Isatis indigotica: from (ethno) botany, biochemistry to synthetic biology

Absorption, distribution, metabolism, and excretion (ADME) of R,S-Goitrin in Radix Isatidis in rats by LC-MS/MS determination

Radix Isatidis (syn. Isatis indigotica Fort.) is employed in the treatment of fever, influenza, acute tonsillitis, viral hepatitis, and COVID-19, demonstrating diverse pharmacological activities, including antibacterial, antiviral, antioxidant, anticancer, and immune-regulatory effects. Furthermore, there is significant potential for the development of new clinical applications. In order to investigate the pharmacokinetic characteristics, a quantitative method for determining R,S-goitrin in rat plasma using liquid chromatography-tandem mass spectrometry (LC-MS/MS) was developed and validated. The established LC-MS/MS method was employed to investigate the pharmacokinetics, tissue distribution, plasma protein binding, excretion, and metabolic characteristics of Radix Isatidis extract following oral administration in rats. Meanwhile, by comparing with the oral monomer group, the absorption profile of the extract in rats was assessed. After oral administration of different doses of Radix Isatidis extract (0.1,0.3,1 g/kg) to male rats, showed dose-dependent increases in R,S-goitrin's Cmax and AUC, with bioavailability at 56.33 %. No gender differences in pharmacokinetics (PK) were observed. Compared with the monomer R,S-goitrin (0.03 mg/kg), it was observed higher in vivo exposure AUC(0-t) and peak concentration Cmax of R,S-goitrin after dosing of the Radix Isatidis extract with equal dosage of R,S-goitrin. R,S-goitrin was widely distributed in immune organs (adrenal glands, thymus, lymph nodes), liver, spleen, and gastrointestinal tract after oral administration of Radix Isatidis extract (0.1 g/kg) in rats. R,S-goitrin was primarily excreted via urine, accounting for 56 % of the administered dose, with plasma protein binding ranging from 13 % to 16.4 % across different species. These findings provide data to support Radix Isatidis clinical use in antibacterial, anti-inflammatory, anticancer therapies, and formulation development.

Genetic Analysis and Fingerprint Construction for Isatis indigotica Fort. Using SSR Markers

Isatis indigotica Fort. is a traditional medicinal plant, which has anti-inflammatory, antioxidant, and antiviral properties. Despite the development and licensing of several cultivars in recent years, morphological similarity among cultivars complicates their identification. The genetic diversity within I. indigotica significantly impacts the biosynthesis of bioactive substances. To elucidate genetic relationships and evaluate bioactive compounds, I. indigotica cultivars were analyzed using SSR markers. A total of 109 alleles were identified across 29 cultivars at 20 SSR loci, exhibiting a genetic diversity with an average polymorphic information content (PIC) of 0.46. Phylogenetic, principal coordinate analysis (PCoA), and Bayesian clustering revealed that genetic relationships were largely independent of geographic origin, potentially due to regional transplantations. Notably, some cultivars with distinct leaf sizes showed clear genetic differentiation, highlighting their potential as candidates for quality evaluation. A fingerprint was successfully constructed using five SSR markers. These findings provide technical support for cultivar identification, quality evaluation, and intellectual property protection of I. indigotica cultivars.

Chromosome-level genome assembly of the tetraploid medicinal and natural dye plant Persicaria tinctoria

Persicaria tinctoria (2n = 40) is an important traditional medicinal plant and natural dye source within the genus Persicaria. P. tinctoria has been utilized for its antibacterial, antiviral, anti-inflammatory, and tumor treatment properties. Additionally, it has served as a natural blue dye for thousands of years worldwide, and continues to be used in countries such as China and Japan. Here, we assembled a tetraploid chromosome-scale genome of P. tinctoria, organized into two subgenomes: subgenome A, which contains 10 pseudochromosomes with a genome size of 888.67 Mb and a scaffold N50 of 90.56 Mb, and subgenome B, which also comprises 10 pseudochromosomes with a genome size of 771.58 Mb and a scaffold N50 of 76.84 Mb. Repeat sequences constitute 77.9% of the genome. A total of 76,742 high-confidence protein-coding genes were annotated, with 94.28% of these genes assigned functional annotations. This high-quality genome assembly of P. tinctoria will provide valuable genomic resources for studying the biosynthesis and evolution of indigoids in indigo plants, as well as for further research on the Polygonaceae family.

Multi-omics analysis on the mechanism of the effect of Isatis leaf on the growth performance of fattening sheep

Introduction

This study evaluated the effects of Isatis Leaf (ISL) on the growth performance, gastrointestinal tissue morphology, rumen and intestinal microbiota, rumen, serum and urine metabolites, and rumen epithelial tissue transcriptome of fattening sheep.

Methods

Twelve 3.5-month-old healthy fattening sheep were randomly divided into two groups, each with 6 replicates, and fed with basal diet (CON) and basal diet supplemented with 80 g/kg ISL for 2.5 months. Gastrointestinal tract was collected for histological analysis, rumen fluid and feces were subjected to metagenomic analysis, rumen fluid, serum, and urine for metabolomics analysis, and rumen epithelial tissue for transcriptomics analysis.

Results

The results showed that in the ISL group, the average daily gain and average daily feed intake of fattening sheep were significantly lower than those of the CON group (P < 0.05), and the rumen ammonia nitrogen level was significantly higher than that of the CON group (P < 0.01). The thickness of the reticulum and abomasum muscle layer was significantly increased (P < 0.05). At the genus level, the addition of ISL modified the composition of rumen and fecal microorganisms, and the relative abundance of Methanobrevibacter and Centipeda was significantly upregulated in rumen microorganisms, The relative abundance of Butyrivibrio, Saccharofermentans, Mogibacterium, and Pirellula was significantly downregulated (P < 0.05). In fecal microorganisms, the relative abundance of Papillibacter, Pseudoflavonifractor, Butyricicoccus, Anaerovorax, and Methanocorpusculum was significantly upregulated, while the relative abundance of Roseburia, Coprococcus, Clostridium XVIII, Butyrivibrio, Parasutterella, Macellibacteroides, and Porphyromonas was significantly downregulated (P < 0.05). There were 164, 107, and 77 different metabolites in the rumen, serum, and urine between the ISL and CON groups (P < 0.05). The differential metabolic pathways mainly included thiamine metabolism, niacin and nicotinamide metabolism, vitamin B6 metabolism, taurine and taurine metabolism, beta-Alanine metabolism and riboflavin metabolism. These metabolic pathways were mainly involved in the regulation of energy metabolism and immune function in fattening sheep. Transcriptome sequencing showed that differentially expressed genes were mainly enriched in cellular physiological processes, development, and immune regulation.

Conclusion

In summary, the addition of ISL to the diet had the effect of increasing rumen ammonia nitrogen levels, regulating gastrointestinal microbiota, promoting body fat metabolism, and enhancing immunity in fattening sheep.

Mass Spectrometry Rearrangement Ions and Metabolic Pathway-Based Discovery of Indole Derivatives during the Aging Process in Citrus reticulata 'Chachi'

The rapid analysis and characterization of compounds using mass spectrometry (MS) may overlook trace compounds. Although targeted analysis methods can significantly improve detection sensitivity, it is hard to discover novel scaffold compounds in the trace. This study developed a strategy for discovering trace compounds in the aging process of traditional Chinese medicine based on MS fragmentation and known metabolic pathways. Specifically, we found that the characteristic component of C. reticulata 'Chachi', methyl N-methyl anthranilate (MMA), fragmented in electrospray ionization coupled with collision-induced dissociation (CID) to produce the rearrangement ion 3-hydroxyindole, which was proven to exist in trace amounts in C. reticulata 'Chachi' based on comparison with the reference substance using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Combining the known metabolic pathways of 3-hydroxyindole and the possible methylation reactions that may occur during aging, a total of 10 possible indole derivatives were untargeted predicted. These compounds were confirmed to originate from MMA using purchased or synthesized reference substances, all of which were detected in C. reticulata 'Chachi' through LC-MS/MS, achieving trace compound analysis from untargeted to targeted. These results may contribute to explaining the aging mechanism of C. reticulata 'Chachi', and the strategy of using the CID-induced special rearrangement ion-binding metabolic pathway has potential application value for discovering trace compounds.

Exploring the pharmacological aspects of natural phytochemicals against SARS-CoV-2 Nsp14 through an in silico approach

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), possesses an important bifunctional nonstructural protein (nsp14) with a C-terminal N7-methyltransferase (N7-MTase) domain and an N-terminal domain with exoribonuclease (ExoN) activity that is required for maintaining high-fidelity viral replication. Viruses use the error-prone replication mechanism, which results in high mutation rates, to adapt quickly to stressful situations. The efficiency with which nsp14 removes mismatched nucleotides due to the presence of ExoN activity protects viruses from mutagenesis. We investigated the pharmacological role of the phytochemicals (Baicalein, Bavachinin, Emodin, Kazinol F, Lycorine, Sinigrin, Procyanidin A2, Tanshinone IIA, Tanshinone IIB, Tomentin A, and Tomentin E) against the highly conserved nsp14 protein using docking-based computational analyses in search of new potential natural drug targets. The selected eleven phytochemicals failed to bind the active site of N7-Mtase in the global docking study, while the local docking study identified the top five phytochemicals with high binding energy scores ranging from - 9.0 to - 6.4 kcal/mol. Procyanidin A2 and Tomentin A showed the highest docking score of - 9.0 and - 8.1 kcal/mol, respectively. Local docking of isoform variants was also conducted, yielding the top five phytochemicals, with Procyanidin A1 having the highest binding energy value of - 9.1 kcal/mol. The phytochemicals were later tested for pharmacokinetics and pharmacodynamics analysis for Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) which resulted in choosing Tomentin A as a potential candidate. The molecular dynamics simulations studies of nsp14 revealed significant conformational changes upon complex formation with the identified compound, implying that these phytochemicals could be used as safe nutraceuticals which will impart long-term immunological competence in the human population against CoVs.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s40203-023-00143-7.

Identification and investigation of a novel NADP+-dependent secoisolariciresinol dehydrogenase from Isatis indigotica

Cofactors are crucial for the biosynthesis of natural compounds, and cofactor engineering is a useful strategy for enzyme optimization due to its potential to enhance enzyme efficiency. Secoisolariciresinol dehydrogenase (SIRD) was reported to convert secoisolariciresinol into matairesinol in an NAD+-dependent reaction. Here, a SIRD designated as IiSIRD2 identified from Isatis indigotica was found to utilize NADP+ as the cofactor. To explore the structural basis for this unique cofactor preference, model-based structural analysis was carried out, and it was postulated that a variation at the GXGGXG glycine-rich motif of IiSIRD2 alters its cofactor preference. This study paves way for future investigations on SIRD cofactor specificity and cofactor engineering to improve SIRD's catalytic efficiency.