yield and quality. Here, we first conducted transcriptome sequencing on two tissues (roots and young leaves) under two different nitrate levels (0.2 and 2.5 mm KNO3) and at six time points (0, 15, and 45 min; 2 and 6 h and 2 days). Differential gene expression patterns were observed for several genes that exhibited altered expression at 2 h. Clustering and enrichment analyses, along with co-expression network construction, provided evidence for the crucial involvement of CsSNACA2 in nitrogen assimilation. CsSNACA2 overexpression elicited pronounced phenotypic changes in nitrogen-deficient plants. Furthermore, CsSNACA2 suppressed the expression of CsNR (encoding nitrate reductase) and CsCLCa (encoding aNO 3 - /H+ exchanger). Moreover, CsSNACA2 served as a downstream target of CsSPL6.1. In addition, we characterized Csi-miR156e and Csi-miR156k, which directly cleave CsSPL6.1. This study identified a transcription factor module participating in nitrogen assimilation in tea plants, providing a genetic foundation for future innovations in tea cultivar improvement. These results broaden our understanding of the genetic mechanisms governing nitrogen assimilation in dicotyledonous plants.

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.

Glycyrrhiza, a commonly used medicinal herb: Review of species classification, pharmacology, active ingredient biosynthesis, and synthetic biology

BACKGROUND

Licorice is extensively and globally utilized as a medicinal herb and is one of the traditional Chinese herbal medicines with valuable pharmacological effects. Its therapeutic components primarily reside within its roots and rhizomes, classifying it as a tonifying herb. As more active ingredients in licorice are unearthed and characterized, licorice germplasm resources are gaining more and more recognition. However, due to the excessive exploitation of wild licorice resources, the degrading germplasm reserves fail to meet the requirements of chemical extraction and clinical application.

AIM OF REVIEW

This article presents a comprehensive review of the classification and phylogenetic relationships of species in genus Glycyrrhiza, types of active components and their pharmacological activities, licorice omics, biosynthetic pathways of active compounds in licorice, and metabolic engineering. It aims to offer a unique and comprehensive perspective on Glycyrrhiza, integrating knowledge from diverse fields to offer a comprehensive understanding of this genus. It will serve as a valuable resource and provide a solid foundation for future research and development in the molecular breeding and synthetic biology fields of Glycyrrhiza.

KEY SCIENTIFIC CONCEPTS OF REVIEW

Licorice has an abundance of active constituents, primarily triterpenoids, flavonoids, and polysaccharides. Modern pharmacological research unveiled its multifaceted effects encompassing anti-inflammatory, analgesic, anticancer, antiviral, antioxidant, and hepatoprotective activities. Many resources of Glycyrrhiza species remain largely untapped, and multiomic studies of the Glycyrrhiza lineage are expected to facilitate new discoveries in the fields of medicine and human health. Therefore, strategies for breeding high-yield licorice plants and developing effective biosynthesis methods for bioactive compounds will provide valuable insights into resource conservation and drug development. Metabolic engineering and microorganism-based green production provide alternative strategies to improve the production efficiency of natural products.

Duplication and sub-functionalization of flavonoid biosynthesis genes plays important role in Leguminosae root nodule symbiosis evolution

Gene innovation plays an essential role in trait evolution. Rhizobial symbioses, the most important N2-fixing agent in agricultural systems that exists mainly in Leguminosae, is one of the most attractive evolution events. However, the gene innovations underlying Leguminosae root nodule symbiosis (RNS) remain largely unknown. Here, we investigated the gene gain event in Leguminosae RNS evolution through comprehensive phylogenomic analyses. We revealed that Leguminosae-gain genes were acquired by gene duplication and underwent a strong purifying selection. Kyoto Encyclopedia of Genes and Genomes analyses showed that the innovated genes were enriched in flavonoid biosynthesis pathways, particular downstream of chalcone synthase (CHS). Among them, Leguminosae-gain type Ⅱ chalcone isomerase (CHI) could be further divided into CHI1A and CHI1B clades, which resulted from the products of tandem duplication. Furthermore, the duplicated CHI genes exhibited exon-intron structural divergences evolved through exon/intron gain/loss and insertion/deletion. Knocking down CHI1B significantly reduced nodulation in Glycine max (soybean) and Medicago truncatula; whereas, knocking down its duplication gene CHI1A had no effect on nodulation. Therefore, Leguminosae-gain type Ⅱ CHI participated in RNS and the duplicated CHI1A and CHI1B genes exhibited RNS functional divergence. This study provides functional insights into Leguminosae-gain genetic innovation and sub-functionalization after gene duplication that contribute to the evolution and adaptation of RNS in Leguminosae.

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.

Metabolomic and transcriptomic analysis of flavonoids biosynthesis mechanisms in mulberry fruit (Hongguo 2) under exogenous hormone treatments

The mulberry fruit is prized for its superior nutrition value and abundant color due to its high flavone content. To enhance comprehension of flavone biogenesis induced by external hormones, we sprayed exogenous ethylene (ETH), indoleacetic acid (IAA) and spermine (SPM) on mulberry fruit (Hongguo 2) during its color-changed period. The levels of anthocyanin, titratable acid, soluble sugar and endogenous hormones were determined after hormone treatment, integrated transcriptome and metabolome analysis were performed for mechanism exploration. Our results indicated that exogenous ETH, SPM, and IAA play important roles in mulberry ripening, including acid reduction, sugar increase and flavonoid synthesis.

R2R3-MYB transcription factor CsMYB60 controls mature fruit skin color by regulating flavonoid accumulation in cucumber

Skin color is an important trait that determines the cosmetic appearance and quality of fruits. In cucumber, the skin color ranges from white to brown in mature fruits. However, the genetic basis for this important trait remains unclear. We conducted a genome-wide association study of natural cucumber populations, along with map-based cloning techniques, on an F2 population resulting from a cross between Pepino (with yellow-brown fruit skin) and Zaoer-N (with creamy fruit skin). We identified CsMYB60 as a candidate gene responsible for skin coloration in mature cucumber fruits. In cucumber accessions with white to pale yellow skin color, a premature stop mutation (C to T) was found in the second exon region of CsMYB60, whereas light yellow cucumber accessions exhibited splicing premature termination caused by an intronic mutator-like element insertion in CsMYB60. Transgenic CsMYB60c cucumber plants displayed a yellow-brown skin color by promoting accumulation of flavonoids, especially hyperoside, a yellow-colored flavonol. CsMYB60c encodes a nuclear protein that primarily acts as a transcriptional activator through its C-terminal activation motif. RNA sequencing and DNA affinity purification sequencing assays revealed that CsMYB60c promotes skin coloration by directly binding to the YYTACCTAMYT motif in the promoter regions of flavonoid biosynthetic genes, including CsF3'H, which encodes flavonoid 3'-hydroxylase. The findings of our study not only offer insight into the function of CsMYB60 as dominantly controlling fruit coloration, but also highlight that intronic DNA mutations can have a similar phenotypic impact as exonic mutations, which may be valuable in future cucumber breeding programs.

EpMYB2 positively regulates chicoric acid biosynthesis by activating both primary and specialized metabolic genes in purple coneflower

Chicoric acid is the major active ingredient of the world-popular medicinal plant purple coneflower (Echinacea purpurea (L.) Menoch). It is recognized as the quality index of commercial hot-selling Echinacea products. While the biosynthetic pathway of chicoric acid in purple coneflower has been elucidated recently, its regulatory network remains elusive. Through co-expression and phylogenetic analysis, we found EpMYB2, a typical R2R3-type MYB transcription factor (TF) responsive to methyl jasmonate (MeJA) simulation, is a positive regulator of chicoric acid biosynthesis. In addition to directly regulating chicoric acid biosynthetic genes, EpMYB2 positively regulates genes of the upstream shikimate pathway. We also found that EpMYC2 could activate the expression of EpMYB2 by binding to its G-box site, and the EpMYC2-EpMYB2 module is involved in the MeJA-induced chicoric acid biosynthesis. Overall, we identified an MYB TF that positively regulates the biosynthesis of chicoric acid by activating both primary and specialized metabolic genes. EpMYB2 links the gap between the JA signaling pathway and chicoric acid biosynthesis. This work opens a new direction toward engineering purple coneflower with higher medicinal qualities.

A functional study reveals CsNAC086 regulated the biosynthesis of flavonols in Camellia sinensis

MAIN CONCLUSION

CsNAC086 was found to promote the expression of CsFLS, thus promoting the accumulation of flavonols in Camellia sinensis. Flavonols, the main flavonoids in tea plants, play an important role in the taste and quality of tea. In this study, a NAC TF gene CsNAC086 was isolated from tea plants and confirmed its regulatory role in the expression of flavonol synthase which is a key gene involved in the biosynthesis of flavonols in tea plant. Yeast transcription-activity assays showed that CsNAC086 has self-activation activity. The transcriptional activator domain of CsNAC086 is located in the non-conserved C-terminal region (positions 171-550), while the conserved NAC domain (positions 1-170) does not have self-activation activity. Silencing the CsNAC086 gene using antisense oligonucleotides significantly decreased the expression of CsFLS. As a result, the concentration of flavonols decreased significantly. In overexpressing CsNAC086 tobacco leaves, the expression of NtFLS was significantly increased. Compared with wild-type tobacco, the flavonols concentration increased. Yeast one-hybrid assays showed CsNAC086 did not directly regulate the gene expression of CsFLS. These findings indicate that CsNAC086 plays a role in regulating flavonols biosynthesis in tea plants, which has important implications for selecting and breeding of high-flavonols-concentration containing tea-plant cultivars.

Transcriptional regulation of flavonol biosynthesis in plants

Flavonols are a class of flavonoids that play a crucial role in regulating plant growth and promoting stress resistance. They are also important dietary components in horticultural crops due to their benefits for human health. In past decades, research on the transcriptional regulation of flavonol biosynthesis in plants has increased rapidly. This review summarizes recent progress in flavonol-specific transcriptional regulation in plants, encompassing characterization of different categories of transcription factors (TFs) and microRNAs as well as elucidation of different transcriptional mechanisms, including direct and cascade transcriptional regulation. Direct transcriptional regulation involves TFs, such as MYB, AP2/ERF, and WRKY, which can directly target the key flavonol synthase gene or other early genes in flavonoid biosynthesis. In addition, different regulation modules in cascade transcriptional regulation involve microRNAs targeting TFs, regulation between activators, interaction between activators and repressors, and degradation of activators or repressors induced by UV-B light or plant hormones. Such sophisticated regulation of the flavonol biosynthetic pathway in response to UV-B radiation or hormones may allow plants to fine-tune flavonol homeostasis, thereby balancing plant growth and stress responses in a timely manner. Based on orchestrated regulation, molecular design strategies will be applied to breed horticultural crops with excellent health-promoting effects and high resistance.

Integration of metabolomics and transcriptomics reveals the regulation mechanism of the phenylpropanoid biosynthesis pathway in insect resistance traits in Solanum habrochaites

Solanum habrochaites (SH), a wild species closely related to 'Ailsa Craig' (AC), is an important germplasm resource for modern tomato breeding. Trichomes, developed from epidermal cells, have a role in defense against insect attack, and their secretions are of non-negligible value. Here, we found that the glandular heads of type VI trichomes were clearly distinguishable between AC and SH under cryo-scanning electron microscopy, the difference indicating that SH could secrete more anti-insect metabolites than AC. Pest preference experiments showed that aphids and mites preferred to feed near AC compared with SH. Integration analysis of transcriptomics and metabolomics data revealed that the phenylpropanoid biosynthesis pathway was an important secondary metabolic pathway in plants, and SH secreted larger amounts of phenylpropanoids and flavonoids than AC by upregulating the expression of relevant genes in this pathway, and this may contribute to the greater resistance of SH to phytophagous insects. Notably, virus-induced silencing of Sl4CLL6 not only decreased the expression of genes downstream of the phenylpropanoid biosynthesis pathway (SlHCT, SlCAD, and SlCHI), but also reduced resistance to mites in tomato. These findings provided new genetic resources for the synthesis of phenylpropanoid compounds and anti-insect breeding in S. habrochaites and a new theoretical basis for the improvement of important traits in cultivated tomato.

Genome-wide identification of the Pyrus R2R3-MYB gene family and PhMYB62 regulation analysis in Pyrus hopeiensis flowers at low temperature

The R2R3-MYB gene family play an important role in plant growth, development and stress responses. In this study, a total of 122 PcoR2R3-MYB genes were identified and grouped into 26 clades in pear. And these PcoMYBs were unevenly distributed among 17 chromosomes. The sequence characteristics, conversed motifs, exon/intron structures, classification, duplication events and cis-acting elements were also investigated. The gene duplication events showed that segmental duplication may play key roles in expansion of the PcoMYB gene family. Pyrus hopeiensis, which is a valuable wild resource, has strong cold resistance. An integrative analyses of miRNA and mRNA showed that PhMYB62 was involved in regulating low-temperature stress in P. hopeiensis flower organs. Subcellular localization analysis showed that PhMYB62 protein was specifically localized to the nucleus. The result of DAP-seq showed that PhMYB62 responded to low-temperature stress in P. hopeiensis by regulating TFs, which were associated with plant stress resistance, and POD, GAUT12, AUX28 and CHS genes. Subsequently, yeast one-hybrid verified that PhMYB62 could bind and activate the promoter of POD gene. The current study would provide a comprehensive information for further functional research on the stress-responsive R2R3-MYB gene candidates in pear, and may help to identify the genes associated with cold resistance for the cultivation of cold-resistant pear varieties.

A metabolomics study in citrus provides insight into bioactive phenylpropanoid metabolism

Citrus fruits are widely consumed worldwide in juices or as fresh and provide a broad range of phytonutrients that are important for human health. Here, a citrus multi-omics resource is presented: comprehensive metabolic profiling of various citrus species was performed and metabolic profiles were compared among species, with a focus on the phenylpropanoid metabolic pathway. A metabolite-based genome-wide association analysis (mGWAS) of 154 pummelo accessions was performed using factored spectrally transformed linear mixed models (FaST-LMM) and efficient mixed-model association eXpedited (EMMAX), and the genetic and biochemical basis of metabolomic variation was comprehensively analysed. A metabolite-single nucleotide polymorphism-gene (metabolite-SNP-gene) interaction network was constructed for pummelo, and many candidate loci controlling the synthesis and regulation of bioactive compounds were identified; among these loci, three BAHD malonyltransferases were involved in the malonylation of flavonoid glycosides. Further investigation revealed that an R2R3-MYB transcription factor CgMYB1 positively controls the metabolism of phenylpropanoid molecules, particularly the flavonoid derivatives. This study provides valuable data resources on the metabolic regulatory networks of bioactive components in citrus, in addition to demonstrating an efficient method for metabolic pathway dissection and providing targets for future breeding work with the aim of improving nutritional value.

Ethylene inhibits ABA-induced stomatal closure via regulating NtMYB184-mediated flavonol biosynthesis in tobacco

Stomatal movement can be regulated by ABA signaling through synthesis of reactive oxygen species (ROS) in guard cells. By contrast, ethylene triggers the biosynthesis of antioxidant flavonols to suppress ROS accumulation and prevent ABA-induced stomatal closure; however, the underlying mechanism remains largely unknown. In this study, we isolated and characterized the tobacco (Nicotiana tabacum) R2R3-MYB transcription factor NtMYB184, which belongs to the flavonol-specific SG7 subgroup. RNAi suppression and CRISPR/Cas9 mutation (myb184) of NtMYB184 in tobacco caused down-regulation of flavonol biosynthetic genes and decreased the concentration of flavonols in the leaves. Yeast one-hybrid assays, transactivation assays, EMSAs, and ChIP-qPCR demonstrated that NtMYB184 specifically binds to the promoters of flavonol biosynthetic genes via MYBPLANT motifs. NtMYB184 regulated flavonol biosynthesis in guard cells to modulate ROS homeostasis and stomatal aperture. ABA-induced ROS production was accompanied by the suppression of NtMYB184 and flavonol biosynthesis, which may accelerate ABA-induced stomatal closure. Furthermore, ethylene stimulated NtMYB184 expression and flavonol biosynthesis to suppress ROS accumulation and curb ABA-induced stomatal closure. In myb184, however, neither the flavonol and ROS concentrations nor the stomatal aperture varied between the ABA and ABA+ethylene treatments, indicating that NtMYB184 was indispensable for the antagonism between ethylene and ABA via regulating flavonol and ROS concentrations in the guard cells.

Transcription factor CsTT8 promotes fruit coloration by positively regulating the methylerythritol 4-phosphate pathway and carotenoid biosynthesis pathway in citrus (Citrus spp.)

Carotenoids directly influence citrus fruit color and nutritional value, which is critical to consumer acceptance. Elucidating the potential molecular mechanism underlying carotenoid metabolism is of great importance for improving fruit quality. Despite the well-established carotenoid biosynthetic pathways, the molecular regulatory mechanism underlying carotenoid metabolism remains poorly understood. Our previous studies have reported that the Myc-type basic helix-loop-helix (bHLH) transcription factor (TF) regulates citrus proanthocyanidin biosynthesis. Transgenic analyses further showed that overexpression of CsTT8 could significantly promote carotenoid accumulation in transgenic citrus calli, but its regulatory mechanism is still unclear. In the present study, we found that overexpression of CsTT8 enhances carotenoid content in citrus fruit and calli by increasing the expression of CsDXR, CsHDS, CsHDR, CsPDS, CsLCYE, CsZEP, and CsNCED2, which was accompanied by changes in the contents of abscisic acid and gibberellin. The in vitro and in vivo assays indicated that CsTT8 directly bound to the promoters of CsDXR, CsHDS, and CsHDR, the key metabolic enzymes of the methylerythritol 4-phosphate (MEP) pathway, thus providing precursors for carotenoid biosynthesis and transcriptionally activating the expression of these three genes. In addition, CsTT8 activated the promoters of four key carotenoid biosynthesis pathway genes, CsPDS, CsLCYE, CsZEP, and CsNCED2, directly promoting carotenoid biosynthesis. This study reveals a novel network of carotenoid metabolism regulated by CsTT8. Our findings will contribute to manipulating carotenoid metabolic engineering to improve the quality of citrus fruit and other crops.

Transcription factor VvWRKY70 inhibits both norisoprenoid and flavonol biosynthesis in grape

Norisoprenoids and flavonols are important secondary metabolites in grape berries (Vitis vinifera L.). The former is a class of ubiquitous flavor and fragrance compounds produced by the cleavage of carotenoids, and the latter, which is derived from the flavonoid metabolic pathway, has been proposed as a general quality marker for red grapes. However, the transcriptional regulatory mechanisms underlying norisoprenoid and flavonol production are still not fully understood. In this study, we characterized a transcription factor, VvWRKY70, as a repressor of both norisoprenoid and flavonol biosynthesis in grape berries, and its expression was downregulated by light and high-temperature treatment. Overexpressing VvWRKY70 in grape calli reduced norisoprenoid and flavonol production, particularly under light exposure or at high temperature, by repressing the expression of several related genes in the isoprenoid and flavonoid metabolic pathways. VvWRKY70 downregulated β-CAROTENE HYDROXYLASE 2 (VvBCH2) and CHALCONE SYNTHASE 3 (VvCHS3) expression based on yeast 1-hybrid analysis combined with electrophoretic mobility shift assay and chromatin immunoprecipitation-quantitative PCR. We discuss the role of VvWRKY70 in the coordinated regulatory network of isoprenoid and flavonoid metabolism. These findings provide a theoretical basis to improve flavor, color, and other comprehensive qualities of fruit crops and their processing products.

Hetero-grafting affects flavonoid biosynthesis in sweet orange 'Newhall' (Citrus sinensis) peels: a metabolomics and transcriptomics analysis

Citrus cultivation involves the widespread practice of grafting, which has a significant impact on citrus development and fruit quality and yield. However, understanding the effect of flavonoid compounds after different rootstock grafting have been limited. Flavonoid compounds, found at the highest levels in citrus peels, contribute to improving fruit quality and nutritional value. In this study, scion-rootstock interaction was investigated at various developmental stages when sweet orange 'Newhall' was hetero-grafted with two commonly used rootstocks (Poncirus trifoliate population, C. junos Siebold ex Tanaka). Physiological index detection showed a higher concentration of total flavonoid content in peels of sweet orange 'Newhall' grafted on Poncirus trifoliate population (ct) than C. junos Siebold ex Tanaka (cj). Further metabolomic analysis identified 703 flavonoid compounds, including flavones, flavonols, and flavanones. Out of the 25 flavonoids affected by different rootstock grafting and developmental stages, most were flavones. Transcriptomic analysis identified 8,562 differentially expressed genes (DEGs). Co-expression and Pearson's correlation analysis discovered six hub structure genes and 19 transcription factors (TFs) that affected flavonoid biosynthesis. In addition to increasing the transcript levels of genes that synthesize flavones, flavonols, and flavanones, the scion-rootstock interaction also affected the expression of many TFs. Taken together, our findings suggested that hetero-grafting could promote the accumulation of flavonoid compounds in citrus peels during the development stages. These results offered fresh perspectives on grafting's application usefulness and the enhancement of the accumulation of nutritive flavonoid components by grafting in citrus.

Time-series transcriptome provides insights into the gene regulation network involved in the icariin-flavonoid metabolism during the leaf development of Epimedium pubescens

Herba Epimedii (Epimedium) leaves are rich in prenylated flavonol glycosides (PFGs) with high medicinal value. However, the dynamics and regulatory network of PFG biosynthesis remain largely unclear. Here, we combined metabolite profiling (targeted to PFGs) and a high-temporal-resolution transcriptome to elucidate PFGs' regulatory network in Epimedium pubescens and identified key candidate structural genes and transcription factors (TFs) involved in PFG accumulation. Chemical profile analysis revealed that PFG content was quite different between buds and leaves and displayed a continuous decline with leaf development. The structural genes are the determinant reasons, and they are strictly regulated by TFs under temporal cues. We further constructed seven time-ordered gene co-expression networks (TO-GCNs) of PFG biosynthesis genes (including EpPAL2, EpC4H, EpCHS2, EpCHI2, EpF3H, EpFLS3, and EpPT8), and three flavonol biosynthesis routines were then predicted. The TFs involved in TO-GCNs were further confirmed by WGCNA analysis. Fourteen hub genes, comprising 5 MYBs, 1 bHLH, 1 WD40, 2 bZIPs, 1 BES1, 1 C2H2, 1 Trihelix, 1 HD-ZIP, and 1 GATA were identified as candidate key TFs. The results were further validated by TF binding site (TFBS) analysis and qRT-PCR. Overall, these findings provide valuable information for understanding the molecular regulatory mechanism of PFGs biosynthesis, enriching the gene resources, which will guide further research on PFG accumulation in Epimedium.

Comparative transcriptome and metabolome analysis identifies a citrus ERF transcription factor CsERF003 as flavonoid activator

Transcription factor (TF) modulation is a promising strategy for plant flavonoid improvement. Here, we observed evident decreases in some major flavones and flavonols and the expression of some key related genes in a 'Newhall' navel orange mutant (MT) relative to the wild type (WT). A consistently downregulated ERF TF CsERF003 in MT could increase the contents of major flavonoids and the precursor phenylalanine when transiently overexpressed in citrus fruit. Overexpression of CsERF003 in 'Micro-Tom' tomato (OE) resulted in a darker and redder fruit color than wild type 'Micro-Tom' (WTm). Two major flavonoids, naringeninchalcone and kaempferolrutinoside, were averagely induced by 7.99- and 36.83-fold in OEs, respectively, while little change was observed in other polyphenols, such as caffeic acid, ferulic acid, and gallic acid. Key genes involved in the initiation of phenylpropanoid (PAL, 4CH, and 4CL) and flavonoid (CHS and CHI) biosynthesis were up-regulated, while most genes participating in the biosynthesis of other polyphenols, such as HCT and CCR, were down-regulated in OEs. Therefore, it could be concluded that carbon flux floods into the phenylpropanoid biosynthetic pathway and is then specifically directed for flavonoid biosynthesis. CsERF003 may be a potentially promising gene for fruit quality improvement and engineering of natural flavonoid components.

Evolution-guided multiomics provide insights into the strengthening of bioactive flavone biosynthesis in medicinal pummelo

Pummelo (Citrus maxima or Citrus grandis) is a basic species and an important type for breeding in Citrus. Pummelo is used not only for fresh consumption but also for medicinal purposes. However, the molecular basis of medicinal traits is unclear. Here, compared with wild citrus species/Citrus-related genera, the content of 43 bioactive metabolites and their derivatives increased in the pummelo. Furthermore, we assembled the genome sequence of a variety for medicinal purposes with a long history, Citrus maxima 'Huazhouyou-tomentosa' (HZY-T), at the chromosome level with a genome size of 349.07 Mb. Comparative genomics showed that the expanded gene family in the pummelo genome was enriched in flavonoids-, terpenoid-, and phenylpropanoid biosynthesis. Using the metabolome and transcriptome of six developmental stages of HZY-T and Citrus maxima 'Huazhouyou-smooth' (HZY-S) fruit peel, we generated the regulatory networks of bioactive metabolites and their derivatives. We identified a novel MYB transcription factor, CmtMYB108, as an important regulator of flavone pathways. Both mutations and expression of CmtMYB108, which targets the genes PAL (phenylalanine ammonia-lyase) and FNS (flavone synthase), displayed differential expression between Citrus-related genera, wild citrus species and pummelo species. This study provides insights into the evolution-associated changes in bioactive metabolism during the origin process of pummelo.

The CmMYB3 transcription factors isolated from the Chrysanthemum morifolium regulate flavonol biosynthesis in Arabidopsis thaliana

Chrysanthemum morifolium MYB3 factors are transcriptional activators for the regulation of flavonol biosynthesis. Flavonol was not only the critical secondary metabolite participating in the growth and development of plants but also the main active ingredient in medicinal chrysanthemum. However, few pieces of research revealed the transcriptional regulation of flavonol biosynthesis in Chrysanthemum morifolium. Here, we isolated two CmMYB3 transcription factors (CmMYB3a and CmMYB3b) from the capitulum of Chrysanthemum morifolium cv 'Hangju'. According to the sequence characteristics, the CmMYB3a and CmMYB3b belonged to the R2R3-MYB subgroup 7, whose members were often reported to regulate flavonol biosynthesis positively. CmMYB3a and CmMYB3b factors were identified to localize in the nucleus by subcellular localization assay. Besides, both of them have obvious transcriptional self-activation activity in their C-terminal. After the overexpression of CmMYB3 genes in Nicotiana benthamiana and Arabidopsis thaliana, the flavonol contents in plants were increased, and the expression of AtCHS, AtCHI, AtF3H, and AtFLS genes in A. thaliana was also improved. Interestingly, the CmMYB3a factor had stronger functions in improving flavonol contents and related gene expression levels than CmMYB3b. The interaction analysis between transcription factors and promoters suggested that CmMYB3 could bind and activate the promoters of CmCHI and CmFLS genes in C. morifolium, and CmMYB3a also functioned more powerfully. Overall, these results indicated that CmMYB3a and CmMYB3b work as transcriptional activators in controlling flavonol biosynthesis.

ART1 and putrescine contribute to rice aluminum resistance via OsMYB30 in cell wall modification

Cell wall is the first physical barrier to aluminum (Al) toxicity. Modification of cell wall properties to change its binding capacity to Al is one of the major strategies for plant Al resistance; nevertheless, how it is regulated in rice remains largely unknown. In this study, we show that exogenous application of putrescines (Put) could significantly restore the Al resistance of art1, a rice mutant lacking the central regulator Al RESISTANCE TRANSCRIPTION FACTOR 1 (ART1), and reduce its Al accumulation particularly in the cell wall of root tips. Based on RNA-sequencing, yeast-one-hybrid and electrophoresis mobility shift assays, we identified an R2R3 MYB transcription factor OsMYB30 as the novel target in both ART1-dependent and Put-promoted Al resistance. Furthermore, transient dual-luciferase assay showed that ART1 directly inhibited the expression of OsMYB30, and in turn repressed Os4CL5-dependent 4-coumaric acid accumulation, hence reducing the Al-binding capacity of cell wall and enhancing Al resistance. Additionally, Put repressed OsMYB30 expression by eliminating Al-induced H₂ O₂ accumulation, while exogenous H₂ O₂ promoted OsMYB30 expression. We concluded that ART1 confers Put-promoted Al resistance via repression of OsMYB30-regulated modification of cell wall properties in rice.

Integrated transcriptome and metabolome analysis revealed that flavonoids enhanced the resistance of Oryza sativa against Meloidogyne graminicola

Rice is a crucial food crop worldwide, but its yield and quality are significantly affected by Meloidogyne graminicola is a root knot nematode. No rice variety is entirely immune to this nematode disease in agricultural production. Thus, the fundamental strategy to combat this disease is to utilize rice resistance genes. In this study, we conducted transcriptome and metabolome analyses on two rice varieties, ZH11 and IR64. The results indicated that ZH11 showed stronger resistance than IR64. Transcriptome analysis revealed that the change in gene expression in ZH11 was more substantial than that in IR64 after M. graminicola infection. Moreover, GO and KEGG enrichment analysis of the upregulated genes in ZH11 showed that they were primarily associated with rice cell wall construction, carbohydrate metabolism, and secondary metabolism relating to disease resistance, which effectively enhanced the resistance of ZH11. However, in rice IR64, the number of genes enriched in disease resistance pathways was significantly lower than that in ZH11, which further explained susceptibility to IR64. Metabolome analysis revealed that the metabolites detected in ZH11 were enriched in flavonoid metabolism and the pentose phosphate pathway, compared to IR64, after M. graminicola infection. The comprehensive analysis of transcriptome and metabolome data indicated that flavonoid metabolism plays a crucial role in rice resistance to M. graminicola infection. The content of kaempferin, apigenin, and quercetin in ZH11 significantly increased after M. graminicola infection, and the expression of genes involved in the synthetic pathway of flavonoids also significantly increased in ZH11. Our study provides theoretical guidance for the precise analysis of rice resistance and disease resistance breeding in further research.

Regulation of the regulators: Transcription factors controlling biosynthesis of plant secondary metabolites during biotic stresses and their regulation by miRNAs

Biotic stresses threaten to destabilize global food security and cause major losses to crop yield worldwide. In response to pest and pathogen attacks, plants trigger many adaptive cellular, morphological, physiological, and metabolic changes. One of the crucial stress-induced adaptive responses is the synthesis and accumulation of plant secondary metabolites (PSMs). PSMs mitigate the adverse effects of stress by maintaining the normal physiological and metabolic functioning of the plants, thereby providing stress tolerance. This differential production of PSMs is tightly orchestrated by master regulatory elements, Transcription factors (TFs) express differentially or undergo transcriptional and translational modifications during stress conditions and influence the production of PSMs. Amongst others, microRNAs, a class of small, non-coding RNA molecules that regulate gene expression post-transcriptionally, also play a vital role in controlling the expression of many such TFs. The present review summarizes the role of stress-inducible TFs in synthesizing and accumulating secondary metabolites and also highlights how miRNAs fine-tune the differential expression of various stress-responsive transcription factors during biotic stress.

DhMYB2 and DhbHLH1 regulates anthocyanin accumulation via activation of late biosynthesis genes in Phalaenopsis-type Dendrobium

Phalaenopsis-type Dendrobium is a popular orchid with good ornamental and market value. Despite their popularity, molecular regulation of anthocyanin biosynthesis during flower development remains poorly understood. In this study, we systematically investigated the regulatory roles of the transcription factors DhMYB2 and DhbHLH1 in anthocyanins biosynthesis. Gene expression analyses indicated that both DhMYB2 and DhbHLH1 are specifically expressed in flowers and have similar expression patterns, showing high expression in purple floral tissues with anthocyanin accumulation. Transcriptomic analyses showed 29 differentially expressed genes corresponding to eight enzymes in anthocyanin biosynthesis pathway have similar expression patterns to DhMYB2 and DhbHLH1, with higher expression in the purple lips than the yellow petals and sepals of Dendrobium 'Suriya Gold'. Further gene expression analyses and Pearson correlation matrix analyses of Dendrobium hybrid progenies revealed expression profiles of DhMYB2 and DhbHLH1 were positively correlated with the structural genes DhF3'H1, DhF3'5'H2, DhDFR, DhANS, and DhGT4. Yeast one-hybrid and dual-luciferase reporter assays revealed DhMYB2 and DhbHLH1 can bind to promoter regions of DhF3'H1, DhF3'5'H2, DhDFR, DhANS and DhGT4, suggesting a role as transcriptional activators. These results provide new evidence of the molecular mechanisms of DhMYB2 and DhbHLH1 in anthocyanin biosynthesis in Phalaenopsis-type Dendrobium.

Metabolomic and transcriptomic exploration of the uric acid-reducing flavonoids biosynthetic pathways in the fruit of Actinidia arguta Sieb. Zucc

Flavonoids from Actinidia arguta Sieb. Zucc. can reduce uric acid in mice. However, the molecular basis of its biosynthesis is still unclear. In this paper, we used a combination of extensively targeted metabolomics and transcriptomics analysis to determine the types and differences of flavonoids in the fruit ripening period (August to September) of two main cultivated varieties in northern China. The ethanol extract was prepared, and the potential flavonoids of Chrysin (Flavone1), Rutin (Flavone2), and Daidzein (Flavone3) in Actinidia arguta Sieb. Zucc. were separated and purified by HPD600 macroporous adsorption resin and preparative liquid chromatography. The structure was identified by MS-HPLC, and the serum uric acid index of male Kunming mice was determined by an animal model test.125 flavonoids and 50 differentially regulated genes were identified. The contents of UA (uric acid), BUN (urea nitrogen), Cr (creatinine), and GAPDH in mouse serum and mouse liver glycogen decreased or increased in varying degrees. This paper reveals the biosynthetic pathway of uric acid-reducing flavonoids in the fruit of Actinidia arguta Sieb. Zucc., a major cultivar in northern China, provides valuable information for the development of food and drug homologous functional foods.

Integration of metabolome and transcriptome analyses reveals the mechanism of anthocyanin accumulation in purple radish leaves

Anthocyanins are natural pigments and play significant roles in multiple growth, development, and stress response processes in plants. The vegetables with high anthocyanin content have better colours, higher antioxidant activity than green vegetables and are potent antioxidants with health benefits. However, the mechanism of anthocyanin accumulation in purple and green leaves of Raphanus sativus (radish) is poorly understood and needs further investigation. In the present study, the pigment content in a green leaf cultivar "RA9" and a purple-leaf cultivar "MU17" was characterized and revealed that the MU17 had significantly increased accumulation of anthocyanins and reduced content of chlorophyll and carotenoid compared with that in RA9. Meanwhile, these two cultivars were subjected to a combination of metabolomic and transcriptome studies. A total of 52 massively content-changed metabolites and 3463 differentially expressed genes were discovered in MU17 compared with RA9. In addition, the content of significantly increased flavonoids (such as pelargonidin and cyanidin) was identified in MU17 compared to RA9 using an integrated analysis of metabolic and transcriptome data. Moreover, the quantitative real-time polymerase chain reaction results also confirmed the differences in the expression of genes related to pathways of flavonoids and anthocyanin metabolism in MU17 leaves. The present findings provide valuable information for anthocyanin metabolism and further genetic manipulation of anthocyanin biosynthesis in radish leaves.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-022-01245-w.

Full-Length Transcriptome Sequencing Provides Insights into Flavonoid Biosynthesis in Camellia nitidissima Petals

Flavonoids are the main medicinal ingredients in Camellia nitidissima, but the regulatory mechanism of flavonoid biosynthesis in flowers is unclear; therefore, the flavonoids in C. nitidissima have not been effectively used. The present study performed full-length transcriptome sequencing of C. nitidissima flower. Furthermore, the reported RNA-sequencing data of C. nitidissima petals were reanalyzed using the full-length transcriptome as a reference, and the regulatory mechanism of flavonoid synthesis in petals was elucidated. The analysis identified 43,350 isoforms annotated in non-redundant protein (Nr), Kyoto Encyclopedia of Genes and Genomes (KEGG), EuKaryotic Orthologous Groups (KOG), and Swiss-Prot databases, among which 34,602 aligned to Camellia sinensis genes. A total of 11,857 differentially expressed genes (DEGs), including 112 related to flavonoid synthesis, were identified by pairwise comparison. Subsequently, analysis of the phylogeny and the conserved motifs of R2R3-MYB using the proteins sequences identified three R2R3-MYB transcription factors that regulated flavonoid biosynthesis. Weighted gene co-expression network analysis (WGCNA) identified phenylalanine ammonia-lyase (PAL) and 4-coumarate: CoA ligase(4CL) as the hub genes and showed that bHLH79 interacted with PAL. Finally, validated the expression of seven DEGs involved in flavonoid biosynthesis using real-time quantitative PCR (qRT-PCR). Thus, the present study generated and used the full-length transcriptome as the reference to analyze the transcriptome of petals and proposed a possible regulatory mechanism of flavonoid synthesis in C. nitidissima. The study's findings unravel the genetic mechanisms underlying flavonoid synthesis and suggest candidate genes for the genetic improvement of C. nitidissima.

Natural products of medicinal plants: biosynthesis and bioengineering in post-genomic era

Globally, medicinal plant natural products (PNPs) are a major source of substances used in traditional and modern medicine. As we human race face the tremendous public health challenge posed by emerging infectious diseases, antibiotic resistance and surging drug prices etc., harnessing the healing power of medicinal plants gifted from mother nature is more urgent than ever in helping us survive future challenge in a sustainable way. PNP research efforts in the pre-genomic era focus on discovering bioactive molecules with pharmaceutical activities, and identifying individual genes responsible for biosynthesis. Critically, systemic biological, multi- and inter-disciplinary approaches integrating and interrogating all accessible data from genomics, metabolomics, structural biology, and chemical informatics are necessary to accelerate the full characterization of biosynthetic and regulatory circuitry for producing PNPs in medicinal plants. In this review, we attempt to provide a brief update on the current research of PNPs in medicinal plants by focusing on how different state-of-the-art biotechnologies facilitate their discovery, the molecular basis of their biosynthesis, as well as synthetic biology. Finally, we humbly provide a foresight of the research trend for understanding the biology of medicinal plants in the coming decades.

MYB transcription factors and their role in Medicinal plants

Transcription factors are multi-domain proteins that regulate gene expression in eukaryotic organisms. They are one of the largest families of proteins, which are structurally and functionally diverse. While there are transcription factors that are plant-specific, such as AP2/ERF, B3, NAC, SBP and WRKY, some transcription factors are present in both plants as well as other eukaryotic organisms. MYB transcription factors are widely distributed among all eukaryotes. In plants, the MYB transcription factors are involved in the regulation of numerous functions such as gene regulation in different metabolic pathways especially secondary metabolic pathways, regulation of different signalling pathways of plant hormones, regulation of genes involved in various developmental and morphological processes etc. Out of the thousands of MYB TFs that have been studied in plants, the majority of them have been studied in the model plants like Arabidopsis thaliana, Oryza sativa etc. The study of MYBs in other plants, especially medicinal plants, has been comparatively limited. But the increasing demand for medicinal plants for the production of biopharmaceuticals and important bioactive compounds has also increased the need to explore more number of these multifaceted transcription factors which play a significant role in the regulation of secondary metabolic pathways. These studies will ultimately contribute to medicinal plants' research and increased production of secondary metabolites, either through transgenic plants or through synthetic biology approaches. This review compiles studies on MYB transcription factors that are involved in the regulation of diverse functions in medicinal plants.

PrMYB5 activates anthocyanin biosynthetic PrDFR to promote the distinct pigmentation pattern in the petal of Paeonia rockii

Paeonia rockii is well-known for its distinctive large dark-purple spot at the white petal base and has been considered to be the main genetic source of spotted tree peony cultivars. In this study, the petal base and petal background of Paeonia ostii (pure white petals without any spot), P. rockii, and other three tree peony cultivars were sampled at four blooming stages from the small bell-like bud stage to the initial blooming stage. There is a distinct difference between the pigmentation processes of spots and petal backgrounds; the spot pigmentation was about 10 days earlier than the petal background. Moreover, the cyanin and peonidin type anthocyanin accumulation at the petal base mainly contributed to the petal spot formation. Then, we identified a C1 subgroup R2R3-MYB transcription factor, PrMYB5, predominantly transcribing at the petal base. This is extremely consistent with PrDFR and PrANS expression, the contents of anthocyanins, and spot formation. Furthermore, PrMYB5 could bind to and activate the promoter of PrDFR in yeast one-hybrid and dual-luciferase assays, which was further verified in overexpression of PrMYB5 in tobacco and PrMYB5-silenced petals of P. rockii by comparing the color change, anthocyanin contents, and gene expression. In summary, these results shed light on the mechanism of petal spot formation in P. rockii and speed up the molecular breeding process of tree peony cultivars with novel spot pigmentation patterns.

EbMYBP1, a R2R3-MYB transcription factor, promotes flavonoid biosynthesis in Erigeron breviscapus

Erigeron breviscapus, a traditional Chinese medicinal plant, is enriched in flavonoids that are beneficial to human health. While we know that R2R3-MYB transcription factors (TFs) are crucial to flavonoid pathway, the transcriptional regulation of flavonoid biosynthesis in E. breviscapus has not been fully elucidated. Here, EbMYBP1, a R2R3-MYB transcription factor, was uncovered as a regulator involved in the regulation of flavonoid accumulation. Transcriptome and metabolome analysis revealed that a large group of genes related to flavonoid biosynthesis were significantly changed, accompanied by significantly increased concentrations of the flavonoid in EbMYBP1-OE transgenic tobacco compared with the wild-type (WT). In vitro and in vivo investigations showed that EbMYBP1 participated in flavonoid biosynthesis, acting as a nucleus-localized transcriptional activator and activating the transcription of flavonoid-associated genes like FLS, F3H, CHS, and CHI by directly binding to their promoters. Collectively, these new findings are advancing our understanding of the transcriptional regulation that modulates the flavonoid biosynthesis.

A Genome-Wide Analysis of StTGA Genes Reveals the Critical Role in Enhanced Bacterial Wilt Tolerance in Potato During Ralstonia solanacearum Infection

TGA is one of the members of TGACG sequence-specific binding protein family, which plays a crucial role in the regulated course of hormone synthesis as a stress-responsive transcription factor (TF). Little is known, however, about its implication in response to bacterial wilt disease in potato (Solanum tuberosum) caused by Ralstonia solanacearum. Here, we performed an in silico identification and analysis of the members of the TGA family based on the whole genome data of potato. In total, 42 StTGAs were predicted to be distributed on four chromosomes in potato genome. Phylogenetic analysis showed that the proteins of StTGAs could be divided into six sub-families. We found that many of these genes have more than one exon according to the conserved motif and gene structure analysis. The heat map inferred that StTGAs are generally expressed in different tissues which are at different stages of development. Genomic collinear analysis showed that there are homologous relationships among potato, tomato, pepper, Arabidopsis, and tobacco TGA genes. Cis-element in silico analysis predicted that there may be many cis-acting elements related to abiotic and biotic stress upstream of StTGA promoter including plant hormone response elements. A representative member StTGA39 was selected to investigate the potential function of the StTGA genes for further analysis. Quantitative real-time polymerase chain reaction (qRT-PCR) assays indicated that the expression of the StTGAs was significantly induced by R. solanacearum infection and upregulated by exogenous salicylic acid (SA), abscisic acid (ABA), gibberellin 3 (GA₃), and methyl jasmonate (MeJA). The results of yeast one-hybrid (Y1H) assay showed that StTGA39 regulates S. tuberosum BRI1-associated receptor kinase 1 (StBAK1) expression. Thus, our study provides a theoretical basis for further research of the molecular mechanism of the StTGA gene of potato tolerance to bacterial wilt.

Review of phytochemical and nutritional characteristics and food applications of Citrus L. fruits

Since the dietary regimen rich in fruits is being widely recognized and encouraged, Citrus L. fruits have been growing in popularity worldwide due to their high amounts of health-promoting phytonutrients and bioactive compounds, such as flavonoids, phenolic acids, vitamins, carotenoids, pectins, and fatty acids. The diverse physicochemical properties and multiple utilization of citrus fruits in food industry are associated with their unique chemical compositions. Throughout the world, citrus has been used for producing various value-added and nutritionally enhanced products, including juices, wines, jams, canned citrus, and dried citrus. However, the current studies regarding the phytochemical and nutritional characteristics and food applications of citrus are scattered. This review systematically summarizes the existing bibliography on the chemical characteristics, functional and nutraceutical benefits, processing, and potential applications of citrus. A thorough understanding of this information may provide scientific guidance for better utilizing citrus as a functional fruit and benefit the extension of citrus value chain.

Two Dof transcription factors promote flavonoid synthesis in kumquat fruit by activating C-glucosyltransferase

Although DNA binding with one finger (Dof) constitutes a crucial plant-specific family of transcription factors (TFs) that plays important roles in a wide range of biological processes, the molecular mechanisms underlying Dof regulation of flavonoid biosynthesis in plants remain largely unknown. Here, we characterized 28 Dof genes (FhDof1-FhDof28) from the 'Hongkong' kumquat (Fortunella hindsii) cultivar genome. Promoter analysis and transcriptome profiling revealed that four FhDofs - FhDof4, FhDof9, FhDof15, and FhDof16 - may be involved in flavonoid biosynthesis through binding to the flavonoid C-glycosyltransferase (FhCGT) promoter. We cloned homologous genes of four FhDofs, designated as FcDof4, FcDof9, FcDof15, FcDof16, and a homologous gene of FhCGT, designated as FcCGT, from the widely cultivated 'HuaPi' kumquat (F. crassifolia). Quantitative reverse transcription-polymerase chain reaction analysis revealed that FcDof4 and FcDof16 were significantly correlated with FcCGT expression during development stages in the 'HuaPi' fruit (Pearson's correlation coefficient > 0.7) and were localized to the nucleus. Results of yeast one-hybrid, electrophoretic mobility shift, and dual-luciferase assays indicated that the two FcDofs trigger FcCGT expression by specifically binding to its promoters. Moreover, transient overexpression of FcDof4 and FcDof16 enhances the transcription of structural genes in the flavonoid biosynthetic pathway and increases C-glycosylflavonoid content. Our results provide strong evidence that the TFs FcDof4 and FcDof16 promote flavonoid synthesis in kumquat fruit by activating FcCGT expression.

Comparative transcriptomics of wild and commercial Citrus during early ripening reveals how domestication shaped fruit gene expression

BACKGROUND

Interspecific hybridizations and admixtures were key in Citrus domestication, but very little is known about their impact at the transcriptomic level. To determine the effects of genome introgressions on gene expression, the transcriptomes of the pulp and flavedo of three pure species (citron, pure mandarin and pummelo) and four derived domesticated genetic admixtures (sour orange, sweet orange, lemon and domesticated mandarin) have been analyzed at color break.

RESULTS

Many genes involved in relevant physiological processes for domestication, such sugar/acid metabolism and carotenoid/flavonoid synthesis, were differentially expressed among samples. In the low-sugar, highly acidic species lemon and citron, many genes involved in sugar metabolism, the TCA cycle and GABA shunt displayed a reduced expression, while the P-type ATPase CitPH5 and most subunits of the vacuolar ATPase were overexpressed. The red-colored species and admixtures were generally characterized by the overexpression in the flavedo of specific pivotal genes involved in the carotenoid biosynthesis, including phytoene synthase, ζ-carotene desaturase, β-lycopene cyclase and CCD4b, a carotenoid cleavage dioxygenase. The expression patterns of many genes involved in flavonoid modifications, especially the flavonoid and phenylpropanoid O-methyltransferases showed extreme diversity. However, the most noticeable differential expression was shown by a chalcone synthase gene, which catalyzes a key step in the biosynthesis of flavonoids. This chalcone synthase was exclusively expressed in mandarins and their admixed species, which only expressed the mandarin allele. In addition, comparisons between wild and domesticated mandarins revealed that the major differences between their transcriptomes concentrate in the admixed regions.

CONCLUSION

In this work we present a first study providing broad evidence that the genome introgressions that took place during citrus domestication largely shaped gene expression in their fruits.

CsNIP5;1 acts as a multifunctional regulator to confer water loss tolerance in citrus fruit

Plant aquaporins facilitate the transport of water across the inner membranes and play an important role in the response to water loss stress. A citrus NOD26-like intrinsic protein, CsNIP5;1, has been investigated to participate in the regulation of water permeability. In the present study, the expression profile indicated that CsNIP5;1 showed high transcription abundance in conducting tissues. Function analysis revealed that CsNIP5;1 reduced water loss of Arabidopsis rosette leaf, as well as promoted the seed germination under hyperosmotic stress. Besides, overexpression of CsNIP5;1 contributed to the alleviation of water loss in citrus fruit and citrus callus during storage. Further metabolomic profiling and RNA-seq analysis of transgenic citrus callus revealed that CsNIP5;1 may modulate the water loss by inducing the accumulation of osmotic adjustment substances and repressing the expression of other AQPs. Moreover, CsWRKY4 and CsWRKY28 were found to directly bind to the promoter and acted as opposite regulators of CsNIP5;1 during the postharvest period. These findings provide new insights into the regulatory mechanism of aquaporins in response to the water loss stress of citrus fruit during postharvest storage.

CsMYB96 confers resistance to water loss in citrus fruit by simultaneous regulation of water transport and wax biosynthesis

A Citrus sinensis R2R3 MYB transcription factor (CsMYB96) has previously been shown to be strongly associated with the expression of many genes related to wax biosynthesis in the fruit. In this study, CsMYB96 was found to alleviate water loss by simultaneously regulating the expression of genes encoding plasma membrane intrinsic proteins (CsPIPs) and wax-related genes. Expression profiling indicated that CsPIP1;1 and CsPIP2;4 had high expression that was representative of other aquaporins, and they were down-regulated in the peel of post-harvest citrus fruit. CsPIP2;4 was further characterized as the predominant CsPIP, with high expression and high-water channel activity. Transient overexpression of CsPIP2;4 accelerated water loss in citrus fruit. In silico analysis further indicated that the expression of CsMYB96 had a significant negative correlation with that of CsPIPs. In vivo and in vitro experiments confirmed that CsMYB96 was able to directly repress the expression of CsPIPs. In addition, CsMYB96 was able to activate wax-related genes and promote wax biosynthesis for defense against water loss. Transient and stable overexpression of CsMYB96 reduced water loss from both citrus fruit and Arabidopsis.

Genome-Wide Association Study of Healthful Flavonoids among Diverse Mandarin Accessions

Mandarins have many unique flavonoids with documented health benefits and that help to prevent chronic human diseases. Flavonoids are difficult to measure and cannot be phenotyped without the use of specialized equipment; consequently, citrus breeders have not used flavonoid contents as selection criteria to develop cultivars with increased benefits for human health or increased tolerance to diseases. In this study, peel, pulp, and seed samples collected from many mandarin accessions and their hybrids were analyzed for the presence of selected flavonoids with documented human health benefits. A genome-wide association study (GWAS) was used to identify SNPs associated with biosynthesis of flavonoids in these mandarin accessions, and there were 420 significant SNPs were found to be associated with 28 compounds in peel, pulp, or seed samples. Four candidate genes involved in flavonoid biosynthesis were identified by enrichment analysis. SNPs that were found to be associated with compounds in pulp samples have the potential to be used as markers to select mandarins with improved phytonutrient content to benefit human health. Mandarin cultivars bred with increased flavonoid content may provide value to growers and consumers.

Cucurbitaceae genome evolution, gene function and molecular breeding

The Cucurbitaceae is one of the most genetically diverse plant families in the world. Many of them are important vegetables or medicinal plants and are widely distributed worldwide. The rapid development of sequencing technologies and bioinformatic algorithms has enabled the generation of genome sequences of numerous important Cucurbitaceae species. This has greatly facilitated research on gene identification, genome evolution, genetic variation and molecular breeding of cucurbit crops. So far, genome sequences of 18 different cucurbit species belonging to tribes Benincaseae, Cucurbiteae, Sicyoeae, Momordiceae and Siraitieae have been deciphered. This review summarizes the genome sequence information, evolutionary relationship, and functional genes associated with important agronomic traits (e.g., fruit quality). The progress of molecular breeding in cucurbit crops and prospects for future applications of Cucurbitaceae genome information are also discussed.

Citrus transcription factor CsHB5 regulates abscisic acid biosynthetic genes and promotes senescence

Senescence is a gradual physiological process involving the integration of numerous internal and environmental signals. Abscisic acid (ABA) is a well-known inducer of senescence. However, the regulatory mechanisms underlying ABA-mediated senescence remain largely unknown. Here, we report that the citrus homeodomain leucine zipper I (HD-ZIP I) transcription factor CsHB5 functions as a regulator of ABA-triggered senescence. CsHB5 acts as a nucleus-localized transcriptional activator, the expression of which appeared to be closely associated with citrus senescence. Overexpression of CsHB5 in citrus calli upregulated the expression of ABA- and reactive oxygen species (ROS)-related genes, and significantly increased the content of ABA and hydrogen peroxide (H₂ O₂ ), whereas silencing CsHB5 in citrus calli downregulated the expression of ABA-related genes. Additionally, heterogenous overexpression of CsHB5 in Solanum lycopersicum (tomato) and Arabidopsis thaliana (Arabidopsis) leads to early leaf yellowing under dark-induced senescence conditions. Meanwhile, the levels of ABA and H₂ O₂ in transgenic tomatoes increased significantly and the lycopene content decreased. Transcriptome analysis of CsHB5-overexpressing citrus calli and tomato showed that CsHB5 was involved in multiple senescence-associated processes, including chlorophyll degradation, nutrient compound biosynthesis and transport, as well as ABA and ROS signal transduction. The results of yeast one-hybrid assays, electrophoretic mobility shift assays and dual luciferase assays indicated that CsHB5 directly binds to the promoters of ABA biosynthetic genes, including β-carotene hydroxylase 1 (BCH1) and 9-cis-epoxycarotenoid dioxygenase 2 (NCED2), thereby activating their transcription. Our findings revealed that CsHB5 participates in senescence, at least partly, by directly controlling ABA accumulation. Our work provides insight into the regulatory mechanisms underlying ABA-mediated senescence.

Emerging roles of NAC transcription factor in medicinal plants: progress and prospects

Transcriptional factors act as mediators in regulating stress response in plants from signal perception to processing the directed gene expression. WRKY, MYB, AP2/ERF, etc. are some of the major families of transcription factors known to mediate stress mechanisms in plants by regulating the production of secondary metabolites. NAC domain-containing proteins are among these large transcription factors families in plants. These proteins play impulsive roles in plant growth, development, and various abiotic as well as biotic stresses. They are involved in regulating the different signaling pathways of plant hormones that direct a plant's immunity against pathogens, thereby affecting their immune responses. However, their role in stress regulation or defence mechanism in plants through the secondary metabolite biosynthesis pathway is studied for very few cases. Emerging concern over the requirement of medicinal plants for the production of biocompatible drugs and antibiotics, the study of these vast, affecting proteins should be focused to improve their qualitative and quantitative production further. In medicinal plants, phytochemicals and secondary metabolites are the major biochemicals that impose antimicrobial and other medicinal properties in these plants. This review compiles the NAC transcription factors reported in selected medicinal plants and their possible roles in different mechanisms. Further, the comprehensive understanding of the molecular mechanism, genetic engineering, and regulation responses of NAC TFs in medicinal plants, can lead to improvement in stress response, immunity, and production of usable secondary metabolites.

Primary Bitter Taste of Citrus is Linked to a Functional Allele of the 1,2-Rhamnosyltransferase Gene Originating from Citrus grandis

1,2-Rhamnosyltransferase (1,2RhaT) catalyzes the final step of production of flavanone neohesperidoside (FNH) that is responsible for the primary bitter taste of citrus fruits. In this study, species-specific flavonoid profiles were determined in 87 Citrus accessions by identifying eight main flavanone glycosides (FGs). Accumulation of FNHs was completely correlated to the presence of the 1,2RhaT gene in 87 citrus accessions analyzed using a novel 1,2RhaT-specific DNA marker. Pummelo (Citrus grandis) was identified as the genetic origin for a function allele of 1,2RhaT that underpinned FNH-bitterness in modern citrus cultivars. In addition, genes encoding six MYB and five bHLH transcription factors were shown to coexpress with 1,2RhaT and other flavonoid pathway genes related to FNH accumulation, indicating that these transcription factors may affect the fruit taste of citrus. This study provides a better understanding of bitterness formation in Citrus varieties and a genetic marker for the early selection of nonbitterness lines in citrus breeding programs.

CsMYB96 enhances citrus fruit resistance against fungal pathogen by activating salicylic acid biosynthesis and facilitating defense metabolite accumulation

Citrus fruit are generally confronted with various fungal diseases that cause fruit deterioration and economic loss. Salicylic acid (SA), a plant hormone, is an important signal molecule required for stimulating the disease resistance of plants. However, there has been limited information about the molecular mechanism of SA biosynthesis involving biotic stress response in citrus fruit. In the present study, an R2R3 MYB transcription factor (CsMYB96) was identified to mediate SA signaling in response to fungal diseases. The transient overexpression assay revealed that CsMYB96 contributed to the strong tolerance of citrus fruit to Penicillium italicum along with an increase in SA content; meanwhile, CsMYB96 conferred resistance to Botrytis cinerea in Arabidopsis plants. Further metabolomic profiling of stable transgenic Arabidopsis revealed that CsMYB96 participated in the regulation of various metabolism pathways and enhanced the accumulation of phenolic acids. RNA-seq analysis confirmed that overexpression of CsMYB96 activated the expression of genes involved in plant-pathogen interaction, phenylpropanoid biosynthesis, and SA signaling. Besides, CsMBY96 directly activated the transcription of calmodulin binding protein 60g (CsCBP60g), a predominant transcription factor required for the activation of SA signaling. In summary, our results reveal that CsMYB96 promotes SA biosynthesis and the accumulation of defense metabolites to enhance the fungal pathogen resistance of citrus fruit and Arabidopsis and provide new insights into the regulation of disease response.

Integrated transcriptomic and metabolomic analysis provides insight into the regulation of leaf senescence in rice

Leaf senescence is one of the most precisely modulated developmental process and affects various agronomic traits of rice. Anti-senescence rice varieties are important for breeding application. However, little is known about the mechanisms underlying the metabolic regulatory process of leaf senescence in rice. In this study, we performed transcriptomic and metabolomic analyses of the flag leaves in Yuenong Simiao (YN) and YB, two indica rice cultivars that differ in terms of their leaf senescence. We found 8524 genes/204 metabolites were differentially expressed/accumulated in YN at 30 days after flowering (DAF) compared to 0 DAF, and 8799 genes/205 metabolites were differentially expressed in YB at 30 DAF compared to 0 DAF. Integrative analyses showed that a set of genes and metabolites involved in flavonoid pathway were significantly enriched. We identified that relative accumulation of PHENYLALANINE AMMONIA-LYASE (PAL), CINNAMATE 4-HYDROXYLASE (C4H), 4-COUMAROYL-COA LIGASE (4CL), CHALCONE SYNTHASE (CHS) and CHALCONE ISOMERASE (CHI) in YN30/0 was higher than that in YB30/0. Three flavonoid derivatives, including phloretin, luteolin and eriodictyol, showed lower abundances in YB than in YN at 30 DAF. We further revealed a MYB transcription factor, which is encoded by OsR498G0101613100 gene, could suppress the expression of CHI and CHS. Our results suggested a comprehensive analysis of leaf senescence in a view of transcriptome and metabolome and would contribute to exploring the molecular mechanism of leaf senescence in rice.

Identification of a delayed leaf greening gene from a mutation of pummelo

Delayed greening of young leaves is an unusual phenomenon of plants in nature. Citrus are mostly evergreen tree species. Here, a natural mutant of "Guanxi" pummelo (Citrus maxima), which shows yellow leaves at the young stage, was characterized to identify the genes underlying the trait of delayed leaf greening in plants. A segregating population with this mutant as the seed parent and a normal genotype as the pollen parent was generated. Two DNA pools respectively from the leaves of segregating seedlings with extreme phenotypes of normal leaf greening and delayed leaf greening were collected for sequencing. Bulked segregant analysis (BSA) and InDel marker analysis demonstrated that the delayed leaf greening trait is governed by a 0.3 Mb candidate region on chromosome 6. Gene expression analysis further identified a key candidate gene (Citrus Delayed Greening gene 1, CDG1) in the 0.3 Mb region, which showed significantly differential expression between the genotypes with delayed and normal leaf greening phenotypes. There was a 67 bp InDel region difference in the CDG1 promoter and the InDel region contains a TATA-box element. Confocal laser-scanning microscopy revealed that the CDG1-GFP fusion protein signals were co-localized with the chloroplast signals in the protoplasts. Overexpression of CDG1 in tobacco and Arabidopsis led to the phenotype of delayed leaf greening. These results suggest that the CDG1 gene is involved in controlling the delayed leaf greening phenotype with important functions in chloroplast development.

Citrus NIP5;1 aquaporin regulates cell membrane water permeability and alters PIPs plasma membrane localization

The ER or donut-like structures localized aquaporin NIP5;1, which interacts with PIPs and alters their localization from plasma membrane to donut-like structures, regulates water permeability. NOD26-like intrinsic proteins (NIPs) play important roles in nutrient uptake and response to various stresses. However, there have been few studies of their functions in water transportation in citrus. Here, we demonstrate the functions of a novel citrus NIP aquaporin (CsNIP5;1) via multiple physiological and biochemical experiments. CsNIP5;1 showed high water permeability when expressed in Xenopus laevis oocytes and yeast. However, subcellular localization assays showed that this protein was localized in the endoplasmic reticulum (ER) or donut-like structures in citrus callus and tobacco leaf. Meanwhile, overexpression of CsNIP5;1 led to a reduction in the water permeability of citrus callus. Protein-protein interaction experiments and subcellular localization assays further revealed that CsNIP5;1 physically interacted with PIPs (CsPIP1;1 and AtPIP2;1), which altered their subcellular localization from the plasma membrane to donut-like structures. Together, CsNIP5;1 was identified as a good water channel when expressed in oocytes and yeast. Meanwhile, CsNIP5;1 participated in the regulation of water permeability of citrus callus, which may be associated with CsNIP5;1-induced re-localization of water channels PIPs. In summary, these results provide new insights into the regulatory mechanism of AQPs-mediated water diffusion.