Modulation of benzylisoquinoline alkaloid biosynthesis by heterologous expression of CjWRKY1 in Eschscholzia californica cells

Estrogenic actions of alkaloids: Structural characteristics and molecular mechanisms

This comprehensive review of estrogenic alkaloids reveals that although the number is small, they exhibit a wide range of structures, biosynthesis pathways, mechanisms of action, and applications. Estrogenic alkaloids belong to different classes, different biosynthetic pathways, different estrogenic actions (estrogenic/synergistic, anti-estrogenic/antagonistic, biphasic, and acting as a selective estrogen receptor modulator or SERM), different receptor-initiated signaling pathways, different ways of modulations of estrogen action, and different applications. The future applications of estrogenic alkaloids, such as those for diagnostics, drug development, and therapeutics, are considered with the help of new databases containing comprehensive descriptions of their relationships and more elaborate artificial intelligence-based prediction technologies. Structure-activity studies reveal the significance of the nitrogen atom for their structural and functional diversity, which may help support their broader applications. Based on the summary of previous reports, estrogenic alkaloids have significant potential for future applications.

Advances in the biosynthesis of naturally occurring benzylisoquinoline alkaloids

Benzylisoquinoline alkaloids (BIAs) are a prominent class of plant metabolites with significant pharmaceutical and industrial significance that have garnered substantial attention from researchers worldwide. BIAs exhibit several pharmacological activities and have been used extensively. Examples include analgesics such as morphine, tetrahydropalmatine, antimicrobials such as berberine, and antineoplastic agents including cepharanthine. Most BIAs are derived and isolated from medicinal plants; however, these plants are predominantly wild resources that are scarce. Their high environmental impact, slow growth rate, scarcity of resources, and expensive direct extraction costs pose a significant challenge. Certain BIAs are present in trace amounts in medicinal plants; moreover, they have complex chemical structures and unstable properties. Designing chemical synthesis routes and processes is challenging. Thus, a major obstacle in developing and utilizing these natural products in the pharmaceutical industry lies in their low abundance in nature. Consequently, the limited supply of these molecules fails to meet high research and market demands. In recent years, biosynthesis approaches have emerged as a novel and efficient method to obtain BIAs. In this review, recent progress in the field of enzymes related to the elucidation of biosynthetic pathways and the biosynthesis of BIAs are discussed, and future perspectives for designing viable strategies for their targeted manipulation are presented.

Regulation of important natural products biosynthesis by WRKY transcription factors in plants

BACKGROUND

Plants produce abundant natural products, among which are species-specific and diversified secondary metabolites that are essential for growth and development, as well as adaptation to adversity and ecology. Moreover, these secondary metabolites are extensively utilized in pharmaceuticals, fragrances, industrial materials, and more. WRKY transcription factors (TFs), as a family of TFs unique to plants, have significant functions in many plant life activities. Especially in recent years, their role in the field of secondary metabolite biosynthesis regulation has received much attention. However, very little comprehensive summarization has been done to review their research progress.

AIM OF REVIEW

The purpose of this work is not only to provide valuable insights into the regulation of WRKY TFs over metabolic pathways through compiling the WRKY TFs involved in these processes, but also to offer research directions for WRKY TFs by summarizing the regulatory modes of WRKY TFs in the biosynthesis of secondary metabolites, thereby increasing the yield of valuable natural products in the future.

KEY SCIENTIFIC CONCEPTS OF REVIEW

Secondary metabolites can be categorized into three major classes-terpenoids, phenolic compounds, and nitrogen-containing compounds-based on their structural characteristics and biosynthetic pathways, and further subdivided into numerous subclasses. We review in detail the research progressregardingthe regulatory roles of WRKY TFs in plant secondary metabolitebiosynthesis and summarize more than 40 major related species. Additionally, we have presented the concepts of action modes of WRKY TFs involved in metabolic pathways, including direct regulation, indirect regulation, co-regulation, and self-regulation. It is helpful for others to investigate the molecular mechanisms of TF-mediated regulation. Furthermore, regarding future research prospects, we believe that research in this area lays the foundation for increasing the yield of important plant-derived natural products by molecular breeding, generating significant economic and social benefits.

Herbgenomics meets Papaveraceae: a promising -omics perspective on medicinal plant research

Herbal medicines were widely used in ancient and modern societies as remedies for human ailments. Notably, the Papaveraceae family includes well-known species, such as Papaver somniferum and Chelidonium majus, which possess medicinal properties due to their latex content. Latex-bearing plants are a rich source of diverse bioactive compounds, with applications ranging from narcotics to analgesics and relaxants. With the advent of high-throughput technologies and advancements in sequencing tools, an opportunity exists to bridge the knowledge gap between the genetic information of herbs and the regulatory networks underlying their medicinal activities. This emerging discipline, known as herbgenomics, combines genomic information with other -omics studies to unravel the genetic foundations, including essential gene functions and secondary metabolite biosynthesis pathways. Furthermore, exploring the genomes of various medicinal plants enables the utilization of modern genetic manipulation techniques, such as Clustered Regularly-Interspaced Short Palindromic Repeats (CRISPR/Cas9) or RNA interference. This technological revolution has facilitated systematic studies of model herbs, targeted breeding of medicinal plants, the establishment of gene banks and the adoption of synthetic biology approaches. In this article, we provide a comprehensive overview of the recent advances in genomic, transcriptomic, proteomic and metabolomic research on species within the Papaveraceae family. Additionally, it briefly explores the potential applications and key opportunities offered by the -omics perspective in the pharmaceutical industry and the agrobiotechnology field.

Integrated metabolite profiling and transcriptome analysis reveal candidate genes involved in the biosynthesis of benzylisoquinoline alkaloids in Corydalis solida

Structurally diverse benzylisoquinoline alkaloids (BIAs) are found in specific plant families, some of which are desirable for their efficient production because of their strong biological activities. Corydalis plants (e.g., Corydalis yanhusuo) of the family Papaveraceae also produce various BIAs; thus, they have been used in traditional Chinese medicine. Because metabolic engineering and synthetic biology using microorganisms are promising technologies for the effective production of useful metabolites, elucidation of the biosynthetic pathway of each BIA is indispensable. Although several enzyme genes involved in the biosynthesis of Corydalis BIAs have recently been isolated, many remain unknown, such as the protoberberine alkaloid C-methyltransferase involved in the biosynthesis of corydaline, one of the main BIAs found in the tubers of Corydalis plants. In this study, we performed transcriptome analysis combined with metabolite profiling of different tissues of Corydalis solida. Based on the high accumulation of several BIAs, including protopine, allocryptopine, and corydaline, genes encoding putative biosynthetic enzymes, including cytochrome P450, methyltransferase, and oxidase proteins, that were highly expressed in the tubers were screened. Two OMT genes, CsOMT1 and CsOMT2, were highly expressed in the tuber, and further characterization using crude enzyme preparations demonstrated that CsOMT1 showed 7-O-methylation activity against reticuline, whereas CsOMT2 catalyzed 9-O-methylation of scoulerine, followed by 2-O-methylation of tetrahydrocolumbamine. Our findings provide valuable information for the isolation of novel biosynthetic enzyme genes in Corydalis species.

Identification of P450 Candidates Associated with the Biosynthesis of Physalin-Class Compounds in Physalis angulata

The Physalis genus has long been used as traditional medicine in the treatment of various diseases. Physalins, the characteristic class of compounds in this genus, are major bioactive constituents. To date, the biogenesis of physalins remains largely unknown, except for the recently established knowledge that 24-methyldesmosterol is a precursor of physalin. To identify the genes encoding P450s that are putatively involved in converting 24-methyldesmosterol to physalins, a total of 306 P450-encoding unigenes were retrieved from our recently constructed P. angulata transcriptome. Extensive phylogenetic analysis proposed 21 P450s that might participate in physalin biosynthesis. To validate the candidates, we developed a virus-induced gene silencing (VIGS) system for P. angulata, and four P450 candidates were selected for the VIGS experiments. The reduction in the transcripts of the four P450 candidates by VIGS all led to decreased levels of physalin-class compounds in the P. angulata leaves. Thus, this study provides a number of P450 candidates that are likely associated with the biosynthesis of physalin-class compounds, forming a strong basis to reveal the unknown physalin biosynthetic pathway in the future.

California poppy (Eschscholzia californica), the Papaveraceae golden girl model organism for evodevo and specialized metabolism

California poppy or golden poppy (Eschscholzia californica) is the iconic state flower of California, with native ranges from Northern California to Southwestern Mexico. It grows well as an ornamental plant in Mediterranean climates, but it might be invasive in many parts of the world. California poppy was also highly prized by Native Americans for its medicinal value, mainly due to its various specialized metabolites, especially benzylisoquinoline alkaloids (BIAs). As a member of the Ranunculales, the sister lineage of core eudicots it occupies an interesting phylogenetic position. California poppy has a short-lived life cycle but can be maintained as a perennial. It has a comparatively simple floral and vegetative morphology. Several genetic resources, including options for genetic manipulation and a draft genome sequence have been established already with many more to come. Efficient cell and tissue culture protocols are established to study secondary metabolite biosynthesis and its regulation. Here, we review the use of California poppy as a model organism for plant genetics, with particular emphasis on the evolution of development and BIA biosynthesis. In the future, California poppy may serve as a model organism to combine two formerly separated lines of research: the regulation of morphogenesis and the regulation of secondary metabolism. This can provide insights into how these two integral aspects of plant biology interact with each other.

Genomic profiling of WRKY transcription factors and functional analysis of CcWRKY7, CcWRKY29, and CcWRKY32 related to protoberberine alkaloids biosynthesis in Coptis chinensis Franch

Coptis chinensis Franch. (Huanglian in Chinese) is an important economic crop with medicinal value. Its rhizome has been used as a traditional herbal medicine for thousands of years in Asia. Protoberberine alkaloids, as the main bioactive component of Coptis chinensis, have a series of pharmacological activities. However, the protoberberine alkaloids content of C. chinensis is relatively low. Understanding the molecular mechanisms affecting the transcriptional regulation of protoberberine alkaloids would be crucial to increase their production via metabolic engineering. WRKY, one of the largest plant-specific gene families, regulates plant defense responses via the biosynthesis of specialized metabolites such as alkaloids. Totally, 41 WRKY transcription factors (TFs) related to protoberberine alkaloid biosynthesis were identified in the C. chinensis genome and classified into three groups based on phylogenetic and conserved motif analyses. Three WRKY genes (CcWRKY7, CcWRKY29, and CcWRKY32) may regulate protoberberine alkaloid biosynthesis, as suggested by gene-specific expression patterns, metabolic pathways, phylogenetic, and dual-luciferase analysis. Furthermore, the CcWRKY7, CcWRKY29, and CcWRKY32 proteins were specifically detected in the nucleus via subcellular localization. This study provides a basis for understanding the regulatory mechanisms of protoberberine alkaloid biosynthesis and valuable information for breeding C. chinensis varieties.

Interplay of transcription factors orchestrating the biosynthesis of plant alkaloids

Plants produce a range of secondary metabolites primarily as defence molecules. A plant has to invest considerable energy to synthesise alkaloids, and sometimes they are even toxic to themselves. Hence, the biosynthesis of alkaloids is a spatiotemporally regulated process under quantitative feedback regulation which is accomplished by the signal reception, transcriptional/translational regulation, transport, storage and accumulation. The transcription factors (TFs) initiate the biosynthesis of alkaloids after appropriate cues. The present study recapitulates last decade understanding of the role of TFs in alkaloid biosynthesis. The present review discusses TF families, viz. AP2/ERF, bHLH, WRKY, MYB involved in the biosynthesis of various types of alkaloids. It also highlights the role of the jasmonic acid cascade and post-translational modifications of TF proteins. A thorough understanding of TFs will help us to decide a strategy to facilitate successful pathway manipulation and in vitro production.

Application of metabolic engineering to enhance the content of alkaloids in medicinal plants

Plants are a rich source of bioactive compounds, many of which have been exploited for cosmetic, nutritional, and medicinal purposes. Through the characterization of metabolic pathways, as well as the mechanisms responsible for the accumulation of secondary metabolites, researchers have been able to increase the production of bioactive compounds in different plant species for research and commercial applications. The intent of the current review is to describe the metabolic engineering methods that have been used to transform in vitro or field-grown medicinal plants over the last decade and to identify the most effective approaches to increase the production of alkaloids. The articles summarized were categorized into six groups: endogenous enzyme overexpression, foreign enzyme overexpression, transcription factor overexpression, gene silencing, genome editing, and co-overexpression. We conclude that, because of the complex and multi-step nature of biosynthetic pathways, the approach that has been most commonly used to increase the biosynthesis of alkaloids, and the most effective in terms of fold increase, is the co-overexpression of two or more rate-limiting enzymes followed by the manipulation of regulatory genes.

An Update of the Sanguinarine and Benzophenanthridine Alkaloids’ Biosynthesis and Their Applications

Benzophenanthridines belong to the benzylisoquinolic alkaloids, representing one of the main groups of this class. These alkaloids include over 120 different compounds, mostly in plants from the Fumariaceae, Papaveraceae, and Rutaceae families, which confer chemical protection against pathogens and herbivores. Industrial uses of BZD include the production of environmentally friendly agrochemicals and livestock food supplements. However, although mainly considered toxic compounds, plants bearing them have been used in traditional medicine and their medical applications as antimicrobials, antiprotozoals, and cytotoxic agents have been envisioned. The biosynthetic pathways for some BZD have been established in different species, allowing for the isolation of the genes and enzymes involved. This knowledge has resulted in a better understanding of the process controlling their synthesis and an opening of the gates towards their exploitation by applying modern biotechnological approaches, such as synthetic biology. This review presents the new advances on BDZ biosynthesis and physiological roles. Industrial applications, mainly with pharmacological approaches, are also revised.

Transcription Factors in Alkaloid Engineering

Plants produce a large variety of low-molecular-weight and specialized secondary compounds. Among them, nitrogen-containing alkaloids are the most biologically active and are often used in the pharmaceutical industry. Although alkaloid chemistry has been intensively investigated, characterization of alkaloid biosynthesis, including biosynthetic enzyme genes and their regulation, especially the transcription factors involved, has been relatively delayed, since only a limited number of plant species produce these specific types of alkaloids in a tissue/cell-specific or developmental-specific manner. Recent advances in molecular biology technologies, such as RNA sequencing, co-expression analysis of transcripts and metabolites, and functional characterization of genes using recombinant technology and cutting-edge technology for metabolite identification, have enabled a more detailed characterization of alkaloid pathways. Thus, transcriptional regulation of alkaloid biosynthesis by transcription factors, such as basic helix-loop-helix (bHLH), APETALA2/ethylene-responsive factor (AP2/ERF), and WRKY, is well elucidated. In addition, jasmonate signaling, an important cue in alkaloid biosynthesis, and its cascade, interaction of transcription factors, and post-transcriptional regulation are also characterized and show cell/tissue-specific or developmental regulation. Furthermore, current sequencing technology provides more information on the genome structure of alkaloid-producing plants with large and complex genomes, for genome-wide characterization. Based on the latest information, we discuss the application of transcription factors in alkaloid engineering.

Genome-Wide Profiling of WRKY Genes Involved in Benzylisoquinoline Alkaloid Biosynthesis in California Poppy (Eschscholzia californica)

Transcription factors of the WRKY family play pivotal roles in plant defense responses, including the biosynthesis of specialized metabolites. Based on the previous findings of WRKY proteins regulating benzylisoquinoline alkaloid (BIA) biosynthesis, such as CjWRKY1-a regulator of berberine biosynthesis in Coptis japonica-and PsWRKY1-a regulator of morphine biosynthesis in Papaver somniferum-we performed genome-wide characterization of the WRKY gene family in Eschscholzia californica (California poppy), which produces various BIAs. Fifty WRKY genes were identified by homology search and classified into three groups based on phylogenetic, gene structure, and conserved motif analyses. RNA sequencing showed that several EcWRKY genes transiently responded to methyl jasmonate, a known alkaloid inducer, and the expression patterns of these EcWRKY genes were rather similar to those of BIA biosynthetic enzyme genes. Furthermore, tissue expression profiling suggested the involvement of a few subgroup IIc EcWRKYs in the regulation of BIA biosynthesis. Transactivation analysis using luciferase reporter genes harboring the promoters of biosynthetic enzyme genes indicated little activity of subgroup IIc EcWRKYs, suggesting that the transcriptional network of BIA biosynthesis constitutes multiple members. Finally, we investigated the coexpression patterns of EcWRKYs with some transporter genes and discussed the diversified functions of WRKY genes based on a previous finding that CjWRKY1 overexpression in California poppy cells enhanced BIA secretion into the medium.

Transcriptomic Analyses Shed Light on Critical Genes Associated with Bibenzyl Biosynthesis in Dendrobium officinale

The Dendrobium plants (members of the Orchidaceae family) are used as traditional Chinese medicinal herbs. Bibenzyl, one of the active compounds in Dendrobium officinale, occurs in low amounts among different tissues. However, market demands require a higher content of thes compounds to meet the threshold for drug production. There is, therefore, an immediate need to dissect the physiological and molecular mechanisms underlying how bibenzyl compounds are biosynthesized in D. officinale tissues. In this study, the accumulation of erianin and gigantol in tissues were studied as representative compounds of bibenzyl. Exogenous application of Methyl-Jasmonate (MeJA) promotes the biosynthesis of bibenzyl compounds; therefore, transcriptomic analyses were conducted between D. officinale-treated root tissues and a control. Our results show that the root tissues contained the highest content of bibenzyl (erianin and gigantol). We identified 1342 differentially expressed genes (DEGs) with 912 up-regulated and 430 down-regulated genes in our transcriptome dataset. Most of the identified DEGs are functionally involved in the JA signaling pathway and the biosynthesis of secondary metabolites. We also identified two candidate cytochrome P450 genes and nine other enzymatic genes functionally involved in bibenzyl biosynthesis. Our study provides insights on the identification of critical genes associated with bibenzyl biosynthesis and accumulation in Dendrobium plants, paving the way for future research on dissecting the physiological and molecular mechanisms of bibenzyl synthesis in plants as well as guide genetic engineering for the improvement of Dendrobium varieties through increasing bibenzyl content for drug production and industrialization.

Genome-wide identification of AP2/ERF transcription factor-encoding genes in California poppy (Eschscholzia californica) and their expression profiles in response to methyl jasmonate

With respect to the biosynthesis of plant alkaloids, that of benzylisoquinoline alkaloids (BIAs) has been the most investigated at the molecular level. Previous investigations have shown that the biosynthesis of BIAs is comprehensively regulated by WRKY and bHLH transcription factors, while promoter analyses of biosynthesis enzyme-encoding genes have also implicated the involvement of members of the APETALA2/ethylene responsive factor (AP2/ERF) superfamily. To investigate the physiological roles of AP2/ERF transcription factors in BIA biosynthesis, 134 AP2/ERF genes were annotated using the draft genome sequence data of Eschscholzia californica (California poppy) together with transcriptomic data. Phylogenetic analysis revealed that these genes could be classified into 20 AP2, 5 RAV, 47 DREB, 60 ERF and 2 Soloist family members. Gene structure, conserved motif and orthologous analyses were also carried out. Gene expression profiling via RNA sequencing in response to methyl jasmonate (MeJA) indicated that approximately 20 EcAP2/ERF genes, including 10 group IX genes, were upregulated by MeJA, with an increase in the expression of the transcription factor-encoding gene EcbHLH1 and the biosynthesis enzyme-encoding genes Ec6OMT and EcCYP719A5. Further quantitative RT-PCR confirmed the MeJA responsiveness of the EcAP2/ERF genes, i.e., the increased expression of 9 group IX, 2 group X and 2 group III ERF subfamily genes. Transactivation activity of group IX EcAP2/ERFs was also confirmed by a luciferase reporter assay in conjunction with the promoters of the Ec6OMT and EcCYP719A5 genes. The physiological roles of AP2/ERF genes in BIA biosynthesis and their evolution in the regulation of alkaloid biosynthesis are discussed.

Systematic characterization of alkaloids in Eomecon chionantha Hance using ultrahigh-performance liquid chromatography-tandem quadrupole Exactive Orbitrap mass spectrometry with a four-step screening strategy

RATIONALE

Eomecon chionantha Hance (ECH), a traditional folk herb, is commonly used to treat traumatic injuries based on its analgesic and anti-inflammatory properties. Previous studies have reported that alkaloids are the major bioactive components in ECH. Therefore, identification of alkaloids from ECH contributes to the discovery of its potential active ingredients and quality control in clinic treatments.

METHODS

A four-step screening strategy was performed as follows. (1) Extracting the accurate masses of ions related to different molecules. (2) Screening different types of compounds using their molecular cations, protonated molecules, diagnostic product ions and fragmentation pathways. (3) Comparing the characteristic product ion formulae to obtain the type and number of substituents. (4) Using the biosynthetic pathways of isoquinoline alkaloids to determine the concentration of alkaloids.

RESULTS

Ultrahigh-performance liquid chromatography-tandem quadrupole Exactive Orbitrap mass spectrometry (UHPLC/Q-Exactive Orbitrap MS) analysis combined with the four-step screening strategy was used to profile the alkaloids in ECH. The structures of 95 alkaloids in ECH were unambiguously identified or reasonably assigned, of which 76 were reported in ECH for the first time. Six types of benzylisoquinoline alkaloids were identified in ECH: six benzyltetrahydroisoquinolines, nine protopines, five N-methyltetrahydroprotoberberines, six protoberberines, eight benzophenanthridines and sixty-one dihydrobenzophenanthridines.

CONCLUSIONS

This comprehensive study identified the alkaloids in ECH, thus providing a practical reference for further research. The UHPLC/Q-Exactive Orbitrap MS method, combined with the four-step screening strategy, which was developed and successfully applied to identify the alkaloids in ECH, may also be applicable for the efficient screening of other herbal medicines.

Harpin-inducible defense signaling components impair infection by the ascomycete Macrophomina phaseolina

Soybean (Glycine max) infection by the charcoal rot (CR) ascomycete Macrophomina phaseolina is enhanced by the soybean cyst nematode (SCN) Heterodera glycines. We hypothesized that G. max genetic lines impairing infection by M. phaseolina would also limit H. glycines parasitism, leading to resistance. As a part of this M. phaseolina resistance process, the genetic line would express defense genes already proven to impair nematode parasitism. Using G. max[DT97-4290/PI 642055], exhibiting partial resistance to M. phaseolina, experiments show the genetic line also impairs H. glycines parasitism. Furthermore, comparative studies show G. max[DT97-4290/PI 642055] exhibits induced expression of the effector triggered immunity (ETI) gene NON-RACE SPECIFIC DISEASE RESISTANCE 1/HARPIN INDUCED1 (NDR1/HIN1) that functions in defense to H. glycines as compared to the H. glycines and M. phaseolina susceptible line G. max[Williams 82/PI 518671]. Other defense genes that are induced in G. max[DT97-4290/PI 642055] include the pathogen associated molecular pattern (PAMP) triggered immunity (PTI) genes ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1), NONEXPRESSOR OF PR1 (NPR1) and TGA2. These observations link G. max defense processes that impede H. glycines parasitism to also potentially function toward impairing M. phaseolina pathogenicity. Testing this hypothesis, G. max[Williams 82/PI 518671] genetically engineered to experimentally induce GmNDR1-1, EDS1-2, NPR1-2 and TGA2-1 expression leads to impaired M. phaseolina pathogenicity. In contrast, G. max[DT97-4290/PI 642055] engineered to experimentally suppress the expression of GmNDR1-1, EDS1-2, NPR1-2 and TGA2-1 by RNA interference (RNAi) enhances M. phaseolina pathogenicity. The results show components of PTI and ETI impair both nematode and M. phaseolina pathogenicity.