@article{xi_wang_cagle_zhu_odle_xie_2023, title={Exploring the Prebiotic Activities of Proanthocyanidins on a Platform Using the Three-Dimensionally (3D)-Cultured Organoids}, volume={101}, ISSN={["1525-3163"]}, DOI={10.1093/jas/skad281.421}, abstractNote={Abstract
               Using antibiotics, the antimicrobial substance active against bacteria and promoting growth efficiency, in feedstuffs and food supply has been attracting great attention due to its side effects and contribution to antibiotic resistance. Therefore, exploring talternatives to antibiotics is of great significance and urgent need for human health and animal industries with a sustainable high efficiency. The objective of this study is to evaluate the biological and medicinal activities of the monomers of proanthocyanidins (PAs), such as epicatechin, epigallocatechin gallate, and flavanols such as quercetin, isoquercetrin, and rutin generated from engineered plants. The evaluations were performed in intestinal organoids isolated from ileum of neonatal piglets. The organoids after expended in vitro were incubated with or without the candidate compounds for 24 hours, and then treated with or without polyinosinic-polycytidylic acid [Poly (I:C), 10 µg/mL] for another 24 hours, a synthetic analog of double-stranded RNA (can induce a molecular pattern associated with viral infections). Cell proliferation, barrier function, toll-like receptor pathway and apoptosis as well as organic cation transporters were assessed by measuring the abundance of the corresponding genes. Concentration gradient (0 to 200 µM) measurements showed that isoquercetrin and epigallocatechin gallate might stimulate the intestinal cell proliferation, promote the uptake of L-carnitine, and increase barrier function and mucin secretion (P < 0.05). Epigallocatechin gallate and epicatechin might affect the inflammation responses via modifying expression of Interleukins but not induce apoptosis. Interactions between the examined these compounds and Poly (I: C) were not observed (P > 0.05), but the influence on the challenged pattern were tested for some of the measured genes (P < 0.05). Based on the data collected from this in vitro study, we conclude that epigallocatechin gallate is a potential PA monomer with all prebiotic characteristics and its applicable values in feedstuff and food supply should be studied in vivo studies in domestic (food) animals with and without antigen challenges. Supported by NC Biotechnology Center project (1107)2022-3082 and the North Carolina Agricultural Research Hatch Projects 02780.}, journal={JOURNAL OF ANIMAL SCIENCE}, author={Xi, Lin and Wang, Feng and Cagle, Daisy and Zhu, Yue and Odle, Jack and Xie, Deyu}, year={2023}, month={Nov}, pages={355–356} }
 @article{zhu_yuzuak_sun_xie_2023, title={Identification and biosynthesis of plant papanridins, a group of novel oligomeric flavonoids}, volume={16}, ISSN={["1752-9867"]}, DOI={10.1016/j.molp.2023.09.015}, abstractNote={The discovery of novel flavonoids and elucidation of their biosynthesis are fundamental to understanding their roles in plants and their benefits for human and animal health. Here, we report a new pathway for polymerization of a group of novel oligomeric flavonoids in plants. We engineered red cells for discovering genes of interest involved in the flavonoid pathway and identified a gene encoding a novel flavanol polymerase (FP) localized in the central vacuole. FP catalyzes the polymerization of flavanols, such as epicatechin and catechin, to produce yellowish dimers or oligomers. Structural elucidation shows that these compounds feature a novel oligomeric flaven–flavan (FF) skeleton linked by interflavan–flaven and interflaven bonds, distinguishing them from proanthocyanidins and dehydrodicatechins. Detailed chemical and physical characterizations further confirmed the novel FFs as flavonoids. Mechanistic investigations demonstrated that FP polymerizes flavan-3-ols and flav-2-en-3-ol carbocation, forming dimeric or oligomeric flaven-4→8-flavans, which we term “papanridins.” Data from transgenic experiments, mutant analysis, metabolic profiling, and phylogenetic analyses show that the biosynthesis of papanridins is prevalent in cacao, grape, blueberry, corn, rice, Arabidopsis, and other species in the plant kingdom. In summary, our study discoveries a group of novel oligomeric flavonoids, namely papanridins, and reveals that a novel FP-mediated polymerization mechanism for the biosynthesis of papanridins in plants.}, number={11}, journal={MOLECULAR PLANT}, author={Zhu, Yue and Yuzuak, Seyit and Sun, Xiaoyan and Xie, De-Yu}, year={2023}, month={Nov}, pages={1773–1793} }
 @article{judd_dong_sun_zhu_li_xie_2023, title={Metabolic engineering of the anthocyanin biosynthetic pathway in Artemisia annua and relation to the expression of the artemisinin biosynthetic pathway}, volume={257}, ISSN={["1432-2048"]}, url={https://doi.org/10.1007/s00425-023-04091-6}, DOI={10.1007/s00425-023-04091-6}, abstractNote={Four types of cells were engineered from Artemisia annua to produce approximately 17 anthocyanins, four of which were elucidated structurally. All of them expressed the artemisinin pathway. Artemisia annua is the only medicinal crop to produce artemisinin for the treatment of malignant malaria. Unfortunately, hundreds of thousands of people still lose their life every year due to the lack of sufficient artemisinin. Artemisinin is considered to result from the spontaneous autoxidation of dihydroartemisinic acid in the presence of reactive oxygen species (ROS) in an oxidative condition of glandular trichomes (GTs); however, whether increasing antioxidative compounds can inhibit artemisinin biosynthesis in plant cells is unknown. Anthocyanins are potent antioxidants that can remove ROS in plant cells. To date, no anthocyanins have been structurally elucidated from A. annua. In this study, we had two goals: (1) to engineer anthocyanins in A. annua cells and (2) to understand the artemisinin biosynthesis in anthocyanin-producing cells. Arabidopsis Production of Anthocyanin Pigment 1 was used to engineer four types of transgenic anthocyanin-producing A. annua (TAPA1-4) cells. Three wild-type cell types were developed as controls. TAPA1 cells produced the highest contents of total anthocyanins. LC-MS analysis detected 17 anthocyanin or anthocyanidin compounds. Crystallization, LC/MS/MS, and NMR analyses identified cyanidin, pelargonidin, one cyanin, and one pelargonin. An integrative analysis characterized that four types of TAPA cells expressed the artemisinin pathway and TAPA1 cells produced the highest artemisinin and artemisinic acid. The contents of arteannuin B were similar in seven cell types. These data showed that the engineering of anthocyanins does not eliminate the biosynthesis of artemisinin in cells. These data allow us to propose a new hypothesis that enzymes catalyze the formation of artemisinin from dihydroartemisinic acid in non-GT cells. These findings show a new platform to increase artemisinin production via non-GT cells of A. annua.}, number={3}, journal={PLANTA}, author={Judd, Rika and Dong, Yilun and Sun, Xiaoyan and Zhu, Yue and Li, Mingzhuo and Xie, De-Yu}, year={2023}, month={Mar} }
 @article{zhu_scholle_kisthardt_xie_2022, title={<p>Flavonols and dihydroflavonols inhibit the main protease activity of SARS-CoV-2 and the replication of human coronavirus 229E</p>}, volume={571}, ISSN={["1089-862X"]}, DOI={10.1016/j.virol.2022.04.005}, abstractNote={Since December 2019, the deadly novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the current COVID-19 pandemic. To date, vaccines are available in the developed countries to prevent the infection of this virus; however, medicines are necessary to help control COVID-19. Human coronavirus 229E (HCoV-229E) causes the common cold. The main protease (M pro ) is an essential enzyme required for the multiplication of these two viruses in the host cells, and thus is an appropriate candidate to screen potential medicinal compounds. Flavonols and dihydroflavonols are two groups of plant flavonoids. In this study, we report docking simulation with two M pro  enzymes and five flavonols and three dihydroflavonols, in vitro inhibition of the SARS-CoV-2 M pro , and in vitro inhibition of the HCoV 229E replication. The docking simulation results predicted that (+)-dihydrokaempferol, (+)- dihydroquercetin, (+)-dihydromyricetin, kaempferol, quercetin, myricentin, isoquercitrin, and rutin could bind to at least two subsites (S1, S1', S2, and S4) in the binding pocket and inhibit the activity of SARS-CoV-2 M pro . Their affinity scores ranged from -8.8 to -7.4 (kcal/mol). Likewise, these compounds were predicted to bind and inhibit the HCoV-229E M pro  activity with affinity scores ranging from -7.1 to -7.8 (kcal/mol). In vitro inhibition assays showed that seven available compounds effectively inhibited the SARS-CoV-2 M pro  activity and their IC 50  values ranged from 0.125 to 12.9 μM. Five compounds inhibited the replication of HCoV-229E in Huh-7 cells. These findings indicate that these antioxidative flavonols and dihydroflavonols are promising candidates for curbing the two viruses.}, journal={VIROLOGY}, author={Zhu, Yue and Scholle, Frank and Kisthardt, Samantha C. and Xie, De-Yu}, year={2022}, month={Jun}, pages={21–33} }
 @article{li_he_la hovary_zhu_dong_liu_xing_liu_jie_ma_et al._2022, title={A de novo regulation design shows an effectiveness in altering plant secondary metabolism}, volume={37}, ISSN={["2090-1224"]}, url={http://dx.doi.org/10.1016/j.jare.2021.06.017}, DOI={10.1016/j.jare.2021.06.017}, abstractNote={Transcription factors (TFs) and}, journal={JOURNAL OF ADVANCED RESEARCH}, publisher={Elsevier BV}, author={Li, Mingzhuo and He, Xianzhi and La Hovary, Christophe and Zhu, Yue and Dong, Yilun and Liu, Shibiao and Xing, Hucheng and Liu, Yajun and Jie, Yucheng and Ma, Dongming and et al.}, year={2022}, month={Mar}, pages={43–60} }
 @article{zhu_xie_2020, title={Docking Characterization and in vitro Inhibitory Activity of Flavan-3-ols and Dimeric Proanthocyanidins Against the Main Protease Activity of SARS-Cov-2}, volume={11}, ISSN={1664-462X}, url={http://dx.doi.org/10.3389/fpls.2020.601316}, DOI={10.3389/fpls.2020.601316}, abstractNote={We report to use the main protease (Mpro) of SARS-Cov-2 to screen plant flavan-3-ols and proanthocyanidins. Twelve compounds, (–)-afzelechin (AF), (–)-epiafzelechin (EAF), (+)-catechin (CA), (–)-epicatechin (EC), (+)-gallocatechin (GC), (–)-epigallocatechin (EGC), (+)-catechin-3-O-gallate (CAG), (–)-epicatechin-3-O-gallate (ECG), (–)-gallocatechin-3-O-gallate (GCG), (–)-epigallocatechin-3-O-gallate (EGCG), procyanidin A2 (PA2), and procyanidin B2 (PB2), were selected for docking simulation. The resulting data predicted that all 12 metabolites could bind to Mpro. The affinity scores of PA2 and PB2 were predicted to be −9.2, followed by ECG, GCG, EGCG, and CAG, −8.3 to −8.7, and then six flavan-3-ol aglycones, −7.0 to −7.7. Docking characterization predicted that these compounds bound to three or four subsites (S1, S1′, S2, and S4) in the binding pocket of Mpro via different spatial ways and various formation of one to four hydrogen bonds. In vitro analysis with 10 available compounds showed that CAG, ECG, GCG, EGCG, and PB2 inhibited the Mpro activity with an IC50 value, 2.98 ± 0.21, 5.21 ± 0.5, 6.38 ± 0.5, 7.51 ± 0.21, and 75.3 ± 1.29 μM, respectively, while CA, EC, EGC, GC, and PA2 did not have inhibitory activities. To further substantiate the inhibitory activities, extracts prepared from green tea (GT), two muscadine grapes (MG), cacao, and dark chocolate (DC), which are rich in CAG, ECG, GAG, EGCG, or/and PB2, were used for inhibitory assay. The resulting data showed that GT, two MG, cacao, and DC extracts inhibited the Mpro activity with an IC50 value, 2.84 ± 0.25, 29.54 ± 0.41, 29.93 ± 0.83, 153.3 ± 47.3, and 256.39 ± 66.3 μg/ml, respectively. These findings indicate that on the one hand, the structural features of flavan-3-ols are closely associated with the affinity scores; on the other hand, the galloylation and oligomeric types of flavan-3-ols are critical in creating the inhibitory activity against the Mpro activity.}, journal={Frontiers in Plant Science}, publisher={Frontiers Media SA}, author={Zhu, Yue and Xie, De-Yu}, year={2020}, month={Nov} }
 @article{ma_li_zhu_xie_2017, title={Overexpression and Suppression of Artemisia annua 4-Hydroxy-3-Methylbut-2-enyl Diphosphate Reductase 1 Gene (AaHDR1) Differentially Regulate Artemisinin and Terpenoid Biosynthesis}, volume={8}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2017.00077}, abstractNote={4-Hydroxy-3-methylbut-2-enyl diphosphate reductase (HDR) catalyzes the last step of the 2-C-methyl-D-erythritol 4- phosphate (MEP) pathway to synthesize isopentenyl pyrophosphate (IPP) and dimethylallyl diphosphate (DMAPP). To date, little is known regarding effects of an increase or a decrease of a HDR expression on terpenoid and other metabolite profiles in plants. In our study, an Artemisia annua HDR cDNA (namely AaHDR1) was cloned from leaves. Expression profiling showed that it was highly expressed in leaves, roots, stems, and flowers with different levels. Green florescence protein fusion and confocal microscope analyses showed that AaHDR1 was localized in chloroplasts. The overexpression of AaHDR1 increased contents of artemisinin, arteannuin B and other sesquiterpenes, and multiple monoterpenes. By contrast, the suppression of AaHDR1 by anti-sense led to opposite results. In addition, an untargeted metabolic profiling showed that the overexpression and suppression altered non-polar metabolite profiles. In conclusion, the overexpression and suppression of AaHDR1 protein level in plastids differentially affect artemisinin and other terpenoid biosynthesis, and alter non-polar metabolite profiles of A. annua. Particularly, its overexpression leading to the increase of artemisinin production is informative to future metabolic engineering of this antimalarial medicine.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Ma, Dongming and Li, Gui and Zhu, Yue and Xie, De-Yu}, year={2017}, month={Jan} }
 @article{ma_li_alejos-gonzalez_zhu_xue_wang_zhang_li_ye_wang_et al._2017, title={Overexpression of a type-I isopentenyl pyrophosphate isomerase of Artemisia annua in the cytosol leads to high arteannuinB production and artemisinin increase}, volume={91}, DOI={10.1111/tpj.13583}, abstractNote={SummaryWe recently characterized a gene–terpene network that is associated with artemisinin biosynthesis in self‐pollinated (SP) Artemisia annua, an effective antimalarial plant. We hypothesize that an alteration of gene expression in the network may improve the production of artemisinin and its precursors. In this study, we cloned an isopentenyl pyrophosphate isomerase (IPPI) cDNA, AaIPPI1, from Artemisia annua (Aa). The full‐length cDNA encodes a type‐I IPPI containing a plastid transit peptide (PTP) at its amino terminus. After the removal of the PTP, the recombinant truncated AaIPPI1 isomerized isopentenyl pyrophosphate (IPP) to dimethyl allyl pyrophosphate (DMAPP) and vice versa. The steady‐state equilibrium ratio of IPP/DMAPP in the enzymatic reactions was approximately 1:7. The truncated AaIPPI1 was overexpressed in the cytosol of the SP A. annua variety. The leaves of transgenic plants produced approximately 4% arteannuin B (g g−1, dry weight, dw) and 0.17–0.25% artemisinin (g g−1, dw), the levels of which were significantly higher than those in the leaves of wild‐type plants. In addition, transgenic plants showed an increase in artemisinic acid production of more than 1% (g g−1, dw). In contrast, isoprene formation was significantly reduced in transgenic plants. These results provide evidence that overexpression of AaIPPI1 in the cytosol can lead to metabolic alterations of terpenoid biosynthesis, and show that these transgenic plants have the potential to yield high production levels of arteannuin B as a new precursor source for artemisinin.}, number={3}, journal={Plant Journal}, author={Ma, D. M. and Li, G. and Alejos-Gonzalez, F. and Zhu, Y. and Xue, Z. and Wang, A. M. and Zhang, H. and Li, X. and Ye, H. C. and Wang, H. and et al.}, year={2017}, pages={466–479} }