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Journal of Agricultural and Food Chemistry

American Chemical Society (ACS)

All preprints, ranked by how well they match Journal of Agricultural and Food Chemistry's content profile, based on 15 papers previously published here. The average preprint has a 0.02% match score for this journal, so anything above that is already an above-average fit. Older preprints may already have been published elsewhere.

1
Metabolic characteristics of taste differences under the soil and hydroponic cultures of sweet potato leaves by using non-targeted metabolomics

Lin, Z.; Li, G.; Zhang, H.; Ji, R.; Xu, Y.; Xu, G.; Li, H.; Liu, Z.; Luo, W.; Qiu, Y.; Qiu, S.; Tang, H.

2021-02-25 plant biology 10.1101/2021.02.24.432602 medRxiv
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Sweet potato leaves are consumed as green leafy vegetables in most of the world due to their nutritional and functional values, and the taste characteristics determine their commodity value and consumer acceptance. However, the metabolic composition and formation mechanism of taste quality in its leaves are not clear. In this study, we found that sweet potato leaves under different growing patterns, soil culture and hydroponic culture, which result in different taste quality. In particular, the taste quality in leafy sweet potato was effectively improved under hydroponic culture. Meanwhile, we further profiled metabolites in leaves of sweet potatoes under different growing patterns by using GC-QToF-MS. A total of 200 metabolites were identified, covering most of the metabolic pathways in plants. A comparison of the good taste and poor taste of sweet potato leaves resulted in 71 metabolites related to taste quality formation. In addition, the leaves with poor taste had lower levels of metabolites regarding amino acids metabolism, whereas was accompanied by high levels of metabolites in carbohydrates and secondary metabolism. This study provides new insights into the improvement of taste quality in leafy sweet potato.

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Metabolite Profiling of Epimedium sagittatum Bee Pollen: Identified Bioactive Flavonoids with Multi-Disease Functional Food Potential

Niu, D. F.; Chen, H.-x.; Lu, C.-y.; Zhang, C.-p.; Zheng, Q.-l.; Su, X.-l.; Fan, X.-m.; Luo, Y.-b.; Li, S.-y.; Yuan, B.; Liu, P.; Hu, F.-l.

2025-10-01 plant biology 10.1101/2025.09.29.679240 medRxiv
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Epimedium sagittatum is a valuable traditional medical plant and an important pollen source for bees. To address the lack of knowledge on its metabolic profile, we systematically analyzed Epimedium bee pollen (EBP) using UPLC-MS/MS and compared it with Brassica rapa bee pollen (BBP), which is widely distributed worldwide, and Camellia sinensis bee pollen (CBP), derived from a common medicinal plant. We firstly identified 1,073 metabolites, mainly flavonoids (30.8%) and phenolic acids (15.3%) in EBP. Although EBP showed fewer overall metabolites than BBP and CBP, it contained the highest total flavonoid content and 19 unique compounds (8 flavonoids). Compared with BBP, EBP had 449 differentially expressed metabolites (DEMs, 410 flavonoids), and 1,083 DEMs (410 flavonoids) compared with CBP. Forty-five flavonoids showed the highest concentrations in EBP. KEGG enrichment revealed flavonoid biosynthesis pathway upregulation. Network pharmacology indicated the potential advantages of EBP in active ingredient content (e.g., kaempferol, tamarixetin, and sinensetin), modulating targets in prostatitis, obesity, and alcoholic fatty liver disease. These findings highlight EBP as a distinctive flavonoid-rich bee pollen with promising functional food potential and underscore the value of Chinese medicinal herbs as high-quality bee pollen sources.

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Action mechanism of a novel agrichemical quinofumelin against Fusarium graminearum

Xiu, Q.; Yin, X.; Chen, Y.; Zhang, Z.; Mao, Y.; Wang, T.; Zhang, J.; Zhou, M.; Duan, Y.

2025-01-15 pathology 10.1101/2025.01.13.632717 medRxiv
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Modern fungicides have made significant contributions to crop disease management, but the development of resistant fungal strains has caused their failure in disease control. Therefore, developing fungicides with novel action mechanisms is the most effective measure to manage resistance. Quinofumelin, a novel quinoline fungicide, exhibits exceptional antifungal activity against phytopathogens. However, there is currently no available information on its mechanism of action. Here, we used transcriptome and metabolome analysis to observe a co-enrichment pattern of differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) within pyrimidine biosynthesis pathway (PBP), identifying down-regulation of dihydroorotate dehydrogenase (DHODH). Exogenous uridine monophosphate (UMP), uridine or uracil (metabolites in PBP) successfully restored quinofumelin-induced inhibition of mycelial growth in Fusarium graminearum and Fusarium asiaticum. Additionally, the deletion of FgDHODHII was determined to be lethal; however, mycelial growth of {Delta}FgDHODHII mutants could be restored by adding UMP, uridine or uracil. These findings indicate that the deficiencies in FgDHODHII are functionally equivalent to complete inhibition of its activity by quinofumelin. Finally, molecular docking, surface plasmon resonance (SPR) and microscale thermophoresis (MST) results strongly support the precise interaction between quinofumelin and FgDHODHII. Collectively, these findings provide compelling evidence for the involvement of de novo uracil biosynthesis as mechanism of action for quinofumelin while identifying FgDHODHII as its specific target.

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Widely targeted metabolomic analysis reveals differences in volatile metabolites among four Angelica species

Wang, L.; Zang, L. l.; Ji, J. j.; Lu, T. t.; Li, C.; Han, X. x.; Lee, S. R.; Ma, L.

2022-12-02 plant biology 10.1101/2022.12.01.518649 medRxiv
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Angelica L. has attracted global interest for its traditional medicinal uses and commercial values. However, few studies have focused on the metabolomic differences among the Angelica species. In this study, employing the widely targeted metabolomics based on gas chromatography-tandem mass spectrometry, the metabolomes of four Angelica species were analyzed (Angelica sinensis (Oliv.) Diels (A. sinensis), Angelica biserrata (R.H.Shan & Yuan) C.Q.Yuan & R.H.Shan (A. biserrata), Angelica dahurica (Hoffm.) Benth. & Hook.f. ex Franch. & Sav. (A. dahurica), Angelica keiskei Koidz. (A. keiskei)). A total of 698 volatile metabolites were identified and classified into fifteen different categories. The metabolomic analysis indicated that 7-hydroxycoumarin and Z-ligustilide were accumulated at significantly higher levels in A. sinensis, whereas the opposite pattern was observed for bornyl acetate. In addition, a high correspondence between the dendrogram of metabolite contents and phylogenetic positions was detected in the four species. This study provides a biochemical map for the exploitation, application and development of the Angelica species as medicinal plants or health-related dietary supplements.

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Identification and Characterization of CtUGT3 as the Key Player of Astragalin Biosynthesis in Safflower

Ren, C.; Xi, Z.; Xian, B.; Chen, C.; Huang, X.; Jiang, H.; Chen, J.; Peng, C.; Pei, J.

2023-06-25 plant biology 10.1101/2023.06.22.546132 medRxiv
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Safflower (Carthamus tinctorius L.) flowers are used as a traditional Chinese medicine for a long history. Flavonoids are the main bioactive components in safflower flowers, and most of them exist in the form of flavonoid glycosides. Only few glycosyltransferases have been identified in safflower. To reveal the uridine diphosphate glycosyltransferase (UGT) involved in flavonoid glycosides biosynthesis in safflower, a metabolomics and transcriptome analysis was performed by using the flowers under different light qualities treatments. Three differentially expressed UGT genes were screened, and their expressions were significantly related with concentrations of 9 flavonoid O-glycosides. Safflower corolla protoplasts were further used to confirm flavonoid O-glycosylation ability of UGT candidates. The astragalin (kaempferol 3-O-glucoside) content was only significantly increased when CtUGT3 was overexpressed in protoplasts. The biochemical properties and kinetic parameters of CtUGT3 were determined. CtUGT3 also showed flavonoid 3-OH and 7-OH glycosylation activities in vitro. Molecular modeling and site-directed mutagenesis revealed that E384 and S276 were critical catalytic residues for the 3-OH glycosylation of CtUGT3. These results demonstrate that CtUGT3 has a flavonoid 3-OH glycosylation function and is involved in the biosynthesis of astragalin in safflower. This study provides insights into the catalytic mechanisms of flavonoid O-glycosyltransferases, and makes a reference for flavonoid biosynthesis genes research in medicinal plants.

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Postharvest partial dehydration of blueberries enhanced blueberry wine aroma via upregulating phenylalanine metabolism and terpene biosynthesis

Wang, Y.; Zhang, Q.; Yang, Q.; Bian, C.; Huang, S.-Q.; Zhao, L.-L.; Huang, Y.-Q.; Chen, Q.; Zhang, H.-W.; Gao, X.-L.

2024-01-31 biochemistry 10.1101/2024.01.29.577155 medRxiv
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Postharvest partial dehydration of blueberries can enhance blueberry wine aroma, while the underlying mechanisms remain unclear. In this study, the key odor-active volatiles in blueberry wines fermented from dehydrated blueberries (30% weight loss) were identified via aroma extract dilution analysis. Results showed that increased levels of phenylalanine-derived compounds such as phenylethanol, and terpenes such as linalool and geraniol, primarily led to the enhancement of sweet, floral and fruity aromas of blueberry wines. Postharvest partial dehydration increased the contents of these compounds, which could be linked to the upregulation of VcGOT2 and VcPAR involved in phenylalanine metabolism, and the upregulation of VcDXS, VcHDR and VcTPS involved in terpene biosynthesis. Notably, the upregulated VcTPS encoded a monoterpene synthase responsible for producing linalool. These findings provided insight into the impact of postharvest dehydration on phenylalanine and terpene metabolism in blueberries, offering a reference for improving blueberry wine aroma through postharvest partial dehydration techniques.

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Functional characterization of five triterpene synthases through De-novo assembly and transcriptome analysis of Euphorbia grantii and Euphorbia tirucalli

Kumar, A.; Mulge, D. S.; Thakar, K. J.; Pandreka, A.; Warhekar, A. D.; Ramkumar, S.; Sharma, P.; Upadrasta, S.; Shanmugam, D.; Thulasiram, H.

2023-04-05 molecular biology 10.1101/2023.04.05.535548 medRxiv
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Euphorbia grantii and Euphorbia tirucalli known to synthesize diverse triterpenes including euphol and tirucallol. These two triterpenes known to possess potent anti-cancer, anti-bacterial, and anti-fungal properties along with various other biological activities. In this study, De-novo assembly and comparative transcriptome analysis of leaf and stem tissues of E. tirucalli and E. grantii were carried out to identify thirteen triterpene synthases from 1,40,227 in correlation with the metabolic profiling. Comparative transcriptome analysis indicated that EutTTS4 and EutTTS5 genes which encodes for euphol/tirucallol and tirucallol synthase were highly expressed in leaf and stem tissue. The genes which encodes -amyrin synthase (EutTTS1) and lupeol synthase (EutTTS2) were characterized by overexpressing them in YPH499 yeast strain. We have developed using hem1 and erg7 knock yeast strain of lanosterol deficient yeast (TMBL17) and used for over expression of friedelin synthase (EutTTS3), and two novel triterpenes synthases such as euphol/tirucallol synthase (EutTTS4) and tirucallol synthase (EutTTS5). These results are very useful in large scale production of triterpenes by genomic integration of respective triterpene synthases in TMBL yeast strain developed in this study. Significance StatementWe have functionally characterized triterpene synthases from E. tirucalli and E. grantii and developed a hem1 and erg7 knock out of lanosterol deficient yeast (TMBL17) for the large-scale production of triterpene and triterpene related products.

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Metabolites with benzene ring from sugarcane leaf play important role in plant-Spodoptera frugiperda interaction

Su, L.; Hu, C.; Wang, C.; Chen, B.; Zhao, Y.

2023-08-31 ecology 10.1101/2023.08.29.555346 medRxiv
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Secondary metabolism plays important role in plant growth and development, however, the relationship between secondary metabolism and adaptive plant-insect communication is largely unknown. The present study used sugarcane line highly susceptible to Spodoptera frugiperda and sister line with medium resistance to analyze the role of plant non-volatile organic compounds (NOCs) and volatile organic compounds (VOCs) in sugarcane-S. frugiperda interaction. A total of 46 plant NOCs and 15 plant VOCs significantly different between resistant and susceptible lines and were continuously up-regulated and down-regulated at different time points before/after S. frugiperda treatment were screened. Phenolic acids containing benzene ring accounted for the largest proportion of differential NOCs. Levels of 66.7% of these phenolic acids were higher in susceptible line. Feeding supplemented with NOCs showed that phenoxyacetic acid (phenolic acid) and 4-methoxybenzaldehyde (aromatic phenolic acid) both increased the male-to-female ratio of S. frugiperda. Aromatics containing benzene ring, accounted for the largest of differential VOCs in susceptible line. Two aromatics, p-cymene and benzene and 1-ethenyl-4-methoxy-, with higher level in susceptible line, were attractive to S. frugiperda. Terpenoids, aldehyde, and esters accounted for most of higher-in-resistant VOCs, with most tested to be repellent to S. frugiperda. Furthermore, transcriptome analysis of S. frugiperda feeding on susceptible and resistant lines combined with feeding assays revealed that tryptophan, as a precursor of aromatic compounds that also contains benzene ring, could promote the growth and development of S. frugiperda in nutritional deficiency condition. These findings together suggested that benzene-ring containing compounds play a critical role in plant-Spodoptera frugiperda interaction.

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Multi-omics analyses reveal the effect of DNA methylation on iridoid glycosides biosynthesis in Rehmannia glutinosa

Dong, T.; Du, Y.; Huang, T.; Su, J.; Yang, Q.; Guo, J.; Chen, P.; Xing, J.; Duan, H.

2025-06-16 molecular biology 10.1101/2025.06.11.659110 medRxiv
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Rehmannia glutinosa roots produce a group of lipophilic bioactive components known as iridoid glycosides. However, the molecular mechanisms by which DNA methylation regulates the biosynthesis of iridoid glycosides in R. glutinosa remain unknown. Herein, the development of R. glutinosa roots and the content of iridoid glycosides in the Wenxian region were significantly higher than those in Xinxiang. Low methylation level contributed to the accumulation of iridoid glycosides and the expression of related enzyme genes. Demethylation promoted both roots growth and development, as well as the accumulation of iridoid glycosides. Up-regulated RgALDH13, RgHDR1, RgG10H4, RgDXR1, RgG10H3, and RgUPD1, along with transcription factors (TFs), form the regulatory network for the biosynthesis of iridoid glycosides. Furthermore, the primary active region of the RgG10H4 promoter is located in the -164 bp region, where the RgMYB2 protein specifically binds to the TAACCA motif in the RgG10H4 promoter. Collectively, low levels of DNA methylation enhance the expression of core genes, followed by inducing the accumulation of iridoid glycosides, which suggests that RgMYB2-RgG10H4 plays a positive role in this process. These findings will contribute to a deeper understanding of the role of DNA methylation in the accumulation of iridoid glycosides. HighlightLow levels of DNA methylation contribute to the accumulation of iridoid glycosides and the expression of key enzyme genes in R. glutinosa.

10
Plant lipid metabolism in susceptible and tolerant soybean (Glycine max) cultivars in response to Phytophthora sojae colonization and infection

Adigun, O. A.; Pham, T. H.; Grapov, D.; Nadeem, M.; Jewell, L. E.; Cheema, M.; Galagedara, L.; Thomas, R.

2021-06-30 pathology 10.1101/2021.06.28.450227 medRxiv
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Soybean is one of the most cultivated crops globally and a staple food for much of the worlds population. The annual global crop losses due to infection by the Phytophthora sojae are currently estimated at approximately $2B USD, yet we have limited understanding of the role of lipid metabolism in the adaptative strategies used to limit infection and crop loss. We employed a multi-modal lipidomics approach to investigate how soybean cultivars remodel their lipid metabolism to successfully limit infection by Phytophthora sojae. Both the tolerant and susceptible soybean cultivars showed alterations in lipid metabolism in response to Phytophthora sojae infection. Relative to non-inoculated controls, induced accumulation of stigmasterol was observed in the susceptible cultivar whereas, induced accumulation of phospholipids and glycerolipids occurred in tolerant soybean cultivar. We have generated a comprehensive metabolic map of susceptible and tolerant soybean root and stem lipid metabolism to identify lipid modulators of host immune or tolerance response to Phytophthora sojae infection and identified potential pathways and unique lipid biomarkers like TG(15:0/22:0/22:5), TG(10:0/10:0/10:0), TG(10:0/10:0/14:0), DG(18:3/18:3), DG(16:0/18:3) and DG(24:0/18:2) as possible targets for the development of future plant protection solutions.

11
Flagellin FLiC Enhances Resistance of Upland Cotton to Verticillium dahliae

Zhou, H.; Xie, Y.; Wang, Y.; Zhu, H.; Tang, C.

2021-10-12 pathology 10.1101/2021.10.11.463976 medRxiv
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The mechanism by which flagellin induces an immune response in plants is still unclear. The purpose of this study is to reveal the effect and mechanism of flagellin in inducing plants to produce an immune response to increase the resistance to Verticillium dahliae (VD). The full-length flagellin gene C (FliC) was cloned from an endophytic bacteria (Pseudomonas) in the root of upland cotton cultivar Zhongmiansuo 41. The FliC protein purified in vitro has 47.50% and 32.42% biocontrol effects on resistant and susceptible cotton cultivars, respectively. FLiC can induce allergic reactions in tobacco leaf cells and immune responses in cotton plants. Smearing FLiC to cotton and performing RNA-seq analysis, it is significantly enriched in the activity of positive ion transporters such as potassium ions and calcium ions (Ca2+), diterpenoid biosynthesis, phenylpropane biosynthesis and other disease-resistant metabolic pathways. FLiC inhibits the expression of calcium antiporter activity gene (GhCAA) to accelerate intracellular Ca2+ influx and stimulate the increase of intracellular hydrogen peroxide (H2O2) and nitric oxide (NO) content. The coordinated regulation of Ca2+, H2O2 and NO enhances disease resistance. The resistance of transgenic FLiC gene Arabidopsis to VD was significantly improved. The FLiC gene can be used as an anti-VD gene and as a regulator to improve resistance to VD.

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Chemoproteomics reveals the epoxidase enzyme for the biosynthesis of camptothecin precursor strictosamide epoxide

Zhang, T.; Wang, Y.; Wu, S. w.; Tian, E. N.; Yang, C. S.; Zhou, Z. H.; Yan, X.; Wang, P. P.

2023-07-27 plant biology 10.1101/2023.07.26.550496 medRxiv
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Camptothecin and its derivatives are the third largest anticancer drugs in the world market, mainly used to treat malignant tumors such as lung, colon and cervical cancer. Camptothecin was firstly discovered in Camptotheca acuminate and extracted mainly from C. acuminate and Nothapodytes nimmoniana for medicine production (Sadre et al. 2016). However, the overharvesting of C. acuminate and N. nimmoniana has greatly reduced their populations in nature, which are currently listed as the second protected plants in China and India. It is estimated there would be 20 million new cancer cases in 2025 all over the world, meeting the growing demand for camptothecin and other anti-cancer drugs has become a daunting challenge (Seca et al. 2018). In this study we tried to elucidate the unknown biosynthetic pathway from strictosamide 1 to strictosamide epoxide 2 by unearthing the candidate enzymes from the proteome of plant Ophiorrhiza pumila using the chemoproteomic strategy.

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Differences in the metabolite profiles of tender leaves of wheat, barley, rye and Triticale based on LC-MS

Xing, P.; Song, Z.; Li, X.

2020-12-03 plant biology 10.1101/2020.12.03.409847 medRxiv
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Wheatgrass has emerged as a functional food source in recent years, but the detailed metabolomics basis for its health benefits remains poorly understood. In this study, liquid chromatography-mass spectrometry (LC-MS) analysis were used to study the metabolic profiling of seedlings from wheat, barley, rye and triticale, which revealed 1800 features in positive mode and 4303 features in negative mode. Principal component analysis (PCA) showed clear differences between species, and 164 differentially expressed metabolites (DEMs) were detected, including amino acids, organic acids, lipids, fatty acids, nucleic acids, flavonoids, amines, polyamines, vitamins, sugar derivatives and others. Unique metabolites in each species were identified. This study provides a glimpse into the metabolomics profiles of wheat and its wild relatives, which may form an important basis for nutrition, health and other parameters. Practical ApplicationThis manuscript present liquid chromatography-mass spectrometry (LC-MS) results of young sprouts of common wheat and its relatives. Our results may help to better understand the natural variation due to the genotype before metabolomics data are considered for application to wheatgrass and can provide a basis (assessment) for its potential pharmaceutical and nutritional value.

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Metabolome and transcriptome analysis reveal components regulating soapberry triterpenoid saponin biosynthesis

Xu, Y.; Zhao, G.; Ji, X.; Liu, J.; Zhao, T.; Gao, Y.; Gao, S.; Hao, Y.; Gao, Y.; Wang, L.; Weng, X.; Chen, Z.; Jia, L.

2022-03-01 molecular biology 10.1101/2022.02.28.482332 medRxiv
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Soapberry (Sapindus mukorossi Gaertn.) pericarps are rich in valuable bioactive triterpenoid saponins. However, the saponin content dynamics and the molecular regulatory network of saponin biosynthesis in soapberry pericarps remain largely unclear. Here, we performed combined metabolite profiling and transcriptome analysis to identify saponin accumulation kinetic patterns, investigate gene networks, and characterize key candidate genes and transcription factors involved in saponin biosynthesis in soapberry pericarps. A total of 54 saponins were tentatively identified, including 25 that were differentially accumulated. Furthermore, 49 genes putatively involved in sapogenin backbone biosynthesis and some candidate genes assumed to be responsible for the backbone modification, including 41 cytochrome P450s and 45 glycosyltransferases, were identified. Saponin-specific clusters/modules were identified by Mfuzz clustering and weighted gene co-expression network analysis, and one TF-gene regulatory network underlying saponin biosynthesis was proposed. The results of yeast one-hybrid assay and electrophoretic mobility shift assay suggested that SmbHLH2, SmTCP4, and SmWRKY27 may play important roles in the triterpenoid saponin biosynthesis by directly regulating the transcription of SmCYP71D-3 in soapberry pericarp. Overall, these findings provide valuable information for understanding the molecular regulatory mechanism of saponin biosynthesis, enriching the gene resources, and guiding further research on triterpenoid saponin accumulation in soapberry pericarps. One-sentence summaryCombining metabolome and transcriptome analysis to identify saponin kinetic patterns, gene networks, and key candidate genes and transcription factors involved in saponin biosynthesis of soapberry.

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The miR156/SPL9 interaction mode regulates the anthocyanin accumulation in potato

Li, N.; Nie, H.; Wu, X.; Wang, P.; Ma, Y.; Yang, E.; Wu, J.; Zhang, Z.; Xie, R.; Wang, D.; Ma, Y.

2025-01-06 molecular biology 10.1101/2025.01.06.631517 medRxiv
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Anthocyanins are an essential class of flavonoids that represent a large group of plant secondary metabolites. microRNAs (miRNAs) can target TFs related to anthocyanin synthesis and inhibit their expression, thereby affecting the expression level of key downstream structural genes and ultimately regulating the synthesis and accumulation of anthocyanins in plants. Nevertheless, the regulatory function of miR156a in anthocyanin synthesis, especially in potatoes, has yet to be investigated. In this study, the miR156a and its target gene StSPL9 were screened and analyzed from small RNA sequencing, degradome sequencing and transient expression assay. The function of miR156a in anthocyanin synthesis of potato tuber was investigated. Overexpression of miR156a (OE-miR156a) in potato tubers promoted anthocyanin synthesis while concurrently reducing flavonoid synthesis compared with wild-type (WT) potatoes. The miR156a-silenced tubers (STTM-miR156a) achieved using short tandem target mimics (STTM) contained significantly lower anthocyanin content and increased flavonoid accumulation compared to WT and OE-miR156a. Notably, overexpression of StSPL9 in potato yielded identical results. The relative expression levels of the anthocyanin-related structural genes PAL, 4CL, CHS, CHI, F3H, DFR, and UFGT in STTM-miR156a transgenic potato tubers showed the opposite trend to that observed in OE-miR156a potato tubers, as demonstrated by RNA sequencing and quantitative real-time PCR (qRT-PCR). The integrated analysis of the transcriptome and metabolome revealed that the accumulation of flavonoids and flavonols in STTM-miR156a was significantly increased than in the wild type, whereas the contents of anthocyanins and phenolic acids were notably reduced. Further analysis showed that the expression of CHS, FG2, BEATH, and CYP75A were up-regulated in STTM-miR156a, and HCT was downregulated, which resulted in a reduced accumulation of methyl 4-caffeoylquinate, a phenolic acid metabolite. Therefore, it is demonstrated that miR156a indirectly modulates the expression of CHS, BEATH, CYP75A, HCT, and FG2 by targeting and degrading its target gene StSPL9 and other SPL genes, thus influencing anthocyanin accumulation in potato tuber. This study provides valuable insights into the complex regulatory network governing anthocyanin biosynthesis in Solanum species.

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Metabolomic and transcriptomic analyses reveal the effects of grafting on anthocyanin synthesis in grapevine

Zhong, H.; Liu, Z.; Zhang, F.; Zhou, X.; Sun, X.; Liu, W.; Xiao, H.; Wang, N.; Pan, M.; Wu, X.; Zhou, Y.

2021-10-09 plant biology 10.1101/2021.10.09.463741 medRxiv
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The grafting has been commonly used in viticulture, which joints the scion from a cultivar with the stem of a rootstock. Grafting has crucial impacts on various phenotypes of the cultivar including berry metabolome and berry coloring, however, the genetics and regulation mechanisms are largely unexplored. In this study, we analyzed the phenotypic, metabolomic and transcriptomic profiles at three stages (45, 75 and105 days after flowering) of the Crimson Seedless (Vitis vinifera, CS) cultivar grafted to four rootstocks (three heterografting: CS/101-14MG, CS/SO4, CS/110R and one self-grafting CS/CS) with an own-rooted grafting-free Crimson Seedless (CS) as a control. All the heterografting plants had a significant influence on berry reddening as early as ~45 days after flowering. The grafting of rootstocks promoted anthocyanin synthesis and accumulation in grape berries. The metabolomic features showed that Cyanidin 3-O-glucoside, Delphinidin 3-O-glucosid, Malvidin 3-O-glucoside, Peonidin 3-O-glucoside and Petunidin 3-O-glucoside were the pigments responsible for the purplish-red color peels. Transcriptomic analyses revealed that the anthocyanins biosynthetic related genes from the upstream (phenylalanine ammonia-lyase) to the downstream (anthocyanidin 3-O-glucosyltransferase and anthocyanidin synthase) were upregulated with the accumulations of anthocyanins in CS/101-14MG, CS/SO4 and CS/110R. At the same time, all these genes were also highly expressed and more anthocyanin was accumulated in CS/CS samples compared to CS samples, suggesting that self-grafting rootstocks might also have promoted berry reddening in grapevine. Our results provide global transcriptomic and metabolomic features in berry coloring regulation under different grafting conditions for improving the berry quality in grapevine production.

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Polysaccharides from Balanophora harlandii Hook: Isolation, Characterization, and Anti-Inflammation Activities

Li, Y.; Li, X.; Yuan, Q.; Zhu, L.; Xia, F.; Wang, Y.; Xue, M.; He, Y.; Yuan, C.

2023-09-28 molecular biology 10.1101/2023.09.27.559774 medRxiv
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Balanophora harlandii Hook (B. harlandii), a folk medicine, has been traditionally employed to treat traumatic bleeding, gastroenteritis, icteric hepatitis, hemorrhoids, and other conditions. In this work, polysaccharides with anti-inflammatory effects were extracted and purified from B. harlandii. The extraction conditions were optimized, and the properties of one purified neutral fraction, denoted as BHPs-W-S3, were analyzed. Gel permeation chromatography (GPC) was carried out to measure the molecular weight. The structure of BHPs-W-S3 was assessed based on monosaccharide composition analysis, Fourier transform infrared (FT-IR) spectroscopy, methylation analysis, and nuclear magnetic resonance (NMR) spectroscopy. BHPs-W-S3 has a molecular weight of 14.1 kDa, and its three main monosaccharides are glucose, galactose, and mannose with a molar ratio of 6.4:1.7:1.1. Its main chain consists of [->]6)--D-Glcp-(1[->], [->]4,6)--D-Glcp-(1[->], [->]6)-{beta}-D-Galp-(1[->], [->]3,6)-{beta}-D-Galp-(1[->], and it has branch chains at the O-4 and/or O-3 positions. In addition, in vitro experiments show that the polysaccharides from B. harlandi can decrease the phosphorylation level of p65 and IKB- in LPS-induced RAW264.7 cells to reduce the expression of the pro-inflammatory genes such as TNF-, IL-6, and IL-1{beta}. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=117 SRC="FIGDIR/small/559774v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@17ccfeforg.highwire.dtl.DTLVardef@137726borg.highwire.dtl.DTLVardef@139100dorg.highwire.dtl.DTLVardef@14cce50_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Comparative metabolomics of wild and cultivated yew: insights into metabolic diversity and environmental adaptability

wang, d.; zhang, y.

2024-07-29 molecular biology 10.1101/2024.07.29.605693 medRxiv
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Taxus cuspidata is a well-known gymnosperm with great ornamental and medicinal value. The study aims to reveal the metabolic differences between wild and cultivated species of T. cuspidata, and to analyze the genetic and ecological factors behind these differences. This study conducted a comparative metabolomics analysis of wild and cultivated T. cuspidata based on LC-MS/MS technology. The results showed: (1) A total of 7030 metabolites were identified, primarily including flavonoids, organic acids, phenolic acids, amino acids and their derivatives, lipids, and alkaloids, among others; (2) 2381 differential metabolites were confirmed: 949 higher in cultivated species and 1432 higher in wild species, which suggesting wild species have more advantageous metabolites. (3) Through KEGG annotation, 20 significant metabolic pathways were identified, with sugar metabolism, photosynthesis, and sulfur metabolism were significantly higher in wild species. In contrast, pathways related to most amino acids and their derivatives, flavonoids, terpenoids, polyphenols, alkaloids, and plant hormones were significantly higher in cultivated species. In conclusion, the wild species are inferior to cultivated species in terms of drought resistance, growth rate, and medicinal value for cancer treatment. However, the advantage of wild species lies in their significantly higher diversity of upregulated secondary metabolites due to their rich genetic resources, which exhibit greater metabolic diversity and environmental adaptability, which enhances their survival capability. Furthermore, the wild species exhibit significantly higher efficiency in photosynthesis and sugar metabolism compared to cultivated species, enabling them to better withstand low-temperature stress. This study has provided the direction for research into the mechanisms of stress resistance in T. cuspidata and has also established a theoretical basis for formulating scientifically and reasonable conservation strategies for wild species.

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Metabolic and transcriptomic insights into a GalNAc/Man-Specific lectin in yeast fermentation

Liu, S.; Li, L.; Niu, H.; Li, W.; Tong, C.

2025-05-26 microbiology 10.1101/2025.05.26.656115 medRxiv
Top 0.1%
15.7%
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Brewers yeast (Saccharomyces cerevisiae) plays a central role in fermentation, and improving its performance is crucial in the brewing industry. This study explored how Cyclina sinensis lectin (CSL), a bioactive peptide from shellfish, influences yeast metabolism using proteomics and metabolomics. CSL bound to yeast peptidoglycan in a concentration-dependent manner and altered cell surface structure. Proteomic analysis revealed 117 differentially expressed proteins after 24 h of CSL treatment, with upregulation of key glycolytic enzymes (e.g., hexokinase, GAPDH) and downregulation of TCA cycle enzymes, suggesting enhanced ethanol production via glycolysis activation and TCA suppression. Metabolomic profiling further confirmed this, showing increased -D-glucose, glucose-6-phosphate, NAD+, and glutathione, alongside reduced TCA intermediates like malic acid. These results indicate CSL promotes ethanol accumulation by reprogramming central carbon metabolism. This study provides novel insight into the metabolic modulation of yeast by marine lectins and suggests potential applications of CSL in improving fermentation

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Dynamic characteristics and Functional Analysis Provide new insights into the role of GauERF105 in resistance against Verticillium wilt in Cotton

UMER, M. J.; Wang, Y.; HOU, Y.; XU, Y.; MEHARI, T. G.; ZHENG, J.; WANG, Y.; ZHOU, Z.; LI, Z.; LIU, F.

2022-01-02 pathology 10.1101/2021.12.30.474616 medRxiv
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15.6%
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Verticillium wilt is the most devastating disease of cotton and it results in huge yield losses every year in the fields. The underlying mechanisms of VW in cotton are not well explored yet. In the current approach we used the transcriptome data from G. australe in response to Verticillium wilt attack to mine the ERF TFs and prove their potential role in resistance against VW attack in cotton. We identified 23 ERFs in total, and on the basis of expression at different time points i.e., 24h, 48h and 72h post inoculation and selected GauERF105 for further validation. We performed VIGS in cotton and over expression in Arabidopsis respectively. Moreover, DAB and trypan staining also suggests that the impact of disease was more in the wildtype as compared to transgene lines. On the basis of our results, we confirmed that GauERF105 is the key candidate and playing a key role for defending cotton against VW attack. Current finding might be helpful for generating resistance germplasm in cotton and it will be beneficial to recover the yield losses in field.