Transcriptome Landscape Variation in the Genus Thymus

In vitro investigations of biological activities of Thymus willdenowii and Thymus atlanticus polyphenol-rich extracts

Thyme species produce a wide variety of phenolic compounds including tannins, phenolic acids, and flavonoids. Thymus atlanticus (T. atlanticus) and Thymus willdenowii (T. willdenowii) are important thyme species in the southeast of Morocco, with numerous biological properties. The polyphenolic extracts of these two thyme species were obtained using ethanol through Soxhlet apparatus. Antioxidant (DPPH, FRAP, and TAC methods), antihemolytic (2,2'-Azobis(2-amidinopropane) dihydrochloride (AAPH) induced hemolysis test), hypolipidemic (3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase activity inhibition test), and anti-inflammatory (protein denaturation inhibition) effects of extracts were carried out using in vitro methods. The results showed that the polyphenolic extracts of these two species revealed important amounts of phenolic compounds. The contents of flavonoids were significant in the two species, while the contents of tannins and anthocyanin were very low. T. atlanticus showed an important antioxidant activity and a considerable antihemolytic effect in AAPH-induced hemolysis test (IC50 = 0.29 mg/mL), while T. willdenowii showed an important anti-inflammatory activity in heat-induced protein denaturation test (IC50 = 1.61 mg/mL). Moreover, both extracts at a dose of 20 µg/mL showed an important in vitro hypolipidemic activity by inhibiting HMG-CoA reductase activity (T. willdenowii: 51.16 %; T. atlanticus: 62.83 %). In conclusion, T. willdenowii and T. atlanticus extracts have considerable antioxidant, antihemolytic, hypolipidemic, and anti-inflammatory effects. The richness of these species in polyphenols gives them a large specter of biological properties, making them a valuable source of natural bioactive compounds that could prevent or treat various diseases.

DNA Barcoding Study of Representative Thymus Species in Bulgaria

We present a study on the taxonomy of eleven Thymus species, belonging to two sections and occurring naturally in Bulgaria. Four DNA barcoding markers—matK, rbcL, trnH-psbA and ITS—were applied to discriminate the species and to reveal their phylogenetic relationships. The results showed that rbcL has the lowest discriminating power regarding the studied species, while the other markers yielded results fitting better to the existing taxonomic schemes based on morphological traits. However, even in the case of better performing markers, the results were not straightforward—morphologically distinct species belonging to different sections were grouped together, and closely related species appeared genetically distinct. The results are typical for taxonomically complex groups, such as the genus Thymus, characterized in Bulgaria with great diversity, high percentage of endemism and still requiring a full and comprehensive taxonomic study. The results are discussed in the light of unresolved taxonomic problems and application of DNA barcoding methods.

Extraction Processes Affect the Composition and Bioavailability of Flavones from Lamiaceae Plants: A Comprehensive Review

Lamiaceae plants are a widespread family of herbaceous plants with around 245 plant genera and nearly 22,576 species distributed in the world. Some of the most representative and widely studied Lamiaceae plants belong to the Ocimum, Origanum, Salvia, and Thymus genera. These plants are a rich source of bioactive molecules such as terpenes, flavonoids, and phenolic acids. In this sense, there is a subgroup of flavonoids classified as flavones. Flavones have antioxidant, anti-inflammatory, anti-cancer, and anti-diabetic potential; thus, efficient extraction techniques from their original plant matrixes have been developed. Currently, conventional extraction methods involving organic solvents are no longer recommended due to their environmental consequences, and new environmentally friendly techniques have been developed. Moreover, once extracted, the bioactivity of flavones is highly linked to their bioavailability, which is often neglected. This review aims to comprehensively gather recent information (2011–2021) regarding extraction techniques and their important relationship with the bioavailability of flavones from Lamiaceae plants including Salvia, Ocimum, Thymus, and Origanum.

Transcriptome and phytochemical analyses provide insights into the organic sulfur pathway in Allium hirtifolium

Allium is one of the well-known genera of the Amaryllidaceae family, which contains over 780 species. Onions, garlic, leeks, and shallots are the most important species of this genus. Allium hirtifolium (shallot) is a rich source of proteins, carbohydrates, lipids, amino acids, and bioactive compounds such as organic sulfur compounds with an expansive range of biological activities and medicinal attributes. To identify the putative compounds and genes involved in the organic sulfur pathway, we applied GC-MS and RNA-seq techniques for the bulb, stem, and flower tissues of A. hirtifolium. The essential oil analysis revealed the maximum amount of sulfur compounds in stem against flower and bulb tissues. Transcriptome profiling showed 6155, 6494, and 4259 DEGs for bulb vs. flower, bulb vs. stem, and flower vs. stem, respectively. Overall, more genes were identified as being up-regulated rather than down-regulated in flower tissue compared to the stem and bulb tissues. Our findings in accordance with other results from different papers, suggest that carbohydrates are vital to bulb formation and development because a high number of identified DEGs (586 genes) were mapped to carbohydrate metabolism. This study has detected the genes in the organic sulfur pathway and indicated that the alliinase gene shows a high variability among different tissues. In general, this study formed a useful genomic resource data to explore tissue-specific sulfur pathway in A. hirtifolium, which is helpful for functional breeding.

Screening and Analysis of Hypolipidemic Components from Shuangdan Capsule Based on Pancreatic Lipase

Background:

Some natural pancreatic lipase inhibitors with fewer side effects are proposed. As a traditional Chinese medicine, Shuangdan Capsule (SDC) has been used for the treatment of higher lipid in blood, which is mainly composed by Radix Salviae and Peony skin.

Objective:

This work is aimed to investigate the molecular mechanism of the constituents from this SDC against metabolic disorders, the molecular flexibility and intermolecular interactional characteristics of these components in the active sites.

Methods:

The small molecules were obtained from the Traditional Chinese Medicine Database TCM database, the systems-level pharmacological database for Traditional Chinese Medicine TCMSP server was used to calculate the ADME-related properties. Autodock Vina was used to perform virtual screening of the selected molecules and to return energy values in several ligand conformations. The network parameters were calculated using the network analyzer plug-in in Cytoscape.

Results:

The most active six molecules are all enclosed by amino acids ASP79, TYR114, GLU175, PRO180, PHE215, GLY216 and LUE264, among which, hydrophobic interaction, hydrogen bond and repulsive forces play extremely important roles. It is worth noting that most of the local minima of molecular electrostatic potentials on van der Waals (vdW) surface are increased while the maxima negative ones are decreased simultaneously, implying that the electrostatic potential tends to be stable. From the topological analysis of the Protein-Protein Interaction (PPI) network, PNLIP related genes are also proved to be pivotal targets for hyperlipidemia, such as LPL, AGK, MGLL, LIPE, LIPF and PNPLA2. Further GO analysis indicated that lipophilic terpenoid compounds may reduce the blood lipid by taking part in the lipid catabolic process, the extracellular space and the cellular components of the extracellular region part and the triacylglycerol lipase activity.

Conclusion:

This study provides some useful information for the development and application of natural hypolipidemic medcines. Further pharmacologically active studies are still needed both in vivo and in vitro.

Thymus zygis subsp. zygis an Endemic Portuguese Plant: Phytochemical Profiling, Antioxidant, Anti-Proliferative and Anti-Inflammatory Activities

Thymus zygis subsp. zygis is an endemic Portuguese plant belonging to the Thymus zygis species. Although T. zygis is commonly used as a condiment and as a medicinal herb, a detailed description of the polyphenol composition of hydroethanolic (HE) and aqueous decoction (AD) extracts is not available. In this work, we describe for the first time a detailed phenolic composition of Thymus zygis subsp. zygis HE and AD extracts, together with their antioxidant, anti-proliferative and anti-inflammatory activities. Unlike other Thymus species, T. zygis subsp. zygis extracts contain higher amounts of luteolin-(?)-O-hexoside. However, the major phenolic compound is rosmarinic acid, and high amounts of salvianolic acids K and I were also detected. T. zygis subsp. zygis extracts exhibited significant scavenging activity of ABTS⁺, hydroxyl (^•OH), and nitric oxide (NO) radicals. Regarding the anti-proliferative/cytotoxic effect, tested against Caco-2 and HepG2 cells, the AD extract only slightly reduced cell viability at higher concentrations (IC₅₀ > 600 µg/mL, 48 h exposure), denoting very low toxicity, while the HE extract showed a high anti-proliferative effect, especially at 48 h exposure (IC₅₀ of 85.01 ± 15.10 μg/mL and 82.19 ± 2.46 μg/mL, for Caco-2 and HepG2, respectively). At non-cytotoxic concentrations, both extracts reduced the nitric oxide (NO) release by lipopolysaccharide (LPS)-stimulated RAW 264.7 cells (at 50 μg/mL, HE and AD extracts inhibited NO release in ~89% and 48%, respectively). In conclusion, the results highlight the non-toxic effect of aqueous extracts, both resembling the consumption of antioxidants in foodstuff or in functional food. Furthermore, the HE extract of T. zygis subsp. zygis is a source of promising molecules with antioxidant, anti-inflammatory and anticancer activities, highlighting its potential as a source of bioactive ingredients for nutraceutical and pharmaceutical industries.

Transcriptome profiling of spike provides expression features of genes related to terpene biosynthesis in lavender

Lavender (Lavandula angustifolia) is an important economic plant because of the value of its essential oil (EO). The Yili Valley in Xinjiang has become the largest lavender planting base in China. However, there is a lack of research on the gene expression regulation of EO biosynthesis and metabolism in local varieties. Here, de novo transcriptome analysis of inflorescence of three development stages from initial flower bud to flowering stage 50% from two lavender cultivars with contrasting EO production revealed the dynamics of 100,177 differentially expressed transcripts (DETs) in various stages of spike development within and across the cultivars. The lavender transcriptome contained 77 DETs with annotations related to terpenoid biosynthesis. The expression profiles of the 27 genes involved in the methylerythritol phosphate (MEP) pathway, 22 genes in the mevalonate (MVA) pathway, 28 genes related to monoterpene and sesquiterpene biosynthesis during inflorescence development were comprehensively characterized, and possible links between the expression changes of genes and contents of EO constituents were explored. The upregulated genes were mainly concentrated in the MEP pathway, while most genes in the MVA pathway were downregulated during flower development, and cultivars with a higher EO content presented higher expression of genes in the MEP pathway, indicating that EOs were chiefly produced through the MEP pathway. Additionally, MYB transcription factors constituted the largest number of transcripts in all samples, suggesting their potential roles in regulating EO biosynthesis. The sequences and transcriptional patterns of the transcripts will be helpful for understanding the molecular basis of lavender terpene biosynthesis.

Sequencing and variation of terpene synthase gene (TPS2) as the major gene in biosynthesis of thymol in different Thymus species

Thyme (Thymus spp.) is a valuable genus of Lamiaceae family with different pharmaceutical and food properties. Thymol has also been considered as the major essential oil compound in most of the studied Thymus species. In this research, the gene encoding γ-terpinene synthase (Ttps2) was sequenced in T. vulgaris and in eight Iranian thymes including T. carmanicus, T. daenensis, T. fedtschenkoi, T. kotschyanus, T. migricus, T. pubescens, T. serpyllum, and T. trautvetteri. Genetic relationships based on terpene synthase genes were also determined among the studied species. Rapid Amplification of cDNA Ends (RACE) PCR was done to complete the sequence of all species. The cDNA of the studied species possessed an open reading frame ranging from 1788 to 1794 bp that encode for a protein of 596-598 amino acids, presenting all the conserved motifs characteristics of monoterpene synthases. The taxonomic status of Thymus species was determined based on eight reported sections. The species were classified in three major groups. The first and second group comprised species of Micantes and Mastichina sections. The third cluster included the species belonging to Serpyllum and Pseudothymbra sections. Overall, phylogenetic analysis according to whole sequence of Ttps2 gene can help providing insights in respect to its evolutionary process. Finally, clustering based on the amount of main essential oils components (thymol and carvacrol) was compared with that based on Ttps2 gene classification in the studied Thymus species, showing that clustering is not always in accordance.