Comprehensive Metabolic and Transcriptomic Profiling of Various
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Metabolic Engineering of Microbial Cell Factories for Biosynthesis of Flavonoids: a Review
molecules Review Metabolic Engineering of Microbial Cell Factories for Biosynthesis of Flavonoids: A Review Hanghang Lou 1,†, Lifei Hu 2,†, Hongyun Lu 1, Tianyu Wei 1 and Qihe Chen 1,* 1 Department of Food Science and Nutrition, Zhejiang University, Hangzhou 310058, China; [email protected] (H.L.); [email protected] (H.L.); [email protected] (T.W.) 2 Hubei Key Lab of Quality and Safety of Traditional Chinese Medicine & Health Food, Huangshi 435100, China; [email protected] * Correspondence: [email protected]; Tel.: +86-0571-8698-4316 † These authors are equally to this manuscript. Abstract: Flavonoids belong to a class of plant secondary metabolites that have a polyphenol structure. Flavonoids show extensive biological activity, such as antioxidative, anti-inflammatory, anti-mutagenic, anti-cancer, and antibacterial properties, so they are widely used in the food, phar- maceutical, and nutraceutical industries. However, traditional sources of flavonoids are no longer sufficient to meet current demands. In recent years, with the clarification of the biosynthetic pathway of flavonoids and the development of synthetic biology, it has become possible to use synthetic metabolic engineering methods with microorganisms as hosts to produce flavonoids. This article mainly reviews the biosynthetic pathways of flavonoids and the development of microbial expression systems for the production of flavonoids in order to provide a useful reference for further research on synthetic metabolic engineering of flavonoids. Meanwhile, the application of co-culture systems in the biosynthesis of flavonoids is emphasized in this review. Citation: Lou, H.; Hu, L.; Lu, H.; Wei, Keywords: flavonoids; metabolic engineering; co-culture system; biosynthesis; microbial cell factories T.; Chen, Q. -
Key Enzymes Involved in the Synthesis of Hops Phytochemical Compounds: from Structure, Functions to Applications
International Journal of Molecular Sciences Review Key Enzymes Involved in the Synthesis of Hops Phytochemical Compounds: From Structure, Functions to Applications Kai Hong , Limin Wang, Agbaka Johnpaul , Chenyan Lv * and Changwei Ma * College of Food Science and Nutritional Engineering, China Agricultural University, 17 Qinghua Donglu Road, Haidian District, Beijing 100083, China; [email protected] (K.H.); [email protected] (L.W.); [email protected] (A.J.) * Correspondence: [email protected] (C.L.); [email protected] (C.M.); Tel./Fax: +86-10-62737643 (C.M.) Abstract: Humulus lupulus L. is an essential source of aroma compounds, hop bitter acids, and xanthohumol derivatives mainly exploited as flavourings in beer brewing and with demonstrated potential for the treatment of certain diseases. To acquire a comprehensive understanding of the biosynthesis of these compounds, the primary enzymes involved in the three major pathways of hops’ phytochemical composition are herein critically summarized. Hops’ phytochemical components impart bitterness, aroma, and antioxidant activity to beers. The biosynthesis pathways have been extensively studied and enzymes play essential roles in the processes. Here, we introduced the enzymes involved in the biosynthesis of hop bitter acids, monoterpenes and xanthohumol deriva- tives, including the branched-chain aminotransferase (BCAT), branched-chain keto-acid dehydroge- nase (BCKDH), carboxyl CoA ligase (CCL), valerophenone synthase (VPS), prenyltransferase (PT), 1-deoxyxylulose-5-phosphate synthase (DXS), 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HDR), Geranyl diphosphate synthase (GPPS), monoterpene synthase enzymes (MTS), cinnamate Citation: Hong, K.; Wang, L.; 4-hydroxylase (C4H), chalcone synthase (CHS_H1), chalcone isomerase (CHI)-like proteins (CHIL), Johnpaul, A.; Lv, C.; Ma, C. -
Building Blue E. Coli: Engineering the Anthocyanin Biosynthetic Pathway
Building blue E. coli: Engineering the anthocyanin biosynthetic pathway Leah Johnston1, Lucas Jarche1, Alexander Porter1, Julie Ryu1, Emma Price1, Emma Finlayson-Trick1, Khaled Aly1, Paul Bissonnette2, Eric Pace3, Dr. John Rohde1 1Department of Microbiology and Immunology, 2Department of Chemistry, 3Department of Agriculture Dalhousie University, Halifax, Canada, B3H 1X5 THE ANTHOCYANIN PATHWAY METHODS RESULTS 1kb (B) Method of Template DNA for each of the genes required for the production of the Anthocyanin biosynthetic Gene Size (bp) Function Epitope ladder (B) Acquisition of pathway in E. coli were acquired from the following sources outlined in Figure 1 (B). (A) Name Tag Template DNA 10 Phenylalanine Lyase involved in Amplified from A. (A) 2762 polyphenol S-Tag thaliana cDNA, Ammonia . synthesis. insert in Phenylalanine Ammonia Lyase and 4-Coumaroyl CoA Ligase were acquired as inserts in a 3.0. Lyase pACYCDuet-1 pACYCDuet-1 plasmid from Sinyuan Wang et. al (2005) at Utah State University. Cinnamate 4- 2.0 Phenylalanine from Utah State Hydroxylase-HA fusion protein was inserted into this plasmid at the end of the PAL coding region 1.5 Phenylalanine ammonia lyase University using restriction enzymes and transformed into BL21 CaCl2 competent E. coli with T7 RNA Cinnamate 4- Oxidoreductase Amplified from A. Cinnamic Acid 1518 involved in HA-Tag thaliana cDNA, Polymerase activity. A western blot with anti-HA antibody was used to detect the presence of the 1.0 Hydroxylase phenylalanine purchased from C4H fusion protein in the resultant cells. Cinnamate 4-hydroxylase metabolism. TAIR database P-Coumaric Acid 4-Coumaroyl Ligase involved in Insert in 2546 phenylpropanoid His-Tag pACYCDuet-1 Chalcone Synthase, Chalcone Isomerase and Flavanone 3-Hydroxylase were amplified from the CoA Ligase 0.5 4-coumaryl-coenzyme A ligase biosynthesis. -
L.) Leaves Tao Jiang1,3, Kunyuan Guo2,3, Lingdi Liu1, Wei Tian1, Xiaoliang Xie1, Saiqun Wen1 & Chunxiu Wen1*
www.nature.com/scientificreports OPEN Integrated transcriptomic and metabolomic data reveal the favonoid biosynthesis metabolic pathway in Perilla frutescens (L.) leaves Tao Jiang1,3, Kunyuan Guo2,3, Lingdi Liu1, Wei Tian1, Xiaoliang Xie1, Saiqun Wen1 & Chunxiu Wen1* Perilla frutescens (L.) is an important medicinal and edible plant in China with nutritional and medical uses. The extract from leaves of Perilla frutescens contains favonoids and volatile oils, which are mainly used in traditional Chinese medicine. In this study, we analyzed the transcriptomic and metabolomic data of the leaves of two Perilla frutescens varieties: JIZI 1 and JIZI 2. A total of 9277 diferentially expressed genes and 223 favonoid metabolites were identifed in these varieties. Chrysoeriol, apigenin, malvidin, cyanidin, kaempferol, and their derivatives were abundant in the leaves of Perilla frutescens, which were more than 70% of total favonoid contents. A total of 77 unigenes encoding 15 enzymes were identifed as candidate genes involved in favonoid biosynthesis in the leaves of Perilla frutescens. High expression of the CHS gene enhances the accumulation of favonoids in the leaves of Perilla frutescens. Our results provide valuable information on the favonoid metabolites and candidate genes involved in the favonoid biosynthesis pathways in the leaves of Perilla frutescens. Perilla frutescens (L.), which is a self-compatible annual herb, belongs to the family Lamiaceae. Tis species has been widely cultivated in China, Japan, and Korea for centuries. Perilla frutescens is an important medicinal and edible plant in China with medical and nutritional uses 1. Its leaves can be utilized as a transitional medicinal herb, as a vegetable, and as a spice, and its seeds can be processed into foods and nutritional edible oils 2. -
Analysis of the Chromosomal Clustering of Fusarium-Responsive
www.nature.com/scientificreports OPEN Analysis of the chromosomal clustering of Fusarium‑responsive wheat genes uncovers new players in the defence against head blight disease Alexandre Perochon1,2, Harriet R. Benbow1,2, Katarzyna Ślęczka‑Brady1, Keshav B. Malla1 & Fiona M. Doohan1* There is increasing evidence that some functionally related, co‑expressed genes cluster within eukaryotic genomes. We present a novel pipeline that delineates such eukaryotic gene clusters. Using this tool for bread wheat, we uncovered 44 clusters of genes that are responsive to the fungal pathogen Fusarium graminearum. As expected, these Fusarium‑responsive gene clusters (FRGCs) included metabolic gene clusters, many of which are associated with disease resistance, but hitherto not described for wheat. However, the majority of the FRGCs are non‑metabolic, many of which contain clusters of paralogues, including those implicated in plant disease responses, such as glutathione transferases, MAP kinases, and germin‑like proteins. 20 of the FRGCs encode nonhomologous, non‑metabolic genes (including defence‑related genes). One of these clusters includes the characterised Fusarium resistance orphan gene, TaFROG. Eight of the FRGCs map within 6 FHB resistance loci. One small QTL on chromosome 7D (4.7 Mb) encodes eight Fusarium‑ responsive genes, fve of which are within a FRGC. This study provides a new tool to identify genomic regions enriched in genes responsive to specifc traits of interest and applied herein it highlighted gene families, genetic loci and biological pathways of importance in the response of wheat to disease. Prokaryote genomes encode co-transcribed genes with related functions that cluster together within operons. Clusters of functionally related genes also exist in eukaryote genomes, including fungi, nematodes, mammals and plants1. -
Next-Generation Sequencing of Representational Difference Analysis
Planta DOI 10.1007/s00425-017-2657-0 ORIGINAL ARTICLE Next-generation sequencing of representational difference analysis products for identification of genes involved in diosgenin biosynthesis in fenugreek (Trigonella foenum-graecum) 1 1 1 1 Joanna Ciura • Magdalena Szeliga • Michalina Grzesik • Mirosław Tyrka Received: 19 August 2016 / Accepted: 30 January 2017 Ó The Author(s) 2017. This article is published with open access at Springerlink.com Abstract Within the transcripts related to sterol and steroidal Main conclusion Representational difference analysis saponin biosynthesis, we discovered novel candidate of cDNA was performed and differential products were genes of diosgenin biosynthesis and validated their sequenced and annotated. Candidate genes involved in expression using quantitative RT-PCR analysis. Based on biosynthesis of diosgenin in fenugreek were identified. these findings, we supported the idea that diosgenin is Detailed mechanism of diosgenin synthesis was biosynthesized from cycloartenol via cholesterol. This is proposed. the first report on the next-generation sequencing of cDNA-RDA products. Analysis of the transcriptomes Fenugreek (Trigonella foenum-graecum L.) is a valuable enriched in low copy sequences contributed substantially medicinal and crop plant. It belongs to Fabaceae family to our understanding of the biochemical pathways of and has a unique potential to synthesize valuable steroidal steroid synthesis in fenugreek. saponins, e.g., diosgenin. Elicitation (methyl jasmonate) and precursor feeding (cholesterol and squalene) were Keywords Diosgenin Á Next-generation sequencing Á used to enhance the content of sterols and steroidal Phytosterols Á Representational difference analysis of sapogenins in in vitro grown plants for representational cDNA Á Steroidal saponins Á Transcriptome user-friendly difference analysis of cDNA (cDNA-RDA). -
Synthesis of Unnatural Alkaloid Scaffolds by Exploiting Plant Polyketide Synthase
Synthesis of unnatural alkaloid scaffolds by exploiting plant polyketide synthase Hiroyuki Moritaa,b, Makoto Yamashitaa, She-Po Shia,1, Toshiyuki Wakimotoa,b, Shin Kondoc, Ryohei Katoc, Shigetoshi Sugioc,2, Toshiyuki Kohnod,2, and Ikuro Abea,b,2 aGraduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; bJapan Science and Technology Agency, Core Research of Evolutional Science and Technology, 5 Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan; cBiotechnology Laboratory, Mitsubishi Chemical Group Science and Technology Research Center Inc., 1000 Kamoshida, Aoba, Yokohama, Kanagawa 227-8502, Japan; and dMitsubishi Kagaku Institute of Life Sciences, 11 Minamiooya, Machida, Tokyo 194-8511, Japan Edited by Jerrold Meinwald, Cornell University, Ithaca, NY, and approved July 12, 2011 (received for review May 15, 2011) HsPKS1 from Huperzia serrata is a type III polyketide synthase (PKS) club moss Huperzia serrata (HsPKS1) (19) (Fig. S1), using precur- with remarkable substrate tolerance and catalytic potential. Here sor-directed and structure-based approaches. As previously re- we present the synthesis of unnatural unique polyketide–alkaloid ported, HsPKS1 is a unique type III PKS that exhibits unusually hybrid molecules by exploiting the enzyme reaction using precur- broad substrate specificity to produce various aromatic polyke- sor-directed and structure-based approaches. HsPKS1 produced tides. For example, HsPKS1, which normally catalyzes the sequen- novel pyridoisoindole (or benzopyridoisoindole) with the 6.5.6- tial condensations of 4-coumaroyl-CoA (1) with three molecules fused (or 6.6.5.6-fused) ring system by the condensation of 2-carba- of malonyl-CoA (2) to produce naringenin chalcone (3)(Fig.1A), moylbenzoyl-CoA (or 3-carbamoyl-2-naphthoyl-CoA), a synthetic also accepts bulky N-methylanthraniloyl-CoA (4)asastarterto nitrogen-containing nonphysiological starter substrate, with two produce 1,3-dihydroxy-N-methylacridone (5), after three conden- molecules of malonyl-CoA. -
(12) United States Patent (10) Patent No.: US 6,441,206 B1 Mikkonen Et Al
USOO64.41206B1 (12) United States Patent (10) Patent No.: US 6,441,206 B1 Mikkonen et al. (45) Date of Patent: Aug. 27, 2002 (54) USE OF ORGANIC ACID ESTERS IN GB 1298047 11/1972 DIETARY FAT GB 2288805 * 7/1995 JP 588.098 A 1/1983 (75) Inventors: Hannu Mikkonen, Rajamäki; Elina JP 9194345 A 7/1997 Heikkilä, Vantaa, Erkki Anttila, Algy o Rajamäki; Anneli Lindeman, Espoo, all WO A19806405 2/1998 of (FI) OTHER PUBLICATIONS (73) Assignee: Raisio Benecol Ltd., Raisio (FI) Miettinen et al., New Technologies for Healthy Foods, pp. * Y NotOtice: Subjubject to anyy disclaimer,disclai theh term off thisthi 71-83 (1997). patent is extended or adjusted under 35 Habib et al., Sci. Pharm. vol. 49, pp. 253–257 (1981). U.S.C. 154(b) by 0 days. Mukhina e al., STN International, vol. 88, No. 7, pp. 1429-1430 (1977). (21) Appl. No.: 09/508,295 Mukhina et al., STN International, vol. 67, No. 9, pp. 587-589 (1967). (22) PCT Filed: Sep. 9, 1998 Tuomisto et al., Farmakologia Ja Toksikologia, pp. 526-534 (86) PCT No.: PCT/FI98/00707 (1982). Ikeda et al., J. Nutr Sci. Vitaminol, vol. 35, pp. 361-369 S371 (c)(1), (1989). (2), (4) Date: May 12, 2000 Heinemann et al., Eur: J. Clin. Pharmacol., 40(Suppl 1), pp. S59–S63 (1991). (87) PCT Pub. No.: WO99/15546 Mattson et al., J. Nutr, vol. 107, pp. 1139-1146 (1977). PCT Pub. Date: Apr. 1, 1999 Herting et al., Fed. Proc., vol. 19, pp. 18, (1960). Takagi et al., J. -
Supplementary Material
CSIRO PUBLISHING www.publish.csiro.au/journals/fpb Functional Plant Biology 33, 1–24 Supplementary material: FP05139_AC Supplementary material Molecular targets of elevated [CO2] in leaves and stems of Populus deltoides: implications for future tree growth and carbon sequestration Nathalie DruartA,B, Marisa Rodríguez-BueyA, Greg Barron-GaffordC, Andreas SjödinA, Rishikesh BhaleraoB and Vaughan HurryA,D AUmeå Plant Science Centre, Department of Plant Physiology, Umeå University, S-901 87 Umeå, Sweden. BUmeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, S-901 83 Umeå, Sweden. CBiosphere 2 Laboratory, Columbia University, Oracle AZ 85623 USA. Current address: Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85719, USA. DCorresponding author. Email: [email protected] Appendix S1 1.0 1.0 A B 0.5 0.5 0.0 0.0 –0.5 –0.5 –1.0 –1.0 Relative gene expression (log gene expression Relative ) 1.0 1.0 2 C D 0.5 0.5 0.0 0.0 –0.5 –0.5 2 ) Relative gene expression (log gene expression Relative –1.0 –1.0 1.0 1.0 E F 0.5 0.5 0.0 0.0 –0.5 –0.5 –1.0 –1.0 400 800 1200 400 800 1200 Ambient [CO2] (µmol mol–1) Validation of reproducibility of the hybridisations by comparing the hybridisation results of three genes for which two independent cDNA clones had been spotted on the array. (A, C, E leaves; B, D, F stems). (A, B) Protein phosphatase 2A, 65 kDa subunit. (C, D) Elicitor-inducible cytochrome P450. -
Flavonoids and Isoflavonoids Biosynthesis in the Model
plants Review Flavonoids and Isoflavonoids Biosynthesis in the Model Legume Lotus japonicus; Connections to Nitrogen Metabolism and Photorespiration Margarita García-Calderón 1, Carmen M. Pérez-Delgado 1, Peter Palove-Balang 2, Marco Betti 1 and Antonio J. Márquez 1,* 1 Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, Universidad de Sevilla, Calle Profesor García González, 1, 41012-Sevilla, Spain; [email protected] (M.G.-C.); [email protected] (C.M.P.-D.); [email protected] (M.B.) 2 Institute of Biology and Ecology, Faculty of Science, P.J. Šafárik University in Košice, Mánesova 23, SK-04001 Košice, Slovakia; [email protected] * Correspondence: [email protected]; Tel.: +34-954557145 Received: 28 April 2020; Accepted: 18 June 2020; Published: 20 June 2020 Abstract: Phenylpropanoid metabolism represents an important metabolic pathway from which originates a wide number of secondary metabolites derived from phenylalanine or tyrosine, such as flavonoids and isoflavonoids, crucial molecules in plants implicated in a large number of biological processes. Therefore, various types of interconnection exist between different aspects of nitrogen metabolism and the biosynthesis of these compounds. For legumes, flavonoids and isoflavonoids are postulated to play pivotal roles in adaptation to their biological environments, both as defensive compounds (phytoalexins) and as chemical signals in symbiotic nitrogen fixation with rhizobia. In this paper, we summarize the recent progress made in the characterization of flavonoid and isoflavonoid biosynthetic pathways in the model legume Lotus japonicus (Regel) Larsen under different abiotic stress situations, such as drought, the impairment of photorespiration and UV-B irradiation. Emphasis is placed on results obtained using photorespiratory mutants deficient in glutamine synthetase. -
Transcription Factors Regulating Terpene Synthases in Tomato Trichomes
UvA-DARE (Digital Academic Repository) Transcription factors regulating terpene synthases in tomato trichomes Spyropoulou, E. Publication date 2012 Document Version Final published version Link to publication Citation for published version (APA): Spyropoulou, E. (2012). Transcription factors regulating terpene synthases in tomato trichomes. General rights It is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), other than for strictly personal, individual use, unless the work is under an open content license (like Creative Commons). Disclaimer/Complaints regulations If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Ask the Library: https://uba.uva.nl/en/contact, or a letter to: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. You will be contacted as soon as possible. UvA-DARE is a service provided by the library of the University of Amsterdam (https://dare.uva.nl) Download date:03 Oct 2021 Transcription factors regulating terpene synthases in tomato trichomes factors regulating Transcription Transcription factors regulating terpene synthases in tomato trichomes Eleni Spyropoulou Eleni Spyropoulou Transcription factors regulating terpene synthases in tomato trichomes ACADEMISCH PROEFSCHRIFT ter verkrijging van de graad van doctor aan de Universiteit van Amsterdam op gezag van de Rector Magnificus prof. dr. D.C. van den Boom ten overstaan van een door het college voor promoties ingestelde commissie, in het openbaar te verdedigen in de Agnietenkapel op dinsdag 03 juli 2012, te 16:00 uur door Eleni Spyropoulou geboren te Marousi, Griekenland PROMOTIECOMISSIE Promotor Prof. -
Noncatalytic Chalcone Isomerase-Fold Proteins in Humulus Lupulus Are Auxiliary Components in Prenylated Flavonoid Biosynthesis
Noncatalytic chalcone isomerase-fold proteins in Humulus lupulus are auxiliary components in prenylated flavonoid biosynthesis Zhaonan Bana,b, Hao Qina, Andrew J. Mitchellc, Baoxiu Liua, Fengxia Zhanga, Jing-Ke Wengc,d, Richard A. Dixone,f,1, and Guodong Wanga,1 aState Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101 Beijing, China; bUniversity of Chinese Academy of Sciences, 100049 Beijing, China; cWhitehead Institute for Biomedical Research, Cambridge, MA 02142; dDepartment of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139; eBioDiscovery Institute, University of North Texas, Denton, TX 76203; and fDepartment of Biological Sciences, University of North Texas, Denton, TX 76203 Contributed by Richard A. Dixon, April 25, 2018 (sent for review February 6, 2018; reviewed by Joerg Bohlmann and Mattheos A. G. Koffas) Xanthohumol (XN) and demethylxanthohumol (DMX) are special- braries have been deposited in the TrichOME database [www. ized prenylated chalconoids with multiple pharmaceutical appli- planttrichome.org (18)], and numerous large RNAseq datasets from cations that accumulate to high levels in the glandular trichomes different hop tissues or cultivars have also been made publically of hops (Humulus lupulus L.). Although all structural enzymes in available. By mining the hops transcriptome data, we and others have the XN pathway have been functionally identified, biochemical functionally identified several key terpenophenolic biosynthetic en- mechanisms underlying highly efficient production of XN have zymes from hop glandular trichomes (1, 18–23); these include car- not been fully resolved. In this study, we characterized two non- boxyl CoA ligase (CCL) genes and two aromatic prenyltransferase catalytic chalcone isomerase (CHI)-like proteins (designated as (PT) genes (HlPT1L and HlPT2) (22, 23).