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Pathway Engineering Using Escherichia coli to Produce Commercialized Carotenoids. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1261:191-199. [PMID: 33783741 DOI: 10.1007/978-981-15-7360-6_16] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The biosynthesis of commercialized carotenoids (e.g., lycopene, β-carotene, zeaxanthin, and astaxanthin) using recombinant microorganisms is one of the reasonable and cost-effective alternatives to extraction from natural sources and chemical synthesis. Among heterologous hosts, Escherichia coli is one of the most useful and manageable. To date, many approaches using recombinant E. coli are available to produce various carotenoids. Here we outline the latest carotenoid production research using recombinant E. coli produced through pathway engineering and its future prospects.
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Cloning and Characterization of the 2-C-Methyl-D-erythritol 4-Phosphate (MEP) Pathway Genes of a Natural-Rubber Producing Plant,Hevea brasiliensis. Biosci Biotechnol Biochem 2014; 72:2903-17. [DOI: 10.1271/bbb.80387] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Perez-Gil J, Uros EM, Sauret-Güeto S, Lois LM, Kirby J, Nishimoto M, Baidoo EEK, Keasling JD, Boronat A, Rodriguez-Concepcion M. Mutations in Escherichia coli aceE and ribB genes allow survival of strains defective in the first step of the isoprenoid biosynthesis pathway. PLoS One 2012; 7:e43775. [PMID: 22928031 PMCID: PMC3424233 DOI: 10.1371/journal.pone.0043775] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Accepted: 07/25/2012] [Indexed: 11/18/2022] Open
Abstract
A functional 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway is required for isoprenoid biosynthesis and hence survival in Escherichia coli and most other bacteria. In the first two steps of the pathway, MEP is produced from the central metabolic intermediates pyruvate and glyceraldehyde 3-phosphate via 1-deoxy-D-xylulose 5-phosphate (DXP) by the activity of the enzymes DXP synthase (DXS) and DXP reductoisomerase (DXR). Because the MEP pathway is absent from humans, it was proposed as a promising new target to develop new antibiotics. However, the lethal phenotype caused by the deletion of DXS or DXR was found to be suppressed with a relatively high efficiency by unidentified mutations. Here we report that several mutations in the unrelated genes aceE and ribB rescue growth of DXS-defective mutants because the encoded enzymes allowed the production of sufficient DXP in vivo. Together, this work unveils the diversity of mechanisms that can evolve in bacteria to circumvent a blockage of the first step of the MEP pathway.
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Affiliation(s)
- Jordi Perez-Gil
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, Barcelona, Spain
| | - Eva Maria Uros
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, Barcelona, Spain
| | - Susanna Sauret-Güeto
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, Barcelona, Spain
| | - L. Maria Lois
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, Barcelona, Spain
| | - James Kirby
- Joint BioEnergy Institute, Emeryville, California, United States of America
| | - Minobu Nishimoto
- Joint BioEnergy Institute, Emeryville, California, United States of America
| | | | - Jay D. Keasling
- Joint BioEnergy Institute, Emeryville, California, United States of America
| | - Albert Boronat
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, Barcelona, Spain
- Department de Bioquímica i Biologia Molecular, Universitat de Barcelona, Barcelona, Spain
| | - Manuel Rodriguez-Concepcion
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, Barcelona, Spain
- * E-mail:
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Synthetic biology and the development of tools for metabolic engineering. Metab Eng 2012; 14:189-95. [DOI: 10.1016/j.ymben.2012.01.004] [Citation(s) in RCA: 321] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 01/24/2012] [Indexed: 12/21/2022]
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Harada H, Misawa N. Novel approach in the biosynthesis of functional carotenoids in Escherichia coli. Methods Mol Biol 2012; 892:133-141. [PMID: 22623299 DOI: 10.1007/978-1-61779-879-5_6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Many carotenoid pigments are present in a small quantity in nature or low yielding from their natural sources, despite these vivid colorations. Thus, the synthesis of useful carotenoids with metabolic pathway-engineered microorganisms should offer an alternative and promising approach for their efficient production. Here, we describe a novel method for an efficient production of such carotenoids, using E. coli cells that carry heterologous mevalonate pathway-based genes. This method also enables relevant researchers to efficiently identify the function of an isolated carotenogenic gene candidate. For example, the recombinant E. coli cells, which harbor a lycopene-producing plasmid, can synthesize 12.5 mg/g dry cell weight of lycopene with the addition of lithium acetoacetate to the medium. This level corresponded to an 11.8-fold increase of that of E. coli cells carrying only the lycopene-producing plasmid.
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Affiliation(s)
- Hisashi Harada
- KNC Bio-Research Center, KNC Laboratories Co. Ltd., Kobe, Hyogo, Japan
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Misawa N. Carotenoid β-ring hydroxylase and ketolase from marine bacteria-promiscuous enzymes for synthesizing functional xanthophylls. Mar Drugs 2011; 9:757-771. [PMID: 21673887 PMCID: PMC3111180 DOI: 10.3390/md9050757] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 04/19/2011] [Accepted: 04/26/2011] [Indexed: 12/05/2022] Open
Abstract
Marine bacteria belonging to genera Paracoccus and Brevundimonas of the α-Proteobacteria class can produce C40-type dicyclic carotenoids containing two β-end groups (β rings) that are modified with keto and hydroxyl groups. These bacteria produce astaxanthin, adonixanthin, and their derivatives, which are ketolated by carotenoid β-ring 4(4′)-ketolase (4(4′)-oxygenase; CrtW) and hydroxylated by carotenoid β-ring 3(3′)-hydroxylase (CrtZ). In addition, the genus Brevundimonas possesses a gene for carotenoid β-ring 2(2′)-hydroxylase (CrtG). This review focuses on these carotenoid β-ring-modifying enzymes that are promiscuous for carotenoid substrates, and pathway engineering for the production of xanthophylls (oxygen-containing carotenoids) in Escherichia coli, using these enzyme genes. Such pathway engineering researches are performed towards efficient production not only of commercially important xanthophylls such as astaxanthin, but also of xanthophylls minor in nature (e.g., β-ring(s)-2(2′)-hydroxylated carotenoids).
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Affiliation(s)
- Norihiko Misawa
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Suematsu, Nonoichi-machi, Ishikawa 921-8836, Japan
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Harada H, Misawa N. Novel approaches and achievements in biosynthesis of functional isoprenoids in Escherichia coli. Appl Microbiol Biotechnol 2009; 84:1021-31. [PMID: 19672590 DOI: 10.1007/s00253-009-2166-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Revised: 07/01/2009] [Accepted: 07/24/2009] [Indexed: 11/25/2022]
Abstract
Isoprenoids, also referred to as terpenes, are the most diverse class of natural products appearing in a variety of natural sources, specifically in higher plants, and have a wide range of biological functions. This review describes novel or recent approaches and achievements in pathway engineering of Escherichia coli towards efficient biosynthesis of functional isoprenoids, specifically carotenoids and sesquiterpene, following description of "regularity and simplicity" in the biosynthesis of isoprenoid basic structures. The introduction of heterologous mevalonate pathway-based genes into E. coli has been shown to improve the productivity of carotenoids or sesquiterpenes that are synthesized from farnesyl diphosphate. This achievement also enables relevant researchers to efficiently analyze an isolated gene candidate for a terpene synthase (terpene cyclase).
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Affiliation(s)
- Hisashi Harada
- Central Laboratories for Frontier Technology, Kirin Holdings Co., Ltd., i-BIRD, Suematsu, Nonoichi-machi, Ishikawa, Japan
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Harada H, Yu F, Okamoto S, Kuzuyama T, Utsumi R, Misawa N. Efficient synthesis of functional isoprenoids from acetoacetate through metabolic pathway-engineered Escherichia coli. Appl Microbiol Biotechnol 2009; 81:915-25. [PMID: 18836713 DOI: 10.1007/s00253-008-1724-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2008] [Revised: 09/12/2008] [Accepted: 09/17/2008] [Indexed: 11/28/2022]
Abstract
We show here an efficient synthesis system of isoprenoids from acetoacetate as the main substrate. We expressed in Escherichia coli a Streptomyces mevalonate pathway gene cluster starting from HMG-CoA synthase and including isopentenyl diphosphate isomerase (idi) type 2 gene and the yeast idi type 1 and rat acetoacetate-CoA ligase (Aacl) genes. When the alpha-humulene synthase (ZSS1) gene of shampoo ginger was expressed in this transformant, the resultant E. coli produced 958 mug/mL culture of alpha-humulene with a lithium acetoacetate (LAA) supplement, which was a 13.6-fold increase compared with a control E. coli strain expressing only ZSS1. Next, we investigated if this E. coli strain engineered to utilize acetoacetate can synthesize carotenoids effectively. When the crtE, crtB, and crtI genes required for lycopene synthesis were expressed in the transformant, lycopene amounts reached 12.5 mg/g dry cell weight with addition of LAA, an 11.8-fold increase compared with a control expressing only the three crt genes. As for astaxanthin production with the E. coli transformant, in which the crtE, crtB, crtI, crtY, crtZ, and crtW genes were expressed, the total amount of carotenoids produced (astaxanthin, lycopene, and phytoene) was significantly increased to 7.5 times that of a control expressing only the six crt genes.
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Affiliation(s)
- Hisashi Harada
- Central Laboratories for Frontier Technology, Kirin Holdings Co., Ltd., i-BIRD 3-570, Suematsu, Nonoichi-machi, Ishikawa 921-8836, Japan
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Yu F, Okamto S, Nakasone K, Adachi K, Matsuda S, Harada H, Misawa N, Utsumi R. Molecular cloning and functional characterization of alpha-humulene synthase, a possible key enzyme of zerumbone biosynthesis in shampoo ginger (Zingiber zerumbet Smith). PLANTA 2008; 227:1291-9. [PMID: 18273640 DOI: 10.1007/s00425-008-0700-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2007] [Accepted: 01/24/2008] [Indexed: 05/25/2023]
Abstract
Shampoo ginger (Zingiber zerumbet Smith) has a high content and large variety of terpenoids in the essential oil of its rhizome. Here, we report on the isolation of a cDNA clone (ZSS1) encoding alpha-humulene synthase, a possible key enzyme of zerumbone biosynthesis. This clone contains an open reading frame of 1,644 bp and is predicted to encode a protein of 548 amino acids with a calculated molecular mass of 64.5 kDa. The deduced amino acid sequence shows 34-63% identity with known sesquiterpene synthases of other angiosperm species. Based on exon-intron organization, ZSS1 is classified as the terpene synthase-III (TPS-III) subfamily. When expressed in Escherichia coli, the recombinant enzyme catalyzed the formation of a major product, alpha-humulene (95%) and a minor by-product, beta-caryophyllene (5%). Introduction of ZSS1 and the foreign mevalonate pathway involved in FPP synthesis into E. coli results in in vivo production of alpha-humulene. Transcript of ZSS1 was detected almost exclusively in rhizomes and was up-regulated in both leaves and rhizomes after treatment with methyl jasmonate (MeJA), suggesting its ecological function in shampoo ginger.
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Affiliation(s)
- Fengnian Yu
- Department of Bioscience, Graduate School of Agriculture, Kinki University, 3327-204 Nakamachi, Nara, 631-8505, Japan
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Abstract
The richness and versatility of biological systems make them ideally suited to solve some of the world's most significant challenges, such as converting cheap, renewable resources into energy-rich molecules; producing high-quality, inexpensive drugs to fight disease; and remediating polluted sites. Over the years, significant strides have been made in engineering microorganisms to produce fuels, bulk chemicals, and valuable drugs from inexpensive starting materials; to detect and degrade nerve agents as well as less toxic organic pollutants; and to accumulate metals and reduce radionuclides. The components needed to engineer the chemistry inside a microbial cell are significantly different from those commonly used to overproduce pharmaceutical proteins. Synthetic biology has had and will continue to have a significant impact on the development of these components to engineer cellular metabolism and microbial chassis to host the chemistry. The ready availability of more well-characterized gene expression components and hosts for chemical synthesis, standards for the connection of these components to make larger functioning devices, computer-aided design software, and debugging tools for biological designs will decrease both the time and the support needed to construct these designs. Some of the most important tools for engineering bacterial metabolism and their use for production of the antimalarial drug artemisinin are reviewed.
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Affiliation(s)
- Jay D. Keasling
- Departments of Chemical Engineering and Bioengineering, University of California, Berkeley, Berkeley, California 94720, and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
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Abstract
Throughout human history, natural products have been the foundation for the discovery and development of therapeutics used to treat diseases ranging from cardiovascular disease to cancer. Their chemical diversity and complexity have provided structural scaffolds for small-molecule drugs and have consistently served as inspiration for medicinal design. However, the chemical complexity of natural products also presents one of the main roadblocks for production of these pharmaceuticals on an industrial scale. Chemical synthesis of natural products is often difficult and expensive, and isolation from their natural sources is also typically low yielding. Synthetic biology and metabolic engineering offer an alternative approach that is becoming more accessible as the tools for engineering microbes are further developed. By reconstructing heterologous metabolic pathways in genetically tractable host organisms, complex natural products can be produced from inexpensive sugar starting materials through large-scale fermentation processes. In this Perspective, we discuss ongoing research aimed toward the production of terpenoid natural products in genetically engineered Escherichia coli and Saccharomyces cerevisiae.
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Affiliation(s)
- Michelle C Y Chang
- California Institute for Quantitative Biomedical Research, University of California-Berkeley, Berkeley, CA 94720, USA
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Yoon SH, Lee YM, Kim JE, Lee SH, Lee JH, Kim JY, Jung KH, Shin YC, Keasling JD, Kim SW. Enhanced lycopene production inEscherichia coli engineered to synthesize isopentenyl diphosphate and dimethylallyl diphosphate from mevalonate. Biotechnol Bioeng 2006; 94:1025-32. [PMID: 16547999 DOI: 10.1002/bit.20912] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
To increase expression of lycopene synthetic genes crtE, crtB, crtI, and ipiHP1, the four exogenous genes were cloned into a high copy pTrc99A vector with a strong trc promoter. Recombinant Escherichia coli harboring pT-LYCm4 produced 17 mg/L of lycopene. The mevalonate lower pathway, composed of mvaK1, mvaK2, mvaD, and idi, was engineered to produce pSSN12Didi for an efficient supply of the lycopene building blocks, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Mevalonate was supplied as a substrate for the mevalonate lower pathway. Lycopene production in E. coli harboring pT-LYCm4 and pSSN12Didi with supplementation of 3.3 mM mevalonate was more than threefold greater than bacteria with pT-LYCm4 only. Lycopene production was dependent on mevalonate concentration supplied in the culture. Clump formation was observed as cells accumulated more lycopene. Further clumping was prevented by adding the surfactant Tween 80 0.5% (w/v), which also increased lycopene production and cell growth. When recombinant E. coli harboring pT-LYCm4 and pSSN12Didi was cultivated in 2YT medium containing 2% (w/v) glycerol as a carbon source, 6.6 mM mevalonate for the mevalonate lower pathway, and 0.5% (w/v) Tween 80 to prevent clump formation, lycopene production was 102 mg/L and 22 mg/g dry cell weight, and cell growth had an OD(600) value of 15 for 72 h.
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Affiliation(s)
- Sang-Hwal Yoon
- Department of Food Science & Nutrition, Gyeongsang National University, Jinju, Korea
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Preparation of highly deuterated zeaxanthin, lycopene, and β-carotene from fully deuterated mevalonate using engineered Escherichia coli. Tetrahedron 2005. [DOI: 10.1016/j.tet.2004.12.056] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Eguchi T, Watanabe E, Kakinuma K. Practical enantioselective synthesis of fully deuterated (R)-mevalonolactone. Tetrahedron 2003. [DOI: 10.1016/s0040-4020(03)00983-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Eguchi T, Dekishima Y, Hamano Y, Dairi T, Seto H, Kakinuma K. A new approach for the investigation of isoprenoid biosynthesis featuring pathway switching, deuterium hyperlabeling, and 1H NMR spectroscopy. The reaction mechanism of a novel streptomyces diterpene cyclase. J Org Chem 2003; 68:5433-8. [PMID: 12839434 DOI: 10.1021/jo026728a] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recent methodology for the investigation of isoprenoid biosynthesis featuring pathway switching and hyperdeuteration has shown significant advantages in elucidating the reaction mechanism of a novel Streptomyces diterpene cyclase with use of precise atom-level analysis. Insight into the cyclization mechanism involved in the conversion of geranylgeranyl diphosphate (GGPP) into a clerodane hydrocarbon terpentetriene was obtained by heterologous expression in doubly engineered Streptomyces lividans of a diterpene cyclase gene derived from Streptomyces griseolosporeus, a producer of an unique diterpenoid cytotoxic antibiotic terpentecin, and by in vivo labeling with mevalonate-d(9). The cyclization involved electrophilic protonation, cationic ring closure, Wagner-Meerwein-type rearrangements, and deprotonation. A key feature was that the labeled metabolite as a mixture of predominantly deuterated mosaic molecules provided sufficient information that close analysis of the labeling pattern for each individual isoprene unit was achieved primarily by (1)H NMR spectroscopy. The cyclization of GGPP into the clerodane skeleton catalyzed by the cyclase appears to involve Si-face specific protonation, intermediates with A/B chair-boat conformation, and specific methyl and hydride migrations to give an intermediary C-4 carbocation. Subsequent collapse of the cation through specific removal of the initiating proton and final elimination of diphosphate gives rise to the terpentetriene hydrocarbon.
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Affiliation(s)
- Tadashi Eguchi
- Department of Chemistry and Materials Science, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan.
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Vaz B, Alvarez R, de Lera AR. Synthesis of symmetrical carotenoids by a two-fold Stille reaction. J Org Chem 2002; 67:5040-3. [PMID: 12098335 DOI: 10.1021/jo025727f] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
beta-Carotene 1 and (3R,3'R)-zeaxanthin 2 have been stereoselectively prepared in a highly convergent fashion by a 2-fold Stille cross-coupling reaction. The C(12)-pentaenylbis-stannane 8 is the central "lynchpin" that connects two units of the terminal C(14)-iodides 9 and 17 to afford 1 and 2, respectively.
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Affiliation(s)
- Belén Vaz
- Departamento de Química Orgánica, Facultad de Ciencias, Universidade de Vigo. 36200 Vigo, Spain
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Eisenreich W, Bacher A, Berry A, Bretzel W, Hümbelin M, Lopez-Ulibarri R, Mayer AF, Yeliseev A. Biosynthesis of zeaxanthin via mevalonate in Paracoccus species strain PTA-3335. A product-based retrobiosynthetic study. J Org Chem 2002; 67:871-5. [PMID: 11856031 DOI: 10.1021/jo016084r] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cultures of the zeaxanthin-producing bacterium Paracoccus species strain PTA-3335 (formerly Flavobacterium) were grown with supplements of (13)C-labeled glucose. Zeaxanthin was isolated and analyzed by (13)C NMR spectroscopy. The data showed that the isoprenoid precursors of zeaxanthin were biosynthesized via the mevalonate pathway. The microorganism was found to utilize glucose mainly via the Entner-Doudoroff pathway.
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Affiliation(s)
- Wolfgang Eisenreich
- Lehrstuhl für Organische Chemie und Biochemie, Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Federal Republic of Germany.
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