Molecular cloning and characterization of a 1-deoxy-D-xylulose 5-phosphate reductoisomerase gene from Ginkgo biloba

Research progress on the types, functions, biosynthesis, and metabolic regulation of ginkgo terpenoids

Ginkgo biloba L. is a relict plant endemic to China that is commonly considered a "living fossil". It contains unique medicinal compounds that play important roles in its response to various stresses and help maintain human health. Ginkgo terpenoids are known to be important active ingredients but have received less attention than flavonoids. Hence, this review focuses on recent progress in research on the pharmacological effects of ginkgo terpenoid and the bioactivities of different terpenoid monomers. Many key structural genes, enzyme-encoding genes, transcription factors, and noncoding RNAs involved in the ginkgo terpenoid pathway were identified. Finally, many external factors (ecological factors, hormones, etc.) that regulate the biosynthesis and metabolism of terpenoids were proposed. All these findings improve the understanding of the biosynthesis, accumulation, and medicinal functions of terpenoids. Finally, this review includes an in-depth discussion regarding the limitations of terpenoid-related studies and potential future research directions.

Functional Characterization of PmDXR, a Critical Rate-Limiting Enzyme, for Turpentine Biosynthesis in Masson Pine (Pinus massoniana Lamb.)

As one of the largest and most diverse classes of specialized metabolites in plants, terpenoids (oprenoid compounds, a type of bio-based material) are widely used in the fields of medicine and light chemical products. They are the most important secondary metabolites in coniferous species and play an important role in the defense system of conifers. Terpene synthesis can be promoted by regulating the expressions of terpene synthase genes, and the terpene biosynthesis pathway has basically been clarified in Pinus massoniana, in which there are multiple rate-limiting enzymes and the rate-limiting steps are difficult to determine, so the terpene synthase gene regulation mechanism has become a hot spot in research. Herein, we amplified a PmDXR gene (GenBank accession no. MK969119.1) of the MEP pathway (methyl-erythritol 4-phosphate) from Pinus massoniana. The DXR enzyme activity and chlorophyll a, chlorophyll b and carotenoid contents of overexpressed Arabidopsis showed positive regulation. The PmDXR gene promoter was a tissue-specific promoter and can respond to ABA, MeJA and GA stresses to drive the expression of the GUS reporter gene in N. benthamiana. The DXR enzyme was identified as a key rate-limiting enzyme in the MEP pathway and an effective target for terpene synthesis regulation in coniferous species, which can further lay the theoretical foundation for the molecularly assisted selection of high-yielding lipid germplasm of P. massoniana, as well as provide help in the pathogenesis of pine wood nematode disease.

Cloning and functional analysis of the DXR gene and promoter region in Osmanthus fragrans var. semperflorens

The precise biological function and activity of the deoxylulose-5-phosphate reductoisomerase (DXR) gene and its promoter in Osmanthus fragrans var. semperflorens remain unclear, even though OfDXR is known as the crucial enzyme involved in plant terpenoid synthesis. This study aimed to shed light on the role and activity of the OfDXR gene and its promoter in O. fragrans var. semperflorens by employing RACE-PCR and Hi-TAIL-PCR techniques for the cloning of the gene and promoter sequence from the petal tissue. Subsequently, genetic transformation and histochemical staining methods were utilized to analyze their function and activity. The OfDXR gene exhibited a DNA sequence length of 5241 bp, encompassing 12 exons and 11 introns. The corresponding cDNA sequence of the OfDXR gene was 1629 bp, encoding 474 amino acid residues. Expression analysis revealed that the OfDXR gene was predominantly active in the petals during the early full blooming stage. Overexpression of the OfDXR gene in Arabidopsis plants at the primary or full blooming stage led to an augmentation in the total terpenoid content. Furthermore, the promoter sequence of the OfDXR gene spanned a length of 1174 bp and contained conserved regulatory/response elements, demonstrating functional activity. These findings indicate that the OfDXR gene plays a pivotal role in terpenoid synthesis, while its promoter exhibits robust activity.

Structure, synthesis, biosynthesis, and activity of the characteristic compounds from Ginkgo biloba L

Covering: 1928-2021Ginkgo biloba L. is one of the most distinctive plants to have emerged on earth and has no close living relatives. Owing to its phylogenetic divergence from other plants, G. biloba contains many compounds with unique structures that have served to broaden the chemical diversity of herbal medicine. Examples of such compounds include terpene trilactones (ginkgolides), acylated flavonol glycosides (ginkgoghrelins), biflavones (ginkgetin), ginkgotides and ginkgolic acids. The extract of G. biloba leaf is used to prevent and/or treat cardiovascular diseases, while many ginkgo-derived compounds are currently at various stages of preclinical and clinical trials worldwide. The global annual sales of G. biloba products are estimated to total US$10 billion. However, the content and purity of the active compounds isolated by traditional methods are usually low and subject to varying environmental factors, making it difficult to meet the huge demand of the international market. This highlights the need to develop new strategies for the preparation of these characteristic compounds from G. biloba. In this review, we provide a detailed description of the structures and bioactivities of these compounds and summarize the recent research on the development of strategies for the synthesis, biosynthesis, and biotechnological production of the characteristic terpenoids, flavonoids, and alkylphenols/alkylphenolic acids of G. biloba. Our aim is to provide an important point of reference for all scientists who research ginkgo-related compounds for medicinal or other purposes.

In silico characterization and differential expression analysis of 1-deoxy-d-xylulose-5-phosphate reductoisomerase (DXR) of Centella asiatica

The 1-deoxy-d-xylulose-5-phosphate reductoisomerase (DXR; EC1.1.1.267), an NADPH-dependent reductase, plays a pivotal role in the methylerythritol 4-phosphate pathway (MEP), in the conversion of 1-deoxy-d-xylulose-5-phosphate (DXP) into MEP. Photochemical profiles, as well as pharmaceutical activities of Centella asiatica (L.), one of the most valuable medicinal plants, divulge the presence of secondary metabolites called Centellosides. Despite well-studied pharmaceutical activities, not much is known about the genes responsible for the synthesis of these compounds. In the present study, the full-length DXR gene sequence (JQ965955) of Centella submitted in NCBI was characterized using various bioinformatics tools and tissue specific differential expression studies were also carried out. The full-length CDNA of CaDXR contains an open reading frame (ORF) of 1425 bp which encodes a peptide of 474 amino acids. The molecular weight of this protein was found to be 51.5 kDa with isoelectric point of 6.33. The protein contains three conserved domain, namely NADPH (GSTGSIGT and LAAGSNV), substrate binding (LPADSEHSAI and NKGLEVIEAHY) and Cys-Ser-(Ala/Met/Val/Thr) cleavage-site domains. Phylogenetic studies of CaDXR sequence show close homology with DXR sequence of Angelica sinensis and Daucus carota subsp sativus as they all belong to Apiaceae family. In silico analysis predicted that CaDXR protein contains 21 α-helix and 11 β-sheets and further DXR protein model was validated by Ramachandran plot analysis. The results of molecular dynamics (MD) simulations unveil dynamic stability of the proposed model and docking studies suggest that the NDP cofactor tightly binds in the active site of the protein with a strong network of hydrogen and hydrophobic interactions. The expression studies by semi-RT followed by qRT-PCR suggests that CaDXR is differentially expressed in different tissues (with maximal expression in the node and lowest in the roots). Thus, characterization and structure-function analysis of DXR gene in Centella facilitate us to understand not only the functions of DXR gene but also regulatory mechanisms involved in the MEP pathway in C. asiatica plant at the molecular level.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02723-w.

Evaluation, characterization, expression profiling, and functional analysis of DXS and DXR genes of Populus trichocarpa

1-Deoxy-D-xylulose-5-phosphate synthasse (DXS) and 1-deoxy-D-xylulose-5-phosphate reductoisomerase (DXR) are key enzymes in terpenoid biosynthesis. DXS catalyzes the formation of 1-deoxy-D-xylulose 5-phosphate (DXP) from pyruvate and D-glyceraldehyde-3-phosphate. DXR catalyzes the formation of 2-C-methyl-D-erythritol 4-phosphate (MEP) from DXP. Previous studies of the DXS and DXR genes have focused on herbs, such as Arabidopsis thaliana, Salvia miltiorrhiza, and Amomum villosum, but few studies have been conducted on woody plants. For that reason, we chose Populus trichocarpa as a model woody plant for investigating the DXS and DXR genes. PtDXS exhibited the highest expression level in leaves and the lowest expression in roots. PtDXR showed maximum expression in young leaves, and the lowest expression in mature leaves. The expression profiles revealed by RT-PCR following different elicitor treatments such as abscisic acid, NaCl, PEG₆₀₀₀, H₂O₂, and cold stress showed that PtDXS and PtDXR were elicitor-responsive genes. Our results showed that the PtDXS gene exhibited diurnal changes, but PtDXR did not. Moreover, overexpression of PtDXR in transgenic poplars improved tolerance to abiotic and biotic stresses. Those results showed that the PtDXR encoded a functional protein, and widely participates in plant growth and development, stress physiological process.

Recent advances in steroidal saponins biosynthesis and in vitro production

Steroidal saponins exhibited numerous pharmacological activities due to the modification of their backbone by different cytochrome P450s (P450) and UDP glycosyltransferases (UGTs). Plant-derived steroidal saponins are not sufficient for utilizing them for commercial purpose so in vitro production of saponin by tissue culture, root culture, embryo culture, etc, is necessary for its large-scale production. Saponin glycosides are the important class of plant secondary metabolites, which consists of either steroidal or terpenoidal backbone. Due to the existence of a wide range of medicinal properties, saponin glycosides are pharmacologically very important. This review is focused on important medicinal properties of steroidal saponin, its occurrence, and biosynthesis. In addition to this, some recently identified plants containing steroidal saponins in different parts were summarized. The high throughput transcriptome sequencing approach elaborates our understanding related to the secondary metabolic pathway and its regulation even in the absence of adequate genomic information of non-model plants. The aim of this review is to encapsulate the information related to applications of steroidal saponin and its biosynthetic enzymes specially P450s and UGTs that are involved at later stage modifications of saponin backbone. Lastly, we discussed the in vitro production of steroidal saponin as the plant-based production of saponin is time-consuming and yield a limited amount of saponins. A large amount of plant material has been used to increase the production of steroidal saponin by employing in vitro culture technique, which has received a lot of attention in past two decades and provides a way to conserve medicinal plants as well as to escape them for being endangered.

Combining Metabolic Profiling and Gene Expression Analysis to Reveal the Biosynthesis Site and Transport of Ginkgolides in Ginkgo biloba L

The most unique components of Ginkgo biloba extracts are terpene trilactones (TTLs) including ginkgolides and bilobalide. Study of TTLs biosynthesis has been stagnant in recent years. Metabolic profiling of 40 compounds, including TTLs, flavonoids, and phenolic acids, were globally analyzed in leaf, fibrous root, main root, old stem and young stem extracts of G. biloba. Most of the flavonoids were mainly distributed in the leaf and old stem. Most of phenolic acids were generally distributed among various tissues. The total content of TTLs decreased in the order of the leaf, fibrous root, main root, old stem and young stem. The TTLs were further analyzed in different parts of the main root and old stem. The content of TTLs decreases in the order of the main root periderm, the main root cortex and phloem and the main root xylem. In old stems, the content of TTLs in the cortex and phloem was much higher than both the old stem periderm and xylem. The expression patterns of five key genes in the ginkgolide biosynthetic pathway were measured by real-time quantitative polymerase chain reaction (RT-Q-PCR). Combining metabolic profiling and RT-Q-PCR, the results showed that the fibrous root and main root periderm tissues were the important biosynthesis sites of ginkgolides. Based on the above results, a model of the ginkgolide biosynthesis site and transport pathway in G. biloba was proposed. In this putative model, ginkgolides are synthesized in the fibrous root and main root periderm, and these compounds are then transported through the old stem cortex and phloem to the leaves.

Novel insights into structure-function mechanism and tissue-specific expression profiling of full-length dxr gene from Cymbopogon winterianus

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We sequenced the complete coding sequence of citronella dxr gene.

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Analysis of CwDXR revealed the plastidial nature of the enzyme.

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Comparative modelling of CwDXR was performed.

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Molecular dynamics simulation and docking explained the mode of cofactor recognition.

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Tissue-specific expression of CwDXR was performed using RT-PCR and qRT-PCR.

The 1-deoxy-d-xylulose-5-phosphate reductoisomerase (DXR; EC1.1.1.267), an NADPH-dependent reductase, plays a pivotal role in the methylerythritol 4-phosphate pathway (MEP), in the conversion of 1-deoxy-d-xylulose-5-phosphate (DXP) into MEP. The sheath and leaf of citronella (Cymbopogon winterianus) accumulates large amount of terpenes and sesquiterpenes with proven medicinal value and economic uses. Thus, sequencing of full length dxr gene and its characterization seems to be a valuable resource in metabolic engineering to alter the flux of isoprenoid active ingredients in plants. In this study, full length DXR from citronella was characterized through in silico and tissue-specific expression studies to explain its structure–function mechanism, mode of cofactor recognition and differential expression. The modelled DXR has a three-domain architecture and its active site comprised of a cofactor (NADPH) binding pocket and the substrate-binding pocket. Molecular dynamics simulation studies indicated that DXR model retained most of its secondary structure during 10 ns simulation in aqueous solution. The modelled DXR superimposes well with its closest structural homolog but subtle variations in the charge distribution over the cofactor recognition site were noticed. Molecular docking study revealed critical residues aiding tight anchoring NADPH within the active pocket of DXR. Tissue-specific differential expression analysis using semi-quantitative RT-PCR and qRT-PCR in various tissues of citronella plant revealed distinct differential expression of DXR. To our knowledge, this is the first ever report on DXR from the important medicinal plant citronella and further characterization of this gene will open up better avenues for metabolic engineering of secondary metabolite pathway genes from medicinal plants in the near future.

Engineering the MEP pathway enhanced ajmalicine biosynthesis

The 2-C-methyl-D-erythritol-4-phosphate (MEP) pathway genes encoding DXR and MECS from Taxus species and STR from Catharanthus roseus were used to genetically modify the ajmalicine biosynthetic pathway in hairy root cultures of C. roseus. As expected, the STR-overexpressed root cultures showed twofold higher accumulation of ajmalicine than the control. It was important to discover that overexpression of the single DXR or MECS gene from the MEP pathway also remarkably enhanced ajmalicine biosynthesis in transgenic hairy root cultures, and this suggested that engineering the MEP pathway by overexpression of DXR or MECS promoted the metabolic flux into ajmalicine biosynthesis. The transgenic hairy root cultures with co-overexpression of DXR and STR or MECS and STR had higher levels of ajmalicine than those with overexpression of a single gene alone such as DXR, MECS, and STR. It could be concluded that transgenic hairy root cultures harboring both DXR/MECS and STR possessed an increased flux in the terpenoid indole alkaloid biosynthetic pathway that enhanced ajmalicine yield, which was more efficient than cultures harboring only one of the three genes.

Biosynthesis pathways of ginkgolides

The ginkgolides, acting as anti-platelet-activating factors, have been studied for many years. The biosynthetic pathway of ginkgolides is still far away from unveiling at the level of molecular genetics and biochemistry. There are at least 11 kinds of enzymes having been cloned from Ginkgo biloba L., which catalyze the formation of ginkgolides via a series of reactions. Some researchers have indicated that the addition of precursors and elicitors can influence the accumulation of ginkgolides in the suspension cell cultures of G. biloba. There are also other factors that can influence the production of ginkgolides. This review focuses on the aforementioned aspects to discuss the biosynthetic pathways of the ginkgolides.

Characterization and functional analysis of the genes encoding 1-deoxy-D-xylulose-5-phosphate reductoisomerase and 1-deoxy-D-xylulose-5-phosphate synthase, the two enzymes in the MEP pathway, from Amomum villosum Lour

A DXR gene, AvDXR (GenBank accession no. FJ459894), and a DXS gene, AvDXS (GenBank accession no. FJ455512), were isolated from the leaves of Amomum villosum, one of the most well-known and authentic herbs in South China. The 1,749-bp full-length cDNA of AvDXR encoded a peptide of 472 amino acids, and the 2,347-bp full-length cDNA of AvDXS encoded a peptide of 715 amino acids. The deduced amino acid sequences of the AvDXR and AvDXS proteins share high homology with DXRs and DXSs from other plant species, and AvDXS belongs to class 1 plant DXS. The characterization based on bioinformatic analysis indicated that the AvDXR and AvDXS encoded functional proteins as DXR and DXS, respectively. The functional color assay in Escherichia coli with pAC-BETA implied that AvDXR and AvDXS encoded functional proteins that manipulated the biosynthesis of isoprenoid precursors. Both AvDXR and AvDXS were expressed extensively in the leaves, stems, roots, pericarps and seeds of A. villosum. AvDXS expression was similar in all tissues investigated, whereas higher levels of AvDXR were observed in the fruits, the main part for the accumulation of volatile oil in this plant. AvDXR was transformed into tobacco to confirm its function further. Overexpression of AvDXR in transgenic T1 generation tobacco increased DXR activity, photosynthetic pigment content and volatile isoprenoid components, and the increase of photosynthetic pigment content was consistent with the AvDXR transcription level. This study demonstrated that AvDXR plays important role in isoprenoid biosynthesis and it is useful for metabolic engineering.

A raison d'être for two distinct pathways in the early steps of plant isoprenoid biosynthesis?

When compared to other organisms, plants are atypical with respect to isoprenoid biosynthesis: they utilize two distinct and separately compartmentalized pathways to build up isoprene units. The co-existence of these pathways in the cytosol and in plastids might permit the synthesis of many vital compounds, being essential for a sessile organism. While substrate exchange across membranes has been shown for a variety of plant species, lack of complementation of strong phenotypes, resulting from inactivation of either the cytosolic pathway (growth and development defects) or the plastidial pathway (pigment bleaching), seems to be surprising at first sight. Hundreds of isoprenoids have been analyzed to determine their biosynthetic origins. It can be concluded that in angiosperms, under standard growth conditions, C₂₀-phytyl moieties, C₃₀-triterpenes and C₄₀-carotenoids are made nearly exclusively within compartmentalized pathways, while mixed origins are widespread for other types of isoprenoid-derived molecules. It seems likely that this coexistence is essential for the interaction of plants with their environment. A major purpose of this review is to summarize such observations, especially within an ecological and functional context and with some emphasis on regulation. This latter aspect still requires more work and present conclusions are preliminary, although some general features seem to exist.

Characterization of reference genes for quantitative real-time PCR analysis in various tissues of Salvia miltiorrhiza

Five reference genes, 18S, EF1alpha, alpha-Tubulin, Ubiquitin and Actin, from Salvia miltiorrhiza were analyzed as internal controls for gene expression profiling assay using quantitative real-time polymerase chain reaction (qRT-PCR). The five candidate genes were measured for their transcriptional level in seven tissues, including roots, stems, leaves, sepals, petals, stamens and pistils. Then they were ranked by the GeNorm tool. The results showed that Actin and Ubiquitin were the most stable whereas EF1alpha and 18S did not favor normalization of qRT-PCR results in these tissues. Expression levels of the SmDXR gene were studied in parallel, with Actin and Ubiquitin both or each as reference in the seven tissues, and varying relative quantifications of the SmDXR gene in seven tissues. This study indicated that selection of the most stable genes plays an important role in gene expression profiling assays.

Molecular cloning, expression profiling and functional analysis of a DXR gene encoding 1-deoxy-D-xylulose 5-phosphate reductoisomerase from Camptotheca acuminata

As the second enzyme of the non-mevalonate terpenoid pathway for isopentenyl diphosphate biosynthesis, DXP reductoisomerase (DXR, EC: 1.1.1.267) catalyzes a committed step of the MEP pathway for camptothecin (CPT) biosynthesis. In order to understand more about the role of DXR involved in the CPT biosynthesis at the molecular level, the full-length DXR cDNA sequence (designated as CaDXR) was isolated and characterized for the first time from a medicinal Nyssaceae plant species, Camptotheca acuminata. The full-length cDNA of CaDXR was 1823 bp containing a 1416 bp open reading frame (ORF) encoding a polypeptide of 472 amino acids. Comparative and bioinformatic analyses revealed that CaDXR showed extensive homology with DXRs from other plant species and contained a conserved transit peptide for plastids, an extended Pro-rich region and a highly conserved NADPH binding motif in its N-terminal region owned by all plant DXRs. Phylogenetic analysis indicated that CaDXR was more ancient than other plant DXRs. Tissue expression pattern analysis revealed that CaDXR expressed strongly in stem, weak in leaf and root. CaDXR was found to be an elicitor-responsive gene, which could be induced by exogenous elicitor of methyl jasmonate. The functional color complementation assay indicated that CaDXR could accelerate the biosynthesis of carotenoids in the Escherichia coli transformant, demonstrating that DXP reductoisomerase plays an influential step in isoprenoid biosynthesis.

Molecular cloning and characterization of 1-hydroxy-2-methyl-2-(E)-butenyl-4-diphosphate reductase gene from Ginkgo biloba

Ginkgo biloba contains terpene triclactones of high pharmaceutical value such as ginkgolides. 1-hydroxy-2-methyl-2-(E)-butenyl-4-diphosphate (HMBPP) reductase (HDR) is proved to be the terminal-acting enzyme in the plastid MEP pathway which provides isoprenoid precursors for the biosynthesis of ginkgolides. The full-length cDNA encoding HDR, designated as GbHDR (Genbank Accession Number DQ364231), was isolated for the first time from G. biloba by RACE method. GbHDR contained a 1,422-bp open reading frame encoding 474 amino acids. The deduced GbHDR protein, showing high identity to HDRs of other plant species, was predicted to possess a chloroplast transit peptide at the N-terminal and four conserved cysteine residues. Two-dimensional structural analysis showed that GbHDR had a similar secondary structure with HDR from Arabidopsis thaliana. Southern blot analysis indicated that GbHDR belonged to a small gene family. Transcription pattern analysis revealed that GbHDR had high transcription in roots, and low in leaves and stems. The cloning of GbHDR gene will enable us to further understand the role of GbHDR involved in terpene triclatones biosynthetic pathway in G. biloba at molecular level.

Cloning and characterization of 2-C-methyl-D: -erythritol 2,4-cyclodiphosphate synthase (MECS) gene from Ginkgo biloba

Ginkgo biloba contains secondary metabolites with interesting pharmacological properties, including highly modified diterpenoid ginkgolide, potent and selective antagonist of platelet-activating factor. 2-C-Methyl-D: -erythritol 2,4-cyclodiphosphate synthase gene (GbMECS) involved in ginkgolide biosynthesis pathway was cloned and characterized from G. biloba embryonic roots, and the full open reading frame was deduced as protein consisting of 238 amino acid residues. Putative mature protein with a 179 residue-long sequence, obtained by deleting N-terminal chloroplast transit peptide region composed of 59 amino acid residues, rescued Esherichia coli NMW26, an E. coli knock-out mutant of ygbB (EcMECS). Transcription levels of GbMECS were two-fold higher in embryo roots compared to leaves. When full-length GbMECS with chloroplast transit peptide sequence was fused to green fluorescent protein gene (GFP), and transiently expressed in Arabidopsis thaliana protoplast, green fluorescence was found in chloroplast, indication of protein transportation into plastid.

Cloning and functional characterization of 2-C-methyl-D-erythritol 4-phosphate cytidyltransferase (GbMECT) gene from Ginkgo biloba

2-C-methyl-D-erythritol 4-phosphate cytidyltransferase (MECT), the third enzyme of the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway, catalyzes formation of 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol from MEP. GbMECT, presumably involved in ginkgolide biosynthesis, was cloned and characterized from Ginkgo biloba embryonic roots. The protein containing the N-terminal chloroplast transit peptide consisted of 327 amino acid residues. Complementation of GbMECT with Escherichia coli NMW33, ygbP (EcMECT) knock-out mutant, rescued the mutant, confirming the function of the protein. Transcription levels of GbMECT remained generally constant in embryonic roots and leaves for 1 month. Full 88 N-terminal residues were necessary to deliver the protein into the chloroplast as shown by protein-targeting analysis with GFP as a reporter protein in Arabidopsis thaliana protoplasts.