Functional Identification of HhUGT74AG11-A Key Glycosyltransferase Involved in Biosynthesis of Oleanane-Type Saponins in Hedera helix.

Hedera helix is a traditional medicinal plant. Its primary active ingredients are oleanane-type saponins, which have extensive pharmacological effects such as gastric mucosal protection, autophagy regulation actions, and antiviral properties. However, the glycosylation-modifying enzymes responsible for catalyzing oleanane-type saponin biosynthesis remain unidentified. Through transcriptome, cluster analysis, and PSPG structural domain, this study preliminarily screened four candidate UDP-glycosyltransferases (UGTs), including Unigene26859, Unigene31717, CL11391.Contig2, and CL144.Contig9. In in vitro enzymatic reactions, it has been observed that Unigene26859 (HhUGT74AG11) has the ability to facilitate the conversion of oleanolic acid, resulting in the production of oleanolic acid 28-O-glucopyranosyl ester. Moreover, HhUGT74AG11 exhibits extensive substrate hybridity and specific stereoselectivity and can transfer glycosyl donors to the C-28 site of various oleanane-type triterpenoids (hederagenin and calenduloside E) and the C-7 site of flavonoids (tectorigenin). Cluster analysis found that HhUGT74AG11 is clustered together with functionally identified genes AeUGT74AG6, CaUGT74AG2, and PgUGT74AE2, further verifying the possible reason for HhUGT74AG11 catalyzing substrate generalization. In this study, a novel glycosyltransferase, HhUGT74AG11, was characterized that plays a role in oleanane-type saponins biosynthesis in H. helix, providing a theoretical basis for the production of rare and valuable triterpenoid saponins.

Metabolic engineering of Yarrowia lipolytica for high-level production of squalene.

Squalene is an important triterpene with a wide range of applications. Given the growing market demand for squalene, the development of microbial cell factories capable of squalene production is considered a sustainable method. This study aimed to investigate the squalene production potential of Yarrowia lipolytica. First, HMG-CoA reductase from Saccharomyces cerevisiae and squalene synthase from Y. lipolytica was co-overexpressed in Y. lipolytica. Second, by enhancing the supply of NADPH in the squalene synthesis pathway, the production of squalene in Y. lipolytica was effectively increased. Furthermore, by constructing an isoprenol utilization pathway and overexpressing YlDGA1, the strain YLSQ9, capable of producing 868.1 mg/L squalene, was obtained. Finally, by optimizing the fermentation conditions, the highest squalene concentration of 1628.2 mg/L (81.0 mg/g DCW) in Y. lipolytica to date was achieved. This study demonstrated the potential for achieving high squalene production using Y. lipolytica.

Performance Optimization in Frequency Estimation of Noisy Signals: Ds-IpDTFT Estimator.

This research presents a comprehensive study of the dichotomous search iterative parabolic discrete time Fourier transform (Ds-IpDTFT) estimator, a novel approach for fine frequency estimation in noisy exponential signals. The proposed estimator leverages a dichotomous search process before iterative interpolation estimation, which significantly reduces computational complexity while maintaining high estimation accuracy. An in-depth exploration of the relationship between the optimal parameter p and the unknown parameter δ forms the backbone of the methodology. Through extensive simulations and real-world experiments, the Ds-IpDTFT estimator exhibits superior performance relative to other established estimators, demonstrating robustness in noisy conditions and stability across varying frequencies. This efficient and accurate estimation method is a significant contribution to the field of signal processing and offers promising potential for practical applications.

Efficient production of cordycepin by engineered Yarrowia lipolytica from agro-industrial residues.

Cordycepin, a nucleoside compound with a variety of biological activities, has been extensively applied in the nutraceutical and pharmaceutical industries. The advancement of microbial cell factories using agro-industrial residues provides a sustainable pathway for cordycepin biosynthesis. Herein, the cordycepin production was enhanced by the modification of glycolysis and pentose phosphate pathway in engineered Yarrowia lipolytica. Then, cordycepin production based on economical and renewable substrates (sugarcane molasses, waste spent yeast, and diammonium hydrogen phosphate) was analyzed. Furthermore, the effects of C/N molar ratio and initial pH on cordycepin production were evaluated. Results indicated that the maximum cordycepin productivity of 656.27 mg/L/d (72 h) and cordycepin titer was 2286.04 mg/L (120 h) by engineered Y. lipolytica in the optimized medium, respectively. The cordycepin productivity in the optimized medium was increased by 28.81% compared with the original medium. This research establishes a promising way for efficient cordycepin production from agro-industrial residues.

Increased Cordycepin Production in Yarrowia lipolytica Using Combinatorial Metabolic Engineering Strategies.

As the first nucleoside antibiotic discovered in fungi, cordycepin, with its various biological activities, has wide applications. At present, cordycepin is mainly obtained from the natural fruiting bodies of Cordyceps militaris. However, due to long production periods, low yields, and low extraction efficiency, harvesting cordycepin from natural C. militaris is not ideal, making it difficult to meet market demands. In this study, an engineered Yarrowia lipolytica YlCor-18 strain, constructed by combining metabolic engineering strategies, achieved efficient de novo cordycepin production from glucose. First, the cordycepin biosynthetic pathway derived from C. militaris was introduced into Y. lipolytica. Furthermore, metabolic engineering strategies including promoter, protein, adenosine triphosphate, and precursor engineering were combined to enhance the synthetic ability of engineered strains of cordycepin. Fermentation conditions were also optimized, after which, the production titer and yields of cordycepin in the engineered strain YlCor-18 under fed-batch fermentation were improved to 4362.54 mg/L and 213.85 mg/g, respectively, after 168 h. This study demonstrates the potential of Y. lipolytica as a cell factory for cordycepin synthesis, which will serve as the model for the green biomanufacturing of other nucleoside antibiotics using artificial cell factories.

The ignored risk: heavy metal pollution of medicine and food homologous substances.

A survey was conducted to investigate the effects of cadmium (Cd), arsenic (As), chromium (Cr), lead (Pb), and copper (Cu) in medicine and food homologous substances (MFHs) on human health. Nine common and typical MFHs (Dendrobium, Bulbus lilii, Poria, Semen nelumbinis, Radix puerariae, Gardenia jasminoides, Hordeum vulgare L, Semen coicis, and Ganoderma Karst) in the form of medicinal slices ready for decoction were purchased from pharmacies. Five among the MFHs (Dendrobium, Bulbus lilii, Poria, Semen nelumbinis, and Radix puerariae) were further obtained from a local field as raw materials for comparison. The results showed that raw materials of MFHs collected from the field had higher contents of heavy metal and greater health risks than medicinal slices purchased from pharmacy. Generally, the heavy metal residues in MFHs of different medicinal parts were different, and MFHs from roots or stems had significantly higher contents of heavy metals than those from fruits or seeds. Most importantly, the contents of Cd in Bulbus lilii and As in wild Poria from field were higher than the contents described in the Pharmacopoeia of the People's Republic of China (ChP). Non-carcinogenic and carcinogenic risk assessments revealed that Poria from field had larger non-carcinogenic and carcinogenic risks to human health; Bulbus lilii showed no non-carcinogenic risk but exhibited carcinogenic risks, whereas Cr showed carcinogenic risks in all samples. Given that MFHs are incorporated in regular foods, care should be taken to minimize health hazards caused by heavy metals to human. This study creates awareness on the safety issues associated with MFHs, and provides basic information for establishing the maximum allowable contents of medicinal and food substances in normal diets.

Acinetobacter tibetensis sp. nov., Isolated from a Soil Under a Greenhouse in Tibet.

A Gram-stain-negative, light yellow, aerobic, non-motile, short rod-shaped bacterium named strain Y-23T with iprodione-degrading capability was isolated from a soil under a greenhouse in Tibet, PR China. Strain Y-23T grew at 4-37 â„ƒ and pH 5.0-9.0 (optimum, 25 â„ƒ and pH 7.0) with 0-3% (w/v) NaCl (optimum, 0%). Phylogenetic analysis based on 16S rRNA gene and chromosome genome indicated that strain Y-23T formed a stable evolutionary branch with Acinetobacter tandoii DSM 14970T. The 16S rRNA gene similarity, digital DNA-DNA hybridization and average nucleotide identity values between strain Y-23T and Acinetobacter tandoii DSM 14970T were 98.31%, 43.2% and 91.2%, respectively. The genome size was 3.39 Mbp with a genomic DNA G+C content of 40.59 mol%. The predominant fatty acids were C18:1 ω9c, Summed feature 3 (C16:1 ω7c/C16:1 ω6c), C12:0, C12:0 3-OH and C16:0. The polar lipids were diphosphatidyl glycerol, phosphatidyl glycerol, phosphatidyl ethanolamine, phosphatidyl choline, unidentified phospholipid, four unidentified aminophospholipids and two unidentified lipids. The isoprenoid quinone was Q-8 (19.43%) and Q-9 (80.57%). Based on phenotypic, phylogenetic, and genotypic data, strain Y-23T is considered to represent a novel species of the genus Acinetobacter, for which the name Acinetobacter tibetensis sp. nov. is proposed. The type strain is Y-23T (= CICC 25150T = JCM 35630T).

Effects of different boiling processes on chemical compositions of Lilii Bulbus soup.

Lilii Bulbus, an edible Chinese herbal medicine, has a long history in medicine. However, research on effectively boiling Lilii Bulbus is rare. To make the more nutritious Lilii Bulbus soup, the optimized boiling process, using an alternate heating mode by decoction pot carrying a mixture of water and Chinese liquor at the ration of 9:1, was established in this study. Compared to the soup prepared by the daily process, the polysaccharide amount improved by 54%, and the total heavy metals decreased by 33.5% using the optimized boiling process. In addition, the total saponins at 34.3 µg/g were determined in the soup prepared by the optimized process. Meanwhile, the colchicine content in the boiled Lilii Bulbus soup was undetectable using the optimized process. This research performs an optimized boiling process for making Lilii Bulbus soup, and provides a reference for generating high commercial value from Lilii Bulbus soup in the future.

High-level de novo biosynthesis of cordycepin by systems metabolic engineering in Yarrowia lipolytica.

Cordycepin is a nucleoside antibiotic with various biological activities, which has wide applications in the area of cosmetic and medicine industries. However, the current production of cordycepin is costly and time-consuming. To construct the promising cell factory for high-level cordycepin production, firstly, the design and construction of cordycepin biosynthetic pathway were performed in Yarrowia lipolytica. Secondly, the adaptivity between cordycepin biosynthetic pathway and Y. lipolytica was enhanced by enzyme fusion and integration site engineering. Then, the production of cordycepin was improved by the enhancement of adenosine supply. Furthermore, through modular engineering, the production of cordycepin was achieved at 3588.59 mg/L from glucose. Finally, 3249.58 mg/L cordycepin with a yield of 76.46 mg/g total sugar was produced by the engineered strain from the mixtures of glucose and molasses. This research is the first report on the de novo high-level production of cordycepin in the engineered Y. lipolytica.

The Formation of Hollow Trait in Cucumber (Cucumis sativus L.) Fruit Is Controlled by CsALMT2.

The hollow trait is crucial for commercial quality of cucumber (Cucumis sativus L.) fruit, and its molecular regulatory mechanism is poorly understood due to its environmental sensitivity. In the previous research, we obtained the hollow and the non-hollow materials of ecotype cucumbers of South China, which were not easily affected by the external environment through a systematic breeding method. In this study, first, we proposed to use the percentage of the hollow area as the criterion to compare the hollow characteristics between two materials, and to analyze the formation mechanism of early hollow trait from the perspective of cytology. The results showed that the hollow trait occurred in the early stage of fruit development, and formed with the opening of carpel ventral zipped bi-cell layer, which formed rapidly from 2 to 4 days, and then slowed to a constant rate from 14 to 16 days. Meanwhile, the different genetic populations were constructed using these materials, and fine mapping was performed by bulked segregant analysis (BSA) and kompetitive allele specific PCR (KASP) method. The Csa1G630860 (CsALMT2), encoding protein ALMT2, was determined as a candidate gene for regulating the hollow trait in fruit. Furthermore, the expression profile of CsALMT2 was analyzed by qRT-PCR and fluorescence in situ hybridization. The expression of CsALMT2 had obvious tissue specificity, and it was abundantly expressed in the ovule development zone inside the fruit. In the hollow material of cucumber fruit, the expression of CsALMT2 was significantly downregulated. The subcellular localization in tobacco leaves indicated that CsALMT2 was distributed on the plasma membrane. In conclusion, in this study, for the first time, we found the regulatory gene of hollow trait in cucumber fruit, which laid the foundation for subsequent research on the molecular mechanism of hollow trait formation in cucumber fruit, and made it possible to apply this gene in cucumber breeding.

Improving the Acid Resistance of Tannase TanBLp (AB379685) from Lactobacillus plantarum ATCC14917T by Site-Specific Mutagenesis.

Tannin acyl hydrolase referred commonly as tannase catalyzes the hydrolysis of the galloyl ester bond of tannin to release gallic acid. The tannase TanBLp which cloned from Lactobacillus plantarum ATCC14917T has high activity in the pH range (7.0-9.0) at 40 °C, it would be detrimental to the utilization at acidic environment. The catalytic sites and stability of TanBLp were analyzed using bioinformatics and site-specific mutagenesis. The results reiterated that the amino acid residues Ala164, Lys343, Glu357, Asp421 and His451 had played an important role in maintaining the activity. The optimum pH of mutants V75A, G77A, N94A, A164S and F243A were shifted from 8.0 to 6.0, and mutant V75A has the highest pH stability and activity at acidic conditions than other mutants, which was more suitable for industrial application to manufacture gallic acid. This study was of great significance to promote the industrialization and efficient utilization of tannase TanBLp.

Heterotrophic ammonium assimilation: An important driving force for aerobic denitrification of Rhodococcus erythropolis strain Y10.

Studies on microbial ammonium removal have focused on the heterotrophic nitrification of microorganisms and have rarely studied the role of ammonium assimilation. In this study, Rhodococcus erythropolis strain Y10 with the capacity of aerobic denitrification was screened from the surface flow constructed wetlands that treat high-strength ammonium swine wastewater. Instead of through nitrification, this strain removed ammonium through heterotrophic ammonium assimilation, with the removal rate of 9.69 mg/L/h. The KEGG nitrogen metabolism pathway analysis combined with nitrogen balance calculation manifested that the removal of nitrate and nitrite by R. erythropolis Y10 was achieved through two pathways: 1) assimilation reduction to biomass nitrogen and 2) aerobic denitrification reduction to gaseous nitrogen. Ammonium addition improved the aerobic denitrification rate of nitrate and nitrite. The maximal reduction rates of nitrate and nitrite increased from 7.82 and 7.23 mg/L/h to 9.09 and 8.09 mg/L/h respectively, when 100 mg/L ammonium was separately added to 150 mg/L nitrate and nitrite. Furthermore, the removal efficiency of total nitrogen increased from 69.80% and 77.65% to 89.19% and 91.88%, respectively. Heterotrophic ammonium assimilation promoted the aerobic denitrification efficiency of Rhodococcus erythropolis strain Y10.

Degradation of iprodione by a novel strain Azospirillum sp. A1-3 isolated from Tibet.

A bacterial strain A1-3 with iprodione-degrading capabilities was isolated from the soil for vegetable growing under greenhouses at Lhasa, Tibet. Based on phenotypic, phylogenetic, and genotypic data, strain A1-3 was considered to represent a novel species of genus Azospirillum. It was able to use iprodione as the sole source of carbon and energy for growth, 27.96 mg/L (50.80%) iprodione was reduced within 108 h at 25°C. During the degradation of iprodione by Azospirillum sp. A1-3, iprodione was firstly degraded to N-(3,5-dichlorophenyl)-2,4-dioxoimidazolidine, and then to (3,5-dichlorophenylurea) acetic acid. However, (3,5-dichlorophenylurea) acetic acid cannot be degraded to 3,5-dichloroaniline by Azospirillum sp. A1-3. A ipaH gene which has a highly similarity (98.72-99.92%) with other previously reported ipaH genes, was presented in Azospirillum sp. A1-3. Azospirillum novel strain with the ability of iprodione degradation associated with nitrogen fixation has never been reported to date, and Azospirillum sp. A1-3 might be a promising candidate for application in the bioremediation of iprodione-contaminated environments.

Effect of Garlic Organic Sulfides on Gene Expression Profiling in HepG2 Cells and Its Biological Function Analysis by Ingenuity Pathway Analysis System and Bio-Plex-Based Assays.

Garlic organic sulfides are dietary bioactive components with multiple biofunctions to prevent chronic diseases/inflammation and promote human health. DADS (diallyl disulfide), DATS (diallyl trisulfide), and DTS (diallyl tetrasulfide) are typical organic sulfides with similar structures from garlic. However, the structure-activity relationship of garlic organic sulfides remained unknown. The aim of the present study was to investigate the effect of DADS, DATS, and DTS on the gene expression profiling of human hepatocellular carcinoma cells (HepG2) by application of microarray and specialized analysis software, GO, Bio-Plex-based cytokines assay and IPA and analyze their structure-activity relationship according to antioxidant, anti-inflammatory, and metabolic-related properties. According to the microarray data, with the increase of S atom in garlic organic sulfides, its biological activity was gradually enhanced. In the general catalog of GO, garlic organic sulfides mainly affect biological process, molecular function, and cellular component. RT-qPCR results indicated that the microarray data is trustworthy, and the structure-activity analysis data found that more sulfur atoms have more powerful properties; thus, microarray data of DTS was preceded to the subsequent IPA analysis. The results of IPA analysis showed that the top 5 signaling pathways and molecular functions were disturbed by DTS; the molecular functions with the highest scores affected by DTS are cancer, cell apoptosis, and cell proliferation, which imply that the occurrence or metabolism of these diseases is related to the differential expression of the above-mentioned related genes and the activation of signaling channels, and the core of the most significant molecular network is inflammation. Finally, the results found that the secretions of 6 cytokines in macrophages were significantly inhibited by DTS treatment. This is the first study that analyzed the structure-activity relationship of garlic organic sulfides, which will provide useful genetic information for its multi-biofunction and promote their clinical application in the near future.

Rhamnolipid Enhances the Nitrogen Fixation Activity of Azotobacter chroococcum by Influencing Lysine Succinylation.

The enhancement of nitrogen fixation activity of diazotrophs is essential for safe crop production. Lysine succinylation (KSuc) is widely present in eukaryotes and prokaryotes and regulates various biological process. However, knowledge of the extent of KSuc in nitrogen fixation of Azotobacter chroococcum is scarce. In this study, we found that 250 mg/l of rhamnolipid (RL) significantly increased the nitrogen fixation activity of A. chroococcum by 39%, as compared with the control. Real-time quantitative reverse transcription PCR (qRT-PCR) confirmed that RL could remarkably increase the transcript levels of nifA and nifHDK genes. In addition, a global KSuc of A. chroococcum was profiled using a 4D label-free quantitative proteomic approach. In total, 5,008 KSuc sites were identified on 1,376 succinylated proteins. Bioinformatics analysis showed that the addition of RL influence on the KSuc level, and the succinylated proteins were involved in various metabolic processes, particularly enriched in oxidative phosphorylation, tricarboxylic acid cycle (TCA) cycle, and nitrogen metabolism. Meanwhile, multiple succinylation sites on MoFe protein (NifDK) may influence nitrogenase activity. These results would provide an experimental basis for the regulation of biological nitrogen fixation with KSuc and shed new light on the mechanistic study of nitrogen fixation.

Roles of Dietary Bioactive Peptides in Redox Balance and Metabolic Disorders.

Bioactive peptides (BPs) are fragments of 2-15 amino acid residues with biological properties. Dietary BPs derived from milk, egg, fish, soybean, corn, rice, quinoa, wheat, oat, potato, common bean, spirulina, and mussel are reported to possess beneficial effects on redox balance and metabolic disorders (obesity, diabetes, hypertension, and inflammatory bowel diseases (IBD)). Peptide length, sequence, and composition significantly affected the bioactive properties of dietary BPs. Numerous studies have demonstrated that various dietary protein-derived BPs exhibited biological activities through the modulation of various molecular mechanisms and signaling pathways, including Kelch-like ECH-associated protein 1/nuclear factor erythroid 2-related factor 2/antioxidant response element in oxidative stress; peroxisome proliferator-activated-γ, CCAAT/enhancer-binding protein-α, and sterol regulatory element binding protein 1 in obesity; insulin receptor substrate-1/phosphatidylinositol 3-kinase/protein kinase B and AMP-activated protein kinase in diabetes; angiotensin-converting enzyme inhibition in hypertension; and mitogen-activated protein kinase and nuclear factor-kappa B in IBD. This review focuses on the action of molecular mechanisms of dietary BPs and provides novel insights in the maintenance of redox balance and metabolic diseases of human.

Diversity of Culturable Bacteria Isolated from Highland Barley Cultivation Soil in Qamdo, Tibet Autonomous Region.

The soil bacterial communities have been widely investigated. However, there has been little study of the bacteria in Qinghai-Tibet Plateau, especially about the culturable bacteria in highland barley cultivation soil. Here, a total of 830 individual strains were obtained at 4°C and 25°C from a highland barley cultivation soil in Qamdo, Tibet Autonomous Region, using fifteen kinds of media. Seventy-seven species were obtained, which belonged to 42 genera and four phyla; the predominant phylum was Actinobacteria (68.82%), followed by Proteobacteria (15.59%), Firmicutes (14.29%), and Bacteroidetes (1.30%). The predominant genus was Streptomyces (22.08%, 17 species), followed by Bacillus (6.49%, five species), Micromonospora (5.19%, four species), Microbacterium (5.19%, four species), and Kribbella (3.90%, three species). The most diverse isolates belonged to a high G+C Gram-positive group; in particular, the Streptomyces genus is a dominant genus in the high G+C Gram-positive group. There were 62 species and 33 genera bacteria isolated at 25°C (80.52%), 23 species, and 18 genera bacteria isolated at 4°C (29.87%). Meanwhile, only eight species and six genera bacteria could be isolated at 25°C and 4°C. Of the 77 species, six isolates related to six genera might be novel taxa. The results showed abundant bacterial species diversity in the soil sample from the Qamdo, Tibet Autonomous Region.

Dihydromyricetin Acts as a Potential Redox Balance Mediator in Cancer Chemoprevention.

Dihydromyricetin (DHM) is a flavonoid extracted from the leaves and stems of the edible plant Ampelopsis grossedentata that has been used for Chinese Traditional Medicine. It has attracted considerable attention from consumers due to its beneficial properties including anticancer, antioxidative, and anti-inflammatory activities. Continuous oxidative stress caused by intracellular redox imbalance can lead to chronic inflammation, which is intimately associated with the initiation, promotion, and progression of cancer. DHM is considered a potential redox regulator for chronic disease prevention, and its biological activities are abundantly evaluated by using diverse cell and animal models. However, clinical investigations are still scanty. This review summarizes the current potential chemopreventive effects of DHM, including its properties such as anticancer, antioxidative, and anti-inflammatory activities, and further discusses the underlying molecular mechanisms of DHM in cancer chemoprevention by targeting redox balance and influencing the gut microbiota.

The ecdysone-induced protein 93 is a key factor regulating gonadotrophic cycles in the adult female mosquito Aedes aegypti.

Repeated blood feedings are required for adult female mosquitoes to maintain their gonadotrophic cycles, enabling them to be important pathogen carriers of human diseases. Elucidating the molecular mechanism underlying developmental switches between these mosquito gonadotrophic cycles will provide valuable insight into mosquito reproduction and could aid in the identification of targets to disrupt these cycles, thereby reducing disease transmission. We report here that the transcription factor ecdysone-induced protein 93 (E93), previously implicated in insect metamorphic transitions, plays a key role in determining the gonadotrophic cyclicity in adult females of the major arboviral vector Aedes aegypti Expression of the E93 gene in mosquitoes is down-regulated by juvenile hormone (JH) and up-regulated by 20-hydroxyecdysone (20E). We find that E93 controls Hormone Receptor 3 (HR3), the transcription factor linked to the termination of reproductive cycles. Moreover, knockdown of E93 expression via RNAi impaired fat body autophagy, suggesting that E93 governs autophagy-induced termination of vitellogenesis. E93 RNAi silencing prior to the first gonadotrophic cycle affected normal progression of the second cycle. Finally, transcriptomic analysis showed a considerable E93-dependent decline in the expression of genes involved in translation and metabolism at the end of a reproductive cycle. In conclusion, our data demonstrate that E93 acts as a crucial factor in regulating reproductive cycle switches in adult female mosquitoes.

Integrated Metabolome and Transcriptome Analysis Unveils Novel Pathway Involved in the Formation of Yellow Peel in Cucumber.

Yellow peel will adversely affect the appearance quality of cucumber fruit, but the metabolites and the molecular mechanism of pigment accumulation in cucumber peel remain unclear. Flavonoid metabolome and transcriptome analyses were carried out on the young peel and old peel of the color mutant L19 and the near-isogenic line L14. The results showed that there were 165 differential flavonoid metabolites in the old peel between L14 and L19. The total content of representative flavonoid metabolites in the old peel of L14 was 95 times that of L19, and 35 times that of young peel of L14, respectively. This might explain the difference of pigment accumulation in yellow peel. Furthermore, transcriptome analysis showed that there were 3396 and 1115 differentially expressed genes in the yellow color difference group (Young L14 vs. Old L14 and Old L14 vs. Old L19), respectively. These differentially expressed genes were significantly enriched in the MAPK signaling pathway-plant, plant-pathogen interaction, flavonoid biosynthesis and cutin, suberine and wax biosynthesis pathways. By analyzing the correlation between differential metabolites and differentially expressed genes, six candidate genes related to the synthesis of glycitein, kaempferol and homoeriodictyol are potentially important. In addition, four key transcription factors that belong to R2R3-MYB, bHLH51 and WRKY23 might be the major drivers of transcriptional changes in the peel between L14 and L19. Then, the expression patterns of these important genes were confirmed by qRT-PCR. These results suggested that the biosynthesis pathway of homoeriodictyol was a novel way to affect the yellowing of cucumber peel. Together, the results of this study provide a research basis for the biosynthesis and regulation of flavonoids in cucumber peel and form a significant step towards identifying the molecular mechanism of cucumber peel yellowing.