Identification of chalcone isomerase in the basal land plants reveals an ancient evolution of enzymatic cyclization activity for synthesis of flavonoids

Flexible control of influx for flavonoids pathway based on diversity of MaCHI-fold proteins in mulberry

Mulberry (Morus spp., Moraceae) is considered as a rapidly evolving plant species with enriched unique gene family members involved in flavonoid biosynthesis. Recently, transcriptional regulatory mechanism controlling flavonoid biosynthesis in mulberry has been extensively reported, yet studies on the regulation of flavonoid biosynthesis beyond the transcriptional level are limited. In present study, our in vivo and in vitro assays have shown that four MaCHI-fold proteins with different roles in flavonoid biosynthesis coordinated to flexibly regulate the influx for flavonoid biosynthesis. MaCHI2N was the dominant CHI to ensure the normal influx. The mulberry-specific type IB MaCHI1 worked as substitute and could also enhance the influx. The MaCHI2 alternative transcript product, MaCHI2D with low activity for naringin chalcone provided a "braker" for flavonoid biosynthesis by competing with MaCHI2N in transcription process. MaCHIL enhanced the influx for flavonoid biosynthesis by interacting with MaCHS1 and increasing the production of naringenin. Therefore, we proposed a transmission box model that presented the complicated regulation of influx for flavonoid biosynthesis based on the diversity of MaCHI-fold proteins and the homeostasis of naringenin chalcone and naringenin in mulberry. Our results reveal the unique regulatory mechanism of influx for flavonoids pathway beyond transcriptional level.

A Comprehensive Evolutionary Analysis of the Dihydroflavonol 4-Reductase (DFR) Gene Family in Plants: Insights from 237 Species

BACKGROUND

Dihydroflavonol 4-reductase (DFR) is a key enzyme in the flavonoid biosynthetic pathway that regulates anthocyanin and proanthocyanidin accumulation in plants. Although DFR genes have been studied in various species, their origin of the DFR gene family, its distribution across the plant kingdom, and the reasons behind the emergence of different DFR subtypes Methods: This study performed a whole-genome analysis of DFR genes in 237 plant species, including algae, mosses, ferns, gymnosperms, and angiosperms, integrating phylogeny, conserved motifs, duplication mechanisms, positive selection, and expression pattern analyses.

RESULTS

These results indicate that the DFR gene family originated from the common ancestor of extant ferns and seed plants, and the emergence of asparagine (Asn)-type and aspartic (Asp)-type DFRs is associated with gymnosperms. Notably, we report for the first time the presence of Asn-type, Asp-type, and arginine (Arg)-type DFRs in some species, which breaks the previous notion that Arg-type DFRs are exclusive to ferns. Tandem duplication is considered the primary driving force behind the expansion of the DFR family and is associated with the formation of different DFR subtypes. Furthermore, Asn-type DFRs were highly expressed during the early stages of seed development, suggesting their important role in seed development.

CONCLUSIONS

Overall, this study revealed the dynamic evolutionary trajectory of the DFR gene family in plants, providing a theoretical foundation for future research on DFR genes.

Effects of CSN1/CSN2 Mutants in Flavonoid Metabolism on Rice (Oryza sativa L.)

The key flavonoid biosynthesis-related genes and their molecular features in rice have not been comprehensively and systematically characterized. In this study, we investigated the glumes of OsCSN1 mutants and OsCSN2 mutants and found the changes in the total flavonoid contents of the OsCSN2 mutants to be more pronounced than those of the OsCSN1 mutants and the changes in the anthocyanin contents of the OsCSN1 mutants to be more pronounced than those of the OsCSN2 mutants. In addition, key genes related to flavonoid synthesis, OsCHI, showed a more pronounced up-regulation trend, and the OsDFR gene, which encodes a precursor enzyme for anthocyanin synthesis, showed a clear down-regulation trend. And yeast two-hybrid experiments showed that OsCSN1 and OsCSN2 had the ability to interact with OsCUL4. In summary, OsCSN1 and OsCSN2 may regulate the metabolism of flavonoids in rice through CUL4-based E3 ligase, and the two subunits play different roles, laying a foundation for the study of the mechanism of flavonoid metabolism in monocotyledonous plants.

Bioinformatics and Expression Analysis of CHI Gene Family in Sweet Potato

Chalcone isomerase (CHI) is not only an enzyme related to flavonoid biosynthesis, but also one of the key enzymes in the flavonoid metabolic pathway. In this study, members of the CHI gene family were identified in the whole genome of sweet potato. Bioinformatics methods were used to analyze the physical and chemical properties, systematic evolution, conserved domain, chromosome location, cis-acting elements of the promoter, and so on, of CHI gene family members. In addition, the tissue site-specific expression of CHI gene family members and their expression patterns under three kinds of abiotic stress were analyzed. The results showed that five members of IbCHI gene family were identified in sweet potato, which were unevenly distributed on four chromosomes. The protein secondary structure and tertiary structure were consistent, and there was a conservative domain related to chalcone isomerase. The prediction of subcellular localization showed that it was mainly located in cytoplasm and chloroplast. Systematic evolution showed that the members of sweet potato CHI gene family could be divided into Type I-IV, and the Type I gene IbCHI1 showed CHI catalytic activity in transgenic callus. The collinearity gene pairs were identified between sweet potato and allied species. Its promoter contains light response elements, hormone response elements, and stress response elements. The results of real-time fluorescence quantitative PCR (qRT-PCR) analysis showed that the expression of the IbCHI gene was tissue-specific and that the catalytic genes IbCHI1 and IbCHI5 serve as primary responders to abiotic stress, while the non-catalytic members IbCHI3 and IbCHI4 may fine-tune metabolic flux or participate in low-temperature, salt, and drought stress signaling. This study can provide a theoretical basis for a follow-up functional genomics study of the chalcone isomerase gene family in sweet potato.

Evolutionary analysis of anthocyanin biosynthetic genes: insights into abiotic stress adaptation

Anthocyanin regulation can be fruitfully explored from a diverse perspective by studying distantly related model organisms. Land plants pioneers faced a huge evolutionary leap, involving substantial physiological and genetic changes. Anthocyanins have evolved alongside these changes, becoming versatile compounds capable of mitigating terrestrial challenges such as drought, salinity, extreme temperatures and high radiation. With the accessibility of whole-genome sequences from ancient plant lineages, deeper insights into the evolution of key metabolic pathways like phenylpropanoids have emerged. Despite understanding the function of anthocyanins under stress, gaps remain in uncovering the precise metabolic and regulatory mechanisms driving their overproduction under stressful conditions. For example, the regulatory effect of reactive oxygen species (ROS) on well-known transcription factors like MYBs is not fully elucidated. This manuscript presents an evolutionary analysis of the anthocyanin biosynthetic pathway to elucidate key genes. CINNAMATE 4-HYDROXYLASE (C4H) and CHALCONE ISOMERASE (CHI2) received particular attention. C4H exposes remarkable differences between aquatic and land plants, while CHI2 demonstrates substantial variation in gene copy number and sequence similarity across species. The role of transcription factors, such as MYB, and the involvement of ROS in the regulation of anthocyanin biosynthesis are discussed. Complementary gene expression analyses under abiotic stress in Arabidopsis thaliana, Selaginella moellendorffii, and Marchantia polymorpha reveal intriguing gene-stress relationships. This study highlights evolutionary trends and the regulatory complexity of anthocyanin production under abiotic stress, providing insights and opening avenues for future research.

The evolution of plant responses underlying specialized metabolism in host-pathogen interactions

In the course of plant evolution from aquatic to terrestrial environments, land plants (embryophytes) acquired a diverse array of specialized metabolites, including phenylpropanoids, flavonoids and cuticle components, enabling adaptation to various environmental stresses. While embryophytes and their closest algal relatives share candidate enzymes responsible for producing some of these compounds, the complete genetic network for their biosynthesis emerged in embryophytes. In this review, we analysed genomic data from chlorophytes, charophytes and embryophytes to identify genes related to phenylpropanoid, flavonoid and cuticle biosynthesis. By integrating published research, transcriptomic data and metabolite studies, we provide a comprehensive overview on how these specialized metabolic pathways have contributed to plant defence responses to pathogens in non-vascular bryophytes and vascular plants throughout evolution. The evidence suggests that these biosynthetic pathways have provided land plants with a repertoire of conserved and lineage-specific compounds, which have shaped immunity against invading pathogens. The discovery of additional enzymes and metabolites involved in bryophyte responses to pathogen infection will provide evolutionary insights into these versatile pathways and their impact on environmental terrestrial challenges.This article is part of the theme issue 'The evolution of plant metabolism'.

SWATH-MS based proteomics reveals the role of photosynthesis related proteins and secondary metabolic pathways in the colored leaves of sweet olive (Osmanthus fragrans)

Colored leaves, a notable horticultural trait, have high research and ornamental value. The evergreen sweet olive (Osmanthus fragrans), one of the top ten traditional flowers in China, has been cultivated for more than two thousand years. However, in recent years, an increasing number of O. fragrans cultivars with colored leaves have been cultivated for their ornamental value. To study the molecular mechanism underlying the observed changes in leaf color, we selected O. fragrans 'Yinbi Shuanghui' (Y), which has yellow-white leaves, and O. fragrans 'Sijigui' (S), which has green leaves, as materials. Pigment content measurement showed that the chlorophyll, carotenoid and anthocyanin contents in Y were lower than in S. According to the SWATH-MS sequencing results, a total of 3,959 proteins were quantitatively identified, 1,300 of which were differentially expressed proteins (DEPs), including 782 up-regulated and 518 down-regulated proteins in Y compared to S. Functional enrichment analysis of DEPs revealed that down-regulated expression of photosynthesis related proteins may lead to the inhibition of chlorophyll synthesis in Y, this may be the main cause of leaf color change. Moreover, a protein interaction prediction model also showed that proteins such as PetC, PsbO, PsbP, and PsbQ were key proteins in the interaction network, and the up-regulated proteins participating in the anthocyanin and carotenoid pathways may be related to the formation of yellow-white leaves. Taken together, our findings represent the first SWATH-MS-based proteomic report on colored leaf O. fragrans and reveal that chlorophyll synthesis and secondary metabolism pathways contribute to the changes in leaf color.

Elucidating the metabolic roles of isoflavone synthase-mediated protein-protein interactions in yeast

Transient plant enzyme complexes formed via protein-protein interactions (PPIs) play crucial regulatory roles in secondary metabolism. Complexes assembled on cytochrome P450s (CYPs) are challenging to characterize metabolically due to difficulties in decoupling the PPIs' metabolic impacts from the CYPs' catalytic activities. Here, we developed a yeast-based synthetic biology approach to elucidate the metabolic roles of PPIs between a soybean-derived CYP, isoflavone synthase (GmIFS2), and other enzymes in isoflavonoid metabolism. By reconstructing multiple complex variants with an inactive GmIFS2 in yeast, we found that GmIFS2-mediated PPIs can regulate metabolic flux between two competing pathways producing deoxyisoflavonoids and isoflavonoids. Specifically, GmIFS2 can recruit chalcone synthase (GmCHS7) and chalcone reductase (GmCHR5) to enhance deoxyisoflavonoid production or GmCHS7 and chalcone isomerase (GmCHI1B1) to enhance isoflavonoid production. Additionally, we identified and characterized two novel isoflavone O-methyltransferases interacting with GmIFS2. This study highlights the potential of yeast synthetic biology for characterizing CYP-mediated complexes.

Step-by-step optimization of a heterologous pathway for de novo naringenin production in Escherichia coli

Naringenin is a plant polyphenol, widely explored due to its interesting biological activities, namely anticancer, antioxidant, and anti-inflammatory. Due to its potential applications and attempt to overcome the industrial demand, there has been an increased interest in its heterologous production. The microbial biosynthetic pathway to produce naringenin is composed of tyrosine ammonia-lyase (TAL), 4-coumarate-CoA ligase (4CL), chalcone synthase (CHS), and chalcone isomerase (CHI). Herein, we targeted the efficient de novo production of naringenin in Escherichia coli by performing a step-by-step validation and optimization of the pathway. For that purpose, we first started by expressing two TAL genes from different sources in three different E. coli strains. The highest p-coumaric acid production (2.54 g/L) was obtained in the tyrosine-overproducing M-PAR-121 strain carrying TAL from Flavobacterium johnsoniae (FjTAL). Afterwards, this platform strain was used to express different combinations of 4CL and CHS genes from different sources. The highest naringenin chalcone production (560.2 mg/L) was achieved by expressing FjTAL combined with 4CL from Arabidopsis thaliana (At4CL) and CHS from Cucurbita maxima (CmCHS). Finally, different CHIs were tested and validated, and 765.9 mg/L of naringenin was produced by expressing CHI from Medicago sativa (MsCHI) combined with the other previously chosen genes. To our knowledge, this titer corresponds to the highest de novo production of naringenin reported so far in E. coli. KEY POINTS: • Best enzyme and strain combination were selected for de novo naringenin production. • After genetic and operational optimizations, 765.9 mg/L of naringenin was produced. • This de novo production is the highest reported so far in E. coli.

Structural and Interactional Analysis of the Flavonoid Pathway Proteins: Chalcone Synthase, Chalcone Isomerase and Chalcone Isomerase-like Protein

Chalcone synthase (CHS) and chalcone isomerase (CHI) catalyze the first two committed steps of the flavonoid pathway that plays a pivotal role in the growth and reproduction of land plants, including UV protection, pigmentation, symbiotic nitrogen fixation, and pathogen resistance. Based on the obtained X-ray crystal structures of CHS, CHI, and chalcone isomerase-like protein (CHIL) from the same monocotyledon, Panicum virgatum, along with the results of the steady-state kinetics, spectroscopic/thermodynamic analyses, intermolecular interactions, and their effect on each catalytic step are proposed. In addition, PvCHI's unique activity for both naringenin chalcone and isoliquiritigenin was analyzed, and the observed hierarchical activity for those type-I and -II substrates was explained with the intrinsic characteristics of the enzyme and two substrates. The structure of PvCHS complexed with naringenin supports uncompetitive inhibition. PvCHS displays intrinsic catalytic promiscuity, evident from the formation of p-coumaroyltriacetic acid lactone (CTAL) in addition to naringenin chalcone. In the presence of PvCHIL, conversion of p-coumaroyl-CoA to naringenin through PvCHS and PvCHI displayed ~400-fold increased Vmax with reduced formation of CTAL by 70%. Supporting this model, molecular docking, ITC (Isothermal Titration Calorimetry), and FRET (Fluorescence Resonance Energy Transfer) indicated that both PvCHI and PvCHIL interact with PvCHS in a non-competitive manner, indicating the plausible allosteric effect of naringenin on CHS. Significantly, the presence of naringenin increased the affinity between PvCHS and PvCHIL, whereas naringenin chalcone decreased the affinity, indicating a plausible feedback mechanism to minimize spontaneous incorrect stereoisomers. These are the first findings from a three-body system from the same species, indicating the importance of the macromolecular assembly of CHS-CHI-CHIL in determining the amount and type of flavonoids produced in plant cells.

Efficient Production of Flavonoid Glucuronides in Escherichia coli Using Flavonoid O-Glucuronosyltransferases Characterized from Marchantia polymorpha

As a model liverwort, Marchantia polymorpha contains various flavone glucuronides with cardiovascular-promoting effects and anti-inflammatory properties. However, the related glucuronosyltransferases have not yet been reported. In this study, two bifunctional UDP-glucuronic acid/UDP-glucose:flavonoid glucuronosyltransferases/glucosyltransferases, MpUGT742A1 and MpUGT736B1, were identified from M. polymorpha. Extensive enzymatic assays found that MpUGT742A1 and MpUGT736B1 exhibited efficient glucuronidation activity for flavones, flavonols, and flavanones and showed promiscuous regioselectivity at positions 3, 6, 7, 3', and 4'. These enzymes catalyzed the production of a variety of flavonoid glucuronides with medicinal value, including apigenin-7-O-glucuronide and scutellarein-7-O-glucuronide. With the use of MpUGT736B1, apigenin-4'-O-glucuronide and apigenin-7,4'-di-O-glucuronide were prepared by scaled-up enzymatic catalysis and structurally identified by NMR spectroscopy. MpUGT742A1 also displayed glucosyltransferase activity on the 7-OH position of the flavanones using UDP-glucose as the sugar donor. Furthermore, we constructed four recombinant strains by combining the pathway for increasing the UDP-glucuronic acid supply with the two novel UGTs MpUGT742A1 and MpUGT736B1. When apigenin was used as a substrate, the extracellular apigenin-4'-O-glucuronide and apigenin-7,4'-di-O-glucuronide production obtained from the Escherichia coli strain BB2 reached 598 and 81 mg/L, respectively. Our study provides new candidate genes and strategies for the biosynthesis of flavonoid glucuronides.

Flavonols affect the interrelated glucosinolate and camalexin biosynthetic pathways in Arabidopsis thaliana

Flavonols are structurally and functionally diverse biomolecules involved in plant biotic and abiotic stress tolerance, pollen development, and inhibition of auxin transport. However, their effects on global gene expression and signaling pathways are unclear. To explore the roles of flavonol metabolites in signaling, we performed comparative transcriptome and targeted metabolite profiling of seedlings from the flavonol-deficient Arabidopsis loss-of-function mutant flavonol synthase1 (fls1) with and without exogenous supplementation of flavonol derivatives (kaempferol, quercetin, and rutin). RNA-seq results indicated that flavonols modulate various biological and metabolic pathways, with significant alterations in camalexin and aliphatic glucosinolate synthesis. Flavonols negatively regulated camalexin biosynthesis but appeared to promote the accumulation of aliphatic glucosinolates via transcription factor-mediated up-regulation of biosynthesis genes. Interestingly, upstream amino acid biosynthesis genes involved in methionine and tryptophan synthesis were altered under flavonol deficiency and exogenous supplementation. Quercetin treatment significantly up-regulated aliphatic glucosinolate biosynthesis genes compared with kaempferol and rutin. In addition, expression and metabolite analysis of the transparent testa7 mutant, which lacks hydroxylated flavonol derivatives, clarified the role of quercetin in the glucosinolate biosynthesis pathway. This study elucidates the molecular mechanisms by which flavonols interfere with signaling pathways, their molecular targets, and the multiple biological activities of flavonols in plants.

Genetic Channelization Mechanism of Four Chalcone Isomerase Homologous Genes for Synergistic Resistance to Fusarium wilt in Gossypium barbadense L

Duplication events occur very frequently during plant evolution. The genes in the duplicated pathway or network can evolve new functions through neofunctionalization and subfunctionalization. Flavonoids are secondary metabolites involved in plant development and defense. Our previous transcriptomic analysis of F6 recombinant inbred lines (RILs) and the parent lines after Fusarium oxysporum f. sp. vasinfectum (Fov) infection showed that CHI genes have important functions in cotton. However, there are few reports on the possible neofunctionalization differences of CHI family paralogous genes involved in Fusarium wilt resistance in cotton. In this study, the resistance to Fusarium wilt, expression of metabolic pathway-related genes, metabolite content, endogenous hormone content, reactive oxygen species (ROS) content and subcellular localization of four paralogous CHI family genes in cotton were investigated. The results show that the four paralogous CHI family genes may play a synergistic role in Fusarium wilt resistance. These results revealed a genetic channelization mechanism that can regulate the metabolic flux homeostasis of flavonoids under the mediation of endogenous salicylic acid (SA) and methyl jasmonate (MeJA) via the four paralogous CHI genes, thereby achieving disease resistance. Our study provides a theoretical basis for studying the evolutionary patterns of homologous plant genes and using homologous genes for molecular breeding.

Stepwise changes in flavonoids in spores/pollen contributed to terrestrial adaptation of plants

Protecting haploid pollen and spores against UV-B light and high temperature, 2 major stresses inherent to the terrestrial environment, is critical for plant reproduction and dispersal. Here, we show flavonoids play an indispensable role in this process. First, we identified the flavanone naringenin, which serves to defend against UV-B damage, in the sporopollenin wall of all vascular plants tested. Second, we found that flavonols are present in the spore/pollen protoplasm of all euphyllophyte plants tested and that these flavonols scavenge reactive oxygen species to protect against environmental stresses, particularly heat. Genetic and biochemical analyses showed that these flavonoids are sequentially synthesized in both the tapetum and microspores during pollen ontogeny in Arabidopsis (Arabidopsis thaliana). We show that stepwise increases in the complexity of flavonoids in spores/pollen during plant evolution mirror their progressive adaptation to terrestrial environments. The close relationship between flavonoid complexity and phylogeny and its strong association with pollen survival phenotypes suggest that flavonoids played a central role in the progression of plants from aquatic environments into progressively dry land habitats.

Identification and Functional Characterization of UDP-Glycosyltransferases Involved in Isoflavone Biosynthesis in Astragalus membranaceus

Isoflavones are rich natural compounds present in legumes and are essential for plant growth and development. Moreover, they are beneficial for animals and humans. Isoflavones are primarily found as glycoconjugates, including calycosin-7-O-β-d-glucoside (CG) in Astragalus membranaceus, a legume. However, the glycosylation mechanism of isoflavones in A. membranaceus remains unclear. In the present study, three uridine diphosphate (UDP)-glycosyltransferases (UGTs) that may be involved in the biosynthesis of isoflavone were identified in the transcriptome of A. membranaceus. Enzymatic analysis revealed that AmUGT88E29 and AmUGT88E30 had high catalytic activity toward isoflavones in vitro. In addition, AmUGT88E29 and AmUGT88E30 could accept various flavones, flavanones, flavonols, dihydroflavonols, and dihydrochalcones as substrates. AmUGT71G10 was only active against phloretin and dihydroresveratrol. Overexpression of AmUGT88E29 significantly increased the contents of CG, an isoflavone glucoside, in the hairy roots of A. membranaceus. This study provided candidate AmUGT genes for the potential metabolic engineering of flavonoid compounds in plants and a valuable resource for studying the calycosin glycosides biosynthesis pathway.

A Polyphenol Oxidase Catalyzes Aurone Synthesis in Marchantia polymorpha

Aurones constitute one of the major classes of flavonoids, with a characteristic furanone structure that acts as the C-ring of flavonoids. Members of various enzyme families are involved in aurone biosynthesis in different higher plants, suggesting that during evolution plants acquired the ability to biosynthesize aurones independently and convergently. Bryophytes also produce aurones, but the biosynthetic pathways and enzymes involved have not been determined. The present study describes the identification and characterization of a polyphenol oxidase (PPO) that acts as an aureusidin synthase (MpAS1) in the model liverwort, Marchantia polymorpha. Crude enzyme assays using an M. polymorpha line overexpressing MpMYB14 with high accumulation of aureusidin showed that aureusidin was biosynthesized from naringenin chalcone and converted to riccionidin A. This activity was inhibited by N-phenylthiourea, an inhibitor specific to enzymes of the PPO family. Of the six PPOs highly induced in the line overexpressing MpMyb14, one, MpAS1, was found to biosynthesize aureusidin from naringenin chalcone when expressed in Saccharomyces cerevisiae. MpAS1 also recognized eriodictyol chalcone, isoliquiritigenin and butein, showing the highest activity for eriodictyol chalcone. Members of the PPO family in M. polymorpha evolved independently from PPOs in higher plants, indicating that aureusidin synthases evolved in parallel in land plants.

Aim18p and Aim46p are chalcone isomerase domain-containing mitochondrial hemoproteins in Saccharomyces cerevisiae

Chalcone isomerases (CHIs) have well-established roles in the biosynthesis of plant flavonoid metabolites. Saccharomyces cerevisiae possesses two predicted CHI-like proteins, Aim18p (encoded by YHR198C) and Aim46p (YHR199C), but it lacks other enzymes of the flavonoid pathway, suggesting that Aim18p and Aim46p employ the CHI fold for distinct purposes. Here, we demonstrate using proteinase K protection assays, sodium carbonate extractions, and crystallography that Aim18p and Aim46p reside on the mitochondrial inner membrane and adopt CHI folds, but they lack select active site residues and possess an extra fungal-specific loop. Consistent with these differences, Aim18p and Aim46p lack CHI activity and also the fatty acid-binding capabilities of other CHI-like proteins, but instead bind heme. We further show that diverse fungal homologs also bind heme and that Aim18p and Aim46p possess structural homology to a bacterial hemoprotein. Collectively, our work reveals a distinct function and cellular localization for two CHI-like proteins, introduces a new variation of a hemoprotein fold, and suggests that ancestral CHI-like proteins were hemoproteins.

Flavonoid Production: Current Trends in Plant Metabolic Engineering and De Novo Microbial Production

Flavonoids are secondary metabolites that represent a heterogeneous family of plant polyphenolic compounds. Recent research has determined that the health benefits of fruits and vegetables, as well as the therapeutic potential of medicinal plants, are based on the presence of various bioactive natural products, including a high proportion of flavonoids. With current trends in plant metabolite research, flavonoids have become the center of attention due to their significant bioactivity associated with anti-cancer, antioxidant, anti-inflammatory, and anti-microbial activities. However, the use of traditional approaches, widely associated with the production of flavonoids, including plant extraction and chemical synthesis, has not been able to establish a scalable route for large-scale production on an industrial level. The renovation of biosynthetic pathways in plants and industrially significant microbes using advanced genetic engineering tools offers substantial promise for the exploration and scalable production of flavonoids. Recently, the co-culture engineering approach has emerged to prevail over the constraints and limitations of the conventional monoculture approach by harnessing the power of two or more strains of engineered microbes to reconstruct the target biosynthetic pathway. In this review, current perspectives on the biosynthesis and metabolic engineering of flavonoids in plants have been summarized. Special emphasis is placed on the most recent developments in the microbial production of major classes of flavonoids. Finally, we describe the recent achievements in genetic engineering for the combinatorial biosynthesis of flavonoids by reconstructing synthesis pathways in microorganisms via a co-culture strategy to obtain high amounts of specific bioactive compounds.

Identification of Chalcone Isomerase Family Genes and Roles of CnCHI4 in Flavonoid Metabolism in Camellia nitidissima

Camellia nitidissima is a woody plant with high ornamental value, and its golden-yellow flowers are rich in a variety of bioactive substances, especially flavonoids, that are beneficial to human health. Chalcone isomerases (CHIs) are key enzymes in the flavonoid biosynthesis pathway; however, there is a scarcity of information regarding the CHI family genes of C. nitidissima. In this study, seven CHI genes of C. nitidissima were identified and divided into three subfamilies by phylogenetic analysis. The results of multiple sequence alignment revealed that, unlike CnCHI1/5/6/7, CnCHI2/3/4 are bona fide CHIs that contain all the active site and critical catalytic residues. Analysis of the expression patterns of CnCHIs and the total flavonoid content of the flowers at different developmental stages revealed that CnCHI4 might play an essential role in the flavonoid biosynthesis pathway of C. nitidissima. CnCHI4 overexpression significantly increased flavonoid production in Nicotiana tabacum and C. nitidissima. The results of the dual-luciferase reporter assay and yeast one-hybrid system revealed that CnMYB7 was the key transcription factor that governed the transcription of CnCHI4. The study provides a comprehensive understanding of the CHI family genes of C. nitidissima and performed a preliminary analysis of their functions and regulatory mechanisms.

Flavonoid Metabolism in Tetrastigma hemsleyanum Diels et Gilg Based on Metabolome Analysis and Transcriptome Sequencing

Tetrastigma hemsleyanum Diels et Gilg, known as a "plant antibiotic", possesses several attractive properties including anti-inflammatory, anti-tumor, and antioxidant effects, with its efficacy being attributed to flavonoids. However, the flavonoid biosynthesis of T. hemsleyanum has rarely been studied. In this study, we investigated the flavonoid metabolism of T. hemsleyanum through metabolome analysis and transcriptome sequencing. The metabolomic results showed differences in the flavonoids of the leaves and root tubers of T. hemsleyanum. A total of 22 flavonoids was detected, and the concentrations of most flavonoids in the leaves were higher than those in the root tubers. Transcriptome analysis revealed that differentially expressed genes (DEGs) in the leaves and root tubers were enriched in photosynthesis-antenna proteins. Pearson correlation analysis indicated that the expression levels of chalcone isomerase (CHI) and UDP-glycose flavonoid glycosyltransferase (UFGT) were highly correlated with the concentrations of most flavonoids. Further, this study found that the photosynthesis-antenna proteins essentially contributed to the difference in the flavonoids in T. hemsleyanum. The gene expressions and concentrations of the total flavonoids of leaves and root tubers in Hangzhou, Jinhua, Lishui, and Taizhou in Zhejiang Province, China, showed that CHI (CL6715.Contig1_All, Unigene19431_All, CL921.Contig4_All) and UFGT (CL11556.Contig3_All, CL11775.Contig1_All) were the potential key genes of accumulation of most flavonoids in T. hemsleyanum.

Evolution and function of red pigmentation in land plants

BACKGROUND

Land plants commonly produce red pigmentation as a response to environmental stressors, both abiotic and biotic. The type of pigment produced varies among different land plant lineages. In the majority of species they are flavonoids, a large branch of the phenylpropanoid pathway. Flavonoids that can confer red colours include 3-hydroxyanthocyanins, 3-deoxyanthocyanins, sphagnorubins and auronidins, which are the predominant red pigments in flowering plants, ferns, mosses and liverworts, respectively. However, some flowering plants have lost the capacity for anthocyanin biosynthesis and produce nitrogen-containing betalain pigments instead. Some terrestrial algal species also produce red pigmentation as an abiotic stress response, and these include both carotenoid and phenolic pigments.

SCOPE

In this review, we examine: which environmental triggers induce red pigmentation in non-reproductive tissues; theories on the functions of stress-induced pigmentation; the evolution of the biosynthetic pathways; and structure-function aspects of different pigment types. We also compare data on stress-induced pigmentation in land plants with those for terrestrial algae, and discuss possible explanations for the lack of red pigmentation in the hornwort lineage of land plants.

CONCLUSIONS

The evidence suggests that pigment biosynthetic pathways have evolved numerous times in land plants to provide compounds that have red colour to screen damaging photosynthetically active radiation but that also have secondary functions that provide specific benefits to the particular land plant lineage.

De Novo Assembly of a Sarcocarp Transcriptome Set Identifies AaMYB1 as a Regulator of Anthocyanin Biosynthesis in Actinidia arguta var. purpurea

The kiwifruit (Actinidia arguta var. purpurea) produces oval shaped fruits containing a slightly green or mauve outer exocarp and a purple-flesh endocarp with rows of tiny black seeds. The flesh color of the fruit results from a range of anthocyanin compounds, and is an important trait for kiwifruit consumers. To elucidate the molecular mechanisms involved in anthocyanin biosynthesis of the sarcocarp during A. arguta fruit development, de novo assembly and transcriptomic profile analyses were performed. Based on significant Gene Ontology (GO) biological terms, differentially expressed genes were identified in flavonoid biosynthetic and metabolic processes, pigment biosynthesis, carbohydrate metabolic processes, and amino acid metabolic processes. The genes closely related to anthocyanin biosynthesis, such as phenylalanine ammonia-lyase (PAL), chalcone synthase (CHS), and anthocyanidin synthase (ANS), displayed significant up-regulation during fruit development according to the transcriptomic data, which was further confirmed by qRT-PCR. Meanwhile, a series of transcription factor genes were identified among the DEGs. Through a correlation analysis. AaMYB1 was found to be significantly correlated with key genes of anthocyanin biosynthesis, especially with CHS. Through a transient expression assay, AaMYB1 induced anthocyanin accumulation in tobacco leaves. These data provide an important basis for exploring the related mechanisms of sarcocarp anthocyanin biosynthesis in A. arguta. This study will provide a strong foundation for functional studies on A. arguta and will facilitate improved breeding of A. arguta fruit.

Flavonoids in vegetables: improvement of dietary flavonoids by metabolic engineering to promote health

Flavonoids are the most abundant polyphenols in plants, and have antioxidant effects as well as other bioactivities (e.g., anti-inflammatory, anti-cancer, anti-allergic, and neuroprotective effects). Vegetables are rich in flavonoids and are indispensable in our daily diet. Moreover, the vegetables as chassis for producing natural products would emerge as a promising means for cost-effective and sustainable production of flavonoids. Understanding the metabolic engineering of flavonoids in vegetables allows us to improve their nutrient composition. In this review, a comprehensive overview of flavonoids in vegetables, including the characterized types and distribution, health-promoting effects, associated metabolic pathways, and applied metabolic engineering are provided. We also introduce breakthroughs in multi-omics approaches that pertain to the elucidation of flavonoids metabolism in vegetables, as well as prospective and potential genome-editing technologies. Based on the varied composition and content of flavonoids among vegetables, dietary suggestions are further provided for human health.

Molecular and structural characterization of a promiscuous chalcone synthase from the fern species Stenoloma chusanum

The key enzymes involved in the flavonoid biosynthesis pathway have been extensively studied in seed plants, but relatively less in ferns. In this study, two 4-Coumarate: coenzyme A ligases (Sc4CL1 and Sc4CL2) and one novel chalcone synthase (ScCHS1) were functionally characterized by mining the Stenoloma chusanum transcriptome database. Recombinant Sc4CLs were able to esterify various hydroxycinnamic acids to corresponding acyl-coenzyme A (CoA). ScCHS1 could catalyze p-coumaroyl-CoA, cinnamoyl-CoA, caffeoyl-CoA, and feruloyl-CoA to form naringenin, pinocembrin, eriodictyol, and homoeriodictyol, respectively. Moreover, enzymatic kinetics studies revealed that the optimal substrates of ScCHS1 were feruloyl-CoA and caffeoyl-CoA, rather than p-coumaroyl-CoA, which was substantially different from the common CHSs. Crystallographic and site-directed mutagenesis experiments indicated that the amino acid residues, Leu87, Leu97, Met165, and Ile200, located in the substrate-binding pocket near the B-ring of products, could exert a significant impact on the unique catalytic activity of ScCHS1. Furthermore, overexpression of ScCHS1 in tt4 mutants could partially rescue the mutant phenotypes. Finally, ScCHS1 and Sc4CL1 were used to synthesize flavanones and flavones with multi-substituted hydroxyl and methoxyl B-ring in Escherichia coli, which can effectively eliminate the need for the cytochrome P450 hydroxylation/O-methyltransferase from simple phenylpropanoid acids. In summary, the identification of these important Stenoloma enzymes provides a springboard for the future production of various flavonoids in E. coli.

Genome-Wide Classification and Evolutionary Analysis Reveal Diverged Patterns of Chalcone Isomerase in Plants

Flavonoids as a class of important secondary metabolites are widely present in land plants, and chalcone isomerase (CHI) is the key rate-limiting enzyme that participates in catalyzing the stereospecific isomerization of chalcones to yield their corresponding flavanones. However, the phylogenetic dynamics and functional divergence of CHI family genes during the evolutionary path of green plants remains poorly understood. Here, a total of 122 CHI genes were identified by performing a genome-wide survey of 15 representative green plants from the most ancestral basal plant chlorophyte algae to higher angiosperm plants. Phylogenetic, orthologous groups (OG) classification, and genome structure analysis showed that the CHI family genes have evolved into four distinct types (types I–IV) containing eight OGs after gene duplication, and further studies indicated type III CHIs consist of three subfamilies (FAP1, FAP2, and FAP3). The phylogeny showed FAP3 CHIs as an ancestral out-group positioned on the outer layers of the main branch, followed by type IV CHIs, which are placed in an evolutionary intermediate between FAP3 CHIs and bona fide CHIs (including type I and type II). The results imply a potential intrinsic evolutionary connection between CHIs existing in the green plants. The amino acid substitutions occurring in several residues have potentially affected the functional divergence between CHI proteins. This is supported by the analysis of transcriptional divergence and cis-acting element analysis. Evolutionary dynamics analyses revealed that the differences in the total number of CHI family genes in each plant are primarily attributed to the lineage-specific expansion by natural selective forces. The current studies provide a deeper understanding of the phylogenetic relationships and functional diversification of CHI family genes in green plants, which will guide further investigation on molecular characteristics and biological functions of CHIs.

Deficiency in flavonoid biosynthesis genes CHS, CHI, and CHIL alters rice flavonoid and lignin profiles

Lignin is a complex phenylpropanoid polymer deposited in the secondary cell walls of vascular plants. Unlike most gymnosperm and eudicot lignins that are generated via the polymerization of monolignols, grass lignins additionally incorporate the flavonoid tricin as a natural lignin monomer. The biosynthesis and functions of tricin-integrated lignin (tricin-lignin) in grass cell walls and its effects on the utility of grass biomass remain largely unknown. We herein report a comparative analysis of rice (Oryza sativa) mutants deficient in the early flavonoid biosynthetic genes encoding CHALCONE SYNTHASE (CHS), CHALCONE ISOMERASE (CHI), and CHI-LIKE (CHIL), with an emphasis on the analyses of disrupted tricin-lignin formation and the concurrent changes in lignin profiles and cell wall digestibility. All examined CHS-, CHI-, and CHIL-deficient rice mutants were largely depleted of extractable flavones, including tricin, and nearly devoid of tricin-lignin in the cell walls, supporting the crucial roles of CHS and CHI as committed enzymes and CHIL as a noncatalytic enhancer in the conserved biosynthetic pathway leading to flavone and tricin-lignin formation. In-depth cell wall structural analyses further indicated that lignin content and composition, including the monolignol-derived units, were differentially altered in the mutants. However, regardless of the extent of the lignin alterations, cell wall saccharification efficiencies of all tested rice mutants were similar to that of the wild-type controls. Together with earlier studies on other tricin-depleted grass mutant and transgenic plants, our results reflect the complexity in the metabolic consequences of tricin pathway perturbations and the relationships between lignin profiles and cell wall properties.

De novo assembly of a fruit transcriptome set identifies AmMYB10 as a key regulator of anthocyanin biosynthesis in Aronia melanocarpa

Aronia is a group of deciduous fruiting shrubs, of the Rosaceae family, native to eastern North America. Interest in Aronia has increased because of the high levels of dietary antioxidants in Aronia fruits. Using Illumina RNA-seq transcriptome analysis, this study investigates the molecular mechanisms of polyphenol biosynthesis during Aronia fruit development. Six A. melanocarpa (diploid) accessions were collected at four fruit developmental stages. De novo assembly was performed with 341 million clean reads from 24 samples and assembled into 90,008 transcripts with an average length of 801 bp. The transcriptome had 96.1% complete according to Benchmarking Universal Single-Copy Orthologs (BUSCOs). The differentially expressed genes (DEGs) were identified in flavonoid biosynthetic and metabolic processes, pigment biosynthesis, carbohydrate metabolic processes, and polysaccharide metabolic processes based on significant Gene Ontology (GO) biological terms. The expression of ten anthocyanin biosynthetic genes showed significant up-regulation during fruit development according to the transcriptomic data, which was further confirmed using qRT-PCR expression analyses. Additionally, transcription factor genes were identified among the DEGs. Using a transient expression assay, we confirmed that AmMYB10 induces anthocyanin biosynthesis. The de novo transcriptome data provides a valuable resource for the understanding the molecular mechanisms of fruit anthocyanin biosynthesis in Aronia and species of the Rosaceae family.

A Moss 2-Oxoglutarate/Fe(II)-Dependent Dioxygenases (2-ODD) Gene of Flavonoids Biosynthesis Positively Regulates Plants Abiotic Stress Tolerance

Flavonoids, the largest group of polyphenolic secondary metabolites present in all land plants, play essential roles in many biological processes and defense against abiotic stresses. In the flavonoid biosynthesis pathway, flavones synthase I (FNSI), flavanone 3-hydroxylase (F3H), flavonol synthase (FLS), and anthocyanidin synthase (ANS) all belong to 2-oxoglutarate/Fe(II)-dependent dioxygenases (2-ODDs) family, which catalyzes the critical oxidative reactions to form different flavonoid subgroups. Here, a novel 2-ODD gene was cloned from Antarctic moss Pohlia nutans (Pn2-ODD1) and its functions were investigated both in two model plants, Physcomitrella patens and Arabidopsis thaliana. Heterologous expression of Pn2-ODD1 increased the accumulation of anthocyanins and flavonol in Arabidopsis. Meanwhile, the transgenic P. patens and Arabidopsis with expressing Pn2-ODD1 exhibited enhanced tolerance to salinity and drought stresses, with larger gametophyte sizes, better seed germination, and longer root growth. Heterologous expression of Pn2-ODD1 in Arabidopsis also conferred the tolerance to UV-B radiation and oxidative stress by increasing antioxidant capacity. Therefore, we showed that Pn2-ODD1 participated in the accumulation of anthocyanins and flavonol in transgenic plants, and regulated the tolerance to abiotic stresses in plants, contributing to the adaptation of P. nutans to the polar environment.

Elusive partners: a review of the auxiliary proteins guiding metabolic flux in flavonoid biosynthesis

Flavonoids are specialized metabolites widely distributed across the plant kingdom. They are involved in the growth and survival of plants, conferring the ability to filter ultra-violet rays, conduct symbiotic partnerships, and respond to stress. While many branches of flavonoid biosynthesis have been resolved, recent discoveries suggest missing auxiliary components. These overlooked elements can guide metabolic flux, enhance production, mediate stereoselectivity, transport intermediates, and exert regulatory functions. This review describes several families of auxiliary proteins from across the plant kingdom, including examples from specialized metabolism. In flavonoid biosynthesis, we discuss the example of chalcone isomerase-like (CHIL) proteins and their non-catalytic role. CHILs mediate the cyclization of tetraketides, forming the chalcone scaffold by interacting with chalcone synthase (CHS). Loss of CHIL activity leads to derailment of the CHS-catalyzed reaction and a loss of pigmentation in fruits and flowers. Similarly, members of the pathogenesis-related 10 (PR10) protein family have been found to differentially bind flavonoid intermediates, guiding the composition of anthocyanins. This role comes within a larger body of PR10 involvement in specialized metabolism, from outright catalysis (e.g., (S)-norcoclaurine synthesis) to controlling stereochemistry (e.g., enhancing cis-trans cyclization in catnip). Both CHILs and PR10s hail from larger families of ligand-binding proteins with a spectrum of activity, complicating the characterization of their enigmatic roles. Strategies for the discovery of auxiliary proteins are discussed, as well as mechanistic models for their function. Targeting such unanticipated components will be crucial in manipulating plants or engineering microbial systems for natural product synthesis.

Biochemical and Molecular Characterization of the Rice Chalcone Isomerase Family

Chalcone isomerase (CHI) is a key enzyme in flavonoid biosynthesis. In plants, CHIs occur in multigene families, and they are divided into four types, types I-IV. Type I and II CHIs are bona fide CHIs with CHI activity, and type III and IV CHIs are non-catalytic members with different functions. Rice contains seven CHI family genes (OsCHIs). Molecular analysis suggested that OsCHI3 is a type I CHI, and the other OsCHIs were classified into types III and IV. To elucidate their biochemical functions, OsCHI1, OsCHI3, OsCHI6, and OsCHI7 were expressed in Escherichia coli, and the recombinant OsCHI proteins were purified. An activity assay of recombinant OsCHIs showed that OsCHI3 catalyzed the isomerization of naringenin chalcone and isoliquiritigenin, whereas the other recombinant OsCHIs had no CHI activity. OsCHI3 also exhibited a strong preference to naringenin chalcone compared to isoliquiritigenin, which agrees well with the catalytic properties of type I CHIs. These results ascertain OsCHI3 to be a bona fide CHI in rice. OsCHI3 and the other OsCHIs were expressed constitutively throughout the rice growth period and different tissues. OsCHI3 expression was induced immediately in response to ultra-violet (UV) stress, suggesting its involvement in the biosynthesis of sakuranetin, a flavonoid phytoalexin in rice.

Cloning and functional characterization of three flavonoid O-glucosyltransferase genes from the liverworts Marchantia emarginata and Marchantia paleacea

Flavonoid glycosides are important plant secondary metabolites with broad pharmacological activities. Flavonoid glycosides are generated from aglycones, in reactions catalyzed by typical uridine diphosphate-dependent glycosyltransferases (UGTs). Liverworts produce various types of flavonoid glycosides; however, only two UGTs have been characterized from liverworts to date. Here, we isolated three genes encoding UGTs (MeUGT1, MeUGT2, and MpalUGT1) from the liverwort species Marchantia emarginata and Marchantia paleacea through transcriptome sequencing. Recombinant MeUGT1, MeUGT2, and MpalUGT1 proteins heterologously produced in Escherichia coli exhibited catalytic activity towards multiple flavonoids. MeUGT1 and MpalUGT1 catalyzed the glycosylation of flavonols into the corresponding 3-O-glucosides with UDP-glucose as the sugar donor, while MeUGT2 exhibited a wider substrate specificity that included flavonols, flavones, and flavanones. When MeUGT2 was expressed in E. coli, the yield of flavonol 3-O-glucosides reached to 40-60% with feeding of the substrates kaempferol or quercetin under optimal conditions. Furthermore, heterologous expression of MeUGT1 in Arabidopsis thaliana increased the flavonol glycoside contents in the plants. Therefore, the UGTs characterized in this study could provide new data that will be useful for examining flavonoid biosynthesis in liverworts.

Evolutionary History of Plant Metabolism

Tremendous chemical diversity is the hallmark of plants and is supported by highly complex biochemical machinery. Plant metabolic enzymes originated and were transferred from eukaryotic and prokaryotic ancestors and further diversified by the unprecedented rates of gene duplication and functionalization experienced in land plants. Unlike microbes, which have frequent horizontal gene transfer events and multiple inputs of energy and organic carbon, land plants predominantly rely on organic carbon generated from CO₂ and have experienced very few, if any, gene transfers during their recent evolutionary history. As such, plant metabolic networks have evolved in a stepwise manner and on existing networks under various evolutionary constraints. This review aims to take a broader view of plant metabolic evolution and lay a framework to further explore evolutionary mechanisms of the complex metabolic network. Understanding the underlying metabolic and genetic constraints is also an empirical prerequisite for rational engineering and redesigning of plant metabolic pathways.

Two putative parallel pathways for naringenin biosynthesis in Epimedium wushanense

Flavonoids that exhibit various biological activities such as antioxidant, antitumor, antiviral, antibacterial and anti-inflammatory properties are found in a wide range of medicinal plants. Among the flavonoid-producing plants identified so far, the genus Epimedium is recognised as a group of prolific prenyl-flavonoid glycoside producers with high economic value in the global dietary supplement market. To date, the biosynthetic genes for prenyl-flavonoid glycosides still remain elusive in Epimedium. Here, we identified five genes in Epimedium wushanense responsible for the biosynthesis of naringenin, the common precursor for flavonoid natural products. We successfully set up the biosynthetic pathway of naringenin using l-tyrosine as the precursor through enzymatic assays of these genes' encoding products, including phenylalanine ammonia-lyase (EwPAL), 4-coumarate-CoA ligase (Ew4CL1), chalcone synthase (EwCHS1), chalcone isomerase (EwCHI1) and CHI-like protein (EwCHIL3). Intriguingly, in vitro characterisation of the above catalytic enzymes' substrate specificity indicated a route parallel to naringenin biosynthesis, which starts from l-phenylalanine and ends in pinocembrin. The fact that there is no pinocembrin or pinocembrin-derived flavonoid accumulated in E. wushanense prompted us to propose that pinocembrin is likely converted into naringenin in vivo, constituting two parallel biosynthetic pathways for naringenin. Therefore, our study provides a basis for the full elucidation of the biosynthetic logic of prenyl-flavonoid glycoside in Epimedium, paving the way for future metabolite engineering and molecular breeding of E. wushanense to acquire a higher titre of desired, bioactive flavonoid compounds.

Functional characterization of two chalcone isomerase (CHI) revealing their responsibility for anthocyanins accumulation in mulberry

Mulberry (Morus sp., Moraceae) is an important economic crop plant and mulberry fruits are rich in anthocyanidins. Chalcone isomerase (CHI) catalyzes the conversion of chalcones to flavanones providing precursors for biosynthesis of anthocyanidins. In this study, bona fide CHIs were cloned and characterized from different Morus species with differently colored fruits (Morus multicaulis, Mm and Morus alba variety LvShenZi, LSZ). Enzymatic assay of MmCHI1 and MmCHI2 showed that they can utilize naringenin chalcone as substrate. The catalytic efficiency of MmCHI2 and LSZCHI2 are approximately 200 and 120-fold greater than that of MmCHI1 respectively. Phylogenetic analysis showed the two mulberry CHIs belonged to different sub-clade of Type I CHI1 named type IA (CHI2) and type IB (CHI1). Type IB CHIs are mulberry specific. MmCHI1 and MmCHI2 had similar expression profiles and showed preferred expression in fruits. In addition, both mulberry CHI1 and CHI2 played roles in the response to excess zinc stress and sclerotiniose pathogen infection. Both MmCHI1 and MmCHI2 expression levels showed positive close relationship with anthocyanins content during fruit ripening process. The co-expression of MmCHI1 and MmCHI2 was observed during fruit ripening process and in transgenic mulberry. VIGS (virus induced gene silence) targeting on MmCHI1 and MmCHI2 showed significant down-regulation of MmCHI2 instead of MmCHI1 would result in significant (about 50%) decrease in anthocyanins content. MmCHI2 is the dominant CHI for anthocyanins accumulation in mulberry. The results presented in this work provided insight on bona fide CHIs in mulberry and reveal their roles in anthocyanins accumulation.

Three AP2/ERF family members modulate flavonoid synthesis by regulating type IV chalcone isomerase in citrus

Flavanones and flavones are excellent source of bioactive compounds but the molecular basis of their highly efficient production remains elusive. Chalcone isomerase (CHI) family proteins play essential roles in flavonoid biosynthesis but little are known about the transcription factors controlling their gene expression. Here, we identified a type IV CHI (designated as CitCHIL1) from citrus which enhances the accumulation of citrus flavanones and flavones (CFLs). CitCHIL1 participates in a CFL biosynthetic metabolon and assists the cyclization of naringenin chalcone to (2S)-naringenin, which leads to the efficient influx of substrates to chalcone synthase (CHS) and improves the catalytic efficiency of CHS. Overexpressing CitCHIL1 in Citrus and Arabidopsis significantly increased flavonoid content and RNA interference-induced silencing of CitCHIL1 in citrus led to a 43% reduction in CFL content. Three AP2/ERF transcription factors were identified as positive regulators of the CitCHIL1 expression. Of these, two dehydration-responsive element binding (DREB) proteins, CitERF32 and CitERF33, activated the transcription by directly binding to the CGCCGC motif in the promoter, while CitRAV1 (RAV: related to ABI3/VP1) formed a transcription complex with CitERF33 that strongly enhanced the activation efficiency and flavonoid accumulation. These results not only illustrate the specific function that CitCHIL1 executes in CFL biosynthesis but also reveal a new DREB-RAV transcriptional complex regulating flavonoid production.

Functional and Structural Investigation of Chalcone Synthases Based on Integrated Metabolomics and Transcriptome Analysis on Flavonoids and Anthocyanins Biosynthesis of the Fern Cyclosorus parasiticus

The biosynthesis of flavonoids and anthocyanidins has been exclusively investigated in angiosperms but largely unknown in ferns. This study integrated metabolomics and transcriptome to analyze the fronds from different development stages (S1 without spores and S2 with brown spores) of Cyclosorus parasiticus. About 221 flavonoid and anthocyanin metabolites were identified between S1 and S2. Transcriptome analysis revealed several genes encoding the key enzymes involved in the biosynthesis of flavonoids, and anthocyanins were upregulated in S2, which were validated by qRT-PCR. Functional characterization of two chalcone synthases (CpCHS1 and CpCHS2) indicated that CpCHS1 can catalyze the formation of pinocembrin, naringenin, and eriodictyol, respectively; however, CpCHS2 was inactive. The crystallization investigation of CpCHS1 indicated that it has a highly similar conformation and shares a similar general catalytic mechanism to other plants CHSs. And by site-directed mutagenesis, we found seven residues, especially Leu199 and Thr203 that are critical to the catalytic activity for CpCHS1.

Identification and Characterization of Chalcone Isomerase Genes Involved in Flavonoid Production in Dracaena cambodiana

Dragon's blood is a traditional medicine in which flavonoids are the main bioactive compounds; however, the underlying formation mechanism of dragon's blood remains largely poorly understood. Chalcone isomerase (CHI) is the key enzyme in the flavonoid biosynthesis pathway. However, CHI family genes are not well understood in Dracaena cambodiana Pierre ex Gagnep, an important source plant of dragon's blood. In this study, 11 CHI family genes were identified from D. cambodiana, and they were classified into three types. Evolutionary and transcriptional profiling analysis revealed that DcCHI1 and DcCHI4 might be involved in flavonoid production. Both DcCHI1 and DcCHI4 displayed low expression levels in stem under normal growth conditions and were induced by methyl jasmonate (MeJA), 6-benzyl aminopurine (6-BA, synthetic cytokinin), ultraviolet-B (UV-B), and wounding. The recombinant proteins DcCHI1 and DcCHI4 were expressed in Escherichia coli and purified by His-Bind resin chromatography. Enzyme activity assay indicated that DcCHI1 catalyzed the formation of naringenin from naringenin chalcone, while DcCHI4 lacked this catalytic activity. Overexpression of DcCHI1 or DcCHI4 enhanced the flavonoid production in D. cambodiana and tobacco. These findings implied that DcCHI1 and DcCHI4 play important roles in flavonoid production. Thus, our study will not only contribute to better understand the function and expression regulation of CHI family genes involved in flavonoid production in D. cambodiana but also lay the foundation for developing the effective inducer of dragon's blood.

Screening of key genes responsible for Pennisetum setaceum 'Rubrum' leaf color using transcriptome sequencing

Pennisetum setaceum 'Rubrum' is an ornamental grass plant that produces purple leaves in high-light environments and light purple or green leaves in low-light environments, the latter of which greatly reduces its aesthetic appeal. Therefore, we aimed to identify the key genes associated with leaf coloration and elucidate the molecular mechanisms involved in the color changes in P. setaceum 'Rubrum' leaves. We performed transcriptome sequencing of P. setaceum 'Rubrum' leaves before and after shading. A total of 19,043 differentially expressed genes were identified, and the numbers of upregulated and downregulated genes at T1 stage, when compared with their expression at the T0 stage, were 10,761 and 8,642, respectively. The possible pathways that determine P. setaceum 'Rubrum' leaf color included flavonoid biosynthesis, flavone and flavonol biosynthesis, and carotenoid biosynthesis. There were 31 differentially expressed genes related to chlorophyll metabolism, of which 21 were related to chlorophyll biosynthesis and 10 to chlorophyll degradation, as well as three transcription factors that may be involved in the regulation of chlorophyll degradation. There were 31 key enzyme genes involved in anthocyanin synthesis and accumulation in P. setaceum 'Rubrum' leaves, with four transcription factors that may be involved in the regulation of anthocyanin metabolism. The transcriptome data were verified and confirmed reliable by real-time fluorescence quantitative PCR analysis. These findings provide a genetic basis for improving leaf color in P. setaceum 'Rubrum.'

Functional characterization of UDP-glycosyltransferases from the liverwort Plagiochasma appendiculatum and their potential for biosynthesizing flavonoid 7-O-glucosides

Flavonoid glucosides, typically generated from aglycones via the action of uridine diphosphate-dependent glycosyltransferases (UGTs), both contribute to plant viability and are pharmacologically active. The properties of UGTs produced by liverworts, one of the basal groups of non-vascular land plants, have not been systematically explored. Here, two UGTs potentially involved in flavonoids synthesis were identified from the transcriptome of Plagiochasma appendiculatum. Enzymatic analysis showed that PaUGT1 and PaUGT2 accepted various flavones, flavonols, flavanones and dihydrochalcones as substrates. A mutated form PaUGT1-Q19A exhibited a higher catalytic efficiency than did the wild type enzyme. When expressed in Escherichia coli, the yield of flavonol 7-O-glucosides reached to over 70 %. Co-expression of PaUGT1-Q19A with the upstream flavone synthase I PaFNS I-1 proved able to convert the flavanone aglycones naringenin and eriodictyol into the higher-yield apigenin 7-O-glucoside (A7G) and luteolin 7-O-glucoside (L7G). The maximum concentration of 81.0 μM A7G and 88.6 μM L7G was achieved upon supplementation with 100 μM naringenin and 100 μM eriodictyol under optimized conditions. This is the first time that flavonoids UGTs have been characterized from liverworts and co-expression of UGTs and FNS Is from the same species serves as an effective strategy to synthesize flavone 7-O-glucosides in E. coli.

The moss flavone synthase I positively regulates the tolerance of plants to drought stress and UV-B radiation

Flavonoids are extensively distributed secondary metabolites in land plants. They play a critical role in plant evolution from aquatic to terrestrial and plant adaption to ultraviolet radiation. However, the downstream branching pathway of flavonoids and its regulatory mechanism in bryophytes, which are the most ancient of terrestrial plants, remain unclear. Here, a type I flavone synthase (PnFNSI) was characterized from the Antarctic moss Pohlia nutans. PnFNSI was primarily distributed in the cytoplasm, as detected by subcellular localization. PnFNSI could catalyze the conversion of naringenin to apigenin with an optimal temperature between 15 and 20 °C in vitro. Overexpression of PnFNSI in Arabidopsis alleviated the growth restriction caused by naringenin and accumulated apigenin product. PnFNSI-overexpressing plants showed enhanced plant tolerance to drought stress and UV-B radiation. PnFNSI also increased the enzyme activities and gene transcription levels of reactive oxygen species (ROS) scavengers, protecting plants against oxidative stress. Moreover, overexpression of PnFNSI enhanced the flavone biosynthesis pathway in Arabidopsis. Therefore, this moss FNSI-type enzyme participates in flavone metabolism, conferring protection against drought stress and UV-B radiation.

Automatic Identification of Players in the Flavonoid Biosynthesis with Application on the Biomedicinal Plant Croton tiglium

The flavonoid biosynthesis is a well-characterised model system for specialised metabolism and transcriptional regulation in plants. Flavonoids have numerous biological functions such as UV protection and pollinator attraction, but also biotechnological potential. Here, we present Knowledge-based Identification of Pathway Enzymes (KIPEs) as an automatic approach for the identification of players in the flavonoid biosynthesis. KIPEs combines comprehensive sequence similarity analyses with the inspection of functionally relevant amino acid residues and domains in subjected peptide sequences. Comprehensive sequence sets of flavonoid biosynthesis enzymes and knowledge about functionally relevant amino acids were collected. As a proof of concept, KIPEs was applied to investigate the flavonoid biosynthesis of the medicinal plant Croton tiglium on the basis of a transcriptome assembly. Enzyme candidates for all steps in the biosynthesis network were identified and matched to previous reports of corresponding metabolites in Croton species.

Phylogenomics reveals convergent evolution of red-violet coloration in land plants and the origins of the anthocyanin biosynthetic pathway

The flavonoids, one of the largest classes of plant secondary metabolites, are found in lineages that span the land plant phylogeny and play important roles in stress responses and as pigments. Perhaps the most well-studied flavonoids are the anthocyanins that have human health benefits and help plants attract pollinators, regulate hormone production, and confer resistance to abiotic and biotic stresses. The canonical biochemical pathway responsible for the production of these pigments is well-characterized for flowering plants yet its conservation across deep divergences in land plants remains debated and poorly understood. Many early land plants such as mosses, liverworts, and ferns produce flavonoid pigments, but their biosynthetic origins and homologies to the anthocyanin pathway remain uncertain. We conducted phylogenetic analyses using full genome sequences representing nearly all major green plant lineages to reconstruct the evolutionary history of the anthocyanin biosynthetic pathway then test the hypothesis that genes in this pathway are present in early land plants. We found that the entire pathway was not intact until the most recent common ancestor of seed plants and that orthologs of many downstream enzymes are absent from seedless plants including mosses, liverworts, and ferns. Our results also highlight the utility of phylogenetic inference, as compared to pairwise sequence similarity, in orthology assessment within large gene families that have complex duplication-loss histories. We suggest that the production of red-violet flavonoid pigments widespread in seedless plants, including the 3-deoxyanthocyanins, requires the activity of novel, as-yet discovered enzymes, and represents convergent evolution of red-violet coloration across land plants.

Overexpression of chalcone isomerase in apple reduces phloridzin accumulation and increases susceptibility to herbivory by two-spotted mites

Apples (Malus spp.) accumulate significant quantities of the dihydrochalcone glycoside, phloridzin, whilst pears (Pyrus spp.) do not. To explain this difference, we hypothesized that a metabolic bottleneck in the phenylpropanoid pathway might exist in apple. Expression analysis indicated that transcript levels of early phenylpropanoid pathway genes in apple and pear leaves were similar, except for chalcone isomerase (CHI), which was much lower in apple. Apples also showed very low CHI activity compared with pear. To relieve the bottleneck at CHI, transgenic apple plants overexpressing the Arabidopsis AtCHI gene were produced. Unlike other transgenic apples where phenylpropanoid flux was manipulated, AtCHI overexpression (CHIox) plants were phenotypically indistinguishable from wild-type, except for an increase in red pigmentation in expanding leaves. CHIox plants accumulated slightly increased levels of flavanols and flavan-3-ols in the leaves, but the major change was a 2.8- to 19-fold drop in phloridzin concentrations compared with wild-type. The impact of these phytochemical changes on insect preference was studied using a two-choice leaf assay with the polyphagous apple pest, the two-spotted spider mite (Tetranychus urticae Koch). Transgenic CHIox leaves were more susceptible to herbivory, an effect that could be reversed (complemented) by application of phloridzin to transgenic leaves. Taken together, these findings shed new light on phenylpropanoid biosynthesis in apple and suggest a new physiological role for phloridzin as an antifeedant in leaves.

Transcriptomic Analysis of Ficus carica Peels with a Focus on the Key Genes for Anthocyanin Biosynthesis

Fig (Ficus carica L.), a deciduous fruit tree of the Moraceae, provides ingredients for human health such as anthocyanins. However, little information is available on its molecular structure. In this study, the fig peels in the yellow (Y) and red (R) stages were used for transcriptomic analyses. Comparing the R with the Y stage, we obtained 6224 differentially expressed genes, specifically, anthocyanin-related genes including five CHS, three CHI, three DFR, three ANS, two UFGT and seven R2R3-MYB genes. Furthermore, three anthocyanin biosynthetic genes, i.e., FcCHS1, FcCHI1 and FcDFR1, and two R2R3-MYB genes, i.e., FcMYB21 and FcMYB123, were cloned; sequences analysis and their molecular characteristics indicated their important roles in fig anthocyanin biosynthesis. Heterologous expression of FcMYB21 and FcMYB123 significantly promoted anthocyanin accumulation in both apple fruits and calli, further suggesting their regulatory roles in fig coloration. These findings provide novel insights into the molecular mechanisms behind fig anthocyanin biosynthesis and coloration, facilitating the genetic improvement of high-anthocyanin cultivars and other horticultural traits in fig fruits.

The Evolution of Flavonoid Biosynthesis: A Bryophyte Perspective

The flavonoid pathway is one of the best characterized specialized metabolite pathways of plants. In angiosperms, the flavonoids have varied roles in assisting with tolerance to abiotic stress and are also key for signaling to pollinators and seed dispersal agents. The pathway is thought to be specific to land plants and to have arisen during the period of land colonization around 550-470 million years ago. In this review we consider current knowledge of the flavonoid pathway in the bryophytes, consisting of the liverworts, hornworts, and mosses. The pathway is less characterized for bryophytes than angiosperms, and the first genetic and molecular studies on bryophytes are finding both commonalities and significant differences in flavonoid biosynthesis and pathway regulation between angiosperms and bryophytes. This includes biosynthetic pathway branches specific to each plant group and the apparent complete absence of flavonoids from the hornworts.

Identification and evolutionary analysis of chalcone isomerase-fold proteins in ferns

The distribution of type I and II chalcone isomerases (CHIs) in plants is highly family specific. We have previously reported that ancient land plants, such as the liverworts and Selaginella moellendorffii, harbor type II CHIs. To better understand the function and evolution of CHI-fold proteins, transcriptomic data obtained from 52 pteridophyte species were subjected to sequence alignment and phylogenetic analysis. The residues determining type I/II CHI identity in the pteridophyte CHIs were identical to those of type I CHIs. The enzymatic characterization of a sample of 24 CHIs, representing all the key pteridophyte lineages, demonstrated that 19 of them were type I enzymes and that five exhibited some type II activity due to an amino acid mutation. Two pteridophyte chalcone synthases (CHSs) were also characterized, and a type IV CHI (CHIL) was demonstrated to interact physically with CHSs and CHI, and to increase CHS activity by decreasing derailment products, thus enhancing flavonoid production. These findings suggest that the emergence of type I CHIs may have coincided with the divergence of the pteridophytes. This study deepens our understanding of the molecular mechanism of CHIL as an enhancer in the flavonoid biosynthesis pathway.

The Chalcone Isomerase Family in Cotton: Whole-Genome Bioinformatic and Expression Analyses of the Gossypium barbadense L. Response to Fusarium Wilt Infection

Chalcone isomerase (CHI) is a key component of phenylalanine metabolism that can produce a variety of flavonoids. However, little information and no systematic analysis of CHI genes is available for cotton. Here, we identified 33 CHI genes in the complete genome sequences of four cotton species (Gossypium arboretum L., Gossypium raimondii L., Gossypium hirsutum L., and Gossypium barbadense L.). Cotton CHI proteins were classified into two main groups, and whole-genome/segmental and dispersed duplication events were important in CHI gene family expansion. qRT-PCR and semiquantitative RT-PCR results suggest that CHI genes exhibit temporal and spatial variation and respond to infection with Fusarium wilt race 7. A preliminary model of CHI gene involvement in cotton evolution was established. Pairwise comparison revealed that seven CHI genes showed higher expression in cultivar 06-146 than in cultivar Xinhai 14. Overall, this whole-genome identification unlocks a new approach to the comprehensive functional analysis of the CHI gene family, which may be involved in adaptation to plant pathogen stress.

Exploiting MATE efflux proteins to improve flavonoid accumulation in Camellia sinensis in silico

Flavonoids in tea plant are the important bioactive compounds for both human health and taste quality. Multidrug and Toxic compound Extrusion (MATE) proteins could improve flavonoid accumulations by transporting and sequestering the flavonoid in vacuoles. We identified 41 putative MATE genes in tea plants. The similar intron-exon structures of tea MATEs clustered within the same gene clade. The correlation analysis of tea flavonoid and transcriptome data showed that TEA006173 might be involve in the tea flavonoid accumulation. The RT-PCR results confirmed that TEA006173 showed high expression in the young leaf tissues. Tertiary structure prediction has shown that TEA006173 contained the 12 helices with three active pockets, comprising 13 critical residues. The present study provided the structural variations and expression patterns of tea MATEs and it would be helpful for taste and nutrient quality improvement in tea plant.

Auronidins are a previously unreported class of flavonoid pigments that challenges when anthocyanin biosynthesis evolved in plants

Anthocyanins are key pigments of plants, providing color to flowers, fruit, and foliage and helping to counter the harmful effects of environmental stresses. It is generally assumed that anthocyanin biosynthesis arose during the evolutionary transition of plants from aquatic to land environments. Liverworts, which may be the closest living relatives to the first land plants, have been reported to produce red cell wall-bound riccionidin pigments in response to stresses such as UV-B light, drought, and nutrient deprivation, and these have been proposed to correspond to the first anthocyanidins present in early land plant ancestors. Taking advantage of the liverwort model species Marchantia polymorpha, we show that the red pigments of Marchantia are formed by a phenylpropanoid biosynthetic branch distinct from that leading to anthocyanins. They constitute a previously unreported flavonoid class, for which we propose the name "auronidin," with similar colors as anthocyanin but different chemistry, including strong fluorescence. Auronidins might contribute to the remarkable ability of liverworts to survive in extreme environments on land, and their discovery calls into question the possible pigment status of the first land plants.