Metabolon formation and metabolic channeling in the biosynthesis of plant natural products

Evidence supporting multienzyme complexes as metabolons: A review

Fungi are widespread organisms with complex multienzyme systems crucial for diverse biochemical processes. This study systematically reviewed research on multienzyme complexes, focusing on their isolation and identification, while examining their potential classification as metabolons. Using a theoretical framework based on PRISMA guidelines, the review analysed literature from 2013 to 2023 across databases such as Medline, Web of Science, and ScienceDirect, employing targeted descriptors to identify relevant studies. The articles were selected by two independent reviewers among those published in English in the last 10 years. From 2313 papers identified through bibliographic searches, 13 were selected for qualitative analysis. Purification methods for fungal multienzyme complexes vary, each offering unique advantages and requiring tailored approaches for specific enzyme systems. The isolation and characterisation of multienzyme complexes face significant challenges. Their classification as metabolons depends on three criteria: substrate channelling, functional coupling, and dynamic assembly. Although research highlights the significance of substrate channelling and the function of stabilising proteins in improving metabolic efficiency, evidence for dynamic assembly is limited. Future research should emphasise new stabilising measures, real-time monitoring of intricate dynamics, and a more profound investigation of molecular causes.

Toward Design Principles for Biomolecular Condensates for Metabolic Pathways

Biology uses membrane-less organelles or biomolecular condensates as dynamic reaction compartments that can form or dissolve to regulate biochemical pathways. This has led to a flurry of research aiming to design new synthetic organelles that function as reaction crucibles for enzymes and biomolecular cascades in biotechnology. The mechanisms by which a condensate can enhance multistep biochemical processes including mass action, tuning the chemical environment, scaffolding and metabolic channelling is reviewed. These mechanisms are not inherently beneficial for the rate of enzymatic processes but can also inhibit a reaction. Similarly, some aspects of condensates are likely intrinsically inhibitory including retardation of diffusion, where the net effect of a condensate will be a trade-off between inhibitory and stimulatory effects. It is discussed which generalizable conclusions can be drawn so far and how close it is to design principles for condensates for enzyme cascades in microbial cell factories including which reactions are likely to be enhanced by condensates and which type of condensate will be suited for which reaction.

Occurrence and characterization of tricin-lignin

Tricin, a flavonoid, is a noncanonical lignin monomer present in grasses and other monocots, but rarely in dicots. This review explores the latest discovery of biosynthesis, transport, and distribution of tricin in plant cell walls, and discusses the missing gaps in this engaging topic. Tricin biosynthesis in grasses involves the phenylpropanoid and flavonoid pathways, with distinct enzymatic processes leading to tricin incorporation into lignin polymers. Methods for characterizing and quantifying tricin in lignin are also highlighted, including NMR spectroscopy and chromatographic techniques with discussion of challenges associated with its low abundance in plant tissues. The stability of tricin during biomass pretreatment processes is discussed, with findings indicating that acidic and alkaline conditions degrade tricin, while milder pretreatments preserve its structure. These insights underscore the potential of tricin in enhancing the functionality of lignin for sustainable bioprocessing, offering promising applications in pharmaceuticals, nutraceuticals, and biorefinery industries.

Integrative omics reveals mechanisms of biosynthesis and regulation of floral scent in Cymbidium tracyanum

Flower scent is a crucial determiner in pollinator attraction and a significant horticultural trait in ornamental plants. Orchids, which have long been of interest in evolutionary biology and horticulture, exhibit remarkable diversity in floral scent type and intensity. However, the mechanisms underlying floral scent biosynthesis and regulation in orchids remain largely unexplored. In this study, we focus on floral scent in Cymbidium tracyanum, a wild species known for its strong floral fragrance and as a primary breeding parent of commercial Cymbidium hybrids. We present a chromosome-level genome assembly of C. tracyanum, totaling 3.79 Gb in size. Comparative genomic analyses reveal significant expansion of gene families associated with terpenoid biosynthesis and related metabolic pathways in C. tracyanum. Integrative analysis of genomic, volatolomic and transcriptomic data identified terpenoids as the predominant volatile components in the flowers of C. tracyanum. We characterized the spatiotemporal patterns of these volatiles and identified CtTPS genes responsible for volatile terpenoid biosynthesis, validating their catalytic functions in vitro. Dual-luciferase reporter assays, yeast one-hybrid assays and EMSA experiments confirmed that CtTPS2, CtTPS3, and CtTPS8 could be activated by various transcription factors (i.e., CtAP2/ERF1, CtbZIP1, CtMYB2, CtMYB3 and CtAP2/ERF4), thereby regulating the production of corresponding monoterpenes and sesquiterpenes. Our study elucidates the biosynthetic and regulatory mechanisms of floral scent in C. tracyanum, which is of great significance for the breeding of fragrant Cymbidium varieties and understanding the ecological adaptability of orchids. This study also highlights the importance of integrating multi-omics data in deciphering key horticultural traits in orchids.

Genomic, transcriptomic, and metabolomic analyses reveal convergent evolution of oxime biosynthesis in Darwin's orchid

Angraecum sesquipedale, also known as Darwin's orchid, possesses an exceptionally long nectar spur. Charles Darwin predicted the orchid to be pollinated by a hawkmoth with a correspondingly long proboscis, later identified as Xanthopan praedicta. In this plant-pollinator interaction, the A. sesquipedale flower emits a complex blend of scent compounds dominated by diurnally regulated oximes (R1R2C = N-OH) to attract crepuscular and nocturnal pollinators. The molecular mechanism of oxime biosynthesis remains unclear in orchids. Here, we present the chromosome-level genome of A. sesquipedale. The haploid genome size is 2.10 Gb and represents 19 pseudochromosomes. Cytochrome P450 encoding genes of the CYP79 family known to be involved in oxime biosynthesis in seed plants are not present in the A. sesquipedale genome nor the genomes of other members of the orchid family. Metabolomic analysis of the A. sesquipedale flower revealed a substantial release of oximes at dusk during the blooming stage. By integrating metabolomic and transcriptomic correlation approaches, flavin-containing monooxygenases (FMOs) encoded by six tandem-repeat genes in the A. sesquipedale genome are identified as catalyzing the formation of oximes present. Further in vitro and in vivo assays confirm the function of FMOs in the oxime biosynthesis. We designate these FMOs as orchid oxime synthases 1-6. The evolutionary aspects related to the CYP79 gene losses and neofunctionalization of FMO-catalyzed biosynthesis of oximes in Darwin's orchid provide new insights into the convergent evolution of biosynthetic pathways.

Designing a microbial factory suited for plant chloroplast-derived enzymes to efficiently and green synthesize natural products: Capsanthin and capsorubin as examples

Specific cellular microenvironment, multi-enzyme complex and expensive essential cofactor make the biological manufacturing of plant chloroplast natural products (PCNPs) extremely challenging. The above difficulties have hampered the biosynthesis of capsanthin and capsorubin in the past 30 years. Here, we take capsanthin and capsorubin as examples to design an innovative microbial factory to promote the heterologous synthesis of PCPNs. Our main strategy is mimicking the microenvironment of chloroplasts in microbial factory. First, accumulation of violaxanthin, which is the key precursor, was increased by 587.9%, through introducing oxidative microenvironment and thioredoxin. The initial capsanthin-producing strain with 0.28 mg g-1 DCW were obtained by introducing capsanthin/capsorubin synthase (CCS). Subsequently, chloroplast-derived chaperones Cpn60α, Cpn60β and Cpn20 created a folding-promoting microenvironment for CCS. At the same time, by imitating the quasi-natural CCS, an artificial homotrimer was constructed and obtained 5.15 mg g-1 DCW capsanthin, and 1.62 mg g-1 DCW capsorubin. Finally, sufficient FADH2 was provided for CCS by feeding 20 mM formate. This process was realized by the continuous catalysis of formate dehydrogenase and flavin reductase. The engineered strain accumulated 6.77 mg g-1 DCW of capsanthin and 2.18 mg g-1 DCW of capsorubin. Compared with the initial strain, the yield of capsanthin was increased by 24.18 times, and 13.54 times of the highest yield reported so far. Artificially designed microbial cell factory and low-cost cofactor supply methods are in line with the current sustainable and green wave of biochemicals. This work not only provides a platform strain for low-cost and sustainable biosynthesis, but also provides a paradigm for heterologous expression of chloroplast-derived enzymes.

Identification and expression of a hydrophobic carboxylic acid reductase from Trichoderma virens

Carboxylic acid reductases (CARs) have been garnering attention in applications for the sustainable synthesis of aldehydes. Despite numerous discoveries, not all characteristics of CAR enzymes have been extensively studied or understood. Herein, we report the discovery and expression of a new CAR enzyme (TvirCAR2) from the ascomycetous fungus, Trichoderma virens. Tvircar2 is one of the five putative CARs identified from analyses of the T. virens genome. In silico, analyses showed that TvirCAR2 has a high hydrophobicity index and that its corresponding gene is part of a biosynthetic gene cluster predicted to synthesize hybrid polyketide synthases-nonribosomal peptide synthetase secondary metabolites. TvirCAR2 was highly expressed as soluble and insoluble forms in an Escherichia coli expression host. The solubility of the purified TvirCAR2 necessitated the addition of glycerol in the purification and assay buffers. Substrate screening via molecular docking showed that benzoic acid was a suitable substrate candidate. The TvirCAR2 enzyme catalyzed the reduction of benzoic acid with a specific activity of around 1.4 µmol/h/mg. Homologs, which are predicted to exhibit similar hydrophobicity, are the CARs from Stachybotrys bisbyi (StbB), which is involved in the production of the meroterpenoid, ilicicolin B, and Trichoderma reesei (TrCAR), which is part of a similar but still uncharacterized biosynthetic gene cluster.

Spatial chromosome organization and adaptation of the radiation-resistant extremophile Deinococcus radiodurans

Radiation-resistant Deinococcus radiodurans is an extremophilic microorganism capable of withstanding high levels of ionizing radiation and chemical mutagens. It possesses remarkable DNA repair capability and serves as a model organism for studying stress resistance mechanisms. However, our understanding of the spatial chromosome organization of this species remains limited. In this study, we employed chromosome conformation capture (3C) technology to determine the 3D genome structure of D. radiodurans and to further investigate the changes of chromosome conformation induced by ultraviolet (UV) irradiation. We observed that UV irradiation reduced short-range chromosome interactions, and smaller chromosomal interaction domains (CIDs) merged to form larger CIDs. Integrating transcriptomic data analysis, we found that the majority of upregulated differentially expressed genes were significantly enriched near specific CID boundaries. Specifically, we comprehensively elucidated that the nucleoid-associated protein DrEbfC as a global regulatory factor for gene expression, may modulate the efficiency of relevant metabolic pathways by altering the local chromosome structure, thereby influencing the physiological state of the bacterium. Overall, our study revealed the chromosome conformations of D. radiodurans under different conditions and offered valuable insights into the molecular response mechanism of this extremophile to survival stresses.

A scaffold protein manages the biosynthesis of steroidal defense metabolites in plants

Solanaceae plants produce two major classes of valuable sterol-derived natural products-steroidal glycoalkaloids and steroidal saponins-from a common cholesterol precursor. Attempts to heterologously produce these molecules have consistently failed, although the genes responsible for each biosynthetic step have been identified. Here we identify a cellulose synthase-like protein, an unexpected biosynthetic component that interacts with the early pathway enzymes, enabling steroidal scaffolds production in plants. Moreover, knockout of this gene in black nightshade, Solanum nigrum, resulted in plants lacking both steroidal alkaloids and saponins. Unexpectedly, these knockout plants also revealed that steroidal saponins deter serious agricultural insect pests. This discovery provides the missing link to engineer these high-value steroidal molecules and also pinpoints the ecological role for steroidal saponins.

Is the TCA cycle malate dehydrogenase-citrate synthase metabolon an illusion?

This review discusses the intriguing yet controversial concept of metabolons, focusing on the malate dehydrogenase-citrate synthase (MDH-CISY) metabolon as a model. Metabolons are multienzyme complexes composed of enzymes that catalyze sequential reactions in metabolic pathways. Metabolons have been proposed to enhance metabolic pathway efficiency by facilitating substrate channeling. However, there is skepticism about the presence of metabolons and their functionality in physiological conditions in vivo. We address the skepticism by reviewing compelling evidence supporting the existence of the MDH-CISY metabolon and highlighting its potential functions in cellular metabolism. The electrostatic interaction between MDH and CISY and the intermediate oxaloacetate, channeled within the metabolon, has been demonstrated using various experimental techniques, including protein-protein interaction assays, isotope dilution studies, and enzyme coupling assays. Regardless of the wealth of in vitro evidence, further validation is required to elucidate the functionality of MDH-CISY metabolons in living systems using advanced structural and spatial analysis techniques.

Exploring the uncharted territory of the potential protein-protein interactions of cytosolic malate dehydrogenase

In this review, we examine the protein-protein interactions of cytosolic malate dehydrogenase (MDH), an under-studied area in cellular metabolism. We provide a comprehensive overview of MDH involvement in metabolism, especially its interactions with metabolic partners and dynamics of changing metabolism. We present an analysis of the biophysical nature of these interactions and the current methods used to study them. Our review includes an assessment of computational docking studies, which offer initial hypotheses about potential MDH interaction partners. Furthermore, we provide a summary of the sparse yet insightful experimental evidence available, establishing a foundation for future research. By integrating biophysical analysis and methodological advancements, this paper aims to illuminate the intricate network of interactions involving cytosolic MDH and their metabolic implications. This work not only contributes to our understanding of MDH's role in metabolism but also highlights the potential impact of these interactions in metabolic disorders.

Global organization of phenylpropanoid and anthocyanin pathways revealed by proximity labeling of trans-cinnamic acid 4-hydroxylase in Petunia inflata petal protoplasts

The phenylpropanoid pathway is one of the main carbon sinks in plants, channeling phenylalanine towards thousands of products including monolignols, stilbenes, flavonoids and volatile compounds. The enzymatic steps involved in many of these pathways are well characterized, however the physical organization of these enzymes within the plant cell remains poorly understood. Proximity-dependent labeling allows untargeted determination of both direct and indirect protein interactions in vivo, and therefore stands as an attractive alternative to targeted binary assays for determining global protein-protein interaction networks. We used TurboID-based proximity labeling to study protein interaction networks of the core phenylpropanoid and anthocyanin pathways in petunia. To do so, we coupled the endoplasmic reticulum (ER) membrane anchored cytochrome P450 cinnamic acid 4-hydroxylase (C4H, CYP73A412) from Petunia inflata to TurboID and expressed it in protoplasts derived from anthocyanin-rich petunia petals. We identified multiple soluble enzymes from the late anthocyanin pathway among enriched proteins, along with other C4H isoforms, and other ER membrane anchored CYPs. Several of these interactions were subsequently confirmed by bimolecular fluorescence complementation (BiFC). Our results suggest that C4H co-localizes with enzymes from the phenylpropanoid- and downstream anthocyanin pathways, supporting the idea that C4H may serve as ER anchoring points for downstream metabolic pathways. Moreover, this study demonstrates the feasibility of using protoplasts to perform global mapping of protein network for enzymes in their native cellular environment.

Metabolic channeling of lipids via the contact zones between different organelles

Various lipid transfer proteins (LTPs) mediate the inter-organelle transport of lipids. By working at membrane contact zones between donor and acceptor organelles, LTPs achieve rapid and accurate inter-organelle transfer of lipids. This article will describe the emerging paradigm that the action of LTPs at organelle contact zones generates metabolic channeling events in lipid metabolism, mainly referring to how ceramide synthesized in the endoplasmic reticulum is preferentially metabolized to sphingomyelin in the distal Golgi region, how cholesterol and phospholipids receive specific metabolic reactions in mitochondria, and how the hijacking of host LTPs by intracellular pathogens may generate new channeling-like events. In addition, the article will discuss how the function of LTPs is regulated, exemplified by a few representative LTP systems, and will briefly touch on experiments that will be necessary to establish the paradigm that LTP-mediated inter-organelle transport of lipids is one of the mechanisms of compartmentalization-based metabolic channeling events.

FhMYB108 Regulates the Expression of Linalool Synthase Gene in Freesia hybrida and Arabidopsis

Acting as the most abundant and widely distributed volatile secondary metabolites in plants, terpenoids play crucial roles in diverse physiological regulations and metabolic processes. Terpene synthases play a decisive role in determining the composition and diversity of terpenoids. Though the regulation of terpene synthases has been extensively investigated across various plant species, limited studies have focused on the upstream transcriptional regulation of terpene synthases. In this study, we have identified linalool as the predominant volatile compound that is released gradually from Freesia hybrida flowers throughout flower blooming. In the context of the transcriptome, a typical MYB transcription factor, FhMYB108, was screened based on homologous gene comparison. FhMYB108 is capable of regulating the expression of FhTPS1, and both their expression levels showed gradual increase during flower opening. Moreover, FhMYB108 exerts a stimulatory effect on the transcription of Arabidopsis thaliana AtTPS14, while no significant increase in AtTPS14 expression is observed upon the stabilization of FhMYB108 in A. thaliana. The highly expressed AtMYC2 in A. thaliana could interact with FhMYB108 to suppress the activation of AtTPS14 by FhMYB108. The present study not only elucidates the regulatory mechanism underlying linalool synthesis but also discovers the synergistic effect of MYB and bHLH transcription factors in governing the biosynthesis of volatile terpenoids.

Disentangling hydroxynitrile glucoside biosynthesis in a barley (Hordeum vulgare) metabolon provides access to elite malting barleys for ethyl carbamate-free whisky production

Barley produces several specialized metabolites, including five α-, β-, and γ-hydroxynitrile glucosides (HNGs). In malting barley, presence of the α-HNG epiheterodendrin gives rise to undesired formation of ethyl carbamate in the beverage production, especially after distilling. Metabolite-GWAS identified QTLs and underlying gene candidates possibly involved in the control of the relative and absolute content of HNGs, including an undescribed MATE transporter. By screening 325 genetically diverse barley accessions, we discovered three H. vulgare ssp. spontaneum (wild barley) lines with drastic changes in the relative ratios of the five HNGs. Knock-out (KO)-lines, isolated from the barley FIND-IT resource and each lacking one of the functional HNG biosynthetic genes (CYP79A12, CYP71C103, CYP71C113, CYP71U5, UGT85F22 and UGT85F23) showed unprecedented changes in HNG ratios enabling assignment of specific and mutually dependent catalytic functions to the biosynthetic enzymes involved. The highly similar relative ratios between the five HNGs found across wild and domesticated barley accessions indicate assembly of the HNG biosynthetic enzymes in a metabolon, the functional output of which was reconfigured in the absence of a single protein component. The absence or altered ratios of the five HNGs in the KO-lines did not change susceptibility to the fungal phytopathogen Pyrenophora teres causing net blotch. The study provides a deeper understanding of the organization of HNG biosynthesis in barley and identifies a novel, single gene HNG-0 line in an elite spring barley background for direct use in breeding of malting barley, eliminating HNGs as a source of ethyl carbamate formation in whisky production.

Ocimum kilimandscharicum 4CL11 negatively regulates adventitious root development via accumulation of flavonoid glycosides

4-Coumarate-CoA Ligase (4CL) is an important enzyme in the phenylpropanoid biosynthesis pathway. Multiple 4CLs are identified in Ocimum species; however, their in planta functions remain enigmatic. In this study, we independently overexpressed three Ok4CL isoforms from Ocimum kilimandscharicum (Ok4CL7, -11, and -15) in Nicotiana benthamiana. Interestingly, Ok4CL11 overexpression (OE) caused a rootless or reduced root growth phenotype, whereas overexpression of Ok4CL15 produced normal adventitious root (AR) growth. Ok4CL11 overexpression in N. benthamiana resulted in upregulation of genes involved in flavonoid biosynthesis and associated glycosyltransferases accompanied by accumulation of specific flavonoid-glycosides (kaempferol-3-rhamnoside, kaempferol-3,7-O-bis-alpha-l-rhamnoside [K3,7R], and quercetin-3-O-rutinoside) that possibly reduced auxin levels in plants, and such effects were not seen for Ok4CL7 and -15. Docking analysis suggested that auxin transporters (PINs/LAXs) have higher binding affinity to these specific flavonoid-glycosides, and thus could disrupt auxin transport/signaling, which cumulatively resulted in a rootless phenotype. Reduced auxin levels, increased K3,7R in the middle and basal stem sections, and grafting experiments (intra and inter-species) indicated a disruption of auxin transport by K3,7R and its negative effect on AR development. Supplementation of flavonoids and the specific glycosides accumulated by Ok4CL11-OE to the wild-type N. benthamiana explants delayed the AR emergence and also inhibited AR growth. While overexpression of all three Ok4CLs increased lignin accumulation, flavonoids, and their specific glycosides were accumulated only in Ok4CL11-OE lines. In summary, our study reveals unique indirect function of Ok4CL11 to increase specific flavonoids and their glycosides, which are negative regulators of root growth, likely involved in inhibition of auxin transport and signaling.

Non-consecutive enzyme interactions within TCA cycle supramolecular assembly regulate carbon-nitrogen metabolism

Enzymes of the central metabolism tend to assemble into transient supramolecular complexes. However, the functional significance of the interactions, particularly between enzymes catalyzing non-consecutive reactions, remains unclear. Here, by co-localizing two non-consecutive enzymes of the TCA cycle from Bacillus subtilis, malate dehydrogenase (MDH) and isocitrate dehydrogenase (ICD), in phase separated droplets we show that MDH-ICD interaction leads to enzyme agglomeration with a concomitant enhancement of ICD catalytic rate and an apparent sequestration of its reaction product, 2-oxoglutarate. Theory demonstrates that MDH-mediated clustering of ICD molecules explains the observed phenomena. In vivo analyses reveal that MDH overexpression leads to accumulation of 2-oxoglutarate and reduction of fluxes flowing through both the catabolic and anabolic branches of the carbon-nitrogen intersection occupied by 2-oxoglutarate, resulting in impeded ammonium assimilation and reduced biomass production. Our findings suggest that the MDH-ICD interaction is an important coordinator of carbon-nitrogen metabolism.

A flavonoid metabolon: cytochrome b5 enhances B-ring trihydroxylated flavan-3-ols synthesis in tea plants

Flavan-3-ols are prominent phenolic compounds found abundantly in the young leaves of tea plants. The enzymes involved in flavan-3-ol biosynthesis in tea plants have been extensively investigated. However, the localization and associations of these numerous functional enzymes within cells have been largely neglected. In this study, we aimed to investigate the synthesis of flavan-3-ols in tea plants, particularly focusing on epigallocatechin gallate. Our analysis involving the DESI-MSI method to reveal a distinct distribution pattern of B-ring trihydroxylated flavonoids, primarily concentrated in the outer layer of buds. Subcellular localization showed that CsC4H, CsF3'H, and CsF3'5'H localizes endoplasmic reticulum. Protein-protein interaction studies demonstrated direct associations between CsC4H, CsF3'H, and cytoplasmic enzymes (CHS, CHI, F3H, DFR, FLS, and ANR), highlighting their interactions within the biosynthetic pathway. Notably, CsF3'5'H, the enzyme for B-ring trihydroxylation, did not directly interact with other enzymes. We identified cytochrome b5 isoform C serving as an essential redox partner, ensuring the proper functioning of CsF3'5'H. Our findings suggest the existence of distinct modules governing the synthesis of different B-ring hydroxylation compounds. This study provides valuable insights into the mechanisms underlying flavonoid diversity and efficient synthesis and enhances our understanding of the substantial accumulation of B-ring trihydroxylated flavan-3-ols in tea plants.

Optimizing the conversion of phosphoenolpyruvate to lactate by enzymatic channeling with mixed nanoparticle display

Co-assembling enzymes with nanoparticles (NPs) into nanoclusters allows them to access channeling, a highly efficient form of multienzyme catalysis. Using pyruvate kinase (PykA) and lactate dehydrogenase (LDH) to convert phosphoenolpyruvic acid to lactic acid with semiconductor quantum dots (QDs) confirms how enzyme cluster formation dictates the rate of coupled catalytic flux (kflux) across a series of differentially sized/shaped QDs and 2D nanoplatelets (NPLs). Enzyme kinetics and coupled flux were used to demonstrate that by mixing different NP systems into clusters, a >10× improvement in kflux is observed relative to free enzymes, which is also ≥2× greater than enhancement on individual NPs. Cluster formation was characterized with gel electrophoresis and transmission electron microscopy (TEM) imaging. The generalizability of this mixed-NP approach to improving flux is confirmed by application to a seven-enzyme system. This represents a powerful approach for accessing channeling with almost any choice of enzymes constituting a multienzyme cascade.

A century of studying plant secondary metabolism-From "what?" to "where, how, and why?"

Over the past century, early advances in understanding the identity of the chemicals that collectively form a living plant have led scientists to deeper investigations exploring where these molecules localize, how they are made, and why they are synthesized in the first place. Many small molecules are specific to the plant kingdom and have been termed plant secondary metabolites, despite the fact that they can play primary and essential roles in plant structure, development, and response to the environment. The past 100 yr have witnessed elucidation of the structure, function, localization, and biosynthesis of selected plant secondary metabolites. Nevertheless, many mysteries remain about the vast diversity of chemicals produced by plants and their roles in plant biology. From early work characterizing unpurified plant extracts, to modern integration of 'omics technology to discover genes in metabolite biosynthesis and perception, research in plant (bio)chemistry has produced knowledge with substantial benefits for society, including human medicine and agricultural biotechnology. Here, we review the history of this work and offer suggestions for future areas of exploration. We also highlight some of the recently developed technologies that are leading to ongoing research advances.

Integrative analysis of the metabolome and transcriptome provides insights into the mechanisms of lignan biosynthesis in Herpetospermum pedunculosum (Cucurbitaceae)

BACKGROUND

Herpetospermum pedunculosum (Ser.) C. B. Clarke is a traditional Chinese herbal medicine that heavily relies on the lignans found in its dried ripe seeds (Herpetospermum caudigerum), which have antioxidant and hepatoprotective functions. However, little is known regarding the lignan biosynthesis in H. pedunculosum. In this study, we used metabolomic (non-targeted UHPLC-MS/MS) and transcriptome (RNA-Seq) analyses to identify key metabolites and genes (both structural and regulatory) associated with lignan production during the green mature (GM) and yellow mature (YM) stages of H. pedunculosum.

RESULTS

The contents of 26 lignan-related metabolites and the expression of 30 genes involved in the lignan pathway differed considerably between the GM and YM stages; most of them were more highly expressed in YM than in GM. UPLC-Q-TOF/MS confirmed that three Herpetospermum-specific lignans (including herpetrione, herpetotriol, and herpetin) were found in YM, but were not detected in GM. In addition, we proposed a lignan biosynthesis pathway for H. pedunculosum based on the fundamental principles of chemistry and biosynthesis. An integrated study of the transcriptome and metabolome identified several transcription factors, including HpGAF1, HpHSFB3, and HpWOX1, that were highly correlated with the metabolism of lignan compounds during seed ripening. Furthermore, functional validation assays revealed that the enzyme 4-Coumarate: CoA ligase (4CL) catalyzes the synthesis of hydroxycinnamate CoA esters.

CONCLUSION

These results will deepen our understanding of seed lignan biosynthesis and establish a theoretical basis for molecular breeding of H. pedunculosum.

Nitrile biosynthesis in nature: how and why?

Covering: up to the end of 2023Natural nitriles comprise a small set of secondary metabolites which however show intriguing chemical and functional diversity. Various patterns of nitrile biosynthesis can be seen in animals, plants, and microorganisms with the characteristics of both evolutionary divergence and convergence. These specialized compounds play important roles in nitrogen metabolism, chemical defense against herbivores, predators and pathogens, and inter- and/or intraspecies communications. Here we review the naturally occurring nitrile-forming pathways from a biochemical perspective and discuss the biological and ecological functions conferred by diversified nitrile biosyntheses in different organisms. Elucidation of the mechanisms and evolutionary trajectories of nitrile biosynthesis underpins better understandings of nitrile-related biology, chemistry, and ecology and will ultimately benefit the development of desirable nitrile-forming biocatalysts for practical applications.

Dynamic Metabolons Using Stimuli-Responsive Protein Cages

Naturally evolved metabolons have the ability to assemble and disassemble in response to environmental stimuli, allowing for the rapid reorganization of chemical reactions in living cells to meet changing cellular needs. However, replicating such capability in synthetic metabolons remains a challenge due to our limited understanding of the mechanisms by which the assembly and disassembly of such naturally occurring multienzyme complexes are controlled. Here, we report the synthesis of chemical- and light-responsive protein cages for assembling synthetic metabolons, enabling the dynamic regulation of enzymatic reactions in living cells. Particularly, a chemically responsive domain was fused to a self-assembled protein cage subunit, generating engineered protein cages capable of displaying proteins containing cognate interaction domains on their surfaces in response to small molecular cues. Chemical-induced colocalization of sequential enzymes on protein cages enhances the specificity of the branched deoxyviolacein biosynthetic reactions by 2.6-fold. Further, by replacing the chemical-inducible domain with a light-inducible dimerization domain, we created an optogenetic protein cage capable of reversibly recruiting and releasing targeted proteins onto and from the exterior of the protein cages in tens of seconds by on-off of blue light. Tethering the optogenetic protein cages to membranes enables the formation of light-switchable, membrane-bound metabolons, which can repeatably recruit-release enzymes, leading to the manipulation of substrate utilization across membranes on demand. Our work demonstrates a powerful and versatile strategy for constructing dynamic metabolons in engineered living cells for efficient and controllable biocatalysis.

Plant-Produced Viral Nanoparticles as a Functionalized Catalytic Support for Metabolic Engineering

Substrate channeling could be very useful for plant metabolic engineering; hence, we propose that functionalized supramolecular self-assembly scaffolds can act as enzymatic hubs able to perform reactions in close contiguity. Virus nanoparticles (VNPs) offer an opportunity in this context, and we present a functionalization strategy to display different enzymes on the outer surface of three different VNPs produced in plants. Tomato bushy stunt virus (TBSV) and Potato virus X (PVX) plant viruses were functionalized by the genetic fusion of the E-coil peptide coding sequence to their respective coat proteins genes, while the enzyme lichenase was tagged with the K-coil peptide. Immobilized E-coil VNPs were able to interact in vitro with the plant-produced functionalized lichenase, and catalysis was demonstrated by employing a lichenase assay. To prove this concept in planta, the Hepatitis B core (HBc) virus-like particles (VLPs) were similarly functionalized by genetic fusion with the E-coil sequence, while acyl-activating enzyme 1, olivetolic acid synthase, and olivetolic acid cyclase enzymes were tagged with the K-coil. The transient co-expression of the K-coil-enzymes together with E-coil-VLPs allowed the establishment of the heterologous cannabinoid precursor biosynthetic pathway. Noteworthy, a significantly higher yield of olivetolic acid glucoside was achieved when the scaffold E-coil-VLPs were employed.

Soybean AROGENATE DEHYDRATASES (GmADTs): involvement in the cytosolic isoflavonoid metabolon or trans-organelle continuity?

Soybean (Glycine max) produces a class of phenylalanine (Phe) derived specialized metabolites, isoflavonoids. Isoflavonoids are unique to legumes and are involved in defense responses in planta, and they are also necessary for nodule formation with nitrogen-fixing bacteria. Since Phe is a precursor of isoflavonoids, it stands to reason that the synthesis of Phe is coordinated with isoflavonoid production. Two putative AROGENATE DEHYDRATASE (ADT) isoforms were previously co-purified with the soybean isoflavonoid metabolon anchor ISOFLAVONE SYNTHASE2 (GmIFS2), however the GmADT family had not been characterized. Here, we present the identification of the nine member GmADT family. We determined that the GmADTs share sequences required for enzymatic activity and allosteric regulation with other characterized plant ADTs. Furthermore, the GmADTs are differentially expressed, and multiple members have dual substrate specificity, also acting as PREPHENATE DEHYDRATASES. All GmADT isoforms were detected in the stromules of chloroplasts, and they all interact with GmIFS2 in the cytosol. In addition, GmADT12A interacts with multiple other isoflavonoid metabolon members. These data substantiate the involvement of GmADT isoforms in the isoflavonoid metabolon.

Immunoprecipitation and FRET-FLIM to Determine Metabolons on the Plant ER

Metabolons are protein complexes that contain all the enzymes necessary for a metabolic pathway but also scaffolding proteins. Such a structure allows efficient channeling of intermediate metabolites form one active site to the next and is highly advantageous for labile or toxic intermediates. Here we describe two methods currently used to identify metabolons via protein-protein interaction methodology: immunoprecipitations using GFP-Trap®_A beads to find novel interaction partners and potential metabolon components and FRET-FLIM to test for and quantify protein-protein interactions in planta.

Structural Characterization and Molecular Dynamics Study of the REPI Fusion Protein from Papaver somniferum L

REPI is a pivotal point enzyme in plant benzylisoquinoline alkaloid metabolism as it promotes the evolution of the biosynthetic branch of morphinan alkaloids. Experimental studies of its activity led to the identification of two modules (DRS and DRR) that catalyze two sequential steps of the epimerization of (S)- to (R)-reticuline. Recently, special attention has been paid to its genetic characterization and evolutionary history, but no structural analyses of the REPI protein have been conducted to date. We present here a computational structural characterization of REPI with heme and NADP cofactors in the apo state and in three complexes with substrate (S)-reticuline in DRS and intermediate 1,2-dehydroreticuline in DRS and in DRR. Since no experimental structure exists for REPI, we used its AlphaFold model as a scaffold to build up these four systems, which were submitted to all-atom molecular dynamics (MD) simulations. A comparison of MD results for the four systems revealed key dynamic changes associated with cofactor and ligand binding and provided a dynamic picture of the evolution of their structures and interactions. We also explored the possible dynamic occurrence of tunnels and electrostatic highways potentially involved in alternative mechanisms for channeling the intermediate from DRS to DRR.

Engineering of CYP82Y1, a cytochrome P450 monooxygenase: a key enzyme in noscapine biosynthesis in opium poppy

Protein engineering provides a powerful base for the circumvention of challenges tied with characteristics accountable for enzyme functions. CYP82Y1 introduces a hydroxyl group (-OH) into C1 of N-methylcanadine as the substrate to yield 1-hydroxy-N-methylcanadine. This chemical process has been found to be the gateway to noscapine biosynthesis. Owning to the importance of CYP82Y1 in this biosynthetic pathway, it has been selected as a target for enzyme engineering. The insertion of tags to the N- and C-terminal of CYP82Y1 was assessed for their efficiencies for improvement of the physiological performances of CYP82Y1. Although these attempts achieved some positive results, further strategies are required to dramatically enhance the CYP82Y1 activity. Here methods that have been adopted to achieve a functionally improved CYP82Y1 will be reviewed. In addition, the possibility of recruitment of other techniques having not yet been implemented in CYP82Y1 engineering, including the substitution of the residues located in the substrate recognition site, formation of the synthetic fusion proteins, and construction of the artificial lipid-based scaffold will be discussed. Given the fact that the pace of noscapine synthesis is constrained by the CYP82Y1-catalyzing step, the methods proposed here are capable of accelerating the rate of reaction performed by CYP82Y1 through improving its properties, resulting in the enhancement of noscapine accumulation.

Subcellular compartmentalization in the biosynthesis and engineering of plant natural products

Plant natural products (PNPs) are specialized metabolites with diverse bioactivities. They are extensively used in the pharmaceutical, cosmeceutical and food industries. PNPs are synthesized in plant cells by enzymes that are distributed in different subcellular compartments with unique microenvironments, such as ions, co-factors and substrates. Plant metabolic engineering is an emerging and promising approach for the sustainable production of PNPs, for which the knowledge of the subcellular compartmentalization of their biosynthesis is instrumental. In this review we describe the state of the art on the role of subcellular compartments in the biosynthesis of major types of PNPs, including terpenoids, phenylpropanoids, alkaloids and glucosinolates, and highlight the efforts to target biosynthetic pathways to subcellular compartments in plants. In addition, we will discuss the challenges and strategies in the field of plant synthetic biology and subcellular engineering. We expect that newly developed methods and tools, together with the knowledge gained from the microbial chassis, will greatly advance plant metabolic engineering.

Golgi ELMO1 binds QUA1, QUA2, GAUT9, and ELMO4 and is required for pectin accumulation in Arabidopsis

Pectin and its modification influence the plasticity and strength of the plant cell wall controlling cell adhesion, size, shape, and pathogen resistance. The Golgi membrane anchored QUA1, QUA2, and GAUT9 Golgi enzymes synthesize and esterify pectin, which is then secreted and selectively de-esterified to potentiate structure influencing crosslinks in the cell wall. Mutations in members of the family of non-enzymatic ELMO Golgi membrane proteins lead to a reduction of pectin levels, cell adhesion, and hypocotyl tensile strength. Results from immunoprecipitation of Golgi protein complexes reveal that ELMO1-GFP is associated with pectin biosynthesis and modifying enzymes QUA1, QUA2, and GAUT9. In a yeast two and three hybrid assay, ELMO1 can bind directly to QUA1, GAUT9 or ELMO4, but QUA1, QUA2 or GAUT9 do not bind to each other. A yeast 3 hybrid assay provides evidence that ELMO1 can mediate the binding of QUA1 and QUA2. Taken together, these results indicate that the 20 kDa ELMO1 serves to facilitate some aspect of pectin synthesis and modification that leads to sufficient accumulation to allow cell adhesion, and we speculate that ELMOs help to scaffold key enzymes in this process.

Deciphering triterpenoid saponin biosynthesis by leveraging transcriptome response to methyl jasmonate elicitation in Saponaria vaccaria

Methyl jasmonate (MeJA) is a known elicitor of plant specialized metabolism, including triterpenoid saponins. Saponaria vaccaria is an annual herb used in traditional Chinese medicine, containing large quantities of oleanane-type triterpenoid saponins with anticancer properties and structural similarities to the vaccine adjuvant QS-21. Leveraging the MeJA-elicited saponin biosynthesis, we identify multiple enzymes catalyzing the oxidation and glycosylation of triterpenoids in S. vaccaria. This exploration is aided by Pacbio full-length transcriptome sequencing and gene expression analysis. A cellulose synthase-like enzyme can not only glucuronidate triterpenoid aglycones but also alter the product profile of a cytochrome P450 monooxygenase via preference for the aldehyde intermediate. Furthermore, the discovery of a UDP-glucose 4,6-dehydratase and a UDP-4-keto-6-deoxy-glucose reductase reveals the biosynthetic pathway for the rare nucleotide sugar UDP-D-fucose, a likely sugar donor for fucosylation of plant natural products. Our work enables the production and optimization of high-value saponins in microorganisms and plants through synthetic biology approaches.

Biotechnological Approaches for Enhancing Polyhydroxyalkanoates (PHAs) Production: Current and Future Perspectives

The benefits of biotechnology are not limited to genetic engineering, but it also displays its great impact on industrial uses of crops (e.g., biodegradable plastics). Polyhydroxyalkanoates (PHAs) make a diverse class of bio-based and biodegradable polymers naturally synthesized by numerous microorganisms. However, several C3 and C4 plants have also been genetically engineered to produce PHAs. The highest production yield of PHAs was obtained with a well-known C3 plant, Arabidopsis thaliana, upto 40% of the dry weight of the leaf. This review summarizes all biotechnological mechanisms that have been adopted with the goal of increasing PHAs production in bacteria and plant species alike. Moreover, the possibility of using some methods that have not been applied in bioplastic science are discussed with special attention to plants. These include producing PHAs in transgenic hairy roots and cell suspension cultures, making transformed bacteria and plants via transposons, constructing an engineered metabolon, and overexpressing of phaP and the ABC operon concurrently. Taken together, that biotechnology will be highly beneficial for reducing plastic pollution through the implementation of biotechnological strategies is taken for granted.

The Role of TCA Cycle Enzymes in Plants

As one of the iconic pathways in plant metabolism, the tricarboxylic acid (TCA) cycle is commonly thought to not only be responsible for the oxidization of respiratory substrate to drive ATP synthesis but also provide carbon skeletons to anabolic processes and contribute to carbon-nitrogen interaction and biotic stress responses. The functions of the TCA cycle enzymes are characterized by a saturation transgenesis approach, whereby the constituent expression of proteins is knocked out or reduced in order to investigate their function in vivo. The alteration of TCA cycle enzyme expression results in changed plant growth and photosynthesis under controlled conditions. Moreover, improvements in plant performance and postharvest properties are reported by overexpression of either endogenous forms or heterologous genes of a number of the enzymes. Given the importance of the TCA cycle in plant metabolism regulation, here, the function of each enzyme and its roles in different tissues are discussed. This article additionally highlights the recent finding that the plant TCA cycle, like that of mammals and microbes, dynamically assembles functional substrate channels or metabolons and discusses the implications of this finding to the current understanding of the metabolic regulation of the plant TCA cycle.

The formation and function of plant metabolons

Metabolons are temporary structural-functional complexes of sequential enzymes of a metabolic pathway that are distinct from stable multi-enzyme complexes. Here we provide a brief history of the study of enzyme-enzyme assemblies with a particular focus on those that mediate substrate channeling in plants. Large numbers of protein complexes have been proposed for both primary and secondary metabolic pathways in plants. However, to date only four substrate channels have been demonstrated. We provide an overview of current knowledge concerning these four metabolons and explain the methodologies that are currently being applied to unravel their functions. Although the assembly of metabolons has been documented to arise through diverse mechanisms, the physical interaction within the characterized plant metabolons all appear to be driven by interaction with structural elements of the cell. We therefore pose the question as to what methodologies could be brought to bear to enhance our knowledge of plant metabolons that assemble via different mechanisms? In addressing this question, we review recent findings in non-plant systems concerning liquid droplet phase separation and enzyme chemotaxis and propose strategies via which such metabolons could be identified in plants. We additionally discuss the possibilities that could be opened up by novel approaches based on: (i) subcellular-level mass spectral imaging, (ii) proteomics, and (iii) emergent methods in structural and computational biology.

Improvement of Cellulomonas fimi endoglucanase CenA by multienzymatic display on a decameric structural scaffold

The development of multifunctional particles using polymeric scaffolds is an emerging technology for many nanobiotechnological applications. Here we present a system for the production of multifunctional complexes, based on the high affinity non-covalent interaction of cohesin and dockerin modules complementary fused to decameric Brucella abortus lumazine synthase (BLS) subunits, and selected target proteins, respectively. The cohesin-BLS scaffold was solubly expressed in high yield in Escherichia coli, and revealed a high thermostability. The production of multienzymatic particles using this system was evaluated using the catalytic domain of Cellulomonas fimi endoglucanase CenA recombinantly fused to a dockerin module. Coupling of the enzyme to the scaffold was highly efficient and occurred with the expected stoichiometry. The decavalent enzymatic complexes obtained showed higher cellulolytic activity and association to the substrate compared to equivalent amounts of the free enzyme. This phenomenon was dependent on the multiplicity and proximity of the enzymes coupled to the scaffold, and was attributed to an avidity effect in the polyvalent enzyme interaction with the substrate. Our results highlight the usefulness of the scaffold presented in this work for the development of multifunctional particles, and the improvement of lignocellulose degradation among other applications. KEY POINTS: • New system for multifunctional particle production using the BLS scaffold • Higher cellulolytic activity of polyvalent endoglucanase compared to the free enzyme • Amount of enzyme associated to cellulose is higher for the polyvalent endoglucanase.

An efficient Pt@MXene platform for the analysis of small-molecule natural products

Small-molecule (m/z<500) natural products have rich biological activity and significant application value thus need to be effectively detected. Surface-assisted laser desorption/ionization mass spectrometry (SALDI MS) has become a powerful detection tool for small-molecule analysis. However, more efficient substrates need to be developed to improve the efficiency of SALDI MS. Thus, platinum nanoparticle-decorated Ti₃C₂ MXene (Pt@MXene) was synthesized in this study as an ideal substrate for SALDI MS in positive ion mode and exhibited excellent performance for the high-throughput detection of small molecules. Compared with using MXene, GO, and CHCA matrix, a stronger signal peak intensity and wider molecular coverage was obtained using Pt@MXene in the detection of small-molecule natural products, with a lower background, excellent salt and protein tolerance, good repeatability, and high detection sensitivity. The Pt@MXene substrate was also successfully used to quantify target molecules in medicinal plants. The proposed method has potentially wide application.

Site-specific dual encoding and labeling of proteins via genetic code expansion

The ability to selectively modify proteins at two or more defined locations opens new avenues for manipulating, engineering, and studying living systems. As a chemical biology tool for the site-specific encoding of non-canonical amino acids into proteins in vivo, genetic code expansion (GCE) represents a powerful tool to achieve such modifications with minimal disruption to structure and function through a two-step "dual encoding and labeling" (DEAL) process. In this review, we summarize the state of the field of DEAL using GCE. In doing so, we describe the basic principles of GCE-based DEAL, catalog compatible encoding systems and reactions, explore demonstrated and potential applications, highlight emerging paradigms in DEAL methodologies, and propose novel solutions to current limitations.

Assembly of Metabolons in Yeast Using Cas6-Mediated RNA Scaffolding

Cells often localize pathway enzymes in close proximity to reduce substrate loss via diffusion and to ensure that carbon flux is directed toward the desired product. To emulate this strategy for the biosynthesis of heterologous products in yeast, we have taken advantage of the highly specific Cas6-RNA interaction and the predictability of RNA hybridizations to demonstrate Cas6-mediated RNA-guided protein assembly within the yeast cytosol. The feasibility of this synthetic scaffolding technique for protein localization was first demonstrated using a split luciferase reporter system with each part fused to a different Cas6 protein. In Saccharomyces cerevisiae, the luminescence signal increased 3.6- to 20-fold when the functional RNA scaffold was also expressed. Expression of a trigger RNA, designed to prevent the formation of a functional scaffold by strand displacement, decreased the luminescence signal by nearly 2.3-fold. Temporal control was also possible, with induction of scaffold expression resulting in an up to 11.6-fold increase in luminescence after 23 h. Cas6-mediated assembly was applied to create a two-enzyme metabolon to redirect a branch of the violacein biosynthesis pathway. Localizing VioC and VioE together increased the amount of deoxyviolacein (desired) relative to prodeoxyviolacein (undesired) by 2-fold. To assess the generality of this colocalization method in other yeast systems, the split luciferase reporter system was evaluated in Kluyveromyces marxianus; RNA scaffold expression resulted in an increase in the luminescence signal of up to 1.9-fold. The simplicity and flexibility of the design suggest that this strategy can be used to create metabolons in a wide range of recombinant hosts of interest.

Metabolic flux enhancement from the translational fusion of terpene synthases is linked to terpene synthase accumulation

The end-to-end fusion of enzymes that catalyse successive steps in a reaction pathway is a metabolic engineering strategy that has been successfully applied in a variety of pathways and is particularly common in terpene bioproduction. Despite its popularity, limited work has been done to interrogate the mechanism of metabolic enhancement from enzyme fusion. We observed a remarkable >110-fold improvement in nerolidol production upon translational fusion of nerolidol synthase (a sesquiterpene synthase) to farnesyl diphosphate synthase. This delivered a titre increase from 29.6 mg/L up to 4.2 g/L nerolidol in a single engineering step. Whole-cell proteomic analysis revealed that nerolidol synthase levels in the fusion strains were greatly elevated compared to the non-fusion control. Similarly, the fusion of nerolidol synthase to non-catalytic domains also produced comparable increases in titre, which coincided with improved enzyme expression. When farnesyl diphosphate synthase was fused to other terpene synthases, we observed more modest improvements in terpene titre (1.9- and 3.8-fold), corresponding with increases of a similar magnitude in terpene synthase levels. Our data demonstrate that increased in vivo enzyme levels - resulting from improved expression and/or improved protein stability - is a major driver of catalytic enhancement from enzyme fusion.

Fine mapping and characterisation of a PV-PUR mediating anthocyanin synthesis in snap bean (Phaseolus vulgaris L.)

Anthocyanin makes snap bean (Phaseolus vulgaris L.) pods purple, which helps seed dispersal and protects against environmental stress. In this study, we characterised the snap bean purple mutant pv-pur, which has purple cotyledon, hypocotyl, stem, leaf vein, flower and pod tissues. Total anthocyanin, delphinidin and malvidin levels in mutant pods were significantly higher than in wild-type plants. We constructed two populations for fine mapping of the PV-PUR purple mutation gene, located in the 243.9-kb region of chromosome 06. We identified Phvul.006g018800.3, encoding F3'5'H, as a candidate gene for PV-PUR. Six single-base mutations occurred in the coding region of this gene, altering protein structure. PV-PUR and pv-pur genes were transferred into Arabidopsis, respectively. Compared with the wild-type, the leaf base and internode of T-PV-PUR plant were purple, and the phenotype of T-pv-pur plant remained unchanged, which verified the function of the mutant gene. The results demonstrated that PV-PUR is a crucial gene for anthocyanin biosynthesis in snap bean, resulting in purple colouration. The findings lay a foundation for future breeding and improvement of snap bean.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01362-8.

Daidzein Hydroxylation by CYP81E63 Is Involved in the Biosynthesis of Miroestrol in Pueraria mirifica

White Kwao Krua (Pueraria candollei var. mirifica), a Thai medicinal plant, is a rich source of phytoestrogens, especially isoflavonoids and chromenes. These phytoestrogens are well known; however, their biosynthetic genes remain largely uncharacterized. Cytochrome P450 (P450) is a large protein family that plays a crucial role in the biosynthesis of various compounds in plants, including phytoestrogens. Thus, we focused on P450s involved in the isoflavone hydroxylation that potentially participates in the biosynthesis of miroestrol. Three candidate P450s were isolated from the transcriptome libraries by considering the phylogenetic and expression data of each tissue of P. mirifica. The candidate P450s were functionally characterized both in vitro and in planta. Accordingly, the yeast microsome harboring PmCYP81E63 regiospecifically exhibited either 2' or 3' daidzein hydroxylation and genistein hydroxylation. Based on in silico calculation, PmCYP81E63 had higher binding energy with daidzein than with genistein, which supported the in vitro result of the isoflavone specificity. To confirm in planta function, the candidate P450s were then transiently co-expressed with isoflavone-related genes in Nicotiana benthamiana. Despite no daidzein in the infiltrated N. benthamiana leaves, genistein and hydroxygenistein biosynthesis were detectable by liquid Chromatography with tandem mass spectrometry (LC-MS/MS). Additionally, we demonstrated that PmCYP81E63 interacted with several enzymes related to isoflavone biosynthesis using bimolecular fluorescence complementation studies and a yeast two-hybrid analysis, suggesting a scheme of metabolon formation in the pathway. Our findings provide compelling evidence regarding the involvement of PmCYP81E63 in the early step of the proposed miroestrol biosynthesis in P. mirifica.

Enhanced UV-B Radiation Induced the Proanthocyanidins Accumulation in Red Rice Grain of Traditional Rice Cultivars and Increased Antioxidant Capacity in Aging Mice

Proanthocyanidins are major UV-absorbing compounds. To clarify the effect of enhanced UV-B radiation on the proanthocyanidin synthesis and antioxidant capacity of traditional rice varieties in Yuanyang terraced fields, we studied the effects of enhanced UV-B radiation (0, 2.5, 5.0, 7.5 kJ·m^-2·d^-1) on the rice grain morphology, proanthocyanidins content, and synthesis. The effects of UV-B radiation on the antioxidant capacity of rice were evaluated by feeding aging model mice. The results showed that UV-B radiation significantly affected the grain morphology of red rice and increased the compactness of starch grains in the starch storage cells of central endosperm. The content of proanthocyanidin B2 and C1 in the grains was significantly increased by 2.5 and 5.0 kJ·m^-2·d^-1 UV-B radiation. The activity of leucoanthocyanidin reductase was higher in rice treated by 5.0 kJ·m^-2·d^-1 than other treatments. The number of neurons in the hippocampus CA1 of mice brain fed red rice increased. After 5.0 kJ·m^-2·d^-1 treatment, red rice has the best antioxidant effect on aging model mice. UV-B radiation induces the synthesis of rice proanthocyanidins B2 and C1, and the antioxidant capacity of rice is related to the content of proanthocyanidins.

RNAseq-Based Working Model for Transcriptional Regulation of Crosstalk between Simultaneous Abiotic UV-B and Biotic Stresses in Plants

Plants adjust their secondary metabolism by altering the expression of corresponding genes to cope with both abiotic and biotic stresses. In the case of UV-B radiation, plants produce protective flavonoids; however, this reaction is impeded during pattern-triggered immunity (PTI) induced by pathogens. Pathogen attack can be mimicked by the application of microbial associated molecular patterns (e.g., flg22) to study crosstalk between PTI and UV-B-induced signaling pathways. Switching from Arabidopsis cell cultures to in planta studies, we analyzed whole transcriptome changes to gain a deeper insight into crosstalk regulation. We performed a comparative transcriptomic analysis by RNAseq with four distinct mRNA libraries and identified 10778, 13620, and 11294 genes, which were differentially expressed after flg22, UV-B, and stress co-treatment, respectively. Focusing on genes being either co-regulated with the UV-B inducible marker gene chalcone synthase CHS or the flg22 inducible marker gene FRK1 identified a large set of transcription factors from diverse families, such as MYB, WRKY, or NAC. These data provide a global view of transcriptomic reprogramming during this crosstalk and constitute a valuable dataset for further deciphering the underlying regulatory mechanism(s), which appear to be much more complex than previously anticipated. The possible involvement of MBW complexes in this context is discussed.

The R2R3MYB transcription factors MaMYBF and MaMYB1 regulate flavonoid biosynthesis in grape hyacinth

R2R3 MYBs play vital roles in the regulation of flavonoid biosynthesis. However, the regulatory network of R2R3 MYBs in flavonoid biosynthesis is not fully understood in grape hyacinth (Muscari spp.). Here, we identified two R2R3 MYBs, MaMYBF and MaMYB1, as potential regulators of flavonol and anthocyanin biosynthesis, respectively. MaMYBF and MaMYB1 expression was elevated during flower development and was light-induced, and the expression patterns were related to those of the flavonoid structural genes MaFLS and MaDFR, respectively. The BiFC assay verified that MaMYB1 interacts with MabHLH1, but MaMYBF does not. A dual luciferase assay revealed that MaMYBF alone strongly activated pMaFLS, and its activation was attenuated at reduced doses of MaMYBF in the presence of MabHLH1, MaMybA, and MaMYB1. MaDFR transcription mediated by MaMybA and MabHLH1 was inhibited by MaMYB1. Moreover, overexpression of MaMYBF and MaMYB1 in tobacco reduced flower pigmentation and repressed the expression of flavonoid pathway key structural genes. Therefore, MaMYBF regulates the flavonol pathway independently of cofactors. Whereas MaMYB1 regulates anthocyanin biosynthesis by binding to MabHLH1 and disrupting the MaMybA-bHLH complex in grape hyacinth. Our results offer new insights into the intricate regulatory network of flavonoids in grape hyacinth involving the regulation of both flavonol and anthocyanin.

Multifaceted roles of flavonoids mediating plant-microbe interactions

Plant-microbe interactions dynamically affect plant growth, health, and development. The mechanisms underpinning these associations are-to a large extent-mediated by specialized host-derived secondary metabolites. Flavonoids are one of the most studied classes of such metabolites, regulating both plant development and the interaction with commensal microbes. Here, we provide a comprehensive review of the multiple roles of flavonoids in mediating plant-microbe interactions. First, we briefly summarize the general aspects of flavonoid synthesis, transport, and exudation in plants. Then, we review the importance of flavonoids regulating plant-microbe interactions and dynamically influencing the overall community assembly of plant-root microbiomes. Last, we highlight potential knowledge gaps in our understanding of how flavonoids determine the interactions between plants and commensal microbes. Collectively, we advocate the importance of advancing research in this area toward innovative strategies to effectively manipulate plant-microbiome composition, in this case, via flavonoid production and exudation in plant roots. Video Abstract.

Genome-edited rice deficient in two 4-COUMARATE:COENZYME A LIGASE genes displays diverse lignin alterations

The 4-coumarate:coenzyme A ligase (4CL) is a key enzyme that contributes to channeling metabolic flux in the cinnamate/monolignol pathway, leading to the production of monolignols, p-hydroxycinnamates, and a flavonoid tricin, the major building blocks of lignin polymer in grass cell walls. Vascular plants often contain multiple 4CL genes; however, the contribution of each 4CL isoform to lignin biosynthesis remains unclear, especially in grasses. In this study, we characterized the functions of two rice (Oryza sativa L.) 4CL isoforms (Os4CL3 and Os4CL4) primarily by analyzing the cell wall chemical structures of rice mutants generated by CRISPR/Cas9-mediated targeted mutagenesis. A series of chemical and nuclear magnetic resonance analyses revealed that loss-of-function of Os4CL3 and Os4CL4 differently altered the composition of lignin polymer units. Loss of function of Os4CL3 induced marked reductions in the major guaiacyl and syringyl lignin units derived from both the conserved non-γ-p-coumaroylated and the grass-specific γ-p-coumaroylated monolignols, with more prominent reductions in guaiacyl units than in syringyl units. In contrast, the loss-of-function mutation to Os4CL4 primarily decreased the abundance of the non-γ-p-coumaroylated guaiacyl units. Loss-of-function of Os4CL4, but not of Os4CL3, reduced the grass-specific lignin-bound tricin units, indicating that Os4CL4 plays a key role not only in monolignol biosynthesis but also in the biosynthesis of tricin used for lignification. Further, the loss-of-function of Os4CL3 and Os4CL4 notably reduced cell-wall-bound ferulates, indicating their roles in cell wall feruloylation. Overall, this study demonstrates the overlapping but divergent roles of 4CL isoforms during the coordinated production of various lignin monomers.

Visualization of a Limonene Synthesis Metabolon Inside Living Bacteria by Hyperspectral SRS Microscopy

Monitoring biosynthesis activity at single-cell level is key to metabolic engineering but is still difficult to achieve in a label-free manner. Using hyperspectral stimulated Raman scattering imaging in the 670-900 cm-1 region, localized limonene synthesis are visualized inside engineered Escherichia coli. The colocalization of limonene and GFP-fused limonene synthase is confirmed by co-registered stimulated Raman scattering and two-photon fluorescence images. The finding suggests a limonene synthesis metabolon with a polar distribution inside the cells. This finding expands the knowledge of de novo limonene biosynthesis in engineered bacteria and highlights the potential of SRS chemical imaging in metabolic engineering research.

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.

Integrating metabolite and transcriptome analysis revealed the different mechanisms of characteristic compound biosynthesis and transcriptional regulation in tea flowers

The flowers of tea plants (Camellia sinensis), as well as tea leaves, contain abundant secondary metabolites and are big potential resources for the extraction of bioactive compounds or preparation of functional foods. However, little is known about the biosynthesis and transcriptional regulation mechanisms of those metabolites in tea flowers, such as terpenoid, flavonol, catechins, caffeine, and theanine. This study finely integrated target and nontarget metabolism analyses to explore the metabolic feature of developing tea flowers. Tea flowers accumulated more abundant terpenoid compounds than young leaves. The transcriptome data of developing flowers and leaves showed that a higher expression level of later genes of terpenoid biosynthesis pathway, such as Terpene synthases gene family, in tea flowers was the candidate reason of the more abundant terpenoid compounds than in tea leaves. Differently, even though flavonol and catechin profiling between tea flowers and leaves was similar, the gene family members of flavonoid biosynthesis were selectively expressed by tea flowers and tea leaves. Transcriptome and phylogenetic analyses indicated that the regulatory mechanism of flavonol biosynthesis was perhaps different between tea flowers and leaves. However, the regulatory mechanism of catechin biosynthesis was perhaps similar between tea flowers and leaves. This study not only provides a global vision of metabolism and transcriptome in tea flowers but also uncovered the different mechanisms of biosynthesis and transcriptional regulation of those important compounds.