GATA and Phytochrome Interacting Factor Transcription Factors Regulate Light-Induced Vindoline Biosynthesis in Catharanthus roseus

Critical parameters for robust Agrobacterium-mediated transient transformation and quantitative promoter assays in Catharanthus roseus seedlings

Agrobacterium-mediated transient expression methods are widely used to study gene function in both model and non-model plants. Using a dual-luciferase assay, we quantified the effect of Agrobacterium-infiltration parameters on the transient transformation efficiency of Catharanthus roseus seedlings. We showed that transformation efficiency is highly sensitive to seedling developmental state and a pre- and post-infiltration dark incubation and is less sensitive to the Agrobacterium growth stage. For example, 5 versus 6 days of germination in the dark increased seedling transformation efficiency by seven- to eight-fold while a dark incubation pre- and post-infiltration increased transformation efficiency by five- to 13-fold. Agrobacterium in exponential compared with stationary phase increased transformation efficiency by two-fold. Finally, we quantified the variation in our Agrobacterium-infiltration method in replicate infiltrations and experiments. Within a given experiment, significant differences of up to 2.6-fold in raw firefly luciferase (FLUC) and raw Renilla luciferase (RLUC) luminescence occurred in replicate infiltrations. These differences were significantly reduced when FLUC was normalized to RLUC values, highlighting the utility of including a reference reporter to minimize false positives. Including a second experimental replicate further reduced the potential for false positives. This optimization and quantitative validation of Agrobacterium infiltration in C. roseus seedlings will facilitate the study of this important medicinal plant and will expand the application of Agrobacterium-mediated transformation methods in other plant species.

The role of the Golden2-like (GLK) transcription factor in regulating terpenoid indole alkaloid biosynthesis in Catharanthus roseus

KEY MESSAGE

A GLK homologue was identified and functionally characterized in Catharanthus roseus. Silencing CrGLK with VIGS or the chloroplast retrograde signaling inducer lincomycin increased terpenoid indole alkaloid biosynthesis. Catharanthus roseus is the sole source of the chemotherapeutic terpenoid indole alkaloids (TIAs) vinblastine and vincristine. TIA pathway genes, particularly genes in the vindoline pathway, are expressed at higher levels in immature versus mature leaves, but the molecular mechanisms responsible for this developmental regulation are unknown. We investigated the role of GOLDEN2-LIKE (GLK) transcription factors in contributing to this ontogenetic regulation since GLKs are active in seedlings upon light exposure and in the leaf's early development, but their activity is repressed as leaves age and senesce. We identified a GLK homologue in C. roseus and functionally characterized its role in regulating TIA biosynthesis, with a focus on the vindoline pathway, by transiently reducing its expression through two separate methods: virus-induced gene silencing (VIGS) and application of chloroplast retrograde signaling inducers, norflurazon and lincomycin. Reducing CrGLK levels with each method reduced chlorophyll accumulation and the expression of the light harvesting complex subunit (LHCB2.2), confirming its functional homology with GLKs in other plant species. In contrast, reducing CrGLK via VIGS or lincomycin increased TIA accumulation and TIA pathway gene expression, suggesting that CrGLK may repress TIA biosynthesis. However, norflurazon had no effect on TIA gene expression, indicating that reducing CrGLK alone is not sufficient to induce TIA biosynthesis. Future work is needed to clarify the specific molecular mechanisms leading to increased TIA biosynthesis with CrGLK silencing. This is the first identification and characterization of GLK in C. roseus and the first investigation of how chloroplast retrograde signaling might regulate TIA biosynthesis.

Integration of cell differentiation and initiation of monoterpenoid indole alkaloid metabolism in seed germination of Catharanthus roseus

In Catharanthus roseus, monoterpenoid indole alkaloids (MIAs) are produced through the cooperation of four cell types, with final products accumulating in specialized cells known as idioblasts and laticifers. To explore the relationship between cellular differentiation and cell type-specific MIA metabolism, we analyzed the expression of MIA biosynthesis in germinating seeds. Embryos from immature and mature seeds were observed via stereomicroscopy, fluorescence microscopy, and electron microscopy. Time-series MIA and iridoid quantification, along with transcriptome analysis, were conducted to determine the initiation of MIA biosynthesis. In addition, the localization of MIAs was examined using alkaloid staining and imaging mass spectrometry (IMS). Laticifers were present in embryos before seed maturation. MIA biosynthesis commenced 12 h after germination. MIAs accumulated in laticifers of embryos following seed germination, and MIA metabolism is induced after germination in a tissue-specific manner. These findings suggest that cellular morphological differentiation precedes metabolic differentiation. Considering the well-known toxicity and defense role of MIAs in matured plants, MIAs may be an important defense strategy already in the delicate developmental phase of seed germination, and biosynthesis and accumulation of MIAs may require the tissue and cellular differentiation.

The Putative GATA Transcription Factor SbGATA22 as a Novel Regulator of Dhurrin Biosynthesis

Cyanogenic glucosides are specialized metabolites produced by over 3000 species of higher plants from more than 130 families. The deployment of cyanogenic glucosides is influenced by biotic and abiotic factors in addition to being developmentally regulated, consistent with their roles in plant defense and stress mitigation. Despite their ubiquity, very little is known regarding the molecular mechanisms that regulate their biosynthesis. The biosynthetic pathway of dhurrin, the cyanogenic glucoside found in the important cereal crop sorghum (Sorghum bicolor (L.) Moench), was described over 20 years ago, and yet no direct regulator of the biosynthetic genes has been identified. To isolate regulatory proteins that bind to the promoter region of the key dhurrin biosynthetic gene of sorghum, SbCYP79A1, yeast one-hybrid screens were performed. A bait fragment containing 1204 base pairs of the SbCYP79A1 5' regulatory region was cloned upstream of a reporter gene and introduced into Saccharomyces cerevisiae. Subsequently, the yeast was transformed with library cDNA representing RNA from two different sorghum developmental stages. From these screens, we identified SbGATA22, an LLM domain B-GATA transcription factor that binds to the putative GATA transcription factor binding motifs in the SbCYP79A1 promoter region. Transient assays in Nicotiana benthamiana show that SbGATA22 localizes to the nucleus. The expression of SbGATA22, in comparison with SbCYP79A1 expression and dhurrin concentration, was analyzed over 14 days of sorghum development and in response to nitrogen application, as these conditions are known to affect dhurrin levels. Collectively, these findings suggest that SbGATA22 may act as a negative regulator of SbCYP79A1 expression and provide a preliminary insight into the molecular regulation of dhurrin biosynthesis in sorghum.

Genome-wide identification of GATA transcription factors in tetraploid potato and expression analysis in differently colored potato flesh

The GATA gene family belongs to a kind of transcriptional regulatory protein featuring a zinc finger motif, which is essential for plant growth and development. However, the identification of the GATA gene family in tetraploid potato is still not performed. In the present research, a total of 88 GATA genes in the tetraploid potato C88.v1 genome were identified by bioinformatics methods. These StGATA genes had an uneven distribution on 44 chromosomes, and the corresponding StGATA proteins were divided into four subfamilies (I-IV) based on phylogenetic analysis. The cis-elements of StGATA genes were identified, including multiple cis-elements related to light-responsive and hormone-responsive. The collinearity analysis indicates that segmental duplication is a key driving force for the expansion of GATA gene family in tetraploid potato, and that the GATA gene families of tetraploid potato and Arabidopsis share a closer evolutionary relationship than rice. The transcript profiling analysis showed that all 88 StGATA genes had tissue-specific expression, indicating that the StGATA gene family members participate in the development of multiple potato tissues. The RNA-seq analysis was also performed on the tuber flesh of two potato varieties with different color, and 18 differentially expressed GATA transcription factor genes were screened, of which eight genes were validated through qRT-PCR. In this study, we identified and characterized StGATA transcription factors in tetraploid potato for the first time, and screened differentially expressed genes in potato flesh with different color. It provides a theoretical basis for further understanding the StGATA gene family and its function in anthocyanin biosynthesis.

Integrated transcriptomic and proteomic analyses uncover the early response mechanisms of Catharanthus roseus under ultraviolet-B radiation

Catharanthus roseus produces a large array of terpenoid indole alkaloids (TIAs) that are important natural source for many drugs. Ultraviolet B (UVB) radiation have been proved to have regulatory effect towards biosynthesis of TIAs, which were meaningful for boost of TIA production. To decipher more comprehensive molecular characteristics in C. roseus under UVB radiation, integrated analysis of the nuclear proteome together with the transcriptome data under UVB radiation were performed. Expression of genes related to transmembrane transporters gradually increased during the prolonged exposure to UVB radiation. Some of known TIA transporters were affected by UVB. Abundance of proteins associated with spliceosome and nucleocytoplasmic transport increased. Homologs belonging to ORCA and CrWRKY transcription factors family increased at both transcriptomic and proteomic levels. At the same time, the numbers of differential alternative splicing events between UVB-radiated and white-light-treated plants continuously increased. These results suggest that the nucleus participated in early response of C. roseus under UVB radiation, where alternative splicing events occurred and might regulate multiple pathways. Furthermore, integrative omics analysis indicates that expression of enzymes at the terminal stages of seco-iridoid pathway decreased with the prolonged radiation exposure, potentially inhibiting further rise of TIA synthesis under extended UVB exposure.

Molecular regulation of the key specialized metabolism pathways in medicinal plants

The basis of modern pharmacology is the human ability to exploit the production of specialized metabolites from medical plants, for example, terpenoids, alkaloids, and phenolic acids. However, in most cases, the availability of these valuable compounds is limited by cellular or organelle barriers or spatio-temporal accumulation patterns within different plant tissues. Transcription factors (TFs) regulate biosynthesis of these specialized metabolites by tightly controlling the expression of biosynthetic genes. Cutting-edge technologies and/or combining multiple strategies and approaches have been applied to elucidate the role of TFs. In this review, we focus on recent progress in the transcription regulation mechanism of representative high-value products and describe the transcriptional regulatory network, and future perspectives are discussed, which will help develop high-yield plant resources.

A Cotyledon-based Virus-Induced Gene Silencing (Cotyledon-VIGS) approach to study specialized metabolism in medicinal plants

BACKGROUND

Virus-induced gene silencing (VIGS) is widely used in plant functional genomics. However, the efficiency of VIGS in young plantlets varies across plant species. Additionally, VIGS is not optimized for many plant species, especially medicinal plants that produce valuable specialized metabolites.

RESULTS

We evaluated the efficacy of five-day-old, etiolated seedlings of Catharanthus roseus (periwinkle) for VIGS. The seedlings were vacuum-infiltrated with Agrobacterium tumefaciens GV3101 cells carrying the tobacco rattle virus (TRV) vectors. The protoporphyrin IX magnesium chelatase subunit H (ChlH) gene, a key gene in chlorophyll biosynthesis, was used as the target for VIGS, and we observed yellow cotyledons 6 days after infiltration. As expected, the expression of CrChlH and the chlorophyll contents of the cotyledons were significantly decreased after VIGS. To validate the cotyledon based-VIGS method, we silenced the genes encoding several transcriptional regulators of the terpenoid indole alkaloid (TIA) biosynthesis in C. roseus, including two activators (CrGATA1 and CrMYC2) and two repressors (CrGBF1 and CrGBF2). Silencing CrGATA1 led to downregulation of the vindoline pathway genes (T3O, T3R, and DAT) and decreased vindoline contents in cotyledons. Silencing CrMYC2, followed by elicitation with methyl jasmonate (MeJA), resulted in the downregulation of ORCA2 and ORCA3. We also co-infiltrated C. roseus seedlings with TRV vectors that silence both CrGBF1 and CrGBF2 and overexpress CrMYC2, aiming to simultaneous silencing two repressors while overexpressing an activator. The simultaneous manipulation of repressors and activator resulted in significant upregulation of the TIA pathway genes. To demonstrate the broad application of the cotyledon-based VIGS method, we optimized the method for two other valuable medicinal plants, Glycyrrhiza inflata (licorice) and Artemisia annua (sweet wormwood). When TRV vectors carrying the fragments of the ChlH genes were infiltrated into the seedlings of these plants, we observed yellow cotyledons with decreased chlorophyll contents.

CONCLUSIONS

The widely applicable cotyledon-based VIGS method is faster, more efficient, and easily accessible to additional treatments than the traditional VIGS method. It can be combined with transient gene overexpression to achieve simultaneous up- and down-regulation of desired genes in non-model plants. This method provides a powerful tool for functional genomics of medicinal plants, facilitating the discovery and production of valuable therapeutic compounds.

Genome-wide identification of GATA transcription factor family and the effect of different light quality on the accumulation of terpenoid indole alkaloids in Uncaria rhynchophylla

Uncaria rhynchophylla is an evergreen vine plant, belonging to the Rubiaceae family, that is rich in terpenoid indole alkaloids (TIAs) that have therapeutic effects on hypertension and Alzheimer's disease. GATA transcription factors (TF) are a class of transcription regulators that participate in the light response regulation, chlorophyll synthesis, and metabolism, with the capability to bind to GATA cis-acting elements in the promoter region of target genes. Currently the charactertics of GATA TFs in U. rhynchophylla and how different light qualities affect the expression of GATA and key enzyme genes, thereby affecting the changes in U. rhynchophylla alkaloids have not been investigated. In this study, 25 UrGATA genes belonging to four subgroups were identified based on genome-wide analysis. Intraspecific collinearity analysis revealed that only segmental duplications were identified among the UrGATA gene family. Collinearity analysis of GATA genes between U. rhynchophylla and four representative plant species, Arabidopsis thaliana, Oryza sativa, Coffea Canephora, and Catharanthus roseus was also performed. U. rhynchophylla seedlings grown in either red lights or under reduced light intensity had altered TIAs content after 21 days. Gene expression analysis reveal a complex pattern of expression from the 25 UrGATA genes as well as a number of key TIA enzyme genes. UrGATA7 and UrGATA8 were found to have similar expression profiles to key enzyme TIA genes in response to altered light treatments, implying that they may be involved in the regulation TIA content. In this research, we comprehensively analyzed the UrGATA TFs, and offered insight into the involvement of UrGATA TFs from U. rhynchophylla in TIAs biosynthesis.

Whole-genome sequencing in medicinal plants: current progress and prospect

Advancements in genomics have dramatically accelerated the research on medicinal plants, and the development of herbgenomics has promoted the "Project of 1K Medicinal Plant Genome" to decipher their genetic code. However, it is difficult to obtain their high-quality whole genomes because of the prevalence of polyploidy and/or high genomic heterozygosity. Whole genomes of 123 medicinal plants were published until September 2022. These published genome sequences were investigated in this review, covering their classification, research teams, ploidy, medicinal functions, and sequencing strategies. More than 1,000 institutes or universities around the world and 50 countries are conducting research on medicinal plant genomes. Diploid species account for a majority of sequenced medicinal plants. The whole genomes of plants in the Poaceae family are the most studied. Almost 40% of the published papers studied species with tonifying, replenishing, and heat-cleaning medicinal effects. Medicinal plants are still in the process of domestication as compared with crops, thereby resulting in unclear genetic backgrounds and the lack of pure lines, thus making their genomes more difficult to complete. In addition, there is still no clear routine framework for a medicinal plant to obtain a high-quality whole genome. Herein, a clear and complete strategy has been originally proposed for creating a high-quality whole genome of medicinal plants. Moreover, whole genome-based biological studies of medicinal plants, including breeding and biosynthesis, were reviewed. We also advocate that a research platform of model medicinal plants should be established to promote the genomics research of medicinal plants.

The leaf idioblastome of the medicinal plant Catharanthus roseus is associated with stress resistance and alkaloid metabolism

Catharanthus roseus leaves produce a range of monoterpenoid indole alkaloids (MIAs) that include low levels of the anticancer drugs vinblastine and vincristine. The MIA pathway displays a complex architecture spanning different subcellular and cell type localizations, and is under complex regulation. As a result, the development of strategies to increase the levels of the anticancer MIAs has remained elusive. The pathway involves mesophyll specialized idioblasts where the late unsolved biosynthetic steps are thought to occur. Here, protoplasts of C. roseus leaf idioblasts were isolated by fluorescence-activated cell sorting, and their differential alkaloid and transcriptomic profiles were characterized. This involved the assembly of an improved C. roseus transcriptome from short- and long-read data, IDIO+. It was observed that C. roseus mesophyll idioblasts possess a distinctive transcriptomic profile associated with protection against biotic and abiotic stresses, and indicative that this cell type is a carbon sink, in contrast to surrounding mesophyll cells. Moreover, it is shown that idioblasts are a hotspot of alkaloid accumulation, suggesting that their transcriptome may hold the key to the in-depth understanding of the MIA pathway and the success of strategies leading to higher levels of the anticancer drugs.

Light regulation of the biosynthesis of phenolics, terpenoids, and alkaloids in plants

Biosynthesis of specialized metabolites (SM), including phenolics, terpenoids, and alkaloids, is stimulated by many environmental factors including light. In recent years, significant progress has been made in understanding the regulatory mechanisms involved in light-stimulated SM biosynthesis at the transcriptional, posttranscriptional, and posttranslational levels of regulation. While several excellent recent reviews have primarily focused on the impacts of general environmental factors, including light, on biosynthesis of an individual class of SM, here we highlight the regulation of three major SM biosynthesis pathways by light-responsive gene expression, microRNA regulation, and posttranslational modification of regulatory proteins. In addition, we present our future perspectives on this topic.

Targeted quantitative analysis of monoterpenoid indole alkaloids in Alstonia scholaris by ultra-high-performance liquid chromatography coupled with quadrupole time of flight mass spectrometry

Monoterpene indole alkaloids exhibit structural diversity in herbal resources and have been developed as promising drugs owing to their significant biological activities. Confidential identification and quantification of monoterpene indole alkaloids is the key to quality control of target plants in industrial production but has rarely been reported. In this study, quantitative performance of three data acquisition modes of ultra-high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry including full scan, auto-MS2 and target-MS2 , was evaluated and compared for specificity, sensitivity, linearity, precision, accuracy, and matrix effect using five monoterpene indole alkaloids (scholaricine, 19-epi-scholaricine, vallesamine, picrinine, and picralinal). Method validations indicated that target-MS2 mode showed predominant performance for simultaneous annotation and quantification of analytes, and was then applied to determine monoterpene indole alkaloids in Alstonia scholaris (leaves, barks) after extraction procedures optimization using Box-Behnken design of response surface methodology. The variations of A. scholaris monoterpene indole alkaloids in different plant parts, harvest periods, and post-handling processes, were subsequently investigated. The results indicated that target-MS2 mode could improve the quantitative capability of ultra-high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry for structure-complex monoterpene indole alkaloids in herbal matrices. Alstonia scholaris, monoterpene indole alkaloids, quadrupole time of flight mass spectrometry, qualitative and quantitative analysis, ultra-high-performance liquid chromatography.

Genome-wide identification, evolution and expression pattern analysis of the GATA gene family in Sorghum bicolor

The GATA family of transcription factors is zinc finger DNA binding proteins involved in a variety of biological processes, including plant growth and development and response to biotic/abiotic stresses, and thus play an essential role in plant response to environmental changes. However, the GATA gene family of Sorghum (SbGATA) has not been systematically analyzed and reported yet. Herein, we used a variety of bioinformatics methods and quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) to explore the evolution and function of the 33 SbGATA genes identified. These SbGATA genes, distributed on 10 chromosomes, are classified into four subfamilies (I-IV) containing one pair of tandem duplications and nine pairs of segment duplications, which are more closely related to the monocot Brachypodium distachyon and Oryza sativa GATA genes. The physicochemical properties of the SbGATAs are significantly different among the subfamilies, while the protein structure and conserved protein motifs are highly conserved in the subfamilies. In addition, the transcription of SbGATAs is tissue-specific during Sorghum growth and development, which allows for functional diversity in response to stress and hormones. Collectively, our study lays a theoretical foundation for an in-depth analysis of the functions, mechanisms and evolutionary relationships of SbGATA during plant growth and development.

High light triggers flavonoid and polysaccharide synthesis through DoHY5-dependent signaling in Dendrobium officinale

Dendrobium officinale is edible and has medicinal and ornamental functions. Polysaccharides and flavonoids, including anthocyanins, are important components of D. officinale that largely determine the nutritional quality and consumer appeal. There is a need to study the molecular mechanisms regulating anthocyanin and polysaccharide biosynthesis to enhance D. officinale quality and its market value. Here, we report that high light (HL) induced the accumulation of polysaccharides, particularly mannose, as well as anthocyanin accumulation, resulting in red stems. Metabolome and transcriptome analyses revealed that most of the flavonoids showed large changes in abundance, and flavonoid and polysaccharide biosynthesis was significantly activated under HL treatment. Interestingly, DoHY5 expression was also highly induced. Biochemical analyses demonstrated that DoHY5 directly binds to the promoters of DoF3H1 (involved in anthocyanin biosynthesis), DoGMPP2, and DoPMT28 (involved in polysaccharide biosynthesis) to activate their expression, thereby promoting anthocyanin and polysaccharide accumulation in D. officinale stems. DoHY5 silencing decreased flavonoid- and polysaccharide-related gene expression and reduced anthocyanin and polysaccharide accumulation, whereas DoHY5 overexpression had the opposite effects. Notably, naturally occurring red-stemmed D. officinale plants similarly have high levels of anthocyanin and polysaccharide accumulation and biosynthesis gene expression. Our results reveal a previously undiscovered role of DoHY5 in co-regulating anthocyanin and polysaccharide biosynthesis under HL conditions, improving our understanding of the mechanisms regulating stem color and determining nutritional quality in D. officinale. Collectively, our results propose a robust and simple strategy for significantly increasing anthocyanin and polysaccharide levels and subsequently improving the nutritional quality of D. officinale.

bHLH transcription factor family identification, phylogeny, and its response to abiotic stress in Chenopodium quinoa

The second-largest transcription factor superfamily in plants is that of the basic helix-loop-helix (bHLH) family, which plays an important complex physiological role in plant growth, tissue development, and environmental adaptation. Systematic research on the Chenopodium quinoa bHLH family will enable a better understanding of this species. Herein, authors used a variety of bioinformatics methods and quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) to explore the evolution and function of the 218 CqbHLH genes identified. A total of 218 CqbHLH transcription factor genes were identified in the whole genome, located on 18 chromosomes. A phylogenetic tree was constructed using the CqbHLH and AtbHLH proteins to determine their homology, and the members were divided into 20 subgroups and one unclustered gene. Authors also analyzed 218 CqbHLH genes, conservative motifs, chromosome diffusion, and gene replication. The author constructed one Neighbor-Joining (NJ) tree and a collinearity analysis map of the bHLH family in C. quinoa and six other plant species to study the evolutionary relationship and homology among multiple species. In addition, the expression levels of 20 CqbHLH members from different subgroups in various tissues, different fruit developmental stages, and six abiotic stresses were analyzed. Authors identified 218 CqbHLH genes and studied their biological functions, providing a basis for better understanding and further studying the bHLH family in quinoa.

Genome-wide analysis revealed the stepwise origin and functional diversification of HSDs from lower to higher plant species

Hydroxysteroid dehydrogenase (HSDs) is an oil-body sterol protein (steroleosin) with an NADP(H) binding domain that belongs to the short-chain dehydrogenase/reductase (SDR) superfamily. There are numerous studies on the characterization of HSDs in plants. However, thus far, the evolutionary differentiation and divergence analysis of these genes remain to be explored. The current study used an integrated method to elucidate the sequential evolution of HSDs in 64 sequenced plant genomes. Analyses were conducted on their origins, distribution, duplication, evolutionary paths, domain functions, motif composition, properties, and cis-elements. Results indicate that except for algae, HSD1 was widely distributed in plant species ranging from lower to higher plants, while HSD5 was restricted to terrestrial plants, and HSD2 was identified in fewer monocots and several dicot plants. Phylogenetic analysis of HSD proteins revealed that monocotyledonous HSD1 in moss and ferns appeared closest to the outgroup, V. carteri HSD-like, M. musculus HSD1, and H. sapiens HSD1. These data support the hypothesis that HSD1 originated in bryophytes and then in non-vascular and vascular plants, followed by HSD5 only in land plants. Gene structure analysis suggests that HSDs in plant species came up with a fixed number of six exons, and the intron phase was primarily 0, 1, 0, 0, and 0. Similarly, duplication analysis revealed that segmental duplications were the main reason for HSDs in plant species. Physicochemical properties suggest that dicotyledonous HSD1s and HSD5s were mainly acidic. The monocotyledonous HSD1s and HSD2s and the dicotyledonous HSD2s, HSD3s, HSD4s, and HSD6s were mainly basic, implying that HSDs in plants may have a variety of functions. Cis-regulatory elements and expression analysis revealed that HSDs in plants might have roles in several abiotic stresses. Due to the high expression of HSD1s and HSD5s in seeds, these HSDs in plants may have roles in fatty acid accumulation and degradation.

Transcriptional regulatory network of high-value active ingredients in medicinal plants

High-value active ingredients in medicinal plants have attracted research attention because of their benefits for human health, such as the antimalarial artemisinin, anticardiovascular disease tanshinones, and anticancer Taxol and vinblastine. Here, we review how hormones and environmental factors promote the accumulation of active ingredients, thereby providing a strategy to produce high-value drugs at a low cost. Focusing on major hormone signaling events and environmental factors, we review the transcriptional regulatory network mediating biosynthesis of representative active ingredients. In this network, many transcription factors (TFs) simultaneously control multiple synthase genes; thus, understanding the molecular mechanisms affecting transcriptional regulation of active ingredients will be crucial to developing new breeding possibilities.

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

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

Metabolic engineering to enhance the accumulation of bioactive flavonoids licochalcone A and echinatin in Glycyrrhiza inflata (Licorice) hairy roots

Echinatin and licochalcone A (LCA) are valuable chalcones preferentially accumulated in roots and rhizomes of licorice (Glycyrrhiza inflata). The licorice chalcones (licochalcones) are valued for their anti-inflammatory, antimicrobial, and antioxidant properties and have been widely used in cosmetic, pharmaceutical, and food industries. However, echinatin and LCA are accumulated in low quantities, and the biosynthesis and regulation of licochalcones have not been fully elucidated. In this study, we explored the potential of a R2R3-MYB transcription factor (TF) AtMYB12, a known regulator of flavonoid biosynthesis in Arabidopsis, for metabolic engineering of the bioactive flavonoids in G. inflata hairy roots. Overexpression of AtMYB12 in the hairy roots greatly enhanced the production of total flavonoids (threefold), echinatin (twofold), and LCA (fivefold). RNA-seq analysis of AtMYB12-overexpressing hairy roots revealed that expression of phenylpropanoid/flavonoid pathway genes, such as phenylalanine ammonia-lyase (PAL), chalcone synthase (CHS), and flavanone 3'-hydroxylase (F3'H), is significantly induced compared to the control. Transient promoter activity assay indicated that AtMYB12 activates the GiCHS1 promoter in plant cells, and mutation to the MYB-binding motif in the GiCHS1 promoter abolished activation. In addition, transcriptomic analysis revealed that AtMYB12 overexpression reprograms carbohydrate metabolism likely to increase carbon flux into flavonoid biosynthesis. Further, AtMYB12 activated the biotic defense pathways possibly by activating the salicylic acid and jasmonic acid signaling, as well as by upregulating WRKY TFs. The transcriptome of AtMYB12-overexpressing hairy roots serves as a valuable source in the identification of potential candidate genes involved in LCA biosynthesis. Taken together, our findings suggest that AtMYB12 is an effective gene for metabolic engineering of valuable bioactive flavonoids in plants.

Hairy roots: An untapped potential for production of plant products

While plants are an abundant source of valuable natural products, it is often challenging to produce those products for commercial application. Often organic synthesis is too expensive for a viable commercial product and the biosynthetic pathways are often so complex that transferring them to a microorganism is not trivial or feasible. For plants not suited to agricultural production of natural products, hairy root cultures offer an attractive option for a production platform which offers genetic and biochemical stability, fast growth, and a hormone free culture media. Advances in metabolic engineering and synthetic biology tools to engineer hairy roots along with bioreactor technology is to a point where commercial application of the technology will soon be realized. We discuss different applications of hairy roots. We also use a case study of the advancements in understanding of the terpenoid indole alkaloid pathway in Catharanthus roseus hairy roots to illustrate the advancements and challenges in pathway discovery and in pathway engineering.

Genome-Wide Identification of the Eucalyptus urophylla GATA Gene Family and Its Diverse Roles in Chlorophyll Biosynthesis

GATA transcription factors have been demonstrated to play key regulatory roles in plant growth, development, and hormonal response. However, the knowledge concerning the evolution of GATA genes in Eucalyptus urophylla and their trans-regulatory interaction is indistinct. Phylogenetic analysis and study of conserved motifs, exon structures, and expression patterns resolved the evolutionary relationships of these GATA proteins. Phylogenetic analysis showed that EgrGATAs are broadly distributed in four subfamilies. Cis-element analysis of promoters revealed that EgrGATA genes respond to light and are influenced by multiple hormones and abiotic stresses. Transcriptome analysis revealed distinct temporal and spatial expression patterns of EgrGATA genes in various tissues of E. urophylla S.T.Blake, which was confirmed by real-time quantitative PCR (RT-qPCR). Further research revealed that EurGNC and EurCGA1 were localized in the nucleus, and EurGNC directly binds to the cis-element of the EurGUN5 promoter, implying its potential roles in the regulation of chlorophyll synthesis. This comprehensive study provides new insights into the evolution of GATAs and could help to improve the photosynthetic assimilation and vegetative growth of E. urophylla at the genetic level.

Genome-wide survey of the GATA gene family in camptothecin-producing plant Ophiorrhiza pumila

Background

Ophiorrhiza pumila (Rubiaceae) is capable of producing camptothecin (CPT), one monoterpene indole alkaloid extensively employed in the treatment of multiple cancers. Transcription factors (TFs) GATA are a group of transcription regulators involved in plant development and metabolism, and show the feature of binding to the GATA motif within the promoters of target genes. However, GATA TFs have not been characterized in O. pumila.

Result

In this study, a total of 18 GATA genes classified into four subfamilies were identified, which randomly distributed on 11 chromosomes of O. pumila. Synteny analysis of GATA genes between O. pumila and other plant species such as Arabidopsis thaliana, Oryza sativa, Glycine max, Solanum lycopersicum, Vitis vinifera, and Catharanthus roseus genomes were analyzed. Tissue expression pattern revealed that OpGATA1 and OpGATA18 were found to be correlated with ASA, MK, CPR and GPPS, which were highly expressed in leaves. OpGATA7, showed high expression in roots as most of the CPT biosynthetic pathway genes did, suggesting that these OpGATAs may be potential candidates regulating CPT biosynthesis in O. pumila.

Conclusions

In this study, we systematically analyzed the OpGATA TFs, and provided insights into the involvement of OpGATA TFs from O. pumila in CPT biosynthesis.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08484-x.

Comparative transcriptome analysis revealed the molecular mechanism of the effect of light intensity on the accumulation of rhynchophylline and isorhynchophylline in Uncaria rhynchophylla

Rhynchophylline (RIN) and isorhynchophylline (IRN), the main medicinal components in plant Uncaria rhynchophylla, have potential effects on Alzheimer's disease. Understanding the influence of environmental factors, especially light intensity, on the production of these active ingredients will help to improve cultivation techniques. Compared with the 100% light intensity (CK), the contents of RIN and IRN in U. rhynchophylla leaves significantly increased at 20% light intensity (HS) after 7 and 21 days. Short-term shading (21d) changed some morphological indicators of U. rhynchophylla, but did not affect its biomass. Transcriptome profile analysis was performed on data from two groups (7 and 21 days) of CK and HS samples and yielded 79,817 unigenes with an average length of 1023 bp. Concurrently, 2391 and 2136 differentially expressed genes were identified in the transcriptome data for, respectively, 7 and 21 days of shade treatment. Notably, unigenes known to be involved upstream in the biosynthesis of RIN and IRN, such as G8O, IO, 7-DLGT, LAMT, TDC, and STR, were mostly upregulated. In addition, 1065 putative transcription factors (TFs) were identified and grouped into 55 TF families; 26 TFs showed differential expression in the shade treatment after 7 and 21 days. HY5 and PIFs, two important TFs of the light signaling pathway, also showed differential expression. This study provides insight into how gene expression was affected by light intensity during RIN and IRN accumulation in U. rhynchophylla.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-022-01142-2.

RNA sequencing-based exploration of the effects of blue laser irradiation on mRNAs involved in functional metabolites of D. officinales

Dendrobium officinale Kimura et Migo (D. officinale) has promising lung moisturizing, detoxifying, and immune boosting properties. Light is an important factor influencing functional metabolite synthesis in D. officinale. The mechanisms by which lasers affect plants are different from those of ordinary light sources; lasers can effectively address the shortcomings of ordinary light sources and have significant interactions with plants. Different light treatments (white, blue, blue laser) were applied, and the number of red leaves under blue laser was greater than that under blue and white light. RNA-seq technology was used to analyze differences in D. officinale under different light treatments. The results showed 465, 2,107 and 1,453 differentially expressed genes (DEGs) in LB-B, LB-W and W-B, respectively. GO, KEGG and other analyses of DEGs indicated that D. officinale has multiple blue laser response modes. Among them, the plasma membrane, cutin, suberine and wax biosynthesis, flavone and flavonol biosynthesis, heat shock proteins, etc. play central roles. Physiological and biochemical results verified that blue laser irradiation significantly increases POD, SOD, and PAL activities in D. officinale. The functional metabolite results showed that blue laser had the greatest promoting effect on total flavonoids, polysaccharides, and alkaloids. qPCR verification combined with other results suggested that CRY DASH, SPA1, HY5, and PIF4 in the blue laser signal transduction pathway affect functional metabolite accumulation in D. officinale through positively regulated expression patterns, while CO16 and MYC2 exhibit negatively regulated expression patterns. These findings provide new ideas for the efficient production of metabolites in D. officinale.

The NAC-like transcription factor CsNAC7 positively regulates the caffeine biosynthesis-related gene yhNMT1 in Camellia sinensis

Caffeine is an important functional substance and is abundant in tea plant, but little is known about how its biosynthesis is regulated by transcription factors. In this study, the NAC-like transcription factor-encoding gene CsNAC7, which is involved in caffeine synthesis, was isolated from a Yinghong 9 cDNA library using a yeast one-hybrid assay; this gene comprises 1371 bp nucleotides and is predicted to encode 456 amino acids. The expression of CsNAC7 at the transcriptional level in tea shoots shared a similar pattern with that of the caffeine synthase gene yhNMT1 in the spring and summer, and its expressed protein was localized in the nucleus. Assays of gene activity showed that CsNAC7 has self-activation activity in yeast, that the active region is at the N-terminus, and that the transient expression of CsNAC7 could significantly promote the expression of yhNMT1 in tobacco leaves. In addition, overexpression or silencing of CsNAC7 significantly increased or decreased the expression of yhNMT1 and the accumulation of caffeine in transgenic tea calli, respectively. Our data suggest that the isolated transcription factor CsNAC7 positively regulates the caffeine synthase gene yhNMT1 and promotes caffeine accumulation in tea plant.

Identification and Characterization of Transcription Factors Regulating Terpenoid Indole Alkaloid Biosynthesis in Catharanthus roseus

Biosynthesis of the therapeutically valuable terpenoid indole alkaloids (TIAs), in the medicinal plant Catharanthus roseus, is one of the most elaborate and complex metabolic processes. Although genomic and transcriptomic resources have significantly accelerated gene discovery in the TIA pathway, relatively few genes of transcription factors (TFs) have been identified and characterized thus far. Systematic identification of TFs and elucidation of their functions are crucial for understanding TIA pathway regulation. The successful discovery of TFs in the TIA pathway has relied mostly on three different approaches, (1) identification of cis-regulatory motifs (CRMs) present in the pathway gene promoters as they often provide clues on potential TFs that bind to the promoters, (2) co-expression analysis, based on the assumption that TFs regulating a metabolic or developmental pathway exhibit similar spatiotemporal expression as the pathway genes, and (3) isolation of homologs of TFs known to regulate structurally similar or diverse specialized metabolites in different plant species. TFs regulating TIA pathway have been isolated using either an individual or a combination of the three approaches. Here we describe transcriptome-based coexpression analysis and cis-element determination to identify TFs in C. roseus. In addition, we describe the protocols for generation of transgenic hairy roots, Agrobacterium infiltration of flowers, and electrophoretic mobility shift assay (EMSA). The methods described here are useful for the identification and characterization of potential TFs involved in the regulation of special metabolism in other medicinal plants.

Virus-Induced Gene Silencing as a Tool to Study Regulation of Alkaloid Biosynthesis in Medicinal Plants

Advancements in genomics and transcriptomics have generated invaluable resources for the discovery of novel genes related to complex specialized metabolic pathways in plants. Virus-induced gene silencing (VIGS) has emerged as a powerful tool that is widely used for rapid functional characterization of genes in planta. VIGS has advantages over other reverse genetic approaches, such as RNAi-mediated suppression or T-DNA knockout, because it does not require the development of stable transgenic lines which is technically challenging and time consuming. Catharanthus roseus is an important medicinal plant that produces more than a hundred monoterpenoid indole alkaloids (MIAs), including the antineoplastic drugs vincristine and vinblastine. Biosynthesis of these alkaloids is strikingly complex, resulting in MIA accumulation in low quantities. Jasmonic acid (JA) is an elicitor of the MIA biosynthesis. Exogenous application of JA in C. roseus induces MIA pathway gene expression and increases MIA accumulation. The core JA signaling module comprises multiple components including the JA coreceptor Coronatine-Insensitive 1(COI1). COI1 plays a key role in JA-responsive gene expression in plants. Because generation of stable transgenic C. roseus plants is challenging, VIGS is being used for functional characterization of genes in the MIA pathway. Here we describe a detailed method for the VIGS-mediated suppression of C. roseus COI1(CrCOI1) expression to decipher the regulatory mechanism of JA-induced elicitation of MIA biosynthesis. When performing VIGS, gene silencing efficiency and the viral spread are monitored by the development of visible phenotype in the control plants. We use the C. roseus phytoene desaturase (CrPDS) and Protoporphyrin IX Mg-chelatase subunit H (CrChlH) as visual markers to access VIGS efficiency and viral spread. The protocol described here could be used for the functional characterization of genes involved in other metabolic pathways and in other medicinal plants.

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.

Terpenoid indole alkaloid biosynthesis in Catharanthus roseus: effects and prospects of environmental factors in metabolic engineering

Plants synthesize a vast array of specialized metabolites that primarily contribute to their defense and survival under adverse conditions. Many of the specialized metabolites have therapeutic values as drugs. Biosynthesis of specialized metabolites is affected by environmental factors including light, temperature, drought, salinity, and nutrients, as well as pathogens and insects. These environmental factors trigger a myriad of changes in gene expression at the transcriptional and posttranscriptional levels. The dynamic changes in gene expression are mediated by several regulatory proteins that perceive and transduce the signals, leading to up- or down-regulation of the metabolic pathways. Exploring the environmental effects and related signal cascades is a strategy in metabolic engineering to produce valuable specialized metabolites. However, mechanistic studies on environmental factors affecting specialized metabolism are limited. The medicinal plant Catharanthus roseus (Madagascar periwinkle) is an important source of bioactive terpenoid indole alkaloids (TIAs), including the anticancer therapeutics vinblastine and vincristine. The emerging picture shows that various environmental factors significantly alter TIA accumulation by affecting the expression of regulatory and enzyme-encoding genes in the pathway. Compared to our understanding of the TIA pathway in response to the phytohormone jasmonate, the impacts of environmental factors on TIA biosynthesis are insufficiently studied and discussed. This review thus focuses on these aspects and discusses possible strategies for metabolic engineering of TIA biosynthesis. PURPOSE OF WORK: Catharanthus roseus is a rich source of bioactive terpenoid indole alkaloids (TIAs). The objective of this work is to present a comprehensive account of the influence of various biotic and abiotic factors on TIA biosynthesis and to discuss possible strategies to enhance TIA production through metabolic engineering.

A comprehensive analysis of transcriptome and phenolic compound profiles suggests the role of flavonoids in cotyledon greening in Catharanthus roseus seedling

During seedling photo-morphogenesis, cotyledon greening is a vital developmental process and a moment of responding to light stress. An increasing number of reports suggest the function of natural antioxidant protection of phenolic compounds in plant growth and development processes. Due to the antioxidant functions, flavonoids allow plants to respond to abiotic or biotic stresses. As one of the plants rich in secondary metabolites, Catharanthus roseus has drawn great academic interest due to its richness of diverse secondary metabolites with medicinal values. To assess the distribution and function of phenolic compounds during cotyledon greening, combined phenolic profiling and transcriptome were applied in C. roseus seedling through ultra-high performance liquid chromatography quadrupole time-of-flight mass spectrometer (UPLC-Q-TOF/MS) and high throughput RNA sequencing, respectively. Results herein showed that light-exposed greening cotyledon accumulated large amounts of C6C3C6-type flavonoids, suggesting the function in repressing reactive oxygen species (ROS) generation to improve light adaptation and seedling survival. Moreover, synergistic up-regulation of relevant genes involved in flavonoids pathway, including PAL, C4H, CHS, FLS, and F3'H, was monitored in response to light. Several crucial candidate transcription factors including bHLH, MYB, and B-box families were likely to function, and thereinto, CrHY5 (CRO_T122304) and CRO_T137938 revealed a prompt response to light, supposing to induce flavonoids accumulation by targeting CHS and FLS. Therefore, this study provided new insight into the potential regulation and underlying roles of flavonoids to improve light acclimation during cotyledon greening.

Subfunctionalization of Paralog Transcription Factors Contributes to Regulation of Alkaloid Pathway Branch Choice in Catharanthus roseus

Catharanthus roseus produces a diverse range of specialized metabolites of the monoterpenoid indole alkaloid (MIA) class in a heavily branched pathway. Recent great progress in identification of MIA biosynthesis genes revealed that the different pathway branch genes are expressed in a highly cell type- and organ-specific and stress-dependent manner. This implies a complex control by specific transcription factors (TFs), only partly revealed today. We generated and mined a comprehensive compendium of publicly available C. roseus transcriptome data for MIA pathway branch-specific TFs. Functional analysis was performed through extensive comparative gene expression analysis and profiling of over 40 MIA metabolites in the C. roseus flower petal expression system. We identified additional members of the known BIS and ORCA regulators. Further detailed study of the ORCA TFs suggests subfunctionalization of ORCA paralogs in terms of target gene-specific regulation and synergistic activity with the central jasmonate response regulator MYC2. Moreover, we identified specific amino acid residues within the ORCA DNA-binding domains that contribute to the differential regulation of some MIA pathway branches. Our results advance our understanding of TF paralog specificity for which, despite the common occurrence of closely related paralogs in many species, comparative studies are scarce.

Transcriptome Analysis Revealed GhWOX4 Intercedes Myriad Regulatory Pathways to Modulate Drought Tolerance and Vascular Growth in Cotton

Cotton is a paramount cash crop around the globe. Among all abiotic stresses, drought is a leading cause of cotton growth and yield loss. However, the molecular link between drought stress and vascular growth and development is relatively uncharted. Here, we validated a crucial role of GhWOX4, a transcription factor, modulating drought stress with that of vasculature growth in cotton. Knock-down of GhWOX4 decreased the stem width and severely compromised vascular growth and drought tolerance. Conversely, ectopic expression of GhWOX4 in Arabidopsis enhanced the tolerance to drought stress. Comparative RNAseq analysis revealed auxin responsive protein (AUX/IAA), abscisic acid (ABA), and ethylene were significantly induced. Additionally, MYC-bHLH, WRKY, MYB, homeodomain, and heat-shock transcription factors (HSF) were differentially expressed in control plants as compared to GhWOX4-silenced plants. The promotor zone of GhWOX4 was found congested with plant growth, light, and stress response related cis-elements. differentially expressed genes (DEGs) related to stress, water deprivation, and desiccation response were repressed in drought treated GhWOX4-virus-induced gene silencing (VIGS) plants as compared to control. Gene ontology (GO) functions related to cell proliferation, light response, fluid transport, and flavonoid biosynthesis were over-induced in TRV: 156-0 h/TRV: 156-1 h (control) in comparison to TRV: VIGS-0 h/TRV: VIGS-1 h (GhWOX4-silenced) plants. This study improves our context for elucidating the pivotal role of GhWOX4 transcription factors (TF), which mediates drought tolerance, plays a decisive role in plant growth and development, and is likely involved in different regulatory pathways in cotton.

ERF Gene Clusters: Working Together to Regulate Metabolism

Plants produce structurally diverse specialized metabolites, including bioactive alkaloids and terpenoids, in response to biotic and abiotic environmental stresses. The APETALA2/ETHYLENE RESPONSE FACTOR (AP2/ERF) family of transcription factors (TFs) play key roles in regulating biosynthesis of specialized metabolites. Increasing genomic and functional evidence shows that a subset of the ERF genes occurs in clusters on the chromosomes. These jasmonate-responsive ERF TF gene clusters control the biosynthesis of many important metabolites, from natural products, such as nicotine and steroidal glycoalkaloids (SGAs), to pharmaceuticals, such as artemisinin, vinblastine, and vincristine. Here, we review the function, regulation, and evolution of ERF clusters and highlight recent advances in understanding the distinct roles of clustered ERF genes and their possible application in metabolic engineering.

BHLH IRIDOID SYNTHESIS 3 is a member of a bHLH gene cluster regulating terpenoid indole alkaloid biosynthesis in Catharanthus roseus

Basic helix-loop-helix (bHLH) transcription factors (TFs) are key regulators of plant specialized metabolites, including terpenoid indole alkaloids (TIAs) in Catharanthus roseus. Two previously characterized subgroup-IVa bHLH TFs, BIS1 (bHLH Iridoid Synthesis 1) and BIS2 regulate iridoid biosynthesis in the TIA pathway. We reanalyzed the recently updated C. roseus genome sequence and discovered that BIS1 and BIS2 are clustered on the same genomic scaffold with a previously uncharacterized bHLH gene, designated as BIS3. Only a few bHLH gene clusters have been studied to date. Comparative analysis of 49 genome sequences from different plant lineages revealed the presence of analogous bHLH clusters in core angiosperms, including the medicinal plants Calotropis gigantea (giant milkweed) and Gelsemium sempervirens (yellow jessamine), but not in the analyzed basal angiosperm and lower plants. Similar to the iridoid pathway genes, BIS3 is highly expressed in roots and induced by methyl jasmonate. BIS3 activates the promoters of iridoid branch genes, geraniol synthase (GES), geraniol 10-hydroxylase (G10H), 8-hydroxygeraniol oxidoreductase (8HGO), iridoid synthase (IS), 7-deoxyloganetic acid glucosyl transferase (7-DLGT), and 7-deoxyloganic acid hydroxylase (7DLH), but not iridoid oxidase (IO). Transactivation of the promoters was abolished when BIS3 is converted to a dominant repressor by fusing with the ERF-associated amphiphilic repression (EAR) sequence. In addition, BIS3 acts synergistically with BIS1 and BIS2 to activate the G10H promoter in tobacco cells. Mutation of the known bHLH TF binding motif, G-box (CACGTG) in the G10H promoter significantly reduced but did not abolish the transactivation by BIS3. Promoter deletion analysis of G10H suggests that the sequences adjacent to the G-box are also involved in the regulation by BIS3. Overexpression of BIS3 in C. roseus flower petals significantly upregulated the expression of iridoid biosynthetic genes and increased loganic acid accumulation. BIS2 expression was significantly induced by BIS3 although BIS3 did not directly activate the BIS2 promoter. Our results advance our understanding of the regulation of plant specialized metabolites by bHLH TF clusters.

Reprogramming plant specialized metabolism by manipulating protein kinases

Being sessile, plants have evolved sophisticated mechanisms to balance between growth and defense to survive in the harsh environment. The transition from growth to defense is commonly achieved by factors, such as protein kinases (PKs) and transcription factors, that initiate signal transduction and regulate specialized metabolism. Plants produce an array of lineage-specific specialized metabolites for chemical defense and stress tolerance. Some of these molecules are also used by humans as drugs. However, many of these defense-responsive metabolites are toxic to plant cells and inhibitory to growth and development. Plants have, thus, evolved complex regulatory networks to balance the accumulation of the toxic metabolites. Perception of external stimuli is a vital part of the regulatory network. Protein kinase-mediated signaling activates a series of defense responses by phosphorylating the target proteins and translating the stimulus into downstream cellular signaling. As biosynthesis of specialized metabolites is triggered when plants perceive stimuli, a possible connection between PKs and specialized metabolism is well recognized. However, the roles of PKs in plant specialized metabolism have not received much attention until recently. Here, we summarize the recent advances in understanding PKs in plant specialized metabolism. We aim to highlight how the stimulatory signals are transduced, leading to the biosynthesis of corresponding metabolites. We discuss the post-translational regulation of specialized metabolism and provide insights into the mechanisms by which plants respond to the external signals. In addition, we propose possible strategies to increase the production of plant specialized metabolites in biotechnological applications using PKs.

The methyl jasmonate-responsive transcription factor SmMYB1 promotes phenolic acid biosynthesis in Salvia miltiorrhiza

Water-soluble phenolic acids are major bioactive compounds in the medicinal plant species Salvia miltiorrhiza. Phenolic acid biosynthesis is induced by methyl jasmonate (MeJA) in this important Chinese herb. Here, we investigated the mechanism underlying this induction by analyzing a transcriptome library of S. miltiorrhiza in response to MeJA. Global transcriptome analysis identified the MeJA-responsive R2R3-MYB transcription factor-encoding gene SmMYB1. Overexpressing SmMYB1 significantly promoted phenolic acid accumulation and upregulated the expression of genes encoding key enzymes in the phenolic acid biosynthesis pathway, including cytochrome P450-dependent monooxygenase (CYP98A14). Dual-luciferase (dual-LUC) assays and/or an electrophoretic mobility shift assays (EMSAs) indicated that SmMYB1 activated the expression of CYP98A14, as well as the expression of genes encoding anthocyanin biosynthesis pathway enzymes, including chalcone isomerase (CHI) and anthocyanidin synthase (ANS). In addition, SmMYB1 was shown to interact with SmMYC2 to additively promote CYP98A14 expression compared to the action of SmMYB1 alone. Taken together, these results demonstrate that SmMYB1 is an activator that improves the accumulation of phenolic acids and anthocyanins in S. miltiorrhiza. These findings lay the foundation for in-depth studies of the molecular mechanism underlying MeJA-mediated phenolic acid biosynthesis and for the metabolic engineering of bioactive ingredients in S. miltiorrhiza.

Effects of Light on Secondary Metabolite Biosynthesis in Medicinal Plants

Secondary metabolites (SMs) found in medicinal plants are one of main sources of drugs, cosmetics, and health products. With the increase in demand for these bioactive compounds, improving the content and yield of SMs in medicinal plants has become increasingly important. The content and distribution of SMs in medicinal plants are closely related to environmental factors, especially light. In recent years, artificial light sources have been used in controlled environments for the production and conservation of medicinal germplasm. Therefore, it is essential to elucidate how light affects the accumulation of SMs in different plant species. Here, we systematically summarize recent advances in our understanding of the regulatory roles of light quality, light intensity, and photoperiod in the biosynthesis of three main types of SMs (polyphenols, alkaloids, and terpenoids), and the underlying mechanisms. This article provides a detailed overview of the role of light signaling pathways in SM biosynthesis, which will further promote the application of artificial light sources in medicinal plant production.

The methyl jasmonate-responsive transcription factor SmMYB1 promotes phenolic acid biosynthesis in Salvia miltiorrhiza

Water-soluble phenolic acids are major bioactive compounds in the medicinal plant species Salvia miltiorrhiza. Phenolic acid biosynthesis is induced by methyl jasmonate (MeJA) in this important Chinese herb. Here, we investigated the mechanism underlying this induction by analyzing a transcriptome library of S. miltiorrhiza in response to MeJA. Global transcriptome analysis identified the MeJA-responsive R2R3-MYB transcription factor-encoding gene SmMYB1. Overexpressing SmMYB1 significantly promoted phenolic acid accumulation and upregulated the expression of genes encoding key enzymes in the phenolic acid biosynthesis pathway, including cytochrome P450-dependent monooxygenase (CYP98A14). Dual-luciferase (dual-LUC) assays and/or an electrophoretic mobility shift assays (EMSAs) indicated that SmMYB1 activated the expression of CYP98A14, as well as the expression of genes encoding anthocyanin biosynthesis pathway enzymes, including chalcone isomerase (CHI) and anthocyanidin synthase (ANS). In addition, SmMYB1 was shown to interact with SmMYC2 to additively promote CYP98A14 expression compared to the action of SmMYB1 alone. Taken together, these results demonstrate that SmMYB1 is an activator that improves the accumulation of phenolic acids and anthocyanins in S. miltiorrhiza. These findings lay the foundation for in-depth studies of the molecular mechanism underlying MeJA-mediated phenolic acid biosynthesis and for the metabolic engineering of bioactive ingredients in S. miltiorrhiza.

Comparative sequence analysis across Brassicaceae, regulatory diversity in KCS5 and KCS6 homologs from Arabidopsis thaliana and Brassica juncea, and intronic fragment as a negative transcriptional regulator

Intra- and epicuticular-waxes primarily comprising of very long chain aliphatic lipid (VLCFA), terpenoids and secondary metabolites such as sterol and flavonoids played a major role in successful colonization of terrestrial ecosystem by aquatic plants and are thus considered as a key evolutionary innovation. The key rate limiting step of Fatty Acid (FA) biosynthesis of condensation/elongation are catalyzed by the enzyme, β-ketoacyl coenzyme A synthase (KCS), part of FAE (Fatty Acid Elongase) complex. KCS6 has been shown to be responsible for elongation using C22 fatty acid as substrate and is considered essential for synthesis of VLCFA for cuticular waxes. Earlier studies have established KCS5 as a close paralog of KCS6 in Arabidopsis thaliana, albeit with non-redundant function. We subsequently established segmental duplication responsible for origin of KCS6-KCS5 paralogy which is exclusive to Brassicaceae. In the present study, we aim to understand impact of duplication on regulatory diversification and evolution, through sequence and functional analysis of cis-regulatory element of KCS5 and KCS6. High level of sequence variation leading to conservation of only the proximal end of the promoter corresponding to the core promoter was observed among Brassicaceae members; such high diversity was also revealed when sliding window analysis revealed only two to three phylogenetic footprints. Profiling of transcription factor binding sites (TFBS) across Brassicaceae shows presence of light, hormone and stress responsive motifs; a few motifs involved in tissue specific expression (Skn-1; endosperm) were also detected. Functional characterization using transcriptional fusion constructs revealed regulatory diversification when promoter activity of homologs from A. thaliana and Brassica juncea were compared. When subjected to 5-Azacytidine, altered promoter activity was observed, implying role of DNA methylation in transcriptional regulation. Finally, investigation of the role of an 87 bp fragment from first intron that is retained in a splice variant, revealed it to be a transcriptional repressor. This is a first report on comparative sequence and functional analysis of transcriptional regulation of KCS5 and KCS6; further studies are required before manipulation of cuticular waxes as a strategy for mitigating stress.

Developmental Methylome of the Medicinal Plant Catharanthus roseus Unravels the Tissue-Specific Control of the Monoterpene Indole Alkaloid Pathway by DNA Methylation

Catharanthus roseus produces a wide spectrum of monoterpene indole alkaloids (MIAs). MIA biosynthesis requires a tightly coordinated pathway involving more than 30 enzymatic steps that are spatio-temporally and environmentally regulated so that some MIAs specifically accumulate in restricted plant parts. The first regulatory layer involves a complex network of transcription factors from the basic Helix Loop Helix (bHLH) or AP2 families. In the present manuscript, we investigated whether an additional epigenetic layer could control the organ-, developmental- and environmental-specificity of MIA accumulation. We used Whole-Genome Bisulfite Sequencing (WGBS) together with RNA-seq to identify differentially methylated and expressed genes among nine samples reflecting different plant organs and experimental conditions. Tissue specific gene expression was associated with specific methylation signatures depending on cytosine contexts and gene parts. Some genes encoding key enzymatic steps from the MIA pathway were found to be simultaneously differentially expressed and methylated in agreement with the corresponding MIA accumulation. In addition, we found that transcription factors were strikingly concerned by DNA methylation variations. Altogether, our integrative analysis supports an epigenetic regulation of specialized metabolisms in plants and more likely targeting transcription factors which in turn may control the expression of enzyme-encoding genes.

Light-regulated expression of terpene synthase gene, AtTPS03, is controlled by the bZIP transcription factor, HY5, in Arabidopsis thaliana

The terpenoid pathway serves as an essential source of all isoprenoid precursors and metabolites that are of great pharmacological importance. The major enzymes for the synthesis of these diverse molecules is the terpene synthases (TPSs), which catalyse the final step of the synthesis of the important secondary products, the terpenes. Previous studies have reported that the various environmental factors, including light govern the synthesis of terpenoids. However, the molecular components and steps involved in the regulation of synthesis of these molecules have not been studied in detail. In this study, we report that the light regulates the expression of the members of terpene synthase gene family in Arabidopsis thaliana. We demonstrate that ELONGATED HYPOCOTYL (HY5), a basic leucine zipper transcription factor, plays a crucial role in light-mediated transcriptional regulation of terpene synthase, AtTPS03. Expression analysis using hy5-215 mutant and HY5 over-expression lines revealed that HY5 acts as a positive regulator of AtTPS03. Additionally, studies including AtTPS03 Promoter::reporter transgenic lines in wild-type and hy5-215, as well as electrophoretic mobility shift assay (EMSA), suggest an interaction of HY5 with the AtTPS03 promoter. Together, our analysis indicate the requirement for HY5 for light-mediated regulation of AtTPS03 for the terpenoid biosynthesis in Arabidopsis.

Revisiting the ORCA gene cluster that regulates terpenoid indole alkaloid biosynthesis in Catharanthus roseus

Transcription factor (TF) gene clusters in plants, such as tomato, potato, petunia, tobacco, and almond, have been characterized for their roles in the biosynthesis of diverse array of specialized metabolites. In Catharanthus roseus, three AP2/ERF TFs, ORCA3, ORCA4, and ORCA5, have been shown to be present on the same genomic scaffold, forming a cluster that regulates the biosynthesis of pharmaceutically important terpenoid indole alkaloids (TIAs). Our analysis of the recently updated C. roseus genome sequence revealed that the ORCA cluster comprises two additional AP2/ERFs, the previously characterized ORCA2 and a newly identified member designated as ORCA6. Transcriptomic analysis revealed that the ORCAs are highly expressed in stems, followed by leaves, roots and flowers. Expression of ORCAs was differentially induced in response to methyl-jasmonate and ethylene treatment. In addition, ORCA6 activated the strictosidine synthase (STR) promoter in tobacco cells. Activation of the STR promoter was significantly higher when ORCA2 or ORCA6 was coexpressed with the mitogen-activated protein kinase kinase, CrMPKK1. Furthermore, transient overexpression of ORCA6 in C. roseus flower petals activated TIA pathway gene expression and TIA accumulation. The results described here advance our understanding of regulation of TIA pathway by the ORCA gene cluster and the evolution for plant ERF gene clusters.

The regulation of ZCT1, a transcriptional repressor of monoterpenoid indole alkaloid biosynthetic genes in Catharanthus roseus

Cys2/His2-type (C2H2) zinc finger proteins, such as ZCT1, are an important class of transcription factors involved in growth, development, and stress responses in plants. In the medicinal plant Catharanthus roseus, the zinc finger Catharanthus transcription factor (ZCT) family represses monoterpenoid indole alkaloid (MIA) biosynthetic gene expression. Here, we report the analysis of the ZCT1 promoter, which contains several hormone-responsive elements. ZCT1 is responsive to not only jasmonate, as was previously known, but is also induced by the synthetic auxin, 1-naphthalene acetic acid (1-NAA). Through promoter deletion analysis, we show that an activation sequence-1-like (as-1-like)-motif and other motifs contribute significantly to ZCT1 expression in seedlings. We also show that the activator ORCA3 does not transactivate the expression of ZCT1 in seedlings, but ZCT1 represses its own promoter, suggesting a feedback mechanism by which the expression of ZCT1 can be limited.

CrERF5, an AP2/ERF Transcription Factor, Positively Regulates the Biosynthesis of Bisindole Alkaloids and Their Precursors in Catharanthus roseus

Catharanthus roseus contains a variety of monoterpenoid indole alkaloids (MIAs), among which bisindole alkaloids vinblastine and vincristine are well-known to have antitumor effects and widely used in clinical treatment. However, their contents in C. roseus is extremely low and difficult to meet market demands. Therefore, it is of great significance to study the transcriptional regulation mechanism of MIAs biosynthesis for high yielding of bisindole alkaloids in C. roseus. Studies have shown that MIAs biosynthesis in C. roseus has complex temporal and spacial specificity and is under tight transcriptional regulation, especially bisindole alkaloids. In this study, an AP2/ERF transcription factor CrERF5 was selected by RNA-seq of C. roseus organs, and its full-length sequence was cloned and characterized. CrERF5 responds to both ethylene and JA signals and is localized in the nucleus. CrERF5 could activate the transcriptional activity of the TDC promoter. Transient overexpressing CrERF5 in C. roseus petals caused a significant increase of the expression levels of key genes in both the upstream and downstream pathways of MIAs biosynthesis while silencing CrERF5 resulted in a decrease of them. Accordingly, the contents of bisindole alkaloids anhydrovinblastine and vinblastine, monoindole alkaloids ajmalicine, vindoline, and catharanthine were strongly enhanced in CrERF5-overexpressing petals while their contents decreased in CrERF5-silenced plants. These results suggested that CrERF5 is a novel positive ethylene-JA-inducible AP2/ERF transcription factor upregulating the MIAs biosynthetic pathway leading to the bisindole alkaloids accumulation.