Genomic survey of bZIP transcription factor genes related to tanshinone biosynthesis in Salvia miltiorrhiza

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.

Comparative transcriptome analysis and identification of candidate bZIP transcription factors involved in anthraquinone biosynthesis in Rheum officinale Baill

Rhubarb is a traditional medicinal plant in China, whose pharmacological effects derive mainly from its anthraquinones. However, the regulatory mechanism affecting anthraquinone biosynthesis in R. officinale remains poorly understood. We assembled a high-quality, full-length transcriptome using single-molecule real-time (SMRT) sequencing. 274 unigenes potentially involved in the biosynthesis of anthraquinones, including those in the shikimate, polyketide, MVA and MEP pathways, were identified based on full-length transcriptome. Differentially expressed genes (DEGs) induced by MeJA treatment and DEGs between different tissues were identified through next-generation sequencing (NGS), revealing the genes that may be involved in the biosynthesis of anthraquinones. The basic leucine zipper (bZIP) transcription factors of R. officinale were systematically identified. Key genes such as RobZIP50 and RobZIP53 were systematically identified and found to be associated with anthraquinone biosynthesis in R. officinale through differential expression, co-expression and protein interaction analyses. RobZIP50 and RobZIP53 were highly expressed in roots and rhizomes, and significantly increased after 12 h of MeJA treatment. Additionally, both RobZIP50 and RobZIP53 were localized exclusively in the nucleus, with RobZIP53 showing significant transcriptional activity. Taken together, our results suggest that RobZIP53 may play a role in regulating anthraquinone biosynthesis in R. officinale.

Engineering the microenvironment of P450s to enhance the production of diterpenoids in Saccharomyces cerevisiae

Cytochrome P450 enzymes play a crucial role as catalysts in the biosynthesis of numerous plant natural products (PNPs). Enhancing the catalytic activity of P450s in host microorganisms is essential for the efficient production of PNPs through synthetic biology. In this study, we engineered Saccharomyces cerevisiae to optimize the microenvironment for boosting the activities of P450s, including coexpression with the redox partner genes, enhancing NADPH supply, expanding the endoplasmic reticulum (ER), strengthening heme biosynthesis, and regulating iron uptake. This created a platform for the efficient production 11,20-dihydroxyferruginol, a key intermediate of the bioactive compound tanshinones. The yield was enhanced by 42.1-fold through 24 effective genetic edits. The optimized strain produced up to 67.69 ± 1.33 mg/L 11,20-dihydroxyferruginol in shake flasks. Our work represents a promising advancement toward constructing yeast cell factories containing P450s and paves the way for microbial biosynthesis of tanshinones in the future.

Transcription factor DcbZIPs regulate secondary metabolism in Dendrobium catenatum during cold stress

Cold stress seriously affects plant development and secondary metabolism. The basic region/leucine zipper (bZIP) is one of the largest transcription factor (TFs) family and widely involved in plant cold stress response. However, the function of bZIP in Dendrobium catenatum has not been well-documented. Cold inhibited the growth of D. catenatum and increased total polysaccharide and alkaloid contents in stems. Here, 62 DcbZIP genes were identified in D. catenatum, which were divided into 13 subfamilies. Among them, 58 DcbZIPs responded to cold stress, which were selected based on the transcriptome database produced from cold-treated D. catenatum seedlings. Specifically, the expression of DcbZIP3/6/28 was highly induced by cold treatment in leaves or stems. Gene sequence analysis indicated that DcbZIP3/6/28 contains the bZIP conserved domain and is localized to the cell nucleus. Co-expression networks showed that DcbZIP6 was significantly negatively correlated with PAL2 (palmitoyl-CoA), which is involved in flavonoid metabolism. Moreover, DcbZIP28 has significant negative correlations with various metabolism-related genes in the polysaccharide metabolic pathway, including PFKA1 (6-phosphofructokinase), ALDO2 (aldose-6-phosphate reductase) and SCRK5 (fructokinase). These results implied that DcbZIP6 or DcbZIP28 are mainly involved in flavonoid or polysaccharide metabolism. Overall, these findings provide new insights into the roles of the DcbZIP gene family in secondary metabolism in D. catenatum under cold stress.

UHPLC-QTOF-MS-Based Targeted Metabolomics Provides Novel Insights into the Accumulative Mechanism of Soil Types on the Bioactive Components of Salvia miltiorrhiza

The root of Salvia miltiorrhiza Bunge (SMB) has been widely used to treat cardiovascular diseases. However, the contents of secondary metabolites in the roots from different production areas are significantly different, and the impact of soil factors on this accumulation remains unclear. Therefore, this study aimed to elucidate the regularity of variation between the active components and soil factors through targeted metabolomics and chemical dosimetry. Soils were collected from five different cities (A, B, C, D, and E) and transplanted into the study area. The results showed that there were significant differences in the soil fertility characteristics and heavy metal pollution levels in different soils. Ten water- and twelve lipid-soluble metabolites were identified in SMBs grown in all soil types. SMBs from D cities exhibited the highest total tanshinone content (p < 0.05). The salvianolic acid B content in SMBs from E cities was the highest (p < 0.05). Interestingly, correlation analysis revealed a significant negative correlation between the accumulation of lipid-soluble and water-soluble metabolites. Double-matrix correlation analysis demonstrated that available potassium (AK) was significantly negatively correlated with salvianolic acid B (r = -0.80, p = 0.0004) and positively correlated with tanshinone IIA (r = 0.66, p = 0.008). Conversely, cadmium (Cd) and cuprum (Cu) were significantly positively and negatively correlated with salvianolic acid B (r = 0.96, p < 0.0001 and r = 0.72, p = 0.0024) and tanshinone IIA (r = 0.40, p = 0.14 and r = 0.73, p = 0.0018), respectively. Mantel's test indicated that AK (r > 0.52, p < 0.001), Cu (r > 0.60, p < 0.005), and Cd (r > 0.31, p < 0.05) were the primary drivers of the differences in the active components of SMBs. These findings provide a theoretical framework for modulating targeted metabolites of SMB through soil factors, with significant implications for the cultivation and quality control of medicinal plants.

Genome-Wide Characterization and Phylogenetic and Stress Response Expression Analysis of the MADS-Box Gene Family in Litchi (Litchi chinensis Sonn.)

The MADS-box protein is an important transcription factor in plants and plays an important role in regulating the plant abiotic stress response. In this study, a total of 94 MADS-box genes were predicted in the litchi genome, and these genes were widely distributed on all the chromosomes. The LcMADS-box gene family was divided into six subgroups (Mα, Mβ, Mγ, Mδ, MIKC, and UN) based on their phylogenetical relationships with Arabidopsis, and the closely linked subgroups exhibited more similarity in terms of motif distribution and intron/exon numbers. Transcriptome analysis indicated that LcMADS-box gene expression varied in different tissues, which can be divided into universal expression and specific expression. Furthermore, we further validated that LcMADS-box genes can exhibit different responses to various stresses using quantitative real-time PCR (qRT-PCR). Moreover, physicochemical properties, subcellular localization, collinearity, and cis-acting elements were also analyzed. The findings of this study provide valuable insights into the MADS-box gene family in litchi, specifically in relation to stress response. The identification of hormone-related and stress-responsive cis-acting elements in the MADS-box gene promoters suggests their involvement in stress signaling pathways. This study contributes to the understanding of stress tolerance mechanisms in litchi and highlights potential regulatory mechanisms underlying stress responses.

Characterization of the basic leucine zipper transcription factor family of Neoporphyra haitanensis and its role in acclimation to dehydration stress

BACKGROUND

Neoporphyra haitanensis, a major marine crop native to southern China, grows in the harsh intertidal habitats of rocky coasts. The thallus can tolerate fluctuating and extreme environmental stresses, for example, repeated desiccation/rehydration due to the turning tides. It is also a typical model system for investigating stress tolerance mechanisms in intertidal seaweed. The basic leucine zipper (bZIP) transcription factors play important roles in the regulation of plants' responses to environmental stress stimuli. However, little information is available regarding the bZIP family in the marine crop Nh. haitanensis.

RESULTS

We identified 19 bZIP genes in the Nh. haitanensis genome and described their conserved domains. Based on phylogenetic analysis, these 19 NhhbZIP genes, distributed unevenly on the 11 superscaffolds, were divided into four groups. In each group, there were analogous exon/intron numbers and motif compositions, along with diverse exon lengths. Cross-species collinearity analysis indicated that 17 and 9 NhhbZIP genes were orthologous to bZIP genes in Neopyropia yezoensis and Porphyra umbilicalis, respectively. Evidence from RNA sequencing (RNA-seq) data showed that the majority of NhhbZIP genes (73.68%) exhibited transcript abundance in all treatments. Furthermore, genes NN 2, 4 and 5 showed significantly altered expression in response to moderate dehydration, severe dehydration, and rehydration, respectively. Gene co-expression network analysis of the representative genes was carried out, followed by gene set enrichment analysis. Two NhhbZIP genes collectively responding to dehydration and rehydration and their co-expressing genes mainly participated in DNA repair, DNA metabolic process, and regulation of helicase activity. Two specific NhhbZIP genes responding to severe dehydration and their corresponding network genes were mainly involved in macromolecule modification, cellular catabolic process, and transmembrane transport. Three specific NhhbZIP genes responding to rehydration and their co-expression gene networks were mainly involved in the regulation of the cell cycle process and defense response.

CONCLUSIONS

This study provides new insights into the structural composition, evolution, and function of the NhhbZIP gene family. Our results will help us to further study the functions of bZIP genes in response to dehydration and rehydration in Nh. haitanensis and improve Nh. haitanensis in southern China.

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.

Systematic evolution of bZIP transcription factors in Malvales and functional exploration of AsbZIP14 and AsbZIP41 in Aquilaria sinensis

Introduction

Agarwood, the dark-brown resin produced by Aquilaria trees, has been widely used as incense, spice, perfume or traditional medicine and 2-(2-phenethyl) chromones (PECs) are the key markers responsible for agarwood formation. But the biosynthesis and regulatory mechanism of PECs were still not illuminated. The transcription factor of basic leucine zipper (bZIP) presented the pivotal regulatory roles in various secondary metabolites biosynthesis in plants, which might also contribute to regulate PECs biosynthesis. However, molecular evolution and function of bZIP are rarely reported in Malvales plants, especially in Aquilaria trees.

Methods and results

Here, 1,150 bZIPs were comprehensively identified from twelve Malvales and model species genomes and the evolutionary process were subsequently analyzed. Duplication types and collinearity indicated that bZIP is an ancient or conserved TF family and recent whole genome duplication drove its evolution. Interesting is that fewer bZIPs in A. sinensis than that species also experienced two genome duplication events in Malvales. 62 AsbZIPs were divided into 13 subfamilies and gene structures, conservative domains, motifs, cis-elements, and nearby genes of AsbZIPs were further characterized. Seven AsbZIPs in subfamily D were significantly regulated by ethylene and agarwood inducer. As the typical representation of subfamily D, AsbZIP14 and AsbZIP41 were localized in nuclear and potentially regulated PECs biosynthesis by activating or suppressing type III polyketide synthases (PKSs) genes expression via interaction with the AsPKS promoters.

Discussion

Our results provide a basis for molecular evolution of bZIP gene family in Malvales and facilitate the understanding the potential functions of AsbZIP in regulating 2-(2-phenethyl) chromone biosynthesis and agarwood formation.

Ginkgo biloba GbbZIP08 transcription factor is involved in the regulation of flavonoid biosynthesis

Ginkgo biloba is the oldest relict plant on Earth and an economic plant resource derived from China. Flavonoids extracted from G. biloba are beneficial to the prevention and treatment of cardiovascular and cerebrovascular diseases. Basic leucine zipper (bZIP) transcription factors (TFs) have been recognized to play important roles in plant secondary metabolism. In this study, GbbZIP08 was isolated and characterized. It encodes a protein containing 154 amino acids, which belongs to hypocotyl 5 in group H of the bZIP family. Tobacco transient expression assay indicated that GbbZIP08 was localized in the plant nucleus. GbbZIP08 overexpression showed that the contents of total flavonoids, kaempferol, and anthocyanin in transgenic tobacco were significantly higher than those in the wild type. Transcriptome sequencing analysis revealed significant upregulation of structural genes in the flavonoid biosynthesis pathway. In addition, phytohormone signal transduction pathways, such as the abscisic acid, salicylic acid, auxin, and jasmonic acid pathways, were enriched with a large number of differentially expressed genes. TFs such as MYB, AP2, WRKY, NAC, bZIP, and bHLH, were also differentially expressed. The above results indicated that GbbZIP08 overexpression promoted flavonoid accumulation and increased the transcription levels of flavonoid-synthesis-related genes in plants.

Role of bZIP transcription factors in the regulation of plant secondary metabolism

MAIN CONCLUSION

This study provides an overview of the structure, classification, regulatory mechanisms, and biological functions of the basic (region) leucine zipper transcription factors and their molecular mechanisms in flavonoid, terpenoid, alkaloid, phenolic acid, and lignin biosynthesis. Basic (region) leucine zippers (bZIPs) are evolutionarily conserved transcription factors (TFs) in eukaryotic organisms. The bZIP TFs are widely distributed in plants and play important roles in plant growth and development, photomorphogenesis, signal transduction, resistance to pathogenic microbes, biotic and abiotic stress, and secondary metabolism. Moreover, the expression of bZIP TFs not only promotes or inhibits the accumulation of secondary metabolites in medicinal plants, but also affects the stress response of plants to the external adverse environment. This paper describes the structure, classification, biological function, and regulatory mechanisms of bZIP TFs. In addition, the molecular mechanism of bZIP TFs regulating the biosynthesis of flavonoids, terpenoids, alkaloids, phenolic acids, and lignin are also elaborated. This review provides a summary for in-depth study of the molecular mechanism of bZIP TFs regulating the synthesis pathway of secondary metabolites and plant molecular breeding, which is of significance for the generation of beneficial secondary metabolites and the improvement of plant varieties.

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.

Genomic characterization of bZIP transcription factors related to andrographolide biosynthesis in Andrographis paniculata

The basic leucine zipper (bZIP) transcription factor family plays an important role in various biological processes in plants. Andrographis paniculata (Burm.f) Nees, belonging to the family Acanthaceae, has been widely used as an important traditional herb with a wide range of pharmacological activities, such as antivenom, antiretroviral, anticancer and so on. However, there was no comprehensive analysis of bZIP gene family in the Andrographis paniculata been reported. In this study, we identified 62 bZIPs in Andrographis paniculata and grouped them into 12 subfamilies through the phylogenetic tree analysis. The bZIPs in the same groups have similar motif composition, exon-intron structure and domain distribution. In addition, the RNA-seq data gave a reference for selecting candidate bZIPs to make further function verification. Lastly, qRT-PCR analyses revealed seven ApbZIPs (ApbZIP4, ApbZIP19, ApbZIP30, ApbZIP42, ApbZIP50, ApbZIP52, ApbZIP62) were the most highly expressed in leaf and significantly up-regulated with MeJA and ABA treatment which may be involved in biosynthesis regulation of andrographolide. These data pave the way for further revealing the function of the bZIPs in Andrographis paniculata.

Isolation and Comprehensive in Silico Characterisation of a New 3-Hydroxy-3-Methylglutaryl-Coenzyme A Reductase 4 (HMGR4) Gene Promoter from Salvia miltiorrhiza: Comparative Analyses of Plant HMGR Promoters

Salvia miltiorrhiza synthesises tanshinones with multidirectional therapeutic effects. These compounds have a complex biosynthetic pathway, whose first rate limiting enzyme is 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGR). In the present study, a new 1646 bp fragment of the S. miltiorrhiza HMGR4 gene consisting of a promoter, 5′ untranslated region and part of a coding sequence was isolated and characterised in silico using bioinformatics tools. The results indicate the presence of a TATA box, tandem repeat and pyrimidine-rich sequence, and the absence of CpG islands. The sequence was rich in motifs recognised by specific transcription factors sensitive mainly to light, salicylic acid, bacterial infection and auxins; it also demonstrated many binding sites for microRNAs. Moreover, our results suggest that HMGR4 expression is possibly regulated during flowering, embryogenesis, organogenesis and the circadian rhythm. The obtained data were verified by comparison with microarray co-expression results obtained for Arabidopsis thaliana. Alignment of the isolated HMGR4 sequence with other plant HMGRs indicated the presence of many common binding sites for transcription factors, including conserved ones. Our findings provide valuable information for understanding the mechanisms that direct transcription of the S. miltiorrhiza HMGR4 gene.

A Global Analysis of Alternative Splicing of Dichocarpum Medicinal Plants, Ranunculales

Background: The multiple isoforms are often generated from a single gene via Alternative Splicing (AS) in plants, and the functional diversity of the plant genome is significantly increased. Despite well-studied gene functions, the specific functions of isoforms are little known, therefore, the accurate prediction of isoform functions is exceedingly wanted. Methods: Here we perform the first global analysis of AS of Dichocarpum, a medicinal genus of Ranunculales, by utilizing full-length transcriptome datasets of five Chinese endemic Dichocarpum taxa. Multiple software were used to identify AS events, the gene function was annotated based on seven databases, and the protein-coding sequence of each AS isoform was translated into an amino acid sequence. The self-developed software DIFFUSE was used to predict the functions of AS isoforms. Results: Among 8,485 genes with AS events, the genes with two isoforms were the most (6,038), followed by those with three isoforms and four isoforms. Retained intron (RI, 551) was predominant among 1,037 AS events, and alternative 3' splice sites and alternative 5' splice sites were second. The software DIFFUSE was effective in predicting functions of Dichocarpum isoforms, which have not been unearthed. When compared with the sequence alignment-based database annotations, DIFFUSE performed better in differentiating isoform functions. The DIFFUSE predictions on the terms GO:0003677 (DNA binding) and GO: 0010333 (terpene synthase activity) agreed with the biological features of transcript isoforms. Conclusion: Numerous AS events were for the first time identified from full-length transcriptome datasets of five Dichocarpum taxa, and functions of AS isoforms were successfully predicted by the self-developed software DIFFUSE. The global analysis of Dichocarpum AS events and predicting isoform functions can help understand the metabolic regulations of medicinal taxa and their pharmaceutical explorations.

Genome-wide analysis of MYB family genes in Tripterygium wilfordii and their potential roles in terpenoid biosynthesis

Terpenoids are a class of significant bioactive components in the woody vine of Tripterygium wilfordii. Previous studies have shown that MYB transcription factors play important roles in plant secondary metabolism, growth, and developmental processes. However, the MYB involved in terpenoid biosynthesis in Tripterygium wilfordii are unknown. To identify Tripterygium wilfordii MYB (TwMYB) genes that are involved in terpenoid biosynthesis, we conducted the genome-wide analysis of the TwMYB gene family. A total of 207 TwMYBs were identified including 84 1R-TwMYB, 117 R2R3-TwMYB, four 3R-TwMYB, and two 4R-TwMYB genes. The most abundant R2R3-TwMYBs together with their Arabidopsis homologs were categorized into 26 subgroups. Intraspecific collinearity analysis found that the 74.9% of the TwMYBs may be generated by segmental duplication events, and 36.7% of duplicated gene pairs were derived from the specific whole genome duplication (WGD) event in Tripterygium wilfordii. In addition, interspecies collinearity analysis found that 16 TwMYB genes formed homologous gene pairs with MYB genes in seven representative species, which indicated they may have a key role in evolution. Notably, we found that the TwMYB genes were differentially expressed in various tissues by expression pattern analysis. In order to further select the candidate genes related to terpenoid biosynthesis, the assay of Methyl jasmonate (MeJA) induction and analysis of phylogenetic tree was conducted. It was speculated that six candidate TwMYB genes (TwMYB33, TwMYB34, TwMYB45, TwMYB67, TwMYB102, and TwMYB103) are involved in regulating terpenoid biosynthesis. This study is the first systematic analysis of the TwMYB gene family and will lay a foundation for the functional characterization of TwMYB genes in the regulation of terpenoid biosynthesis.

Molecular insights into AabZIP1-mediated regulation on artemisinin biosynthesis and drought tolerance in Artemisia annua

Artemisia annua is the main natural source of artemisinin production. In A. annua, extended drought stress severely reduces its biomass and artemisinin production while short-term water-withholding or abscisic acid (ABA) treatment can increase artemisinin biosynthesis. ABA-responsive transcription factor AabZIP1 and JA signaling AaMYC2 have been shown in separate studies to promote artemisinin production by targeting several artemisinin biosynthesis genes. Here, we found AabZIP1 promote the expression of multiple artemisinin biosynthesis genes including AaDBR2 and AaALDH1, which AabZIP1 does not directly activate. Subsequently, it was found that AabZIP1 up-regulates AaMYC2 expression through direct binding to its promoter, and that AaMYC2 binds to the promoter of AaALDH1 to activate its transcription. In addition, AabZIP1 directly transactivates wax biosynthesis genes AaCER1 and AaCYP86A1. The biosynthesis of artemisinin and cuticular wax and the tolerance of drought stress were significantly increased by AabZIP1 overexpression, whereas they were significantly decreased in RNAi-AabZIP1 plants. Collectively, we have uncovered the AabZIP1-AaMYC2 transcriptional module as a point of cross-talk between ABA and JA signaling in artemisinin biosynthesis, which may have general implications. We have also identified AabZIP1 as a promising candidate gene for the development of A. annua plants with high artemisinin content and drought tolerance in metabolic engineering breeding.

Genome-wide characterization of bZIP gene family identifies potential members involved in flavonoids biosynthesis in Ginkgo biloba L

Ginkgo biloba L. is an ancient relict plant with rich pharmacological activity and nutritional value, and its main physiologically active components are flavonoids and terpene lactones. The bZIP gene family is one of the largest gene families in plants and regulates many processes including pathogen defense, secondary metabolism, stress response, seed maturation, and flower development. In this study, genome-wide distribution of the bZIP transcription factors was screened from G. biloba database in silico analysis. A total of 40 bZIP genes were identified in G. biloba and were divided into 10 subclasses. GbbZIP members in the same group share a similar gene structure, number of introns and exons, and motif distribution. Analysis of tissue expression pattern based on transcriptome indicated that GbbZIP08 and GbbZIP15 were most highly expressed in mature leaf. And the expression level of GbbZIP13 was high in all eight tissues. Correlation analysis and phylogenetic tree analysis suggested that GbbZIP08 and GbbZIP15 might be involved in the flavonoid biosynthesis. The transcriptional levels of 20 GbbZIP genes after SA, MeJA, and low temperature treatment were analyzed by qRT-PCR. The expression level of GbbZIP08 was significantly upregulated under 4°C. Protein–protein interaction network analysis indicated that GbbZIP09 might participate in seed germination by interacting with GbbZIP32. Based on transcriptome and degradome data, we found that 32 out of 117 miRNAs were annotated to 17 miRNA families. The results of this study may provide a theoretical foundation for the functional validation of GbbZIP genes in the future.

Genome-Wide Identification of Circular RNAs Potentially Involved in the Biosynthesis of Secondary Metabolites in Salvia miltiorrhiza

Circular RNAs (circRNAs) play various roles in cellular functions. However, no studies have been reported on the potential involvement of circRNAs in the biosynthesis of secondary metabolites in plants. Here, we performed a genome-wide discovery of circRNAs from root, stem and leaf samples of Salvia miltiorrhiza using RNA-Seq. We predicted a total of 2,476 circRNAs with at least two junction reads using circRNA_finder and CIRI, of which 2,096, 151 and 229 were exonic, intronic and intergenic circRNAs, respectively. Sequence similarity analysis showed that 294 out of 2,476 circRNAs were conserved amongst multiple plants. Of the 55 predicted circRNAs, 31 (56%) were validated successfully by PCR and Sanger sequencing using convergent and divergent primer pairs. Alternative circularisation analysis showed that most parental genes produced two circRNAs. Functional enrichment analyses of the parental genes showed that the primary metabolism pathways were significantly enriched, particularly the carbon metabolism. Differential expression analysis showed that the expression profiles of circRNAs were tissue-specific. Co-expression analysis showed 275 circRNAs, and their parental genes had significantly positive correlations. However, 14 had significantly negative correlations. Weighted gene co-expression network analysis showed that nine circRNAs were co-expressed with four modules of protein-coding genes. Next, we found 416 exonic circRNAs with miRNA-binding sites, suggesting possible interactions between circRNAs and miRNAs. Lastly, we found six validated circRNAs, namely, SMscf2473-46693-46978, SMscf3091-29256-29724, SMscf16-111773-112193, SMscf432-13232-13866, SMscf7007-10563-10888 and SMscf1730-1749-2013, which were originated from the genes involved in the biosynthesis of secondary metabolites. Their parental genes were acetyl-CoA C-acetyltransferase 1 (SmAACT1), 1-deoxy-d-xylulose-5-phosphate synthase 2 (SmDXS2), 4-hydroxy-3-methylbut-2-enyl diphosphate reductase 1 (SmHDR1), kaurene synthase-like 2 (SmKSL2), DWF4 and CYP88A3, respectively. In particular, the correlation coefficient of SMscf2473-46693-46978 and SmDXS2 gene was 0.86 (p = 0.003), indicating a potential interaction between this pair of circRNA and its parent gene. Our results provided the first comprehensive catalogue of circRNAs in S. miltiorrhiza and identified one circRNA that might play important roles in the biosynthesis of secondary metabolites.

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.

Isolation and Functional Characterization of the Promoters of Miltiradiene Synthase Genes, TwTPS27a and TwTPS27b, and Interaction Analysis with the Transcription Factor TwTGA1 from Tripterygium wilfordii

Miltiradiene synthase (MS) genes, TwTPS27a and TwTPS27b, are the key diterpene synthase genes in the biosynthesis of triptolide, which is an important medicinally active diterpenoid in Tripterygium wilfordii. However, the mechanism underlying the regulation of key genes TwTPS27a/b in triptolide biosynthesis remains unclear. In this study, the promoters of TwTPS27a (1496 bp) and TwTPS27b (1862 bp) were isolated and analyzed. Some hormone-/stress-responsive elements and transcription factor (TF) binding sites were predicted in both promoters, which might be responsible for the regulation mechanism of TwTPS27a/b. The β-glucuronidase (GUS) activity analysis in promoter deletion assays under normal and methyl jasmonate (MeJA) conditions showed that the sequence of −921 to −391 bp is the potential core region of the TwTPS27b promoter. And the TGACG-motif, a MeJA-responsive element found in this core region, might be responsible for MeJA-mediated stress induction of GUS activity. Moreover, the TGACG-motif is also known as the TGA TF-binding site. Yeast one-hybrid and GUS transactivation assays confirmed the interaction between the TwTPS27a/b promoters and the TwTGA1 TF (a MeJA-inducible TGA TF upregulating triptolide biosynthesis in T. wilfordii), indicating that TwTPS27a/b are two target genes regulated by TwTGA1. In conclusion, our results provide important information for elucidating the regulatory mechanism of MS genes, TwTPS27a and TwTPS27b, as two target genes of TwTGA1, in jasmonic acid (JA)-inducible triptolide biosynthesis.

IiWRKY34 positively regulates yield, lignan biosynthesis and stress tolerance in Isatis indigotica

Yield potential, pharmaceutical compounds production and stress tolerance capacity are 3 classes of traits that determine the quality of medicinal plants. The autotetraploid Isatis indigotica has greater yield, higher bioactive lignan accumulation and enhanced stress tolerance compared with its diploid progenitor. Here we show that the transcription factor IiWRKY34, with higher expression levels in tetraploid than in diploid I. indigotica, has large pleiotropic effects on an array of traits, including biomass growth rates, lignan biosynthesis, as well as salt and drought stress tolerance. Integrated analysis of transcriptome and metabolome profiling demonstrated that IiWRKY34 expression had far-reaching consequences on both primary and secondary metabolism, reprograming carbon flux towards phenylpropanoids, such as lignans and flavonoids. Transcript–metabolite correlation analysis was applied to construct the regulatory network of IiWRKY34 for lignan biosynthesis. One candidate target Ii4CL3, a key rate-limiting enzyme of lignan biosynthesis as indicated in our previous study, has been demonstrated to indeed be activated by IiWRKY34. Collectively, the results indicate that the differentially expressed IiWRKY34 has contributed significantly to the polyploidy vigor of I. indigotica, and manipulation of this gene will facilitate comprehensive improvements of I. indigotica herb.

Gene and genome duplications in the evolution of chemodiversity: perspectives from studies of Lamiaceae

Plants are reservoirs of extreme chemical diversity, yet biosynthetic pathways remain underexplored in the majority of taxa. Access to improved, inexpensive genomic and computational technologies has recently enhanced our understanding of plant specialized metabolism at the biochemical and evolutionary levels including the elucidation of pathways leading to key metabolites. Furthermore, these approaches have provided insights into the mechanisms of chemical evolution, including neofunctionalization and subfunctionalization, structural variation, and modulation of gene expression. The broader utilization of genomic tools across the plant tree of life, and an expansion of genomic resources from multiple accessions within species or populations, will improve our overall understanding of chemodiversity. These data and knowledge will also lead to greater insight into the selective pressures contributing to and maintaining this diversity, which in turn will enable the development of more accurate predictive models of specialized metabolism in plants.

Transcriptional Factors Regulate Plant Stress Responses through Mediating Secondary Metabolism

Plants are adapted to sense numerous stress stimuli and mount efficient defense responses by directing intricate signaling pathways. They respond to undesirable circumstances to produce stress-inducible phytochemicals that play indispensable roles in plant immunity. Extensive studies have been made to elucidate the underpinnings of defensive molecular mechanisms in various plant species. Transcriptional factors (TFs) are involved in plant defense regulations through acting as mediators by perceiving stress signals and directing downstream defense gene expression. The cross interactions of TFs and stress signaling crosstalk are decisive in determining accumulation of defense metabolites. Here, we collected the major TFs that are efficient in stress responses through regulating secondary metabolism for the direct cessation of stress factors. We focused on six major TF families including AP2/ERF, WRKY, bHLH, bZIP, MYB, and NAC. This review is the compilation of studies where researches were conducted to explore the roles of TFs in stress responses and the contribution of secondary metabolites in combating stress influences. Modulation of these TFs at transcriptional and post-transcriptional levels can facilitate molecular breeding and genetic improvement of crop plants regarding stress sensitivity and response through production of defensive compounds.

Genome-wide identification, phylogeny, evolutionary expansion and expression analyses of bZIP transcription factor family in tartaty buckwheat

Background

In reported plants, the bZIP family is one of the largest transcription factor families. bZIP genes play roles in the light signal, seed maturation, flower development, cell elongation, seed accumulation protein, abiotic and biological stress and other biological processes. While, no detailed identification and genome-wide analysis of bZIP family genes in Fagopyum talaricum (tartary buckwheat) has previously been published. The recently reported genome sequence of tartary buckwheat provides theoretical basis for us to study and discuss the characteristics and expression of bZIP genes in tartary buckwheat based on the whole genome.

Results

In this study, 96 FtbZIP genes named from FtbZIP1 to FtbZIP96 were identified and divided into 11 subfamilies according to their genetic relationship with 70 bZIPs of A. thaliana. FtbZIP genes are not evenly distributed on the chromosomes, and we found tandem and segmental duplication events of FtbZIP genes on 8 tartary buckwheat chromosomes. According to the results of gene and motif composition, FtbZIP located in the same group contained analogous intron/exon organizations and motif composition. By qRT-PCR, we quantified the expression of FtbZIP members in stem, root, leaf, fruit, and flower and during fruit development. Exogenous ABA treatment increased the weight of tartary buckwheat fruit and changed the expressions of FtbZIP genes in group A.

Conclusions

Through our study, we identified 96 FtbZIP genes in tartary buckwheat and synthetically further analyzed the structure composition, evolution analysis and expression pattern of FtbZIP proteins. The expression pattern indicates that FtbZIP is important in the course of plant growth and development of tartary buckwheat. Through comprehensively analyzing fruit weight and FtbZIP genes expression after ABA treatment and endogenous ABA content of tartary buckwheat fruit, ABA may regulate downstream gene expression by regulating the expression of FtPinG0003523300.01 and FtPinG0003196200.01, thus indirectly affecting the fruit development of tartary buckwheat. This will help us to further study the function of FtbZIP genes in the tartary buckwheat growth and improve the fruit of tartary buckwheat.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5882-z) contains supplementary material, which is available to authorized users.

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

The novel AP2/ERF transcription factor SmERF128 positively regulates diterpenoid tanshinone biosynthesis by activating the expression of SmCPS1, SmKSL1, and SmCYP76AH1 in Salvia miltiorrhiza. Certain members of the APETALA2/ethylene-responsive factor (AP2/ERF) family regulate plant secondary metabolism. Although it is clearly documented that AP2/ERF transcription factors (TFs) are involved in sesquiterpenoid biosynthesis, the regulation of diterpenoid biosynthesis by AP2/ERF TFs remains elusive. Here, we report that the novel AP2/ERF TF SmERF128 positively regulates diterpenoid tanshinone biosynthesis in Salvia miltiorrhiza. Overexpression of SmERF128 increased the expression levels of copalyl diphosphate synthase 1 (SmCPS1), kaurene synthase-like 1 (SmKSL1) and cytochrome P450 monooxygenase 76AH1 (SmCYP76AH1), whereas their expression levels were decreased when SmERF128 was silenced. Accordingly, the content of tanshinone was reduced in SmERF128 RNA interference (RNAi) hairy roots and dramatically increased in SmERF128 overexpression hairy roots, as demonstrated through Ultra Performance Liquid Chromatography (UPLC) and Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) analysis. Furthermore, SmERF128 activated the expression of SmCPS1, SmKSL1, and SmCYP76AH1 by binding to the GCC box, and to the CRTDREHVCBF2 (CBF2) and RAV1AAT (RAA) motifs within their promoters during in vivo and in vitro assays. Our findings not only reveal the molecular basis of how the AP2/ERF transcription factor SmERF128 regulates diterpenoid biosynthesis, but also provide useful information for improving tanshinone production through genetic engineering.

Comparative transcriptome analysis of roots, stems and leaves of Isodon amethystoides reveals candidate genes involved in Wangzaozins biosynthesis

BACKGROUND

Isodon amethystoides (Ben-th) Cy Wu et Hsuan is an important traditional medicinal plant endowed with pharmacological properties effective in the treatment of various diseases, including pulmonary tuberculosis. The tetracyclic diterpenoids, Wangzaozins (Wangzaozin A, glaucocalyxin A, glaucocalyxin B), are the major bioactive compounds of I. amethystoides. However, the molecular information about the biosynthesis of these compounds still remains unclear.

RESULTS

An examination of the accumulated levels of Wangzaozins in I. amethystoides revealed considerable variations in the root, stem, and leaf tissues of this plant, indicating possible differences in metabolite biosynthesis and accumulation among various tissues. To better elucidate the tetracyclic diterpenoid biosynthesis pathway, we generated transcriptome sequences from the root, stem, and leaf tissues, and performed de novo sequence assembly, yielding 230,974 transcripts and 114,488 unigenes, with average N50 lengths of 1914 and 1241 bp, respectively. Putative functions could be assigned to 73,693 transcripts (31.9%) based on BLAST searches against annotation databases, including GO, KEGG, Swiss-Prot, NR, and Pfam. Moreover, the candidate genes involving in the diterpenoid biosynthesis, such as CPS, KSL, were also analyzed. The expression profiles of eight transcripts, involving the tetracyclic diterpenoid biosynthesis, were validated in different I. amethystoides tissues by qRT-PCR, unraveling the gene expression profile of the pathway. The differential expressions of ISPD, ISPF and ISPH (MEP pathway), and IaCPS and IaKSL (diterpenoid pathway) candidate genes in leaves and roots, may contribute to the high accumulation of Wangzaozins in I. amethystoides leaves.

CONCLUSION

The genomic dataset and analyses reported here lay the foundations for further research on this important medicinal plant.

Trends in herbgenomics

From Shen Nong's Herbal Classic (Shennong Bencao Jing) to the Compendium of Materia Medica (Bencao Gangmu) and the first scientific Nobel Prize for the mainland of China, each milestone in the historical process of the development of traditional Chinese medicine (TCM) involves screening, testing and integrating. After thousands of years of inheritance and development, herbgenomics (bencaogenomics) has bridged the gap between TCM and international advanced omics studies, promoting the application of frontier technologies in TCM. It is a discipline that uncovers the genetic information and regulatory networks of herbs to clarify their molecular mechanism in the prevention and treatment of human diseases. The main theoretical system includes genomics, functional genomics, proteomics, transcriptomics, metabolomics, epigenomics, metagenomics, synthetic biology, pharmacogenomics of TCM, and bioinformatics, among other fields. Herbgenomics is mainly applicable to the study of medicinal model plants, genomic-assisted breeding, herbal synthetic biology, protection and utilization of gene resources, TCM quality evaluation and control, and TCM drug development. Such studies will accelerate the application of cutting-edge technologies, revitalize herbal research, and strongly promote the development and modernization of TCM.

Genome-wide characterization and analysis of bHLH transcription factors in Panax ginseng

Ginseng (Panax ginseng C.A. Meyer) is one of the best-selling herbal medicines, with ginsenosides as its main pharmacologically active constituents. Although extensive chemical and pharmaceutical studies of these compounds have been performed, genome-wide studies of the basic helix-loop-helix (bHLH) transcription factors of ginseng are still limited. The bHLH transcription factor family is one of the largest transcription factor families found in eukaryotic organisms, and these proteins are involved in a myriad of regulatory processes. In our study, 169 bHLH transcription factor genes were identified in the genome of P. ginseng, and phylogenetic analysis indicated that these PGbHLHs could be classified into 24 subfamilies. A total of 21 RNA-seq data sets, including two sequencing libraries for jasmonate (JA)-responsive and 19 reported libraries for organ-specific expression analyses were constructed. Through a combination of gene-specific expression patterns and chemical contents, 6 PGbHLH genes from 4 subfamilies were revealed to be potentially involved in the regulation of ginsenoside biosynthesis. These 6 PGbHLHs, which had distinct target genes, were further divided into two groups depending on the absence of MYC-N structure. Our results would provide a foundation for understanding the molecular basis and regulatory mechanisms of bHLH transcription factor action in P. ginseng.

Plastome-wide comparison reveals new SNV resources for the authentication of Dendrobium huoshanense and its corresponding medicinal slice (Huoshan Fengdou)

Dendrobium species and their corresponding medicinal slices have been extensively used as traditional Chinese medicine (TCM) in many Asian countries. However, it is extremely difficult to identify Dendrobium species based on their morphological and chemical features. In this study, the plastomes of D. huoshanense were used as a model system to investigate the hypothesis that plastomic mutational hotspot regions could provide a useful single nucleotide variants (SNVs) resource for authentication studies. We surveyed the plastomes of 17 Dendrobium species, including the newly sequenced plastome of D. huoshanense. A total of 19 SNVs that could be used for the authentication of D. huoshanense were detected. On the basis of this comprehensive comparison, we identified the four most informative hotspot regions in the Dendrobium plastome that encompass ccsA to ndhF, matK to 3'trnG, rpoB to psbD, and trnT to rbcL. Furthermore, to established a simple and accurate method for the authentication of D. huoshanense and its medicinal slices, a total of 127 samples from 20 Dendrobium species including their corresponding medicinal slices (Fengdous) were used in this study. Our results suggest that D. huoshanense and its medicinal slices can be rapidly and unequivocally identified using this method that combines real-time PCR with the amplification refractory mutation system (ARMS).