Transcriptome and metabolome analysis of Ferula gummosa Boiss. to reveal major biosynthetic pathways of galbanum compounds

A comprehensive review of the molecular and genetic mechanisms underlying gum and resin synthesis in Ferula species

Ferula spp. are plants that produce oleo-gum-resins (OGRs), which are plant exudates with various colors. These OGRs have various industrial applications in pharmacology, perfumery, and food. The main constituents of these OGRs are terpenoids, a diverse group of organic compounds with different structures and functions. The biosynthesis of OGRs in Ferula spp., particularly galbanum, holds considerable economic and ecological importance. However, the molecular and genetic underpinnings of this biosynthetic pathway remain largely enigmatic. This review provides an overview of the current state of knowledge on the biosynthesis of OGRs in Ferula spp., highlighting the major enzymes, genes, and pathways involved in the synthesis of different terpenoid classes, such as monoterpenes, sesquiterpenes, and triterpenes. It also examines the potential of using omics techniques, such as transcriptomics and metabolomics, and genome editing tools, such as CRISPR/Cas, to increase the yield and quality of Ferula OGRs, as well as to create novel bioactive compounds with enhanced properties. Moreover, this review addresses the current challenges and opportunities of applying gene editing in Ferula spp., and suggests some directions for future research and development.

RNA-seq analysis reveals narrow differential gene expression in MEP and MVA pathways responsible for phytochemical divergence in extreme genotypes of Thymus daenensis Celak

BACKGROUND

Here, we investigated the underlying transcriptional-level evidence behind phytochemical differences between two metabolically extreme genotypes of Thymus daenensis. The genotypes 'Zagheh-11' (thymol/carvacrol type, poor in essential oil [EO] [2.9%] but rich in triterpenic acids) and 'Malayer-21' (thymol type and rich in EO [3.8%]) were selected from an ongoing breeding program and then clonally propagated for further experimental use.

MATERIALS AND METHODS

GC-MS, GC-FID, and HPLC-PDA were utilized to monitor the fluctuation of secondary metabolites at four phenological stages (vegetative, bud burst, early, and full-flowering stages). The highest phytochemical divergence was observed at early flowering stage. Both genotypes were subjected to mRNA sequencing (approximately 100 million paired reads) at the aforementioned stage. The expression patterns of four key genes involved in the biosynthesis of terpenoids were also validated using qRT-PCR.

RESULTS

Carvacrol content in 'Zagheh-11' (26.13%) was approximately 23 times higher than 'Malayer-21' (1.12%). Reciprocally, about 10% higher thymol was found in 'Malayer-21' (62.15%). Moreover, the concentrations of three major triterpenic acids in 'Zagheh-11' were approximately as twice as those found in 'Malayer-21'. Transcriptome analysis revealed a total of 1840 unigenes that were differentially expressed, including terpene synthases, cytochrome P450, and terpenoid backbone genes. Several differentially expressed transcription factors (such as MYB, bZIP, HB-HD-ZIP, and WRKY families) were also identified. These results suggest that an active cytosolic mevalonate (MVA) pathway may be linked to higher levels of sesquiterpenes, triterpenic acids, and carvacrol in 'Zagheh-11'. The chloroplastic pathway of methyl erythritol phosphate (MEP) may have also contributed to a higher accumulation of thymol in Malayer-21. Indeed, 'Zagheh-11' showed higher expression of certain genes (HMGR, CYP71D180, β-amyrin 28-monooxygenase, and sesquiterpene synthases) in the MVA pathway, while some genes in the MEP pathway (including DXR, ispG, and γ-terpinene synthase) were distinctly expressed in Malayer-21. Future efforts in metabolic engineering of MVA/MEP pathways may benefit from these findings to produce increased levels of desired secondary metabolites at commercial scale.

In silico molecular modeling, neuro-behavioral profile, and toxicity assessment of the essential oil of Ferula gummosa Boiss. as an anti-seizure agent

ETHNOPHARMACOLOGICAL RELEVANCE

Ferula gummosa Boiss., known in Persian as "Baridje," belongs to the Apiaceae family. All parts of this plant, especially the root, contain galbanum. Galbanum, the oleo-gum resin of F. gummosa, is one of the essential traditional herbal medicines in Iran, which is used as a tonic for epilepsy and chorea, memory enhancement, gastrointestinal diseases, and wound healing.

AIM OF THE STUDY

We investigated the toxicity, anticonvulsant effects, and molecular modeling of the essential oil (EO) distilled from the oleo-gum resin of F. gummosa.

MATERIALS AND METHODS

Gas chromatography-mass spectrometry was used to identify the EO components. The cytotoxicity of EO on HepG2 cell lines was assessed by the MTT method. Male mice were arranged as follows: negative control groups (sunflower oil (10 ml/kg, i.p.) or saline (10 ml/kg, p.o.)), EO groups (0.5, 1, 1.5, and 2.5 ml/kg, p.o.), and positive control groups (ethosuximide (150 mg/kg, p.o.) or diazepam (1.0 or 2 mg/kg, i.p.)). The motor coordination and neurotoxicity of EO were studied using the rota-rod test. Open-field, novel object recognition, and passive avoidance learning tests were used to investigate the effect of EO on locomotor activity and memory function. An acute pentylenetetrazole-induced seizure model was utilized to evaluate the anticonvulsant properties of the EO. The interaction of the EO main components with the GABA_A receptor was investigated by coarse-grained molecular dynamics simulations.

RESULTS

β-pinene, sabinene, α-pinene, and ρ-cymene were the main components of EO. The IC₅₀ of the EO at 24, 48, and 72 h was found to be 59.90, 12.96, and 3.93 μl/ml, respectively. No adverse effects were observed in memory, motor coordination, and locomotor activity in mice treated with EO. Administration of EO (1, 1.5, and 2.5 ml/kg) improved survival rates in mice receiving pentylenetetrazole (PTZ; to induce an epileptic seizure). Sabinene was able to bind to the binding site of benzodiazepines at the GABA_A receptor.

CONCLUSIONS

Acute treatment with the EO of F. gummosa caused antiepileptic effects and could effectively increase the survival rate in PTZ-treated mice with no significant toxicity.

Biosynthesize, physicochemical characterization and biological investigations of chitosan-Ferula gummosa essential oil (CS-FEO) nanocomposite

The bioavailability, solubility, stability, and evaporation rate of essential oils can all be improved by using appropriate nanocarriers. This study describes the simple biosynthesize, physicochemical, optical, and biological activity of Chitosan-Ferula gummosa essential oil (CS-FEO) nanocomposite. The prepared nanocomposite was evaluated by X-ray diffraction (XRD), scanning electron microscopy (SEM), energy dispersive X-ray (EDX) mapping, transmission electron microscopy (TEM), Fourier-transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA), UV-vis and photoluminescence (PL) techniques. The XRD investigation showed that crystallinity indexes of CS-FEO nanocomposite were lower than that of the pure CS and higher than nano-CS. According to SEM/TEM images, a spherical shape with a particle size distribution of around 50-250 nm for nanocomposite was obtained. PL measurement exhibited the addition of FEO caused a strong red emission. GC-MS analysis showed 40 various components in FEO. The antibacterial activity was studied using broth micro-dilution, disc diffusion, colony counts, and well agar diffusion methods against Gram-positive and Gram-negative bacteria. The results revealed that CS-FEO has stronger antibacterial activities than pure CS. It was also observed that the combined use of CS with FEO resulted in synergistic effects against studied bacteria. Obtained results imply that the CS-FEO may provide a new outlook in biomedical applications.

Plant Metabolic Network 15: A resource of genome-wide metabolism databases for 126 plants and algae

To understand and engineer plant metabolism, we need a comprehensive and accurate annotation of all metabolic information across plant species. As a step towards this goal, we generated genome-scale metabolic pathway databases of 126 algal and plant genomes, ranging from model organisms to crops to medicinal plants (https://plantcyc.org). Of these, 104 have not been reported before. We systematically evaluated the quality of the databases, which revealed that our semi-automated validation pipeline dramatically improves the quality. We then compared the metabolic content across the 126 organisms using multiple correspondence analysis and found that Brassicaceae, Poaceae, and Chlorophyta appeared as metabolically distinct groups. To demonstrate the utility of this resource, we used recently published sorghum transcriptomics data to discover previously unreported trends of metabolism underlying drought tolerance. We also used single-cell transcriptomics data from the Arabidopsis root to infer cell type-specific metabolic pathways. This work shows the quality and quantity of our resource and demonstrates its wide-ranging utility in integrating metabolism with other areas of plant biology.

Impact of Genomic and Transcriptomic Resources on Apiaceae Crop Breeding Strategies

The Apiaceae taxon is one of the most important families of flowering plants and includes thousands of species used for food, flavoring, fragrance, medical and industrial purposes. This study had the specific intent of reviewing the main genomics and transcriptomic data available for this family and their use for the constitution of new varieties. This was achieved starting from the description of the main reproductive systems and barriers, with particular reference to cytoplasmic (CMS) and nuclear (NMS) male sterility. We found that CMS and NMS systems have been discovered and successfully exploited for the development of varieties only in Foeniculum vulgare, Daucus carota, Apium graveolens and Pastinaca sativa; whereas, strategies to limit self-pollination have been poorly considered. Since the constitution of new varieties benefits from the synergistic use of marker-assisted breeding in combination with conventional breeding schemes, we also analyzed and discussed the available SNP and SSR marker datasets (20 species) and genomes (8 species). Furthermore, the RNA-seq studies aimed at elucidating key pathways in stress tolerance or biosynthesis of the metabolites of interest were limited and proportional to the economic weight of each species. Finally, by aligning 53 plastid genomes from as many species as possible, we demonstrated the precision offered by the super barcoding approach to reconstruct the phylogenetic relationships of Apiaceae species. Overall, despite the impressive size of this family, we documented an evident lack of molecular data, especially because genomic and transcriptomic resources are circumscribed to a small number of species. We believe that our contribution can help future studies aimed at developing molecular tools for boosting breeding programs in crop plants of the Apiaceae family.

Metabolic differences of two Ferula species as potential sources of galbanum: An NMR-based metabolomics study

INTRODUCTION

Ferula gummosa Boiss. and Ferula galbaniflua Boiss. & Buhse (Apiaceae) are two important Iranian plants that are considered as potential sources of galbanum (barijeh). Galbanum is traditionally used for treating different diseases including flatulence and memory impairment.

OBJECTIVE

According to a phylogenetic analysis of the nrDNA ITS sequence and the Flora Iranica, F. gummosa has been considered as a synonym of F. galbaniflua. However, F. galbaniflua and F. gummosa grow in two different geographical locations and have different metabolic patterns. Some researchers believe that F. gummosa and F. galbaniflua are two distinct species. To discriminate these species, we compared metabolic profiles of F. gummosa and F. galbaniflua samples.

METHODS

¹ H-NMR-based metabolomics analysis was used for classification of F. gummosa and F. galbaniflua samples collected from northeast Iran. The acquired data were analyzed using hierarchical cluster analysis (HCA), partial least squares discriminant analysis (PLS-DA) and orthogonal projection to latent structures discriminant analysis (OPLS-DA).

RESULTS

The result showed a clear separation between the two species that may be related to the quantity and diversity of their metabolites. Ferula gummosa had higher mogoltacin levels, while F. galbaniflua had higher feselol levels. Ligupersin A and conferdione were significantly detected in F. gummosa, whereas sterol compounds were significantly detected in F. galbaniflua.

CONCLUSION

Our findings indicate that clear metabolomics discrimination of F. gummosa and F. galbaniflua makes their chemotaxonomic classification possible.

CRISPR-based metabolic editing: Next-generation metabolic engineering in plants

Plants generate many secondary metabolites, so called phyto-metabolites, which can be used as toxins, dyes, drugs, and insecticides in bio-warfare plus bio-terrorism, industry, medicine, and agriculture, respectively. To 2013, the first generation metabolic engineering approaches like miRNA-based manipulation were widely adopted by researchers in biosciences. However, the discovery of the clustered regularly interspaced short palindromic repeat (CRISPR) genome editing system revolutionized metabolic engineering due to its unique features so that scientists could manipulate the biosynthetic pathways of phyto-metabolites through approaches like miRNA-mediated CRISPR-Cas9. According to the increasing importance of the genome editing in plant sciences, we discussed the current findings on CRISPR-based manipulation of phyto-metabolites in plants, especially medicinal ones, and suggested the ideas to phyto-metabolic editing.

The volatile oils from the oleo-gum-resins of Ferula assa-foetida and Ferula gummosa: A comprehensive investigation of their insecticidal activity and eco-toxicological effects

Since time immemorial, the oleo-gum-resins of Ferula assa-foetida and F. gummosa are used in the traditional medical systems as well as in foodstuffs, perfumery and cosmetics. In the present study, we explored the insecticidal efficacy of the essential oils obtained from these oleo-gum-resins to widen their fields of industrial applications. The two essential oils were mainly composed of sulfides [sec-butyl (Z)-propenyl disulfide, sec-butyl (E)-propenyl disulfide, sec-butyl (Z)-propenyl trisulfide and sec-butyl (E)-propenyl trisulfide)] and monoterpenes (α-pinene, β-pinene and β-phellandrene), respectively, as determined by GC-MS analysis. The two essential oils were assayed for toxicity on a panel of insects, represented by species of public health relevance (Culex quinquefasciatus and Musca domestica), agricultural (Spodoptera littoralis) and stored-product pests (Prostephanus truncatus and Trogoderma granarium). The ecotoxicological effects of the essential oils were assessed on the aquatic microcrustacean Daphnia magna and the earthworm Eisenia fetida, as well as on human cells. Overall, the two essential oils were effective against important insect pests and vectors. On the other hand, they resulted cytotoxic to fibroblasts and non-target aquatic microcrustaceans. Thus, further insights are needed to determine the full spectrum of their eco-toxicological effects.

Phyto-miRNAs-based regulation of metabolites biosynthesis in medicinal plants

Medicinal plants, are known to produce a wide range of plant secondary metabolites (PSMs) applied as insecticides, drugs, dyes and toxins in agriculture, medicine, industry and bio-warfare plus bio-terrorism, respectively. However, production of PSMs is usually in small quantities, so we need to find novel ways to increase both quantity and quality of them. Fortunately, biotechnology suggests several options through which secondary metabolism in plants can be engineered in innovative ways to: 1) over-produce the useful metabolites, 2) down-produce the toxic metabolites, 3) produce the new metabolites. Among the ways, RNA interference (RNAi) technology which involves gene-specific regulation by small non-coding RNAs (sncRNAs) have been recently emerged as a promising tool for plant biotechnologist, not only to decipher the function of plant genes, but also for development of the plants with improved and novel traits through manipulation of both desirable and undesirable genes. Among sncRNAs, miRNAs have been recorded various regulatory roles in plants such as development, signal transduction, response to environmental stresses, metabolism. Certainly, the use of miRNAs in metabolic engineering requires identification of miRNAs involved in metabolites biosynthesis, understanding of the biosynthetic pathways, as well as the identification of key points of the pathways in which the miRNAs have their own effect. Thus, we firstly consider these three issues on metabolic engineering of medicinal plants. Our review shows, application of miRNAs can open a novel perspective to metabolic engineering of medicinal plants.

Candidate genes of flavonoid biosynthesis in Selaginella bryopteris (L.) Baker identified by RNA-Seq

In the present study, de novo transcriptome analysis of Selaginella bryopteris in frond and root was performed to understand the regulation of flavonoid (FL) biosynthesis. High-quality data of 5.84 and 5.86 Gb was generated for frond and root, respectively, that assembled into 94,713 and 81,567 transcripts. A total of 87,471 and 73,395 unigenes were obtained from frond and root, respectively. A total of 41,267 and 31,048 CDS of frond and root, respectively, were annotated by BLASTX, which showed maximum hits against S. moellendorffii. Out of 11,285 differentially expressed genes, a total of 5639 genes were found to be down-regulated and 5628 genes up-regulated in frond as compared to those in root. In silico analysis of expression of genes in frond as compared to that in root was done for those related to phenylpropanoid (PP)/FL biosynthesis along with transcription factors (TFs) after DESeq and MapMan-based information. Results showed that genes of PP/FL biosynthesis pathway namely SbCHS, SbCHI, SbF3H, SbF3'H, SbDFR, SbUF3GT, SbCCOAMT, and SbCATOMT and TFs (SbMYB1, SbMYB2, SbMYB3, SbBHLH1, and SbWD40-5) were up-regulated in frond in comparison to those in root. Further, this in silico expression data was validated by RT-PCR analysis which showed predominant expression of most of these genes in frond and indicated their importance in the biosynthesis of flavonoids in S. bryopteris. A total of 9074 simple sequence repeats (SSRs) were also identified for frond and 3811 SSRs for root; these can be used for experimental validation.