The AP2/ERF transcription factor SmERF128 positively regulates diterpenoid biosynthesis in Salvia miltiorrhiza

APETALA2/ethylene-responsive factors in higher plant and their roles in regulation of plant stress response

Plants, anchored throughout their life cycles, face a unique set of challenges from fluctuating environments and pathogenic assaults. Central to their adaptative mechanisms are transcription factors (TFs), particularly the AP2/ERF superfamily-one of the most extensive TF families unique to plants. This family plays instrumental roles in orchestrating diverse biological processes ranging from growth and development to secondary metabolism, and notably, responses to both biotic and abiotic stresses. Distinguished by the presence of the signature AP2 domain or its responsiveness to ethylene signals, the AP2/ERF superfamily has become a nexus of research focus, with increasing literature elucidating its multifaceted roles. This review provides a synoptic overview of the latest research advancements on the AP2/ERF family, spanning its taxonomy, structural nuances, prevalence in higher plants, transcriptional and post-transcriptional dynamics, and the intricate interplay in DNA-binding and target gene regulation. Special attention is accorded to the ethylene response factor B3 subgroup protein Pti5 and its role in stress response, with speculative insights into its functionalities and interaction matrix in tomatoes. The overarching goal is to pave the way for harnessing these TFs in the realms of plant genetic enhancement and novel germplasm development.

Transcription factors in tanshinones: Emerging mechanisms of transcriptional regulation

Transcription factors play a crucial role in the biosynthesis of tanshinones, which are significant secondary metabolites derived from Salvia miltiorrhiza, commonly known as Danshen. These compounds have extensive pharmacological properties, including anti-inflammatory and cardioprotective effects. This review delves into the roles of various transcription factor families, such as APETALA2/ethylene response factor, basic helix-loop-helix, myeloblastosis, basic leucine zipper, and WRKY domain-binding protein, in regulating the biosynthetic pathways of tanshinones. We discuss the emerging mechanisms by which these transcription factors influence the synthesis of tanshinones, both positively and negatively, by directly regulating gene expression or forming complex regulatory networks. Additionally, the review highlights the potential applications of these insights in enhancing tanshinone production through genetic and metabolic engineering, setting the stage for future advancements in medicinal plant research.

Physiological response of microalga Dunaliella parva when treated with MeJA, GA3

DpAP2 is a transcription factor regulating carotenoid biosynthesis pathway. It was speculated that MeJA significantly decreased expression of DpAP2 gene, then the decreasing DpAP2 expression significantly inhibited expression of some key enzyme genes such as PSY, PDS and GGPS in carotenoid biosynthesis pathway. In contrast, it was speculated that GA3 significantly increased expression of DpAP2 gene, then the increasing DpAP2 expression significantly increased expression of some key enzyme genes such as PDS and GGPS in carotenoid biosynthesis pathway. To increase the content of carotenoid, we evaluated the effect of DpAP2 overexpression on carotenoid accumulation in D. parva. Transgenic D. parva showed a higher carotenoid content (3.18 mg/g DW) compared with control group (2.13 mg/g DW) at 9 d. The dosage effects of exogenous hormones MeJA and GA3 were found in D. parva cells treated with different concentrations of MeJA (10, 20, 50, 100 μM) and GA3 (10, 20, 50, 100 μM). The high concentrations of MeJA (10-100 μM) inhibited the accumulation of carotenoid, and the relative expression of DpAP2, PSY, PDS and GGPS decreased significantly. On the contrary, the relative expression of DpAP2, PDS and GGPS increased significantly when D. parva was treated with 10, 20, 50 and 100 μM GA3, which promoted the biosynthesis of carotenoid. Therefore, we inferred that there was a hierarchical regulation from hormone, transcription factor, key enzyme gene to carotenoid accumulation in carotenoid biosynthesis. Carotenoid biosynthesis was enhanced by DpAP2 overexpression (1.4930 fold of control) and exogenous substances such as GA3 (1.5889 fold of control), which laid a foundation for massive accumulation of carotenoids in microalgae. In the future, further studies were required to demonstrate the complex regulatory network.

PfERF106, a novel key transcription factor regulating the biosynthesis of floral terpenoids in Primula forbesii Franch

BACKGROUND

Flowers can be a source of essential oils used in the manufacture of substances with high economic value. The ethylene response factor (ERF) gene family plays a key role in regulating secondary metabolite biosynthesis in plants. However, until now, little has been known about the involvement of ERF transcription factors (TFs) in floral terpenoid biosynthesis.

RESULTS

In this study, an aromatic plant, Primula forbesii Franch., was used as research material to explore the key regulatory effects of PfERF106 on the biosynthesis of terpenoids. PfERF106, which encodes an IXb group ERF transcription factor, exhibited a consistent expression trend in the flowers of P. forbesii and was transcriptionally induced by exogenous ethylene. Transient silencing of PfERF106 in P. forbesii significantly decreased the relative contents of key floral terpenes, including (z)-β-ocimene, sabinene, β-pinene, γ-terpinene, linalool, eremophilene, α-ionone, and α-terpineol. In contrast, constitutive overexpression of PfERF106 in transgenic tobacco significantly increased the relative contents of key floral terpenes, including cis-3-hexen-1-ol, linalool, caryophyllene, cembrene, and sclareol. RNA sequencing of petals of PfERF106-silenced plants and empty-vector control plants revealed 52,711 expressed unigenes and 9,060 differentially expressed genes (DEGs). KEGG annotation analysis revealed that the DEGs were enriched for involvement in secondary metabolic biosynthetic pathways, including monoterpene and diterpene synthesis. Notably, 10 downregulated DEGs were determined to be the downstream target genes of PfERF106 affecting the biosynthesis of terpenoids in P. forbesii.

CONCLUSION

This study characterized the key positive regulatory effects of PfERF106 on the biosynthesis of terpenoids, indicating high-quality genetic resources for aroma improvement in P. forbesii. Thus, this study advances the artificial and precise directional regulation of metabolic engineering of aromatic substances.

The methyl jasmonate-responsive transcription factor SmERF106 promotes tanshinone accumulation in Salvia miltiorrhiza

Understanding the regulatory biosynthesis mechanisms of active compounds in herbs is vital for the preservation and sustainable use of natural medicine resources. Diterpenoids, which play a key role in plant growth and resistance, also serve as practical products for humans. Tanshinone, a class of abietane-type diterpenes unique to the Salvia genus, such as Salvia miltiorrhiza, is an excellent model for studying diterpenoids. In this study, we discovered that a transcription factor, SmERF106, responds to MeJA induction and is located in the nucleus. It exhibits a positive correlation with the expression of SmKSL1 and SmIDI1, which are associated with tanshinone biosynthesis. We performed DNA affinity purification sequencing (DAP-seq) to predict genes that may be transcriptionally regulated by SmERF106. Our cis-elements analysis suggested that SmERF106 might bind to GCC-boxes in the promoters of SmKSL1 and SmIDI1. This indicates that SmKSL1 and SmIDI1 could be potential target genes regulated by SmERF106 in the tanshinone biosynthesis pathway. Their interaction was then demonstrated through a series of in vitro and in vivo binding experiments, including Y1H, EMSA, and Dual-LUC. Overexpression of SmERF106 in the hairy root of S. miltiorrhiza led to a significant increase in tanshinone content and the transcriptional levels of SmKSL1 and SmIDI1. In summary, we found that SmERF106 can activate the transcription of SmKSL1 and SmIDI1 in response to MeJA induction, thereby promoting tanshinone biosynthesis. This discovery provides new insights into the regulatory mechanisms of tanshinones in response to JA and offers a potential gene tool for tanshinone metabolic engineering strategy.

Biosynthesis and signal transduction of plant growth regulators and their effects on bioactive compound production in Salvia miltiorrhiza (Danshen)

Plant growth regulators (PGRs) are involved in multiple aspects of plant life, including plant growth, development, and response to environmental stimuli. They are also vital for the formation of secondary metabolites in various plants. Salvia miltiorrhiza is a famous herbal medicine and has been used commonly for > 2000 years in China, as well as widely used in many other countries. S. miltiorrhiza is extensively used to treat cardiovascular and cerebrovascular diseases in clinical practices and has specific merit against various diseases. Owing to its outstanding medicinal and commercial potential, S. miltiorrhiza has been extensively investigated as an ideal model system for medicinal plant biology. Tanshinones and phenolic acids are primary pharmacological constituents of S. miltiorrhiza. As the growing market for S. miltiorrhiza, the enhancement of its bioactive compounds has become a research hotspot. S. miltiorrhiza exhibits a significant response to various PGRs in the production of phenolic acids and tanshinones. Here, we briefly review the biosynthesis and signal transduction of PGRs in plants. The effects and mechanisms of PGRs on bioactive compound production in S. miltiorrhiza are systematically summarized and future research is discussed. This article provides a scientific basis for further research, cultivation, and metabolic engineering in S. miltiorrhiza.

The Ginkgo biloba microRNA160-ERF4 module participates in terpene trilactone biosynthesis

Terpene trilactones (TTLs) are important secondary metabolites in ginkgo (Ginkgo biloba); however, their biosynthesis gene regulatory network remains unclear. Here, we isolated a G. biloba ethylene response factor 4 (GbERF4) involved in TTL synthesis. Overexpression of GbERF4 in tobacco (Nicotiana tabacum) significantly increased terpenoid content and upregulated the expression of key enzyme genes (3-hydroxy-3-methylglutaryl-CoA reductase [HMGR], 3-hydroxy-3-methylglutaryl-CoA synthase [HMGS], 1-deoxy-D-xylulose-5-phosphate reductoisomerase [DXR], 1-deoxy-D-xylulose-5-phosphate synthase [DXS], acetyl-CoA C-acetyltransferase [AACT], and geranylgeranyl diphosphate synthase [GGPPS]) in the terpenoid pathway in tobacco, suggesting that GbERF4 functions in regulating the synthesis of terpenoids. The expression pattern analysis and previous microRNA (miRNA) sequencing showed that gb-miR160 negatively regulates the biosynthesis of TTLs. Transgenic experiments showed that overexpression of gb-miR160 could significantly inhibit the accumulation of terpenoids in tobacco. Targeted inhibition and dual-luciferase reporter assays confirmed that gb-miR160 targets and negatively regulates GbERF4. Transient overexpression of GbERF4 increased TTL content in G. biloba, and further transcriptome analysis revealed that DXS, HMGS, CYPs, and transcription factor genes were upregulated. In addition, yeast 1-hybrid and dual-luciferase reporter assays showed that GbERF4 could bind to the promoters of the HMGS1, AACT1, DXS1, levopimaradiene synthase (LPS2), and GGPPS2 genes in the TTL biosynthesis pathway and activate their expression. In summary, this study investigated the molecular mechanism of the gb-miR160-GbERF4 regulatory module in regulating the biosynthesis of TTLs. It provides information for enriching the understanding of the regulatory network of TTL biosynthesis and offers important gene resources for the genetic improvement of G. biloba with high contents of TTLs.

Integrating GC-MS and comparative transcriptome analysis reveals that TsERF66 promotes the biosynthesis of caryophyllene in Toona sinensis tender leaves

Introduction

The strong aromatic characteristics of the tender leaves of Toona sinensis determine their quality and economic value.

Methods and results

Here, GC-MS analysis revealed that caryophyllene is a key volatile compound in the tender leaves of two different T. sinensis varieties, however, the transcriptional mechanisms controlling its gene expression are unknown. Comparative transcriptome analysis revealed significant enrichment of terpenoid synthesis pathway genes, suggesting that the regulation of terpenoid synthesis-related gene expression is an important factor leading to differences in aroma between the two varieties. Further analysis of expression levels and genetic evolution revealed that TsTPS18 is a caryophyllene synthase, which was confirmed by transient overexpression in T. sinensis and Nicotiana benthamiana leaves. Furthermore, we screened an AP2/ERF transcriptional factor ERF-IX member, TsERF66, for the potential regulation of caryophyllene synthesis. The TsERF66 had a similar expression trend to that of TsTPS18 and was highly expressed in high-aroma varieties and tender leaves. Exogenous spraying of MeJA also induced the expression of TsERF66 and TsTPS18 and promoted the biosynthesis of caryophyllene. Transient overexpression of TsERF66 in T. sinensis significantly promoted TsTPS18 expression and caryophyllene biosynthesis.

Discussion

Our results showed that TsERF66 promoted the expression of TsTPS18 and the biosynthesis of caryophyllene in T. sinensis leaves, providing a strategy for improving the aroma of tender leaves.

Genome-wide identification and characterization of the AP2/ERF gene family in loblolly pine (Pinus taeda L.)

The loblolly pine (Pinus taeda L.) is one of the most profitable forest species worldwide owing to its quick growth, high wood yields, and strong adaptability. The AP2/ERF gene family plays a widespread role in the physiological processes of plant defense responses and the biosynthesis of metabolites. Nevertheless, there are no reports on this gene family in loblolly pine (P. taeda). In this study, a total of 303 members of the AP2/ERF gene family were identified. Through multiple sequence alignment and phylogenetic analysis, they were classified into four subfamilies, including AP2 (34), RAV (17), ERF (251), and Soloist (1). An analysis of the conservation domains, conserved motifs, and gene structure revealed that every PtAP2/ERF transcription factor (TF) had at least one AP2 domain. While evolutionary conservation was displayed within the same subfamilies, the distribution of conserved domains, conserved motifs, and gene architectures varied between subfamilies. Cis-element analysis revealed abundant light-responsive elements, phytohormone-responsive elements, and stress-responsive elements in the promoter of the PtAP2/ERF genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of potential target genes showed that the AP2/ERF gene family might play a critical role in plant growth and development, the response to environmental stresses, and metabolite biosynthesis. Utilizing quantitative real-time PCR (qRT-PCR), we examined the expression patterns of 10 randomly selected genes from Group IX after 6 h of treatments with mechanical injury, ethephon (Eth), and methyl jasmonate (MeJA). The AP2/ERF gene family in the loblolly pine was systematically analyzed for the first time in this study, offering a theoretical basis for exploring the functions and applications of AP2/ERF genes.

The grapevine miR827a regulates the synthesis of stilbenes by targeting VqMYB14 and gives rise to susceptibility in plant immunity

Grapevine (Vitis vinifera L.) is an economically important fruit crop cultivated worldwide. In China, grapevine cultivation is very extensive, and a few Vitis grapes have excellent pathogen and stress resistance, but the molecular mechanisms underlying the grapevine response to stress remain unclear. In this study, a microRNA (miRNA; miR827a), which negatively regulates its target gene VqMYB14, a key regulatory role in the synthesis of stilbenes, was identified in Vitis quinquangularis (V. quinquangularis) using transcriptome sequencing. Using overexpression and silencing approaches, we found that miR827a regulates the synthesis of stilbenes by targeting VqMYB14. We used flagellin N-terminal 22-amino-acid peptide (flg22), the representative elicitor in plant basal immunity, as the elicitor to verify whether miR827a is involved in the basal immunity of V. quinquangularis. Furthermore, the promoter activity of miR827a was alleviated in transgenic grape protoplasts and Arabidopsis thaliana following treatment with flg22 and Pseudomonas syringae pv. Tomato DC3000 (Pst DC3000), respectively. In addition, yeast one-hybrid and dual luciferase reporter assay revealed that the ethylene transcription factor VqERF057 acted as a key regulator in the inhibition of miR827a transcription. These results will contribute to the understanding of the biological functions of miR827a in grapevine and clarify the molecular mechanism of the interaction between miR827a and VqMYB14.

Potential Regulatory Networks and Heterosis for Flavonoid and Terpenoid Contents in Pak Choi: Metabolomic and Transcriptome Analyses

Pak choi exhibits a diverse color range and serves as a rich source of flavonoids and terpenoids. However, the mechanisms underlying the heterosis and coordinated regulation of these compounds-particularly isorhamnetin-remain unclear. This study involved three hybrid combinations and the detection of 528 metabolites from all combinations, including 26 flavonoids and 88 terpenoids, through untargeted metabolomics. Analysis of differential metabolites indicated that the heterosis for the flavonoid and terpenoid contents was parent-dependent, and positive heterosis was observed for isorhamnetin in the two hybrid combinations (SZQ, 002 and HMG, ZMG). Moreover, there was a high transcription level of flavone 3'-O-methyltransferase, which is involved in isorhamnetin biosynthesis. The third group was considered the ideal hybrid combination for investigating the heterosis of flavonoid and terpenoid contents. Transcriptome analysis identified a total of 12,652 DEGs (TPM > 1) in various groups that were used for comparison, and DEGs encoding enzymes involved in various categories, including "carotenoid bio-synthesis" and "anthocyanin biosynthesis", were enriched in the hybrid combination (SZQ, 002). Moreover, the category of anthocyanin biosynthesis also was enriched in the hybrid combination (HMG, ZMG). The flavonoid pathway demonstrated more differential metabolites than the terpenoid pathway did. The WGCNA demonstrated notable positive correlations between the dark-green modules and many flavonoids and terpenoids. Moreover, there were 23 ERF genes in the co-expression network (r ≥ 0.90 and p < 0.05). Thus, ERF genes may play a significant role in regulating flavonoid and terpenoid biosynthesis. These findings enhance our understanding of the heterosis and coordinated regulation of flavonoid and terpenoid biosynthesis in pak choi, offering insights for genomics-based breeding improvements.

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.

DoAP2/ERF89 activated the terpene synthase gene DoPAES in Dendrobium officinale and participated in the synthesis of β-patchoulene

Dendrobium officinale Kimura et Migo is a tonic plant that has both ornamental and medicinal properties. Terpenoids are significant and diverse secondary metabolites in plants, and are one of the important natural active ingredients in D. officinale. The AP2/ERF gene family plays a major role in primary and secondary metabolism. However, the AP2/ERF transcription factor family has not been identified in D. officinale, and it is unclear if it is involved in the regulation of terpenoid biosynthesis. This study identified a sesquiterpene synthetase-β-patchoulene synthase (DoPAES) using transcriptome and terpenic metabolic profile analyses. A total of 111 members of the AP2/ERF family were identified through the whole genome of D. officinale. The tissue-specific expression and gene co-expression pattern of the DoAP2/ERF family members were analyzed. The results showed that the expression of DoPAES was highly correlated with the expression of DoAP2/ERF89 and DoAP2/ERF47. The yeast one-hybrid (Y1H) assays and dual-luciferase experiments demonstrated that DoAP2/ERF89 and DoAP2/ERF47 could regulate the expression of DoPAES. The transcriptional regulatory effects were examined using homologous transient expression of DoAP2/ERF89 in protocorms of D. officinale. DoAP2/ERF89 positively regulated the biosynthesis of β-patchoulene. This study showed that DoAP2/ERF89 can bind to the promoter region of DoPAES to control its expression and further regulate the biosynthesis of β-patchoulene in D. officinale. These results provide new insights on the regulation of terpenoid biosynthesis.

The SmERF1b-like regulates tanshinone biosynthesis in Salvia miltiorrhiza hairy root

The ethylene response factor family genes are involved in the regulation of secondary metabolism in Salvia miltiorrhiza, but the mechanism underlying this regulation remains elusive. In the present study, based on the cDNA library of S. miltiorrhiza, an AP2/ERF gene was cloned and named SmERF1b-like. This gene exhibited a significant response to exogenous ethylene supply, such that ethylene remarkably upregulated SmERF1b-like expression levels in the leaves of S. miltiorrhiza. Subcellular localization showed that SmERF1b-like is located in the nucleus. Furthermore, SmERF1b-like showed a binding affinity with a GCC-box motif in the promoter region of genes associated with tanshinone biosynthesis in S. miltiorrhiza. Overexpression of SmERF1b-like in hairy roots of S. miltiorrhiza substantially upregulated SmCPS1 and SmKSL1 expression levels, resulting in increased biosynthesis of tanshinone I and cryptotanshinone contents. This finding provides valuable theoretical support for the utilization of a plant genetic engineering strategy to enhance S. miltiorrhiza resources.

Functions of Representative Terpenoids and Their Biosynthesis Mechanisms in Medicinal Plants

Terpenoids are the broadest and richest group of chemicals obtained from plants. These plant-derived terpenoids have been extensively utilized in various industries, including food and pharmaceuticals. Several specific terpenoids have been identified and isolated from medicinal plants, emphasizing the diversity of biosynthesis and specific functionality of terpenoids. With advances in the technology of sequencing, the genomes of certain important medicinal plants have been assembled. This has improved our knowledge of the biosynthesis and regulatory molecular functions of terpenoids with medicinal functions. In this review, we introduce several notable medicinal plants that produce distinct terpenoids (e.g., Cannabis sativa, Artemisia annua, Salvia miltiorrhiza, Ginkgo biloba, and Taxus media). We summarize the specialized roles of these terpenoids in plant-environment interactions as well as their significance in the pharmaceutical and food industries. Additionally, we highlight recent findings in the fields of molecular regulation mechanisms involved in these distinct terpenoids biosynthesis, and propose future opportunities in terpenoid research, including biology seeding, and genetic engineering in medicinal plants.

Contemporary understanding of transcription factor regulation of terpenoid biosynthesis in plants

KEY MESSAGE

This review summarized how TFs function independently or in response to environmental factors to regulate terpenoid biosynthesis via fine-tuning the expression of rate-limiting enzymes. Terpenoids are derived from various species and sources. They are essential for interacting with the environment and defense mechanisms, such as antimicrobial, antifungal, antiviral, and antiparasitic properties. Almost all terpenoids have high medicinal value and economic performance. Recently, the control of enzyme genes on terpenoid biosynthesis has received a great deal of attention, but transcriptional factors regulatory network on terpenoid biosynthesis and accumulation has yet to get a thorough review. Transcription factors function as activators or suppressors independently or in response to environmental stimuli, fine-tuning terpenoid accumulation through regulating rate-limiting enzyme expression. This study investigates the advancements in transcription factors related to terpenoid biosynthesis and systematically summarizes previous works on the specific mechanisms of transcription factors that regulate terpenoid biosynthesis via hormone signal-transcription regulatory networks in plants. This will help us to better comprehend the regulatory network of terpenoid biosynthesis and build the groundwork for terpenoid development and effective utilization.

The transcription factor ERF108 interacts with AUXIN RESPONSE FACTORs to mediate cotton fiber secondary cell wall biosynthesis

Phytohormones play indispensable roles in plant growth and development. However, the molecular mechanisms underlying phytohormone-mediated regulation of fiber secondary cell wall (SCW) formation in cotton (Gossypium hirsutum) remain largely underexplored. Here, we provide mechanistic evidence for functional interplay between the APETALA2/ethylene response factor (AP2/ERF) transcription factor GhERF108 and auxin response factors GhARF7-1 and GhARF7-2 in dictating the ethylene-auxin signaling crosstalk that regulates fiber SCW biosynthesis. Specifically, in vitro cotton ovule culture revealed that ethylene and auxin promote fiber SCW deposition. GhERF108 RNA interference (RNAi) cotton displayed remarkably reduced cell wall thickness compared with controls. GhERF108 interacted with GhARF7-1 and GhARF7-2 to enhance the activation of the MYB transcription factor gene GhMYBL1 (MYB domain-like protein 1) in fibers. GhARF7-1 and GhARF7-2 respond to auxin signals that promote fiber SCW thickening. GhMYBL1 RNAi and GhARF7-1 and GhARF7-2 virus-induced gene silencing (VIGS) cotton displayed similar defects in fiber SCW formation as GhERF108 RNAi cotton. Moreover, the ethylene and auxin responses were reduced in GhMYBL1 RNAi plants. GhMYBL1 directly binds to the promoters of GhCesA4-1, GhCesA4-2, and GhCesA8-1 and activates their expression to promote cellulose biosynthesis, thereby boosting fiber SCW formation. Collectively, our findings demonstrate that the collaboration between GhERF108 and GhARF7-1 or GhARF7-2 establishes ethylene-auxin signaling crosstalk to activate GhMYBL1, ultimately leading to the activation of fiber SCW biosynthesis.

Advances in the Biosynthesis of Terpenoids and Their Ecological Functions in Plant Resistance

Secondary metabolism plays an important role in the adaptation of plants to their environments, particularly by mediating bio-interactions and protecting plants from herbivores, insects, and pathogens. Terpenoids form the largest group of plant secondary metabolites, and their biosynthesis and regulation are extremely complicated. Terpenoids are key players in the interactions and defense reactions between plants, microorganisms, and animals. Terpene compounds are of great significance both to plants themselves and the ecological environment. On the one hand, while protecting plants themselves, they can also have an impact on the environment, thereby affecting the evolution of plant communities and even ecosystems. On the other hand, their economic value is gradually becoming clear in various aspects of human life; their potential is enormous, and they have broad application prospects. Therefore, research on terpenoids is crucial for plants, especially crops. This review paper is mainly focused on the following six aspects: plant terpenes (especially terpene volatiles and plant defense); their ecological functions; their biosynthesis and transport; related synthesis genes and their regulation; terpene homologues; and research and application prospects. We will provide readers with a systematic introduction to terpenoids covering the above aspects.

Multilayered regulation of secondary metabolism in medicinal plants

Medicinal plants represent a huge reservoir of secondary metabolites (SMs), substances with significant pharmaceutical and industrial potential. However, obtaining secondary metabolites remains a challenge due to their low-yield accumulation in medicinal plants; moreover, these secondary metabolites are produced through tightly coordinated pathways involving many spatiotemporally and environmentally regulated steps. The first regulatory layer involves a complex network of transcription factors; a second, more recently discovered layer of complexity in the regulation of SMs is epigenetic modification, such as DNA methylation, histone modification and small RNA-based mechanisms, which can jointly or separately influence secondary metabolites by regulating gene expression. Here, we summarize the findings in the fields of genetic and epigenetic regulation with a special emphasis on SMs in medicinal plants, providing a new perspective on the multiple layers of regulation of gene expression.

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.

Isolation of Salvia miltiorrhiza Kaurene Synthase-like (KSL) Gene Promoter and Its Regulation by Ethephon and Yeast Extract

The presented study describes the regulation of the promoter region of the Salvia miltiorrhiza kaurene synthase-like gene (SmKSL) by ethylene and yeast extract. The isolated fragment is 897 bp and is composed of a promoter (763 bp), 5'UTR (109 bp), and a short CDS (25 bp). The initial in silico analysis revealed the presence of numerous putative cis-active sites for trans-factors responding to different stress conditions. However, this study examines the influence of ethylene and yeast extract on SmKSL gene expression and tanshinone biosynthesis regulation. The results of 72h RT-PCR indicate an antagonistic interaction between ethylene, provided as ethephon (0.05, 0.10, 0.25, and 0.50 mM), and yeast extract (0.5%) on SmKSL gene expression in callus cultures of S. miltiorrhiza. A similar antagonistic effect was observed on total tanshinone concentration for up to 60 days. Ethylene provided as ethephon (0.05, 0.10, 0.25, and 0.50 mM) is a weak inducer of total tanshinone biosynthesis, increasing them only up to the maximum value of 0.67 ± 0.04 mg g^-1 DW (60-day induction with 0.50 mM ethephon). Among the tanshinones elicited by ethephon, cryptotanshinone (52.21%) dominates, followed by dihydrotanshinone (45.00%) and tanshinone IIA (3.79%). In contrast, the 0.5% yeast extract strongly increases the total tanshinone concentration up to a maximum value of 13.30 ± 1.09 mg g^-1 DW, observed after 50 days of induction. Yeast extract and ethylene appear to activate different fragments of the tanshinone biosynthesis route; hence the primary tanshinones induced by yeast extract were cryptotanshinone (81.42%), followed by dihydrotanshinone (17.06%) and tanshinone IIA (1.52%).

Genome-wide transcriptome analysis reveals the regulatory network governing terpene trilactones biosynthesis in Ginkgo biloba

Ginkgo biloba L. is currently the only remaining gymnosperm of the Ginkgoaceae Ginkgo genus, and its history can be traced back to the Carboniferous 200 million years ago. Terpene trilactones (TTLs) are one of the main active ingredients in G. biloba, including ginkgolides and bilobalide. They have a good curative effect on cardiovascular and cerebrovascular diseases because of their special antagonistic effect on platelet-activating factors. Therefore, it is necessary to deeply mine genes related to TTLs and to analyze their transcriptional regulation mechanism, which will hold vitally important scientific and practical significance for quality improvement and regulation of G. biloba. In this study, we performed RNA-Seq on the root, stem, immature leaf, mature leaf, microstrobilus, ovulate strobilus, immature fruit and mature fruit of G. biloba. The TTL regulatory network of G. biloba in different organs was revealed by different transcriptomic analysis strategies. Weighted gene co-expression network analysis (WGCNA) revealed that the five modules were closely correlated with organs. The 12 transcription factors, 5 structural genes and 24 Cytochrome P450 (CYP450) were identified as candidate regulators for TTL accumulation by WGCNA and cytoscape visualization. Finally, 6 APETALA2/ethylene response factors, 2 CYP450s and bHLH were inferred to regulate the metabolism of TTLs by correlation analysis. This study is the comprehensive in authenticating transcription factors, structural genes and CYP450 involved in TTL biosynthesis, thereby providing molecular evidence for revealing the comprehensive regulatory network involved in TTL metabolism in G. biloba.

Comparative transcriptomics of Pinus massoniana organs provides insights on terpene biosynthesis regulation

Terpenoids are the most important natural products collected from conifer species. However, the molecular mechanisms and core factors underlying terpenoid biosynthesis in Pinus massoniana remain unclear. To clarify these mechanisms, this study aimed to identify potential genes that might participate in the terpenoid biosynthesis of P. massoniana. In this study, single molecule real-time (SMRT) sequencing and expression analysis were used to confirm the expression patterns of genes involved in the cones, immature needles, mature needles, immature branches, and mature branches of P. massoniana. A total of 31,331 lncRNAs and 71,240 mRNAs were identified from these organs, and the greatest number of differentially expressed genes (DEGs) was discovered between needles and branches. Weighted gene coexpression network analysis (WGCNA) classified all expressed genes into nine typical modules with 11 kinds of transcription factors (TFs), namely, AP2-ERF, ARF, AUX-IAA, C2H2, Dof, F-box, SBP, WRKY, bHLH, bZIP, and GRAS, and seven kinds of functional genes, namely, ABC transporter, cellulose synthase (CesA), leucine-rich repeats (LRR), cytochrome P450 (CYT P450), pathogenesis-related protein (PR), terpene synthase (TPS), and chlorophyllase enzyme. A molecular network was constructed for hub genes, TFs, and functional genes in three modules. The potential function of eight candidate genes, including PmbHLH2, PmERF1, PmRGA, PmGAI, PmbZIP1, PmLOB1, PmMADS1, and PmMYB1, was validated through correlation analysis between terpenoid contents and expression levels, subcellular localization, and transcriptional activation activity, which provides us with probable regulators of terpenoid biosynthesis in conifers.

RNA-Seq analysis reveals the important co-expressed genes associated with polyphyllin biosynthesis during the developmental stages of Paris polyphylla

Background

Plants synthesize metabolites to adapt to a continuously changing environment. Metabolite biosynthesis often occurs in response to the tissue-specific combinatorial developmental cues that are transcriptionally regulated. Polyphyllins are the major bioactive components in Paris species that demonstrate hemostatic, anti-inflammatory and antitumor effects and have considerable market demands. However, the mechanisms underlying polyphyllin biosynthesis and regulation during plant development have not been fully elucidated.

Results

Tissue samples of P. polyphylla var. yunnanensis during the four dominant developmental stages were collected and investigated using high-performance liquid chromatography and RNA sequencing. Polyphyllin concentrations in the different tissues were found to be highly dynamic across developmental stages. Specifically, decreasing trends in polyphyllin concentration were observed in the aerial vegetative tissues, whereas an increasing trend was observed in the rhizomes. Consistent with the aforementioned polyphyllin concentration trends, different patterns of spatiotemporal gene expression in the vegetative tissues were found to be closely related with polyphyllin biosynthesis. Additionally, molecular dissection of the pathway components revealed 137 candidate genes involved in the upstream pathway of polyphyllin backbone biosynthesis. Furthermore, gene co-expression network analysis revealed 74 transcription factor genes and one transporter gene associated with polyphyllin biosynthesis and allocation.

Conclusions

Our findings outline the framework for understanding the biosynthesis and accumulation of polyphyllins during plant development and contribute to future research in elucidating the molecular mechanism underlying polyphyllin regulation and accumulation in P. polyphylla.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08792-2.

Cold stress regulates accumulation of flavonoids and terpenoids in plants by phytohormone, transcription process, functional enzyme, and epigenetics

Plants make different defense mechanisms in response to different environmental stresses. One common way is to produce secondary metabolites. Temperature is the main environmental factor that regulates plant secondary metabolites, especially flavonoids and terpenoids. Stress caused by temperature decreasing to 4-10 °C is conducive to the accumulation of flavonoids and terpenoids. However, the accumulation mechanism under cold stress still lacks a systematic explanation. In this review, we summarize three aspects of cold stress promoting the accumulation of flavonoids and terpenoids in plants, that is, by affecting (1) the content of endogenous plant hormones, especially jasmonic acid and abscisic acid; (2) the expression level and activity of important transcription factors, such as bHLH and MYB families. This aspect also includes post-translational modification of transcription factors caused by cold stress; (3) key enzyme genes expression and activity in the biosynthesis pathway, in addition, the rate-limiting enzyme and glycosyltransferases genes are responsive to cold stress. The systematic understanding of cold stress regulates flavonoids, and terpenoids will contribute to the future research of genetic engineering breeding, metabolism regulation, glycosyltransferases mining, and plant synthetic biology.

Genome-wide Investigation and Expression Analysis of the AP2/ERF Family for Selection of Agarwood Related Genes in Aquilaria sinensis (Lour.) Gilg

Aquilaria sinensis is an important non-timber tree species for producing high-value agarwood, which is widely used as a traditional medicine and incense. Agarwood is the product of Aquilaria trees in response to injury and fungal infection. AP2/ERF transcription factors play important roles in plant stress responses and metabolite biosynthesis. In this study, 119 AsAP2/ERF genes were identified from the A. sinensis genome and divided into ERF, AP2, RAV and Soloist subfamilies. Their conserved motif, gene structure, chromosomal localization, and subcellular localization were characterized. A stress/defense-related ERF-associated amphiphilic repression (EAR) motif and an EDLL motif were identified. Moreover, 11 genes that were highly expressed in the agarwood layer in response to whole-tree agarwood induction technique (Agar-Wit) treatment were chosen, and their expression levels in response to MeJA, SA or salt treatment were further analyzed using qRT-PCR. Among the 11 genes, eight belonged to subgroup B-3. All 11 genes were significantly upregulated under salt treatment, while eight genes were significantly induced by both MeJA and SA. In addition, the gene clusters containing these upregulated genes on chromosomes were observed. The results obtained from this research not only provide useful information for understanding the functions of AP2/ERF genes in A. sinensis but also identify candidate genes and gene clusters to dissect their regulatory roles in agarwood formation for future research.

Phosphate-Solubilizing Pseudomonas sp. Strain WS32 Rhizosphere Colonization-Induced Expression Changes in Wheat Roots

Rhizosphere colonization is a pre-requisite for the favorable application of plant growth-promoting rhizobacteria (PGPR). Exchange and mutual recognition of signaling molecules occur frequently between plants and microbes. Here, the luciferase luxAB gene was electrotransformed into the phosphate-solubilizing strain Pseudomonas sp. WS32, a type of plant growth-promoting rhizobacterium with specific affinity for wheat. A labeled WS32 strain (WS32-L) was applied to determine the temporal and spatial traits of colonization within the wheat rhizosphere using rhizoboxes experimentation under natural condition. The effects of colonization on wheat root development and seedling growth were evaluated, and RNA sequencing (RNA-seq) was performed to explore the transcriptional changes that occur in wheat roots under WS32 colonization. The results showed that WS32-L could survive in the wheat rhizosphere for long periods and could expand into new zones following wheat root extension. Significant increases in seedling fresh and dry weight, root fresh and dry weight, root surface area, number of root tips, and phosphorus accumulation in the wheat leaves occurred in response to WS32 rhizosphere colonization. RNA-seq analysis showed that a total of 1485 genes in wheat roots were differentially expressed between the inoculated conditions and the uninoculated conditions. Most of the transcriptional changes occurred for genes annotated to the following functional categories: "phosphorus and other nutrient transport," "hormone metabolism and organic acid secretion," "flavonoid signal recognition," "membrane transport," and "transcription factor regulation." These results are therefore valuable to future studies focused on the molecular mechanisms underlying the growth-promoting activities of PGPR on their host plants.

Tomato zonate spot virus induced hypersensitive resistance via an auxin-related pathway in pepper

Tomato zonate spotvirus (TZSV) often incurs significant losses in many food and ornamental crops in Yunnan province, China, and the surrounding areas. The pepper (Capsicum chinensePI152225)can develop hypersensitive resistance following infection with TZSV, through an as yet unknown mechanism. The transcriptome dataset showed a total of 45.81 GB of clean data were obtained from six libraries, and the average percentage of the reads mapped to the pepper genome was over 90.00 %. A total of 1403 differentially expressed genes (DEGs) were obtained after TZSV infection, including 825significantly up-regulated genes and 578 down-regulated genes. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses indicated that most up-regulated DEGs were involved in basal defenses. RT-qPCR, and virus induced gene silencing (VIGS) were used preliminarily to identifyBBC_22506 and BBC_18917, among total of 71 differentially expressed genes (DEGs), that play a key role in mediating the auxin-induced signaling pathway that might take part in hypersensitive response (HR) conferred resistance to viral infection in pepper (PI152225) byTZSV. This is the first study on the mechanism of auxin resistance, involved in defense responses of pepper against viral diseases, which lay the foundation for further study on the pathogenic mechanism of TZSV, as well as the mechanism of resistance to TZSV, in peppers.

CRISPR-Cas gene editing technology and its application prospect in medicinal plants

The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas gene editing technology has opened a new era of genome interrogation and genome engineering because of its ease operation and high efficiency. An increasing number of plant species have been subjected to site-directed gene editing through this technology. However, the application of CRISPR-Cas technology to medicinal plants is still in the early stages. Here, we review the research history, structural characteristics, working mechanism and the latest derivatives of CRISPR-Cas technology, and discussed their application in medicinal plants for the first time. Furthermore, we creatively put forward the development direction of CRISPR technology applied to medicinal plant gene editing. The aim is to provide a reference for the application of this technology to genome functional studies, synthetic biology, genetic improvement, and germplasm innovation of medicinal plants. CRISPR-Cas is expected to revolutionize medicinal plant biotechnology in the near future.

Function Analysis of the ERF and DREB Subfamilies in Tomato Fruit Development and Ripening

APETALA2/ethylene responsive factors (AP2/ERF) are unique regulators in the plant kingdom and are involved in the whole life activity processes such as development, ripening, and biotic and abiotic stresses. In tomato (Solanum lycopersicum), there are 140 AP2/ERF genes; however, their functionality remains poorly understood. In this work, the 14th and 19th amino acid differences in the AP2 domain were used to distinguish DREB and ERF subfamily members. Even when the AP2 domain of 68 ERF proteins from 20 plant species and motifs in tomato DREB and ERF proteins were compared, the binding ability of DREB and ERF proteins with DRE/CRT and/or GCC boxes remained unknown. During fruit development and ripening, the expressions of 13 DREB and 19 ERF subfamily genes showed some regular changes, and the promoters of most genes had ARF, DRE/CRT, and/or GCC boxes. This suggests that these genes directly or indirectly respond to IAA and/or ethylene (ET) signals during fruit development and ripening. Moreover, some of these may feedback regulate IAA or ET biosynthesis. In addition, 16 EAR motif-containing ERF genes in tomato were expressed in many organs and their total transcripts per million (TPM) values exceeded those of other ERF genes in most organs. To determine whether the EAR motif in EAR motif-containing ERF proteins has repression function, their EAR motifs were retained or deleted in a yeast one-hybrid (YIH) assay. The results indicate that most of EAR motif-containing ERF proteins lost repression activity after deleting the EAR motif. Moreover, some of these were expressed during ripening. Thus, these EAR motif-containing ERF proteins play vital roles in balancing the regulatory functions of other ERF proteins by completing the DRE/CRT and/or GCC box sites of target genes to ensure normal growth and development in tomato.

Overexpression of SmSCR1 Promotes Tanshinone Accumulation and Hairy Root Growth in Salvia miltiorrhiza

Lipid-soluble tanshinone is one of the main bioactive substances in the medicinal plant Salvia miltiorrhiza, and its medicinal demand is growing rapidly. Yeast extract (YE) modulates the tanshinone biosynthesis, but the underlying regulatory network remains obscure. In this study, a YE-responsive transcriptional factor Scarecrow1 (SCR1) was identified in S. miltiorrhiza from the YE-induced transcriptome dataset. SmSCR1 is located in the nucleus. Overexpression of SmSCR1 in S. miltiorrhiza roots resulted in a significantly higher accumulation of tanshinone than the control, with the highest 1.49-fold increase. We also detected upregulation of tanshinone biosynthetic genes, SmSCR1 and SmHMGR1, and distinct alteration of growth and development of the hairy roots in the overexpression lines compared to the control. An inverse phenotype was observed in SmSCR1-SRDX suppression expression lines. We found that SmSCR1 can bind to the promoter of SmCPS1 to induce its expression. This study provides new insight into the regulatory mechanism on the growth and development of hairy roots, tanshinone accumulation, and the metabolic engineering of bioactive compounds in S. miltiorrhiza.

Analysis of long non-coding RNAs and mRNAs in harvested kiwifruit in response to the yeast antagonist, Wickerhamomyces anomalus

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W. anomalus exhibits good biocontrol activity against blue and gray mold on kiwifruit.

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LncRNAs in kiwifruit may be involved in activating plant hormone signal transduction pathways in response to the biocontrol yeast.

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LncRNAs in kiwifruit may modulate the production of related TFs and secondary metabolites.

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The expression of downstream defense-related genes in kiwifruit increases in response to the application of the biocontrol yeast.

Biological control utilizing antagonistic yeasts is an effective method for controlling postharvest diseases. Long non-coding RNAs (lncRNAs) have been found to be involved in a variety of plant growth and development processes, including those associated with plant disease resistance. In the present study, the yeast antagonist, Wickerhamomyces anomalus, was found to strongly inhibit postharvest blue mold (Penicillium expansum) and gray mold (Botrytis cinerea) decay of kiwifruit. Additionally, lncRNA high-throughput sequencing and bioinformatic analysis was used to identify lncRNAs in W. anomalus-treated wounds in kiwifruit and predict their function based on putative target genes. Our results indicate that lncRNAs may be involved in increasing ethylene (ET), jasmonic acid (JA), abscisic acid (ABA), and auxin (IAA) levels, as well as activating signal transduction pathways that regulate the expression of several transcription factors (WRKY72, WRKY53, JUB1AP2). These transcription factors (TFs) then mediate the expression of downstream, defense-related genes (ZAR1, PAD4, CCR4, NPR4) and the synthesis of secondary metabolites, thus, potentially enhancing disease resistance. Notably, by stimulating the accumulation of antifungal compounds, such as phenols and lignin, disease resistance in kiwifruit was enhanced. Our study provides new information on the mechanism underlying the induction of disease resistance in kiwifruit by W. anomalus, as well as a new disease resistance strategy that can be used to enhance the defense response of fruit to pathogenic fungi.

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.

The ERF-VII transcription factor SmERF73 coordinately regulates tanshinone biosynthesis in response to stress elicitors in Salvia miltiorrhiza

Here, we investigate the role of SmERF73, a group VII ETHYLENE RESPONSE FACTOR stress response transcription factor, in the regulation of post-modification of the skeleton precursors of diterpene tanshinones in Salvia miltiorrhiza. Most genes found to be involved in tanshinone biosynthesis are located on chromosome 6, and five of these genes comprise a large gene cluster in S. miltiorrhiza. We found that SmERF73 overexpression in S. miltiorrhiza coordinately up-regulated the transcription of seven tanshinone biosynthetic genes, four of which were located in the tanshinone gene cluster, consequently increasing tanshinone accumulation, while SmERF73 silencing reduced corresponding gene transcription and tanshinone accumulation. SmERF73 recognizes GCC-box promoter elements of four tanshinone-associated genes (DXR1, CPS1, KSL1 and CYP76AH3) and activates their expression. Moreover, SmERF73 and its targets were up-regulated by stress elicitors; SmERF73 appears to be at least partly mediated by the jasmonic acid (JA) signaling pathway via interaction with SmJAZ3. SmERF73 coordinately regulates tanshinone biosynthetic gene expression, suggesting a potential link between tanshinone production and plant stress responses.

Mechanism by which salt stress induces physiological responses and regulates tanshinone synthesis

Salvia miltiorrhiza is a traditional Chinese herbal medicine with tanshinone as one of the main bioactive components and has antitumor, antibacterial, anti-inflammatory properties, as well as other physiological functions. Tanshinone, as a secondary metabolite, is synthesized under salt stress or other environmental stresses. Oxidative stress is an important physiological response of plants to salt stress. Transcription factors (TFs) are believed to play regulatory roles in this process, and AP2/ERF TFs have significant effects on defense against the adversity of plants. However, investigations on the regulation of AP2/ERF TFs in tanshinone synthesis under salt stress are limited. In this research, the tanshinone content, related gene expression and activities of enzymes, and the markers of oxidative stress were determined. The results showed that SmAP1, SmAP2 and SmERF2 were AP2/ERF TFs with AP conserved sequences, whose relative expression levels increased and were positively correlated with the contents of tanshinone I (T-I), tanshinone IIA (T-IIA) and cryptotanshinone (CT) in the roots of Salvia miltiorrhiza. The content of malondialdehyde (MDA) and the activities of superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) increased in the roots of Salvia miltiorrhiza. The expression levels of genes encoding enzymes and the activities of key enzymes in the tanshinone biosynthesis pathway increased accordingly. The results showed that AP2/ERF TFs could positively regulate the biosynthesis of tanshinone in the roots of Salvia miltiorrhiza under salt stress.

Transcriptional Factor-Mediated Regulation of Active Component Biosynthesis in Medicinal Plants

Plants produce thousands of chemically diverse secondary metabolites, many of which have valuable pharmaceutical properties. There is much interest in the synthesis of these pharmaceuticallyvaluable compounds, including the key enzymes and the transcription factors involved. The function and regulatory mechanism of transcription factors in biotic and abiotic stresses have been studied in depth. However, their regulatory roles in the biosynthesis of bioactive compounds, especially in medicinal plants, have only begun. Here, we review what is currently known about how transcription factors contribute to the synthesis of bioactive compounds (alkaloids, terpenoids, flavonoids, and phenolic acids) in medicinal plants. Recent progress has been made in the cloning and characterization of transcription factors in medicinal plants on the genome scale. So far, several large transcription factors have been identified in MYB, WRKY, bHLH, ZIP, AP2/ERF transcription factors. These transcription factors have been predicted to regulate bioactive compound production. These transcription factors positively or negatively regulate the expression of multiple genes encoding key enzymes, and thereby control the metabolic flow through the biosynthetic pathway. Although the research addressing this niche topic is in its infancy, significant progress has been made, and advances in high-throughput sequencing technology are expected to accelerate the discovery of key regulatory transcription factors in medicinal plants. This review is likely to be useful for those interested in the synthesis of pharmaceutically- valuable plant compounds, especially those aiming to breed or engineer plants that produce greater yields of these compounds.

Transcriptome Analysis of Light-Regulated Monoterpenes Biosynthesis in Leaves of Mentha canadensis L

Light is a key environmental aspect that regulates secondary metabolic synthesis. The essential oil produced in mint (Mentha canadensis L.) leaves is used widely in the aromatics industry and in medicine. Under low-light treatment, significant reductions in peltate glandular trichome densities were observed. GC-MS analysis showed dramatically reduced essential oil and menthol contents. Light affected the peltate glandular trichomes’ development and essential oil yield production. However, the underlying mechanisms of this regulation were elusive. To identify the critical genes during light-regulated changes in oil content, following a 24 h darkness treatment and a 24 h recovery light treatment, leaves were collected for transcriptome analysis. A total of 95,579 unigenes were obtained, with an average length of 754 bp. About 56.58% of the unigenes were annotated using four public protein databases: 10,977 differentially expressed genes (DEGs) were found to be involved in the light signaling pathway and monoterpene synthesis pathway. Most of the TPs showed a similar expression pattern: downregulation after darkness treatment and upregulation after the return of light. In addition, the genes involved in the light signal transduction pathway were analyzed. A series of responsive transcription factors (TFs) were identified and could be used in metabolic engineering as an effective strategy for increasing essential oil yields.

MYC2 Transcription Factors TwMYC2a and TwMYC2b Negatively Regulate Triptolide Biosynthesis in Tripterygium wilfordii Hairy Roots

Triptolide, an important bioactive diterpenoid extracted from the plant Tripterygium wilfordii, exhibits many pharmacological activities. MYC2 transcription factor (TF) plays an important role in the regulation of various secondary metabolites in plants. However, whether MYC2 TF could regulate the biosynthesis of triptolide in T. wilfordii is still unknown. In this study, two homologous MYC2 TF genes, TwMYC2a and TwMYC2b, were isolated from T. wilfordii hairy roots and functionally characterized. The analyses of the phylogenetic tree and subcellular localization showed that they were grouped into the IIIe clade of the bHLH superfamily with other functional MYC2 proteins and localized in the nucleus. Furthermore, yeast one-hybrid and GUS transactivation assays suggested that TwMYC2a and TwMYC2b inhibited the promoter activity of the miltiradiene synthase genes, TwTPS27a and TwTPS27b, by binding to the E-box (CACATG) and T/G-box (CACGTT) motifs in their promoters. Transgenic results revealed that RNA interference of TwMYC2a/b significantly enhanced the triptolide accumulation in hairy roots and liquid medium by upregulating the expression of several key biosynthetic genes, including TwMS (TwTPS27a/b), TwCPS (TwTPS7/9), TwDXR, and TwHMGR1. In summary, our findings show that TwMYC2a and TwMYC2b act as two negative regulators of triptolide biosynthesis in T. wilfordii hairy roots and also provide new insights on metabolic engineering of triptolide in the future.

Transcription Factor: A Powerful Tool to Regulate Biosynthesis of Active Ingredients in Salvia miltiorrhiza

Salvia miltiorrhiza Bunge is a common Chinese herbal medicine, and its major active ingredients are phenolic acids and tanshinones, which are widely used to treat vascular diseases. However, the wild form of S. miltiorrhiza possess low levels of these important pharmaceutical agents; thus, improving their levels is an active area of research. Transcription factors, which promote or inhibit the expressions of multiple genes involved in one or more biosynthetic pathways, are powerful tools for controlling gene expression in biosynthesis. Several families of transcription factors have been reported to participate in regulating phenolic acid and tanshinone biosynthesis and influence their accumulation. This review summarizes the current status in this field, with focus on the transcription factors which have been identified in recent years and their functions in the biosynthetic regulation of phenolic acids and tanshinones. Otherwise, the new insight for further research is provided. Finally, the application of the biosynthetic regulation of active ingredients by the transcription factors in S. miltiorrhiza are discussed, and new insights for future research are explored.

Genome-wide identification and analysis of AP2/ERF transcription factors related to camptothecin biosynthesis in Camptotheca acuminata

Camptotheca acuminata produces camptothecin (CPT), a monoterpene indole alkaloid (MIA) that is widely used in the treatment of lung, colorectal, cervical, and ovarian cancers. Its biosynthesis pathway has attracted significant attention, but the regulation of CPT biosynthesis by the APETALA2/ethylene-responsive factor (AP2/ERF) transcription factors (TFs) remains unclear. In this study, a systematic analysis of the AP2/ERF TFs family in C. acuminata was performed, including phylogeny, gene structure, conserved motifs, and gene expression profiles in different tissues and organs (immature bark, cotyledons, young flower, immature fruit, mature fruit, mature leaf, roots, upper stem, and lower stem) of C. acuminata. A total of 198 AP2/ERF genes were identified and divided into five relatively conserved subfamilies, including AP2 (26 genes), DREB (61 genes), ERF (92 genes), RAV (18 genes), and Soloist (one gene). The combination of gene expression patterns in different C. acuminata tissues and organs, the phylogenetic tree, the co-expression analysis with biosynthetic genes, and the analysis of promoter sequences of key enzymes genes involved in CPT biosynthesis pathways revealed that eight AP2/ERF TFs in C. acuminata might be involved in CPT synthesis regulation, which exhibit relatively high expression levels in the upper stem or immature bark. Among these, four genes (CacAP2/ERF123, CacAP2/ERF125, CacAP2/ERF126, and CacAP2/ERF127) belong to the ERF-B2 subgroup; two genes (CacAP2/ERF149 and CacAP2/ERF152) belong to the ERF-B3 subgroup; and two more genes (CacAP2/ERF095 and CacAP2/ERF096) belong to the DREB-A6 subgroup. These results provide a foundation for future functional characterization of the AP2/ERF genes to enhance the biosynthesis of CPT compounds of C. acuminata.

Genomic Characterization of WRKY Transcription Factors Related to Andrographolide Biosynthesis in Andrographis paniculata

Andrographolide, which is enriched in the leaves of Andrographis paniculata, has been known as “natural antibiotic” due to its pharmacological activities such as anti-inflammatory, antimicrobial and antioxidant effects. Several key enzymes in andrographolide biosynthetic pathway have been studied since the genome sequences were released, but its regulatory mechanism remains unknown. WRKY transcription factors proteins have been reported to regulate plant secondary metabolism, development as well as biotic and abiotic stresses. Here, WRKY transcription factors related to andrographolide biosynthesis were systematically identified, including sequences alignment, phylogenetic analysis, chromosomal distribution, gene structure, conserved motifs, synteny, alternative splicing event and Gene ontology (GO) annotation. A total of 58 WRKYs were identified in Chuanxinlian genome and phylogenetically classified into three groups. Moreover, nine WRKY genes underwent alternative splicing events. Furthermore, the combination of binding site prediction, gene-specific expression patterns, and phylogenetic analysis suggested that 7 WRKYs (ApWRKY01, ApWRKY08, ApWRKY12, ApWRKY14, ApWRKY19, ApWRKY20, and ApWRKY50) might regulate andrographolide biosynthesis. This study laid a foundation for understanding the regulatory mechanism of andrographolide biosynthesis and the improvement and breeding of Andrographis paniculata varieties.

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.

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.

JA-Responsive Transcription Factor SmMYB97 Promotes Phenolic Acid and Tanshinone Accumulation in Salvia miltiorrhiza

Phenolic acids and tanshinones are active principles in Salvia miltiorrhiza Bunge administered for cardiovascular and cerebrovascular diseases. Jasmonic acid (JA) promotes secondary metabolite accumulation, but the regulatory mechanism is unknown in S. miltiorrhiza. We identified and characterized the JA-responsive gene SmMYB97. Multiple sequence alignment and phylogenetic tree analyses showed that SmMYB97 was clustered with AtMYB11, AtMYB12, and ZmP1 in the subgroup S7 regulating flavonol biosynthesis. SmMYB97 was highly expressed in S. miltiorrhiza leaves and induced by methyl jasmonate (MeJA). SmMYB97 was localized in the nucleus and had strong transcriptional activation activity. SmMYB97 overexpression increased phenolic acid and tanshinone biosynthesis and upregulated the genes implicated in these processes. Yeast one-hybrid and transient transcriptional activity assays disclosed that SmMYB97 binds the PAL1, TAT1, CPS1, and KSL1 promoter regions. SmJAZ8 interacts with SmMYB97 and downregulates the genes that it controls. This study partially clarified the regulatory network of MeJA-mediated secondary metabolite biosynthesis in S. miltiorrhiza.

Transcriptomic analysis reveals the GRAS family genes respond to gibberellin in Salvia miltiorrhiza hairy roots

BACKGROUND

Salvia miltiorrhiza is one of the most important traditional Chinese medicinal plants with high medicinal value. Gibberellins are growth-promoting phytohormones that regulate numerous growth and developmental processes in plants. However, their role on the secondary metabolism regulation has not been investigated.

RESULTS

In this study, we found that gibberellic acid (GA) can promote hairy roots growth and increase the contents of tanshinones and phenolic acids. Transcriptomic sequencing revealed that many genes involved in the secondary metabolism pathway were the GA-responsive. After further analysis of GA signaling pathway genes, which their expression profiles have significantly changed, it was found that the GRAS transcription factor family had a significant response to GA. We identified 35 SmGRAS genes in S. miltiorrhiza, which can be divided into 10 subfamilies. Thereafter, members of the same subfamily showed similar conserved motifs and gene structures, suggesting possible conserved functions.

CONCLUSIONS

Most SmGRAS genes were significantly responsive to GA, indicating that they may play an important role in the GA signaling pathway, also participating in the GA regulation of root growth and secondary metabolism in S. miltiorrhiza.

Advances in AP2/ERF super-family transcription factors in plant

In the whole life process, many factors including external and internal factors affect plant growth and development. The morphogenesis, growth, and development of plants are controlled by genetic elements and are influenced by environmental stress. Transcription factors contain one or more specific DNA-binding domains, which are essential in the whole life cycle of higher plants. The AP2/ERF (APETALA2/ethylene-responsive element binding factors) transcription factors are a large group of factors that are mainly found in plants. The transcription factors of this family serve as important regulators in many biological and physiological processes, such as plant morphogenesis, responsive mechanisms to various stresses, hormone signal transduction, and metabolite regulation. In this review, we summarized the advances in identification, classification, function, regulatory mechanisms, and the evolution of AP2/ERF transcription factors in plants. AP2/ERF family factors are mainly classified into four major subfamilies: DREB (Dehydration Responsive Element-Binding), ERF (Ethylene-Responsive-Element-Binding protein), AP2 (APETALA2) and RAV (Related to ABI3/VP), and Soloists (few unclassified factors). The review summarized the reports about multiple regulatory functions of AP2/ERF transcription factors in plants. In addition to growth regulation and stress responses, the regulatory functions of AP2/ERF in plant metabolite biosynthesis have been described. We also discussed the roles of AP2/ERF transcription factors in different phytohormone-mediated signaling pathways in plants. Genomic-wide analysis indicated that AP2/ERF transcription factors were highly conserved during plant evolution. Some public databases containing the information of AP2/ERF have been introduced. The studies of AP2/ERF factors will provide important bases for plant regulatory mechanisms and molecular breeding.

Advances in biosynthesis, regulation, and metabolic engineering of plant specialized terpenoids

Plant specialized terpenoids are natural products that have no obvious role in growth and development, but play many important functional roles to improve the plant's overall fitness. Besides, plant specialized terpenoids have immense value to humans due to their applications in fragrance, flavor, cosmetic, and biofuel industries. Understanding the fundamental aspects involved in the biosynthesis and regulation of these high-value molecules in plants not only paves the path to enhance plant traits, but also facilitates homologous or heterologous engineering for overproduction of target molecules of importance. Recent developments in functional genomics and high-throughput analytical techniques have led to unraveling of several novel aspects involved in the biosynthesis and regulation of plant specialized terpenoids. The knowledge thus derived has been successfully utilized to produce target specialized terpenoids of plant origin in homologous or heterologous host systems by metabolic engineering and synthetic biology approaches. Here, we provide an overview and highlights on advances related to the biosynthetic steps, regulation, and metabolic engineering of plant specialized terpenoids.

Genome-Wide Characterization and Analysis of bHLH Transcription Factors Related to Crocin Biosynthesis in Gardenia jasminoides Ellis (Rubiaceae)

Crocins, enriched in Gardenia jasminoides fruits, have a pharmacological activity against central nervous system diseases, cardiovascular diseases, and cancer cell growth. The biosynthesis of crocins has been widely explored, but its regulatory mechanism remains unknown. Here, the basic helix-loop-helix (bHLH) transcription factors related to crocin biosynthesis were systematically identified on the basis of the genome of G. jasminoides. A total of 95 GjbHLH transcription factor genes were identified, and their phylogenetic analysis indicated that they could be classified into 23 subfamilies. The combination of gene-specific bHLH expression patterns, the coexpression analysis of biosynthesis genes, and the analysis of promoter sequences in crocin biosynthesis pathways suggested that nine bHLHs in G. jasminoides might negatively regulate crocin biosynthesis. This study laid a foundation for understanding the regulatory mechanism of crocin biosynthesis and the improvement and breeding of G. jasminoides varieties.