Combined Analysis of Transcriptome and Metabolome Reveals the Potential Mechanism of the Enantioselective Effect of Chiral Penthiopyrad on Tomato Fruit Flavor Quality

Metabolomics as a Tool for Unraveling the Impact of Enantioselectivity in Cellular Metabolism

Metabolomics is an emerging interdisciplinary field focused on the comprehensive analysis of all metabolites within biological samples, making it valuable for areas such as drug development, and environmental analysis. Many compounds, including pharmaceuticals and agrochemicals that have been extensively studied by metabolomics are chiral. The intrinsic chirality of biological targets can lead to a selective recognition of enantiomers resulting in distinct pharmacokinetic, pharmacodynamic and/or toxicological profiles (enantioselectivity). Given that metabolomics captures an instant snapshot of an organism's metabolic state, it serves as a powerful tool to investigate chiral compounds and understand enantioselective effects. Herein, a systematic compilation of scientific literature was performed and 48 enantioselectivity studies using metabolomics were selected. These studies revealed an increasing focus on chiral pesticides (77%), the use of animal models (59%), reliance on LC-MS techniques (52%), and predominantly untargeted approaches (83%). Enantioselective effects were described in most studies. This review describes significant advances in this emerging field and highlights the use of metabolomics to unravel the role of stereochemistry in cellular metabolism by the examination of enantiomer-specific metabolic effects. Furthermore, it elucidates enantioselectivity mechanism that can be further applied to other groups of chiral compounds.

Transcriptomic and Metabolomic Analyses Provide Insights Into the Flavonoid Biosynthesis in Dangshen

INTRODUCTION

Dangshen (DS) has been used for hundreds of years as a traditional Chinese medicine. It has a wide range of biological activities. Flavonoids are one of the important bioactive components with strong free radical scavenging and antioxidant capacity in DS. However, the biosynthesis process of flavonoids in DS remains unclear.

OBJECTIVE

The aim of this study was to understand the biosynthesis molecular mechanism of flavonoids in DS.

METHODS

In this study, metabolomics research and transcriptome sequencing for DS were carried out. Transcript and metabolite profiles were generated by high-throughput RNA sequencing (RNA-seq) data analysis and liquid chromatography-tandem mass spectrometry, respectively.

RESULTS

In total, 256 metabolites were identified in the root, stem, leaf, and flower of DS using untargeted metabolomics. Among them, 55 flavonoids, including pinobanksin, butein, fustin, pelargonidin, apigenin, luteolin, and eriodictyol, were closely related to flavonoid metabolism, and most of them were upregulated in different tissues of DS. Furthermore, the differentially expressed genes identified by transcriptomics were mainly enriched in the biosynthesis of flavonoid, isoflavonoid, flavone, and flavonol. A number of genes, including ANS, CCOAOMT, CHI, CHS, CYP75B1, CYP75A, CYP93B2_16, CYP98A/C3'H, DFR, F3H, FLS, and HCT, may regulate the production of flavonoids in different tissues of DS. An integrated analysis of transcriptome and metabolome revealed the flavonoid biosynthetic network in DS and elucidated the diversity of flavonoid biosynthetic pathway in roots, stems, leaves, and flowers of DS.

CONCLUSION

Our findings provide a molecular basis and new insights into flavonoid biosynthesis in DS and lay the foundation for breeding new valuable DS cultivars.

Assessing the stereoselective bioactivity and biotoxicity of penthiopyrad in soil environment for efficacy improvement and hazard reduction

Penthiopyrad, a chiral pesticide, has been widely used in agricultural production. However, systematic evaluation of stereoselective bioactivity and biotoxicity of penthiopyrad in soil environment is insufficient. In this study, the stereoselective bioactivity of penthiopyrad against three soil-borne disease pathogens and its stereoselective biotoxicity to soil non-target organisms were investigated. The present results showed that the bioactivities of S-penthiopyrad were 546, 76 and 1.1-fold higher than those of R-penthiopyrad due to their different interaction modes with SDH in different target pathogens. S-penthiopyrad was more persistent in the soil environment and had stronger bioaccumulation than R-penthiopyrad. The accumulation of penthiopyrad in earthworms induced the response of detoxification system, resulting in the significant increases in the activity of detoxifying enzymes, such as GST, CarE, and CYP450. Additionally, both S-penthiopyrad and R-penthiopyrad induced cell apoptosis, intestinal damage and differentially expressed genes in earthworms, especially S-penthiopyrad. Furthermore, S-penthiopyrad has stronger binding capacity with COL6A and ACE proteins, while R-penthiopyrad has stronger binding capacity with CYP450 family proteins, which may be the main reason for the differences in biotoxicity between PEN enantiomers. Considering the differences in bioactivity and biotoxicity of penthiopyrad enantiomers, as well as the modes of action of pesticides on target and non-target organisms, S-penthiopyrad has greater potential for future development.

LC-MS and GC-MS Metabolomics Analyses Revealed That Different Exogenous Substances Improved the Quality of Blueberry Fruits under Soil Cadmium Toxicity

Exogenous substances (ESs) can regulate plant growth and respond to environmental stress, but the effects of different ESs on blueberry fruit quality under soil cadmium (Cd) toxicity and related metabolic mechanisms are still unclear. In this study, four ES treatments [salicylic acid (SA), spermidine (Spd), 2,4-epibrassinolide (EBR), and melatonin (MT)] significantly increased blueberry fruit size, single-fruit weight, sweetness, and anthocyanin content under soil Cd toxicity and effectively reduced fruit Cd content to safe consumption levels by promoting mineral uptake (Ca, Mg, Mn, Cu and Zn). Furthermore, a total of 445, 360, 429, and 554 differentially abundant metabolites (DAMs) (LC-MS) and 63, 48, 79, and 73 DAMs (GC-MS) were identified from four comparison groups (SA/CK, Spd/CK, EBR/CK and MT/CK), respectively. The analyses revealed that ESs improved blueberry fruit quality and tolerance to Cd toxicity mainly by regulating the changes in metabolites related to ABC transporters, the TCA cycle, flavonoid biosynthesis, and phenylpropanoid biosynthesis.

Development of S-penthiopyrad for bioactivity improvement and risk reduction from the systemic evaluation at the enantiomeric level

For the purpose of screening high-efficiency and low-risk green pesticides, a systematic study on fungicide penthiopyrad was conducted at the enantiomeric level. The bioactivity of S-(+)-penthiopyrad (median effective concentration (EC50), 0.035 mg/L) against Rhizoctonia solani was 988 times higher than R-(-)-penthiopyrad (EC50, 34.6 mg/L), which would reduce 75% usage of rac-penthiopyrad under the same efficacy. Furthermore, their antagonistic interaction (toxic unit (TUrac), 2.07) indicated the existence of R-(-)-penthiopyrad would reduce the fungicidal activity of S-(+)-penthiopyrad. AlphaFold2 modeling and molecular docking illustrated that S-(+)-penthiopyrad had the higher binding ability with the target protein than R-(-)-penthiopyrad, showing higher bioactivity. For model organism Danio rerio, S-(+)-penthiopyrad (median lethal concentrations (LC50), 3.02 mg/L) and R-(-)-penthiopyrad (LC50, 4.89 mg/L) were both less toxic than rac-penthiopyrad (LC50, 2.73 mg/L), and the existence of R-(-)-penthiopyrad could synergistically enhance the toxicity of S-(+)-penthiopyrad (TUrac, 0.73), using S-(+)-penthiopyrad would reduce at least 23% toxicity to fish. The enantioselective dissipation and residues of rac-penthiopyrad were tested in three kinds of fruits, and their dissipation half-lives ranged from 1.91 to 23.7 d. S-(+)-penthiopyrad was dissipated preferentially in grapes, which was R-(-)-penthiopyrad in pears. On the 60th d, the residue concentrations of rac-penthiopyrad in grapes were still higher than its maximum residue limit (MRL), but the initial concentrations were lower than their MRL values in watermelons and pears. Thus, more tests in different cultivars of grapes and planting environments should be encouraged. Based on the acute and chronic dietary intake risk assessments, the risks in the three fruits were all acceptable. In conclusion, S-(+)-penthiopyrad is a high-efficiency and low-risk alternative to rac-penthiopyrad.

Integrated Analysis of Transcriptome and Metabolome Provides Insight into Camellia oleifera Oil Alleviating Fat Accumulation in High-Fat Caenorhabditis elegans

Camellia oil (CO) is a high medicinal and nutritional value edible oil. However, its ability to alleviate fat accumulation in high-fat Caenorhabditis elegans has not been well elucidated. Therefore, this study aimed to investigate the effect of CO on fat accumulation in high-fat C. elegans via transcriptome and metabolome analysis. The results showed that CO significantly reduced fat accumulation in high-fat C. elegans by 10.34% (Oil Red O method) and 11.54% (TG content method), respectively. Furthermore, CO primarily altered the transcription levels of genes involved in longevity regulating pathway. Specifically, CO decreased lipid storage in high-fat C. elegans by inhibiting fat synthesis. In addition, CO supplementation modulated the abundance of metabolic biomarkers related to pyrimidine metabolism and riboflavin metabolism. The integrated transcriptome and metabolome analyses indicated that CO supplementation could alleviate fat accumulation in high-fat C. elegans by regulating retinol metabolism, drug metabolism-cytochrome P450, metabolism of xenobiotics by cytochrome P450, ascorbate and aldarate metabolism, and pentose and glucuronate interconversions. Overall, these findings highlight the potential health benefits of CO that could potentially be used as a functional edible oil.

Insights into the Mechanism of Flavor Loss in Strawberries Induced by Two Fungicides Integrating Transcriptome and Metabolome Analysis

Consumers have been complaining about the deterioration of the flavor of strawberries. The use of pesticides could have potential impacts on fruit flavor but the mechanisms are unclear. Here, we spayed boscalid and difenoconazole on the small green fruit of strawberries to investigate their effect on fruit flavor quality and the mechanism. The results indicated that both fungicides decreased the contents of soluble sugar and nutrients but increased acids in mature fruits, changed the levels of volatiles, and caused oxidative damage, which ultimately reduced the flavor quality of strawberries, and the negative effect of boscalid was greater. Combined with transcriptome and metabolome, boscalid altered the genes in sugar-acid metabolism (SUT, SPS, and INV), volatiles (FaQR, FaOMT, FaLOX, and FaAAT), and amino acid synthesis pathways and metabolites. This study elaborated on the effects of fungicides on the flavor quality of strawberries from physiological-biochemical and molecular levels and laid the foundation for improving the strawberry flavor quality.

Enantioselective toxic effects of the novel chiral antifungal agrochemical penthiopyrad in the early life stage of zebrafish (Danio rerio)

Penthiopyrad was extensively applied in agricultural production, however, the toxicities information of the penthiopyrad enantiomers on early life stages of aquatic organism were limited. This study investigated the enantioselective toxicity of penthiopyrad on the early life stage of zebrafish by acute toxicity, sublethal toxic effects and the mRNA relative expression levels of genes related to succinate dehydrogenase, cardiac development, and lipid metabolism. The results showed that the 96-h-LC₅₀ of penthiopyrad racemate and enantiomers to zebrafish embryos were Rac-: 2.784 mg/L; R-(-)-: 3.528 mg/L; S-(+)-: 1.882 mg/L. Penthiopyrad exposure induced autonomous movement abnormalities, slowed heart rate and delayed hatching in zebrafish embryos, and caused developmental toxic effects such as pericardial edema and yolk sac edema. The mRNA relative expression levels results showed that penthiopyrad exposure induced significant enantioselectivity effect for the expression of the Sdha, Pr1 and Nkx2.5 with a 1.94-4.98-fold difference between different enantiomers, and significantly affected succinate dehydrogenase (energy metabolism), lipid metabolism and cardiac development-related genes expression. In general, S-(+)-penthiopyrad induced higher toxic effects in zebrafish embryos, and mitochondrial dysfunction may be an important cause of abnormal development. This study contributed to improve the comprehensive risk assessment and enantiomeric research system of penthiopyrad to early life stage of zebrafish.