Biosynthesis-inspired mining and identification of untapped alkaloids in Camptotheca acuminate for enzyme discovery using ultra-high performance liquid chromatography coupled with quadrupole-time of flight-mass spectrometry

Unlocking plant bioactive pathways: omics data harnessing and machine learning assisting

Plant bioactives hold immense potential in the medicine and food industry. The recent advancements in omics applied in deciphering specialized metabolic pathways underscore the importance of high-quality genome releases and the wealth of data in metabolomics and transcriptomics. While harnessing data, whether integrated or standalone, has proven successful in unveiling plant natural product (PNP) biosynthetic pathways, the democratization of machine learning in biology opens exciting new opportunities for enhancing the exploration of these pathways. This review highlights the recent breakthroughs in disrupting plant-specialized biosynthetic pathways through the utilization of omics data harnessing and machine learning techniques.

Discovery of a novel flavonol O-methyltransferase possessing sequential 4'- and 7-O-methyltransferase activity from Camptotheca acuminata Decne

The biosynthetic route for flavonol in Camptotheca acuminata has been recently elucidated from a chemical point of view. However, the genes involved in flavonol methylation remain unclear. It is a critical step for fully uncovering the flavonol metabolism in this ancient plant. In this study, the multi-omics resource of this plant was utilized to perform flavonol O-methyltransferase-oriented mining and screening. Two genes, CaFOMT1 and CaFOMT2 are identified, and their recombinant CaFOMT proteins are purified to homogeneity. CaFOMT1 exhibits strict substrate and catalytic position specificity for quercetin, and selectively methylates only the 4'-OH group. CaFOMT2 possesses sequential O-methyltransferase activity for the 4'-OH and 7-OH of quercetin. These CaFOMT genes are enriched in the leaf and root tissues. The catalytic dyad and critical substrate-binding sites of the CaFOMTs are determined by molecular docking and further verified through site-mutation experiments. PHE181 and MET185 are designated as the critical sites for flavonol substrate selectivity. Genomic environment analysis indicates that CaFOMTs evolved independently and that their ancestral genes are different from that of the known Ca10OMT. This study provides molecular insights into the substrate-binding pockets of two new CaFOMTs responsible for flavonol metabolism in C. acuminata.

The efficacy of polyphenols as an antioxidant agent: An updated review

Global production of the two major poultry products, meat and eggs, has increased quickly. This, in turn, indicates both the relatively low cost and the customers' desire for these secure and high-quality products. Natural feed additives have become increasingly popular to preserve and enhance the health and productivity of poultry and livestock. We consume a lot of polyphenols, which are a kind of micronutrient. These are phytochemicals with positive effects on cardiovascular, cognitive, anti-inflammatory, detoxifying, anti-tumor, anti-pathogen, a catalyst for growth, and immunomodulating functions, among extra health advantages. Furthermore, high quantities of polyphenols have unknown and occasionally unfavorable impacts on the digestive tract health, nutrient assimilation, the activity of digestive enzymes, vitamin and mineral assimilation, the performance of the laying hens, and the quality of the eggs. This review clarifies the numerous sources, categories, biological functions, potential limitations on usage, and effects of polyphenols on poultry performance, egg composition, exterior and interior quality traits.

Discovery of unique CYP716C oxidase involved in pentacyclic triterpene biosynthesis from Camptotheca acuminata

Dozens of triterpenes have been isolated from Camptotheca acuminata, however, triterpene metabolism in this plant remains poorly understood. The common C28 carboxy located in the oleanane-type and ursane-type triterpenes indicates the existence of a functionally active triterpene, C28 oxidase, in this plant. Thorough mining and screening of the CYP716 genes were initiated using the multi-omics database for C. acuminata. Two CYP716A (CYP716A394 and CYP716A395) and three CYP716C (CYP716C80-CYP716C82) were identified based on conserved domain analyses and hierarchical cluster analyses. CYP716 microsomal proteins were prepared and their enzymatic activities were evaluated in vitro. The CYP716 classified into the CYP716C subfamily displays β-amyrin oxidation activity, and CYP716A displays α-amyrin and lupeol oxidation activity, based on gas chromatography-mass spectrometry analyses. The oxidation products were determined based on their mass and nuclear magnetic resonance spectrums. The optimum reaction conditions and kinetic parameters for CYP716C were determined, and functions were verified in Nicotiana benthaminana. Relative quantitative analyses revealed that these CYP716C genes were enriched in the leaves of C. acuminata plantlets after 60 d. These results indicate that CYP716C plays a dominant role in oleanane-type triterpene metabolism in the leaves of C. acuminata via a substrate-specific manner, and CYP716A is responsible for ursane- and lupane-type triterpene metabolism in fruit. This study provides valuable insights into the unique CYP716C-mediated oxidation step of pentacyclic triterpene biosynthesis in C. acuminata.

Proteomics-Guided Mining and Characterization of Epoxidase Involved in Camptothecin Biosynthesis from Camptotheca acuminata

The detailed metabolic map for camptothecin (CPT) biosynthesis in Camptotheca acuminata has been proposed according to our combined omics results. However, the CYP450-mediated epoxidation step in CPT biosynthesis remains unexplored. A proteomics-guided approach was used to identify and annotate the proteins enriched during the vigorous CPT metabolism period in mature C. acuminata and seedlings. Comparative analyses revealed that the CPT and flavonoid biosyntheses were vigorous in stems and all of the samples except the leaves, respectively. The CYP71BE genes were screened based on their enrichment patterns at the transcriptomic-proteomic level and biochemically characterized in Saccharomyces cerevisiae WAT11. Four CYP71BE proteins exhibited in vitro isoliquiritigenin epoxidase activity. Additionally, CYP71BE206 showed epoxidase activity toward strictosamide, the critical precursor for CPT biosynthesis, both in vitro and in Nicotiana benthamiana. In planta functional verification suggested that CYP71BE206 is involved in CPT biosynthesis. Their catalytic conditions were optimized, and the enzymatic parameters were determined. This study provides valuable insight into the CYP71BE-mediated epoxidation step for CPT biosynthesis and offers evidence to verify that the newly characterized epoxidase (CYP71BE206) is simultaneously responsible for the biosynthesis of CPT and the flavonoid in this plant. An evolution event probably happened on ancestral CYP71BE, resulting in the neofunctionalization of CYP71BE206.

OpNAC1 transcription factor regulates the biosynthesis of the anticancer drug camptothecin by targeting loganic acid O-methyltransferase in Ophiorrhiza pumila

Camptothecin (CPT) is an anticancer pentacyclic quinoline alkaloid widely used to treat cancer patients worldwide. However, the biosynthetic pathway and transcriptional regulation of camptothecin are largely unknown. Ophiorrhiza pumila, the herbaceous plant from the Rubiaceae family, has emerged as a model plant for studying camptothecin biosynthesis and regulation. In this study, a high-quality reference genome of O. pumila with estimated size of ~456.90 Mb was reported, and the accumulation level of camptothecin in roots was higher than that in stems and leaves. Based on its spatial distribution in the plant, we examined gene functions and expression by combining genomics with transcriptomic analysis. Two loganic acid O-methyltransferase (OpLAMTs) were identified in strictosidine-producing plant O. pumila, and enzyme catalysis assays showed that OpLAMT1 and not OpLAMT2 could convert loganic acid into loganin. Further knock-out of OpLAMT1 expression led to the elimination of loganin and camptothecin accumulation in O. pumila hairy roots. Four key residues were identified in OpLAMT1 protein crucial for the catalytic activity of loganic acid to loganin. By co-expression network, we identified a NAC transcription factor, OpNAC1, as a candidate gene for regulating camptothecin biosynthesis. Transgenic hairy roots and biochemical assays demonstrated that OpNAC1 suppressed OpLAMT1 expression. Here, we reported on two camptothecin metabolic engineering strategies paving the road for industrial-scale production of camptothecin in CPT-producing plants.

Impacts of polyphenols on laying hens' productivity and egg quality: A review

There has been a rapid increase in the world's output of main poultry products (meat and eggs). This reflects customer desire for these high-quality and safe products and the comparatively low price. Recently, natural feed additives, plants and products have been increasingly popular in the poultry and livestock industries to maintain and improve their health and production. Polyphenols are a type of micronutrient that is plentiful in our diet. They are phytochemicals that have health benefits, notably cardiovascular, cognitive function, antioxidant, anti-mutagenic, anti-inflammatory, antistress, anti-tumour, anti-pathogen, detoxification, growth-promoting and immunomodulating activities. On the other hand, excessive polyphenol levels have an unclear and sometimes negative impact on gastrointestinal tract health, nutrient digestion, digestive enzyme activity, vitamin, mineral absorption, laying hens performance and egg quality. As a result, this review illuminated polyphenols' various sources, classifications, biological activities, potential usage restrictions and effects on poultry, layer productivity and egg external and internal quality.

Structure-based identification and pathway elucidation of flavonoids in Camptotheca acuminate

Flavonoid metabolism in Camptotheca acuminate remained an untapped area for years. A tandem MS approach was used and focused on the mining and characterizing of flavonoids in mature C. acuminate. Fifteen new flavonoids and forty-three known flavonoids, including fifteen flavone analogs, sixteen flavonol analogs, seven flavanone analogs, six chalcone analogs, four xanthone analogs, ten flavane analogs were mined and identified based on their MS/MS fragments. Fifty-three of them were firstly characterized in C. acuminate. Eight biosynthetic precursors for these flavonoids were also identified. We constructed a specific metabolic map for flavonoids according to their relative contents in the flowers, fruits, stems, and leaves of C. acuminate. Furthermore, the most probable genes involved in chalcone biosynthesis, flavonoid hydroxylation, methylation, and glycosylation were further mined and fished in the gene reservoir of C. acuminate according to their conserved domains and co-expression analysis. These findings enable us to acquire a better understanding of versatile flavonoid metabolism in C. acuminate.

Integrative Analysis of Elicitor-Induced Camptothecin Biosynthesis in Camptotheca acuminata Plantlets Through a Combined Omics Approach

Treatments with abiotic elicitors can efficiently induce the accumulation of specialized metabolites in plants. We used a combined omics approach to analyze the elicitation effects of MeJa, AgNO₃, and PEG on camptothecin (CPT) biosynthesis in Camptotheca acuminata plantlets. Untargeted analyses revealed that treatments with MeJa, AgNO₃, and PEG significantly inhibited the photosynthetic pathway and promoted carbon metabolism and secondary metabolic pathways. The CPT levels increased by 78.6, 73.3, and 50.0% in the MeJa, AgNO₃, and PEG treatment groups, respectively. Using C. acuminata plantlets after elicitation treatment, we mined and characterized 15 new alkaloids, 25 known CPT analogs and precursors, 9 iridoid biosynthetic precursors, and 15 tryptamine biosynthetic precursors based on their MS/MS fragmentation spectra. Using 32 characterized genes involved in CPT biosynthesis as bait, we mined 12 prioritized CYP450 genes from the 416 CYP450 candidates that had been identified based on co-expression analysis, conserved domain analysis, and their elicitation-associated upregulation patterns. This study provides a comprehensive perspective on CPT biosynthesis in C. acuminata plantlets after abiotic elicitation. The findings enable us to elucidate the previously unexplored CYP450-mediated oxidation steps for CPT biosynthesis.

Application of Amino Acids in the Structural Modification of Natural Products: A Review

Natural products and their derivatives are important sources for drug discovery; however, they usually have poor solubility and low activity and require structural modification. Amino acids are highly soluble in water and have a wide range of activities. The introduction of amino acids into natural products is expected to improve the performance of these products and minimize their adverse effects. Therefore, this review summarizes the application of amino acids in the structural modification of natural products and provides a theoretical basis for the structural modification of natural products in the future. The articles were divided into six types based on the backbone structures of the natural products, and the related applications of amino acids in the structural modification of natural products were discussed in detail.

Moringa oleifera polysaccharides regulates caecal microbiota and small intestinal metabolic profile in C57BL/6 mice

This study investigated the effects of Moringa oleifera polysaccharides (MOP) on the serum indexes, small intestinal morphology, small intestinal metabolic profile, and caecal microbiota of mice. A new type of polysaccharides with 104,031 Da molecular weight and triple helix structure was isolated from M. oleifera leaves for in vivo experiment. Forty male SPF C57BL/6 mice aged 4 weeks were average divided into four groups randomly according to the MOP gavaged daily (0, 20, 40 and 60 mg/kg body weight MOP). After a 7-day preliminary trial period and a 28-day official trial period, the mice were slaughtered. Results showed that MOP reduced glucose, total cholesterol, and malondialdehyde. It also improved superoxide dismutase and catalase in serum (P < 0.05). For small intestinal morphology, MOP improved the villi length and crypt depth in both ileum and jejunum (P < 0.05); the ratio of villi length to crypt depth in jejunum increased (P < 0.05). MOP could cause the increase of beneficial bacteria and the decrease of harmful bacteria in caecum, further affecting the function of microbiota. In addition, MOP regulated 114 metabolites enriched in the pathway related to the synthesis and metabolism of micromolecules. In sum, MOP exerted positive effects on the serum indexes and intestinal health of mice.