Transcriptomic analysis of key genes involved in chlorogenic acid biosynthetic pathway and characterization of MaHCT from Morus alba L

Soil Application of Bacillus subtilis Regulates Flavonoid and Alkaloids Biosynthesis in Mulberry Leaves

Flavonoids and alkaloids are the major active ingredients in mulberry leaves that have outstanding medicinal value. Bacillus subtilis can effectively activate the plants defense response and regulate the plant secondary metabolism. In this study, we explored the effects of soil application of B. subtilis on the content of flavonoids and the most important alkaloids (1-deoxynojirimycin, DNJ) in mulberry leaves. Significant decreases in flavonoid content were observed in tender leaves and mature leaves after treatment with B. subtilis; at the same time, significant increases in DNJ content were observed in tender leaves. Based on widely targeted LC-MS/MS and high-throughput approaches, we screened out 904 differentially synthesized metabolites (DSMs) and 9715 differentially expressed genes (DEGs). KEGG analyses showed that these DSMs and DEGs were both significantly enriched in the biosynthesis of secondary metabolites, flavonoid synthesis and plant hormone signal transduction. Further correlation analysis of DEMs and DEGs showed that 40 key genes were involved in flavonoid biosynthesis, with 6 key genes involved in DNJ biosynthesis. The expression of CHS, CHI, F3H, F3'H, FLS, UGT and AOC significantly responded to B. subtilis soil application. This study broadens our understanding of the molecular mechanisms underlying the accumulation of flavonoids and alkaloids in mulberry leaves.

Mining and functional characterization of NADPH-cytochrome P450 reductases of the DNJ biosynthetic pathway in mulberry leaves

BACKGROUND

1-Deoxynojirimycin (DNJ), the main active ingredient in mulberry leaves, with wide applications in the medicine and food industries due to its significant functions in lowering blood sugar, and lipids, and combating viral infections. Cytochrome P450 is a key enzyme for DNJ biosynthesis, its activity depends on the electron supply of NADPH-cytochrome P450 reductases (CPRs). However, the gene for MaCPRs in mulberry leaves remains unknown.

RESULTS

In this study, we successfully cloned and functionally characterized two key genes, MaCPR1 and MaCPR2, based on the transcriptional profile of mulberry leaves. The MaCPR1 gene comprised 2064 bp, with its open reading frame (ORF) encoding 687 amino acids. The MaCPR2 gene comprised 2148 bp, and its ORF encoding 715 amino acids. The phylogenetic tree indicates that MaCPR1 and MaCPR2 belong to Class I and Class II, respectively. In vitro, we found that the recombinant enzymes MaCPR2 protein could reduce cytochrome c and ferricyanide using NADPH as an electron donor, while MaCPR1 did not. In yeast, heterologous co-expression indicates that MaCPR2 delivers electrons to MaC3'H hydroxylase, a key enzyme catalyzing the production of chlorogenic acid from 3-O-p-coumaroylquinic acid.

CONCLUSIONS

These findings highlight the orchestration of hydroxylation process mediated by MaCPR2 during the biosynthesis of secondary metabolite biosynthesis in mulberry leaves. These results provided a foundational understanding for fully elucidating the DNJ biosynthetic pathway within mulberry leaves.

Biosynthetic pathways and related genes regulation of bioactive ingredients in mulberry leaves

Mulberry leaves are served not only as fodder for silkworms but also as potential functional food, exhibiting nutritional and medical benefits due to the complex and diverse constituents, including alkaloids, flavonoids, phenolic acids, and benzofurans, which possess a wide range of biological activities, such as anti-diabete, anti-oxidant, anti-inflammatory, and so on. Nevertheless, compared with the well-studied phytochemistry and pharmacology of mulberry leaves, the current understanding of the biosynthesis mechanisms and regulatory mechanisms of active ingredients in mulberry leaves remain unclear. Natural resources of these active ingredients are limited owing to their low contents in mulberry leaves tissues and the long growth cycle of mulberry. Biosynthesis is emerging as an alternative means for accumulation of the desired high-value compounds, which can broaden channels for their large-scale green productions. Therefore, this review summarizes the recent research advance on the correlative key genes, enzyme biocatalytic reactions and biosynthetic pathways of valuable natural ingredients (i.e. alkaloids, flavonoids, phenolic acids, and benzofurans) in mulberry leaves, thereby offering important insights for their further biomanufacturing.

Advances in Production of Hydroxycinnamoyl-Quinic Acids: From Natural Sources to Biotechnology

Hydroxycinnamoyl-quinic acids (HCQAs) are polyphenol esters formed of hydroxycinnamic acids and (-)-quinic acid. They are naturally synthesized by plants and some micro-organisms. The ester of caffeic acid and quinic acid, the chlorogenic acid, is an intermediate of lignin biosynthesis. HCQAs are biologically active dietary compounds exhibiting several important therapeutic properties, including antioxidant, antimicrobial, anti-inflammatory, neuroprotective, and other activities. They can also be used in the synthesis of nanoparticles or drugs. However, extraction of these compounds from biomass is a complex process and their synthesis requires costly precursors, limiting the industrial production and availability of a wider variety of HCQAs. The recently emerged production through the bioconversion is still in an early stage of development. In this paper, we discuss existing and potential future strategies for production of HCQAs.

Metabolomic and transcriptomic analyses identify quinic acid protecting eggplant from damage caused by western flower thrips

BACKGROUND

Western flower thrips are considered the major insect pest of horticultural crops worldwide, causing economic and yield loss to Solanaceae crops. The eggplant (Solanum melongena L.) resistance against thrips remains largely unexplored. This work aims to identify thrips-resistant eggplants and dissect the molecular mechanisms underlying this resistance using the integrated metabolomic and transcriptomic analyses of thrips-resistant and -susceptible cultivars.

RESULTS

We developed a micro-cage thrips bioassay to identify thrips-resistant eggplant cultivars, and highly resistant cultivars were identified from wild eggplant relatives. Metabolomic profiles of thrips-resistant and -susceptible eggplant were compared using the gas chromatography-mass spectrometry (GC-MS)-based approach, resulting in the identification of a higher amount of quinic acid in thrips-resistant eggplant compared to the thrips-susceptible plant. RNA-sequencing analysis identified differentially expressed genes (DEGs) by comparing genome-wide gene expression changes between thrips-resistant and -susceptible eggplants. Consistent with metabolomic analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of DEGs revealed that the starch and sucrose metabolic pathway in which quinic acid is a metabolic by-product was highly enriched. External application of quinic acid enhances the resistance of susceptible eggplant to thrips.

CONCLUSION

Our results showed that quinic acid plays a key role in the resistance to thrips. These findings highlight a potential application of quinic acid as a biocontrol agent to manage thrips and expand our knowledge to breed thrips-resistant eggplant. © 2022 Society of Chemical Industry.

Probing the transcriptome of Boehmeria nivea reveals candidate genes associated with the biosynthesis of chlorogenic acid

Boehmeria nivea (L.) Gaudich is used in traditional Chinese medicine. Chlorogenic acids are major medically active components of Boehmeria nivea, which can be used clinically to treat hyperglycemia, pneumonia, and cancer. To identify the genes involved in chlorogenic acid biosynthesis, we analyzed transcriptome data from leaf, root, and stem tissues of Boehmeria nivea using the Illumina Hi-Seq 4000 platform. A total of 146,790 unigenes were obtained from Boehmeria nivea, of which 106,786 were annotated in public databases. In analyses of the KEGG (Kyoto Encyclopedia of Genes and Genome) database, 484 unigenes that encode the five key enzymes involved in chlorogenic acid biosynthesis were identified, and shikimate O-hydroxycinnamoyl transferase was spatially simulated. Some of these key enzyme unigenes expression levels were verified by RT-qPCR (real-time quantitative Polymerase Chain Reaction). Furthermore, multiple genes encoding plant resistance proteins or transcription factors were identified and analyzed. Differentially expressed genes were identified by performing pairwise comparison of genes between tissues. This study increases the number of public transcript datasets of this species and identifies candidate genes related to the biosynthesis of chlorogenic acid, laying a foundation for the further exploration of this pathway in Boehmeria nivea.

The Biological Activity Mechanism of Chlorogenic Acid and Its Applications in Food Industry: A Review

Chlorogenic acid (CGA), also known as coffee tannic acid and 3-caffeoylquinic acid, is a water-soluble polyphenolic phenylacrylate compound produced by plants through the shikimic acid pathway during aerobic respiration. CGA is widely found in higher dicotyledonous plants, ferns, and many Chinese medicine plants, which enjoy the reputation of “plant gold.” We have summarized the biological activities of CGA, which are mainly shown as anti-oxidant, liver and kidney protection, anti-bacterial, anti-tumor, regulation of glucose metabolism and lipid metabolism, anti-inflammatory, protection of the nervous system, and action on blood vessels. We further determined the main applications of CGA in the food industry, including food additives, food storage, food composition modification, food packaging materials, functional food materials, and prebiotics. With a view to the theoretical improvement of CGA, biological activity mechanism, and subsequent development and utilization provide reference and scientific basis.

Metabolome and transcriptome analysis of eleutheroside B biosynthesis pathway in Eleutherococcus senticosus

Eleutheroside B (syringin) is a medicinal active ingredient extracted from Eleutherococcus senticosus (Ruper. et Maxim.) Maxim with high clinical application value. However, its synthesis pathway remains unknown. Here, we analyzed the eleutheroside B biosynthesis pathway in E. senticosus. Consequently, metabolomic and transcriptomic analyses identified 461 differentially expressed genes (DEGs) and 425 metabolites. Further, we identified 7 DEGs and 67 metabolites involved in the eleutheroside B biosynthetic pathway in the eleutheroside B high and low plants. The correlation between the gene and metabolites was explored using the pearson correlation coefficient (PCC) analysis. Caffeoyl-CoA O-methyltransferase, caffeic acid-O-methyltransferase, β-amyrin synthase (β-AS) genes, NAC5, and HB5 transcription factors were identified as candidate genes and transcription factors related to the eleutheroside B synthesis. Eleutheroside B content was the highest at the young stage of the leaves both in the high and low eleutheroside B plants. Quantitative real-time polymerase chain reaction revealed that phenylalanine ammonia-lyase1, cinnamate 4-hydroxylase, β-AS, and leucoanthocyanidin reductase gene had higher expression levels at the young stage of the leaves in the low eleutheroside B plants but lower expression levels in the high eleutheroside B plants. In the present study, we complemented the eleutheroside B biosynthetic pathway by analyzing the expression levels of relevant genes and metabolite accumulation patterns.

Screening, cloning and functional characterization of key methyltransferase genes involved in the methylation step of 1-deoxynojirimycin alkaloids biosynthesis in mulberry leaves

The novel C-methyltransferase, MaMT1, could catalyze the conversion of piperidine to 2-methylpiperidine, which may be involved in the methylation step of DNJ biosynthesis in mulberry leaves. Mulberry (Morus alba L.) is a worldwide crop with medicinal, feeding and nutritional value, and 1-deoxynojirimycin ((2R, 3R, 4R, 5S)-2-hydroxymethyl-3, 4, 5-trihydroxypiperidine, DNJ) alkaloid, a potent α-glucosidase inhibitor, is its main active ingredient. Our previous researches clarified the biosynthetic pathway of DNJ from lysine to Δ¹-piperideine, but its downstream pathway is unclear. Herein, eight differential methyltransferases (MTs) genes were screened from transcriptome profiles of mulberry leaves with significant differences in DNJ content (P < 0.01). Subsequently, MaMT1 (OM140666) and MaMT2 (OM140667) were hypothesized as candidate genes related to DNJ biosynthesis by correlation analysis of genes expression levels and DNJ content of mulberry leaves at different dates. Functional characterization of MaMT1 and MaMT2 were performed by cloning, prokaryotic expression and enzymatic reaction in vitro, and it showed that MaMT1 protein could catalyze the conversion of piperidine to 2-methylpiperidine. Moreover, molecular docking confirmed the interaction of MaMT1 protein with piperidine and S-adenosyl-L-methionine (SAM), indicating that MaMT1 had C-methyltransferase activity, while MaMT2 did not. The above results suggested that MaMT1 may be involved in the methylation step of DNJ alkaloid biosynthesis in mulberry leaves, which is a breakthrough in the analysis of DNJ alkaloid biosynthetic pathway. It is worth mentioning that the novel MaMT1, annotated as serine hydroxymethyltransferase, could rely on SAM to perform C-methyltransferase function. Therefore, our findings contribute new insights into the research of DNJ alkaloid biosynthesis and C-methyltransferase family.

Phytochemical‑rich herbal formula ATG‑125 protects against sucrose‑induced gastrocnemius muscle atrophy by rescuing Akt signaling and improving mitochondrial dysfunction in young adult mice

The antioxidant capability of herbal remedies has attracted widespread attention, but their molecular mechanisms in a muscle atrophy model have not been explored. The aim of the present study was to compare the bioactivity of sucrose challenged mice following treatment with ATG‑125. Here, through a combination of transcriptomic and biomedical analysis, herbal formula ATG‑125, a phytochemical‑rich formula, was identified as a protective factor against muscle atrophy in sucrose challenged mice. Gene ontology (GO) identified differentially expressed genes that were primarily enriched in the 'negative regulation of proteolysis', 'cellular amino acid metabolic process', 'lipoprotein particle' and 'cell cycle', all of which were associated with the ATG‑125‑mediated prevention of muscle atrophy, particularly with regard to mitochondrial biogenesis. In skeletal muscle, a set of mitochondrial‑related genes, including angiopoietin‑like 4, nicotinamide riboside kinase 2 (Nmrk2), pyruvate dehydrogenase lipoamide kinase isozyme 4, Asc‑type amino acid transporter 1 and mitochondrial uncoupling protein 3 (Ucp3) were markedly upregulated following ATG‑125 intervention. An increase in Nmrk2 and Ucp3 expression were noted after ATG‑125 treatment, in parallel with upregulation of the 'nicotinate and nicotinamide metabolism' pathway, as determined using the Kyoto Encyclopedia of Genes and Genomes (KEGG). Furthermore, KEGG pathway analysis revealed the downregulation of 'complement and coagulation cascades', 'cholesterol metabolism', 'biosynthesis of amino acids' and 'PPAR signaling pathway', which were associated with the downregulation of serine (or cysteine) peptidase inhibitor clade A member (Serpina)3, Serpina1b, Serpina1d, Serpina1e, apolipoprotein (Apo)a1 and Apoa2, all of which were cardiovascular and diabetes‑associated risk factors and were regulated by ATG‑125. In addition, ATG‑125 treatment resulted in downregulated mRNA expression levels of ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 2, troponin‑I1, troponin‑C1 and troponin‑T1 in young adult gastrocnemius muscle compared with the sucrose group. Nuclear factor‑κB‑hypoxia inducible factor‑1α‑TGFβ receptor type‑II‑vascular endothelial growth factor staining indicated that ATG‑125 decreased sucrose‑induced chronic inflammation. ATG‑125 was sufficient to prevent muscle atrophy, and this protective effect may be mediated through upregulation of AKT phosphorylation, upregulating the insulin growth factor‑1R‑insulin receptor substrate‑PI3K‑AKT pathway, which in turn resulted in a forkhead box O‑dependent decrease in protein degradation pathways, including regulation of atrogin1 and E3 ubiquitin‑protein ligase TRIM63. Peroxisome‑proliferator activated receptor γ coactivator 1α (PGC1α) was decreased in young adult mice challenged with sucrose. ATG‑125 treatment significantly increased PGC1α and significantly increased UCP‑1,2,3 expression levels, which suggested ATG‑125 poised the mitochondria for uncoupling of respiration. This effect is consistent with the increased SIRT1 levels and may explain an increase in mitochondria biogenesis. Taken together, the present study showed that ATG‑125, as an integrator of protein synthesis and degradative pathways, prevented muscle wasting.

In Vivo Functional Verification of Four Related Genes Involved in the 1-Deoxynojirimycin Biosynthetic Pathway in Mulberry Leaves

The alkaloid 1-deoxynojirimycin (DNJ) is one of the major bioactive compounds in mulberry leaves (Morus alba L.). Previously, we discovered four key genes involved in the pathway from lysine to piperidine in the biosynthesis of DNJ in mulberry leaves, MaLDC (MG727866), MaCAO (MH205733), MaSDR1 (MT989445), and MaSDR2 (MT989446), which encoded lysine decarboxylase, copper amine oxidase, and short-chain dehydrogenase/reductase 1 and 2, respectively. However, the in vivo functions of these four genes have not been verified yet. Here, these four genes were successfully cloned and used for the establishment of C58C1 Agrobacterium rhizogenes mediated overexpression genetic transformation systems and GV3101 Agrobacterium-mediated virus-induced gene silencing transformation systems in order to verify the influence of these four genes on the biosynthetic content of DNJ in mulberry leaves. The results showed that the content of DNJ increased after the four genes were overexpressed. When these four genes were silenced, the gene expression was blocked, which affected the biosynthesis of DNJ, and the DNJ content decreased. The above results indicated that these four genes participated in DNJ biosynthesis. This study provided a foundation for further elucidating the regulatory mechanisms of DNJ biosynthesis in mulberry leaves.

CsHCT-Mediated Lignin Synthesis Pathway Involved in the Response of Tea Plants to Biotic and Abiotic Stresses

Many studies have shown that phenolic compounds such as lignin and flavonoids enhance plant resistance. Tea plants are rich in flavonoid compounds. Whether these compounds are related to tea plant resistance is unclear. In this study, an interesting conclusion was drawn on the basis of experimental results: in response to abiotic stress (except for sucrose treatment), gene expression was increased in the phenylpropanoid and lignin pathways and was reduced in the flavonoid pathway in tea plants. CsHCTs, the genes located at the branch point of the lignin and flavonoid pathways, are most suitable for regulating the ratio of carbon flow in the lignin pathway and flavonoid synthesis. Enzymatic and genetic modification experiments proved that CsHCTs encode hydroxycinnamoyl-coenzyme A:shikimate/quinate hydroxycinnamoyl transferase in vitro and in vivo. Furthermore, the genetic modification results showed that the contents of phenolic acids and lignin were increased in tobacco and Arabidopsis plants overexpressing CsHCTs, whereas the content of flavonol glycosides was decreased. Both types of transgenic plants showed resistance to many abiotic stresses and bacterial infections. We speculate that CsHCTs participate in regulation of the metabolic flow of carbon from the flavonoid pathway to the chlorogenic acid, caffeoylshikimic acid, and lignin pathways to increase resistance to biotic and abiotic stresses.

Genetic Architecture Underlying the Metabolites of Chlorogenic Acid Biosynthesis in Populus tomentosa

Chlorogenic acid (CGA) plays a crucial role in defense response, immune regulation, and the response to abiotic stress in plants. However, the genetic regulatory network of CGA biosynthesis pathways in perennial plants remains unclear. Here, we investigated the genetic architecture for CGA biosynthesis using a metabolite-based genome-wide association study (mGWAS) and expression quantitative trait nucleotide (eQTN) mapping in a population of 300 accessions of Populus tomentosa. In total, we investigated 204 SNPs which were significantly associated with 11 metabolic traits, corresponding to 206 genes, and were mainly involved in metabolism and cell growth processes of P. tomentosa. We identified 874 eQTNs representing 1066 genes, in which the expression and interaction of causal genes affected phenotypic variation. Of these, 102 genes showed significant signatures of selection in three geographical populations, which provided insights into the adaptation of CGA biosynthesis to the local environment. Finally, we constructed a genetic network of six causal genes that coordinately regulate CGA biosynthesis, revealing the multiple regulatory patterns affecting CGA accumulation in P. tomentosa. Our study provides a multiomics strategy for understanding the genetic basis underlying the natural variation in the CGA biosynthetic metabolites of Populus, which will enhance the genetic development of abiotic-resistance varieties in forest trees.

Quantitative Comparison of the Marker Compounds in Different Medicinal Parts of Morus alba L. Using High-Performance Liquid Chromatography-Diode Array Detector with Chemometric Analysis

It is thought that the therapeutic efficacy of Morus alba L. is determined by its biological compounds. We investigated the chemical differences in the medicinal parts of M. alba by analyzing a total of 57 samples (15 root barks, 11 twigs, 12 fruits, and 19 leaves). Twelve marker compounds, including seven flavonoids, two stilbenoids, two phenolic acids, and a coumarin, were quantitatively analyzed using a high-performance liquid chromatography-diode array detector and chemometric analyses (principal component and heatmap analysis). The results demonstrated that the levels and compositions of the marker compounds varied in each medicinal part. The leaves contained higher levels of six compounds, the root barks contained higher levels of four compounds, and the twigs contained higher levels of two compounds. The results of chemometric analysis showed clustering of the samples according to the medicinal part, with the marker compounds strongly associated with each part: mulberroside A, taxifolin, kuwanon G, and morusin for the root barks; 4-hydroxycinnamic acid and oxyresveratrol for the twigs and skimmin; chlorogenic acid, rutin, isoquercitrin, astragalin, and quercitrin for the leaves. Our approach plays a fundamental role in the quality evaluation and further understanding of biological actions of herbal medicines derived from various medicinal plant parts.

Comparative Transcriptome Analysis of Key Reductase Genes Involved in the 1-Deoxynojirimycin Biosynthetic Pathway in Mulberry Leaves and Cloning, Prokaryotic Expression, and Functional Analysis of MaSDR1 and MaSDR2

The alkaloid 1-deoxynojirimycin (DNJ) is the main bioactive ingredient in the hypoglycemic action of mulberry leaves (Morus alba L.). Our previous research clarified the upstream pathway from lysine to Δ1-piperideine in the biosynthesis of DNJ in mulberry leaves, but the pathway and related reductase genes from Δ1-piperideine to piperidine are still unclear. Here, a comparative transcriptome was used to analyze the transcriptome data of two samples (July and November) of mulberry leaves with significant differences in the content of DNJ and screen-related reductase genes. Results showed that expression levels of MaSDR1 and MaSDR2 were significantly and positively correlated with the content of DNJ (P < 0.05) in different seasons. MaSDR1 (GenBank accession no. MT989445) and MaSDR2 (GenBank accession no. MT989446) were successfully cloned and used for prokaryotic expression and functional analysis in vitro. MaSDR1 and MaSDR2 could catalyze the reaction of Δ1-piperideine with the coenzyme NADPH to generate piperidine. The kinetic parameters of MaSDR1 and MaSDR2 indicated that MaSDR2 had a higher binding ability to Δ1-piperideine than MaSDR1. This study provided insights into the biosynthesis of DNJ in mulberry leaves.