Journal of Ginseng Research

The Korean Society of Ginseng (고려인삼학회)
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Sustainable production of natural products using synthetic biology: Ginsenosides

  • So-Hee Son (Research Center for Bio-Based Chemistry, Korea Research Institute of Chemical Technology (KRICT)) ;
  • Jin Kang (Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB)) ;
  • YuJin Shin (School of Pharmacy, Sungkyunkwan University) ;
  • ChaeYoung Lee (School of Pharmacy, Sungkyunkwan University) ;
  • Bong Hyun Sung (Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB)) ;
  • Ju Young Lee (Research Center for Bio-Based Chemistry, Korea Research Institute of Chemical Technology (KRICT)) ;
  • Wonsik Lee (Graduate School of Engineering Biology, Korea Advanced Institute of Science and Technology (KAIST))
  • Received : 2023.11.17
  • Accepted : 2023.12.30
  • Published : 2024.03.01
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Abstract

Synthetic biology approaches offer potential for large-scale and sustainable production of natural products with bioactive potency, including ginsenosides, providing a means to produce novel compounds with enhanced therapeutic properties. Ginseng, known for its non-toxic and potent qualities in traditional medicine, has been used for various medical needs. Ginseng has shown promise for its antioxidant and neuroprotective properties, and it has been used as a potential agent to boost immunity against various infections when used together with other drugs and vaccines. Given the increasing demand for ginsenosides and the challenges associated with traditional extraction methods, synthetic biology holds promise in the development of therapeutics. In this review, we discuss recent developments in microorganism producer engineering and ginsenoside production in microorganisms using synthetic biology approaches.

Keywords

Acknowledgement

This work was supported by the Basic Science Research Program (NRF-2019R1A2C1090726 to B.S.) and the Bio & Medical Technology Development Program through the National Research Foundation (NRF) grant funded by the Ministry of Science, ICT (MSIT) (NRF-2022M3A9B6082671 to B.S, NRF-2021M3A9I5023254 to J.L.), and by the Ministry of Education (NRF-2022R1A6A1A03054419 to W. L.)

References

  1. Pichersky E, Gang DR. Genetics and biochemistry of secondary metabolites in plants: an evolutionary perspective. Trends Plant Sci 2000;5(10):439-45.  https://doi.org/10.1016/S1360-1385(00)01741-6
  2. Delgoda R, Murray J. Evolutionary perspectives on the role of plant secondary metabolites. In: Pharmacognosy. Elsevier; 2017. p. 93-100. 
  3. Abdulhafiz F, et al. Plant cell culture technologies: a promising alternatives to produce high-value secondary metabolites. Arab J Chem 2022;15(11):104161. 
  4. Fan M, et al. Anti-cancer effect and potential microRNAs targets of ginsenosides against breast cancer. Front Pharmacol 2022;13:1033017. 
  5. Nag SA, et al. Ginsenosides as anticancer agents: in vitro and in vivo activities, structure-activity relationships, and molecular mechanisms of action. Front Pharmacol 2012;3:25. 
  6. Ye XW, et al. Saponins of ginseng products: a review of their transformation in processing. Front Pharmacol 2023;14. 
  7. Liang Y, Zhao S. Progress in understanding of ginsenoside biosynthesis. Plant Biol 2008;10(4):415-21.  https://doi.org/10.1111/j.1438-8677.2008.00064.x
  8. Kim Y-J, Zhang D, Yang D-C. Biosynthesis and biotechnological production of ginsenosides. Biotechnol Adv 2015;33(6):717-35.  https://doi.org/10.1016/j.biotechadv.2015.03.001
  9. Duan L, et al. Panax notoginseng saponins for treating coronary artery disease: a functional and mechanistic overview. Front Pharmacol 2017;8:702. 
  10. Mancuso C, Santangelo R. Panax ginseng and Panax quinquefolius: from pharmacology to toxicology. Food Chem Toxicol 2017;107:362-72.  https://doi.org/10.1016/j.fct.2017.07.019
  11. Lee JW, et al. Systems metabolic engineering of microorganisms for natural and non-natural chemicals. Nat Chem Biol 2012;8(6):536-46.  https://doi.org/10.1038/nchembio.970
  12. Krivoruchko A, Nielsen J. Production of natural products through metabolic engineering of Saccharomyces cerevisiae. Curr Opin Biotechnol 2015;35:7-15.  https://doi.org/10.1016/j.copbio.2014.12.004
  13. Church GM, et al. Realizing the potential of synthetic biology. Nat Rev Mol Cell Biol 2014;15(4):289-94.  https://doi.org/10.1038/nrm3767
  14. Latchman DS. Inhibitory transcription factors. Int J Biochem Cell Biol 1996;28(9):965-74.  https://doi.org/10.1016/1357-2725(96)00039-8
  15. McLaughlin JA, et al. The Synthetic Biology Open Language (SBOL) version 3: simplified data exchange for bioengineering. Front Bioeng Biotechnol 2020;8:1009. 
  16. Villalobos A, et al. Gene Designer: a synthetic biology tool for constructing artificial DNA segments. BMC Bioinf 2006;7:1-8.  https://doi.org/10.1186/1471-2105-7-1
  17. Mante J, et al. Synthetic biology knowledge system. ACS Synth Biol 2021;10(9):2276-85.  https://doi.org/10.1021/acssynbio.1c00188
  18. Cai P, et al. SynBioTools: a one-stop facility for searching and selecting synthetic biology tools. BMC Bioinf 2023;24(1):1-11.  https://doi.org/10.1186/s12859-022-05124-9
  19. Plahar HA, et al. BioParts-a biological parts search portal and updates to the ICE parts registry software platform. ACS Synth Biol 2021;10(10):2649-60.  https://doi.org/10.1021/acssynbio.1c00263
  20. Brophy JAN, Voigt CA. Principles of genetic circuit design. Nat Methods 2014;11(5):508-20.  https://doi.org/10.1038/nmeth.2926
  21. Davidson E, Levin M. Gene regulatory networks. Proc Natl Acad Sci USA 2005;102(14). 4935-4935.  https://doi.org/10.1073/pnas.0502024102
  22. Chen Y, et al. Genetic circuit design automation for yeast. Nature Microbiology 2020;5(11):1349-60.  https://doi.org/10.1038/s41564-020-0757-2
  23. Cho JS, et al. Designing microbial cell factories for the production of chemicals. JACS Au 2022;2(8):1781-99.  https://doi.org/10.1021/jacsau.2c00344
  24. Gomes DG, et al. Bioreactors and engineering of filamentous fungi cultivation. In: Current developments in biotechnology and bioengineering. Elsevier; 2023. p. 219-50. 
  25. Buddingh' BC, Van Hest JCM. Artificial cells: synthetic compartments with life-like functionality and adaptivity. Accounts Chem Res 2017;50(4):769-77.  https://doi.org/10.1021/acs.accounts.6b00512
  26. Pelletier JF, et al. Genetic requirements for cell division in a genomically minimal cell. Cell 2021;184(9):2430-40. e16.  https://doi.org/10.1016/j.cell.2021.03.008
  27. Paddon CJ, et al. High-level semi-synthetic production of the potent antimalarial artemisinin. Nature 2013;496(7446):528-32.  https://doi.org/10.1038/nature12051
  28. Paddon CJ, Keasling JD. Semi-synthetic artemisinin: a model for the use of synthetic biology in pharmaceutical development. Nat Rev Microbiol 2014;12(5):355-67.  https://doi.org/10.1038/nrmicro3240
  29. Ro D-K, et al. Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature 2006;440(7086):940-3.  https://doi.org/10.1038/nature04640
  30. Cravens A, Payne J, Smolke CD. Synthetic biology strategies for microbial biosynthesis of plant natural products. Nat Commun 2019;10(1). 
  31. Hayden EC. Biology software promises easier way to program living cells. Nat News [Internet]; 2016. 
  32. Carbonell P, et al. An automated Design-Build-Test-Learn pipeline for enhanced microbial production of fine chemicals. Commun Biol 2018;1(1). 
  33. Holowko MB, et al. Building a biofoundry. Synthetic Biology 2021;6(1):ysaa026. 
  34. Wu M-R, et al. A high-throughput screening and computation platform for identifying synthetic promoters with enhanced cell-state specificity (SPECS). Nat Commun 2019;10(1). 
  35. Radivojevi'c T, et al. A machine learning Automated Recommendation Tool for synthetic biology. Nat Commun 2020;11(1). 
  36. Vickers CE, Freemont PS. Pandemic preparedness: synthetic biology and publicly funded biofoundries can rapidly accelerate response time. Nat Commun 2022;13(1). 
  37. Hillson N, et al. Building a global alliance of biofoundries. Nat Commun 2019;10(1). 
  38. Butler MS, Robertson AA, Cooper MA. Natural product and natural product derived drugs in clinical trials. Nat Prod Rep 2014;31(11):1612-61.  https://doi.org/10.1039/C4NP00064A
  39. Sussmuth RD, Mainz A. Nonribosomal peptide synthesis-principles and prospects. Angew Chem Int Ed Engl 2017;56(14):3770-821.  https://doi.org/10.1002/anie.201609079
  40. Walsh CT. Polyketide and nonribosomal peptide antibiotics: modularity and versatility. Science 2004;303(5665):1805-10.  https://doi.org/10.1126/science.1094318
  41. Sattely ES, Fischbach MA, Walsh CT. Total biosynthesis: in vitro reconstitution of polyketide and nonribosomal peptide pathways. Nat Prod Rep 2008;25(4):757-93.  https://doi.org/10.1039/b801747f
  42. Du L, Sanchez C, Shen B. Hybrid peptide-polyketide natural products: biosynthesis and prospects toward engineering novel molecules. Metab Eng 2001;3(1):78-95.  https://doi.org/10.1006/mben.2000.0171
  43. Nivina A, et al. Evolution and diversity of assembly-line polyketide synthases. Chem Rev 2019;119(24):12524-47.  https://doi.org/10.1021/acs.chemrev.9b00525
  44. Herbst DA, Townsend CA, Maier T. The architectures of iterative type I PKS and FAS. Nat Prod Rep 2018;35(10):1046-69.  https://doi.org/10.1039/C8NP00039E
  45. Miyazawa T, et al. An in vitro platform for engineering and harnessing modular polyketide synthases. Nat Commun 2020;11(1):80. 
  46. Bedewitz MA, et al. Tropinone synthesis via an atypical polyketide synthase and P450-mediated cyclization. Nat Commun 2018;9(1):5281. 
  47. Li W, et al. Asperphenamate biosynthesis reveals a novel two-module NRPS system to synthesize amino acid esters in fungi. Chem Sci 2018;9(9):2589-94.  https://doi.org/10.1039/C7SC02396K
  48. Fischbach MA, et al. Directed evolution can rapidly improve the activity of chimeric assembly-line enzymes. Proc Natl Acad Sci U S A 2007;104(29):11951-6.  https://doi.org/10.1073/pnas.0705348104
  49. Yang W-z, et al. Saponins in the genus Panax L.(Araliaceae): a systematic review of their chemical diversity. Phytochemistry 2014;106:7-24.  https://doi.org/10.1016/j.phytochem.2014.07.012
  50. Piao X, et al. Advances in saponin diversity of Panax ginseng. Molecules 2020;25(15):3452. 
  51. Xue-Ni N, et al. Research progress on naturally-occurring and semi-synthetic ocotillol-type ginsenosides in the genus Panax L.(Araliaceae). Chin J Nat Med 2021;19(9):648-55.  https://doi.org/10.1016/S1875-5364(21)60089-4
  52. Rohmer M. The discovery of a mevalonate-independent pathway for isoprenoid biosynthesis in bacteria, algae and higher plants. Nat Prod Rep 1999;16(5):565-74.  https://doi.org/10.1039/a709175c
  53. Boucher Y, Doolittle WF. The role of lateral gene transfer in the evolution of isoprenoid biosynthesis pathways. Mol Microbiol 2000;37(4):703-16.  https://doi.org/10.1046/j.1365-2958.2000.02004.x
  54. Lange BM, et al. Isoprenoid biosynthesis: the evolution of two ancient and distinct pathways across genomes. Proc Natl Acad Sci USA 2000;97(24):13172-7.  https://doi.org/10.1073/pnas.240454797
  55. Lombard J, Moreira D. Origins and early evolution of the mevalonate pathway of isoprenoid biosynthesis in the three domains of life. Mol Biol Evol 2010;28(1):87-99.  https://doi.org/10.1093/molbev/msq177
  56. Liao P, et al. The potential of the mevalonate pathway for enhanced isoprenoid production. Biotechnol Adv 2016;34(5):697-713. https://doi.org/10.1016/j.biotechadv.2016.03.005
  57. Xie S-s, et al. Advances in the metabolic engineering of Escherichia coli for the manufacture of monoterpenes. Catalysts 2019;9(5):433. 
  58. Bochar DA, et al. Biosynthesis of mevalonic acid from acetyl-CoA. Comprehensive natural products chemistry 1999;2:15-44.  https://doi.org/10.1016/B978-0-08-091283-7.00035-7
  59. Kaneda K, et al. An unusual isopentenyl diphosphate isomerase found in the mevalonate pathway gene cluster from Streptomyces sp. strain CL190. Proc Natl Acad Sci USA 2001;98(3):932-7.  https://doi.org/10.1073/pnas.98.3.932
  60. Banerjee A, Sharkey T. Methylerythritol 4-phosphate (MEP) pathway metabolic regulation. Nat Prod Rep 2014;31(8):1043-55.  https://doi.org/10.1039/C3NP70124G
  61. Lu X, Tang K, Li P. Plant metabolic engineering strategies for the production of pharmaceutical terpenoids. Front Plant Sci 2016;7. 
  62. Thimmappa R, et al. Triterpene biosynthesis in plants. Annu Rev Plant Biol 2014;65(1):225-57.  https://doi.org/10.1146/annurev-arplant-050312-120229
  63. Chu LL, et al. Hydroxylation of diverse flavonoids by CYP450 BM3 variants: biosynthesis of eriodictyol from naringenin in whole cells and its biological activities. Microb Cell Factories 2016;15(1). 
  64. Chu LL, et al. Synthetic analog of anticancer drug daunorubicin from daunorubicinone using one-pot enzymatic UDP-recycling glycosylation. J Mol Catal B Enzym 2016;124:1-10.  https://doi.org/10.1016/j.molcatb.2015.11.020
  65. Shin JY, et al. In vitro single-vessel enzymatic synthesis of novel Resvera-A glucosides. Carbohydr Res 2016;424:8-14.  https://doi.org/10.1016/j.carres.2016.02.001
  66. Chu LL, et al. Synthesis of umbelliferone derivatives in Escherichia coli and their biological activities. J Biol Eng 2017;11(1). 
  67. Wang P, et al. Production of bioactive ginsenosides Rh2 and Rg3 by metabolically engineered yeasts. Metab Eng 2015;29:97-105.  https://doi.org/10.1016/j.ymben.2015.03.003
  68. Li C, et al. Pathway elucidation of bioactive rhamnosylated ginsenosides in Panax ginseng and their de novo high-level production by engineered Saccharomyces cerevisiae. Commun Biol 2022;5(1). 
  69. Yan X, et al. Production of bioactive ginsenoside compound K in metabolically engineered yeast. Cell Res 2014;24(6):770-3.  https://doi.org/10.1038/cr.2014.28
  70. Ren H, Hu P, Zhao H. A plug-and-play pathway refactoring workflow for natural product research in Escherichia coli and Saccharomyces cerevisiae. Biotechnol Bioeng 2017;114(8):1847-54.  https://doi.org/10.1002/bit.26309
  71. Wang C, et al. Microbial platform for terpenoid production: Escherichia coli and yeast. Front Microbiol 2018;9:2460. 
  72. Zhu Y, et al. High-yield production of protopanaxadiol from sugarcane molasses by metabolically engineered Saccharomyces cerevisiae. Microb Cell Factories 2022;21(1). 
  73. Hu Z-F, et al. Construction and optimization of microbial cell factories for sustainable production of bioactive dammarenediol-II glucosides. Green Chem 2019;21(12):3286-99.  https://doi.org/10.1039/C8GC04066D
  74. Jiang F, et al. Metabolic engineering of yeasts for green and sustainable production of bioactive ginsenosides F2 and 3β, 20S-Di-O-Glc-DM. Acta Pharm Sin B 2022;12(7):3167-76.  https://doi.org/10.1016/j.apsb.2022.04.012
  75. Pompon D, et al. [6] Yeast expression of animal and plant P450s in optimized redox environments. In: Methods in enzymology. Elsevier; 1996. p. 51-64. 
  76. Dai Z, et al. Identification of a novel cytochrome P450 enzyme that catalyzes the C2α hydroxylation of pentacyclic triterpenoids and its application in yeast cell factories. Metab Eng 2019;51:70-8.  https://doi.org/10.1016/j.ymben.2018.10.001
  77. Zhao Y, et al. Enhancing oleanolic acid production in engineered Saccharomyces cerevisiae. Bioresour Technol 2018;257:339-43.  https://doi.org/10.1016/j.biortech.2018.02.096
  78. Kim JE, et al. Pairing of orthogonal chaperones with a cytochrome P450 enhances terpene synthesis in Saccharomyces cerevisiae. Biotechnol J 2022;17(3):2000452. 
  79. Zhao F, et al. Optimization of a cytochrome P450 oxidation system for enhancing protopanaxadiol production in Saccharomyces cerevisiae. Biotechnol Bioeng 2016;113(8):1787-95.  https://doi.org/10.1002/bit.25934
  80. Jung S-C, et al. Two ginseng UDP-glycosyltransferases synthesize ginsenoside Rg3 and rd. Plant Cell Physiol 2014;55(12):2177-88.  https://doi.org/10.1093/pcp/pcu147
  81. Nan W, et al. Promotion of compound K production in Saccharomyces cerevisiae by glycerol. Microb Cell Factories 2020;19(1). 
  82. Wang P, et al. Systematic optimization of the yeast cell factory for sustainable and high efficiency production of bioactive ginsenoside compound K. Synthetic and systems biotechnology 2021;6(2):69-76.  https://doi.org/10.1016/j.synbio.2021.03.002
  83. Wang P, et al. Synthesizing ginsenoside Rh2 in Saccharomyces cerevisiae cell factory at high-efficiency. Cell Discovery 2019;5(1). 
  84. Li D, et al. Heterologous biosynthesis of triterpenoid dammarenediol-II in engineered Escherichia coli. Biotechnol Lett 2016;38(4):603-9.  https://doi.org/10.1007/s10529-015-2032-9
  85. Cui C-H, et al. Enhanced production of gypenoside LXXV using a novel ginsenoside-transforming β-glucosidase from ginseng-cultivating soil bacteria and its anticancer property. Molecules 2017;22(5):844. 
  86. Yu L, et al. Biosynthesis of rare 20 (R)-protopanaxadiol/protopanaxatriol type ginsenosides through Escherichia coli engineered with uridine diphosphate glycosyltransferase genes. J ginseng research 2019;43(1):116-24.  https://doi.org/10.1016/j.jgr.2017.09.005
  87. Deloache WC, Russ ZN, Dueber JE. Towards repurposing the yeast peroxisome for compartmentalizing heterologous metabolic pathways. Nat Commun 2016;7(1):11152. 
  88. Kim J-E, et al. Tailoring the Saccharomyces cerevisiae endoplasmic reticulum for functional assembly of terpene synthesis pathway. Metab Eng 2019;56:50-9.  https://doi.org/10.1016/j.ymben.2019.08.013
  89. Grewal PS, et al. Peroxisome compartmentalization of a toxic enzyme improves alkaloid production. Nat Chem Biol 2021;17(1):96-103.  https://doi.org/10.1038/s41589-020-00668-4
  90. Choi B, et al. Organelle engineering in yeast: enhanced production of protopanaxadiol through manipulation of peroxisome proliferation in Saccharomyces cerevisiae. Microorganisms 2022;10(3):650. 
  91. Lee C-H, et al. Novel split intein-mediated enzymatic channeling accelerates the multimeric bioconversion pathway of ginsenoside. ACS Synth Biol 2022;11(10):3296-304.  https://doi.org/10.1021/acssynbio.2c00216
  92. Son S-H, et al. Chain flexibility of medicinal lipids determines their selective partitioning into lipid droplets. Nat Commun 2022;13(1). 
  93. Sweetlove LJ, Fernie AR. The role of dynamic enzyme assemblies and substrate channelling in metabolic regulation. Nat Commun 2018;9(1). 
  94. Cao X, et al. Harnessing sub-organelle metabolism for biosynthesis of isoprenoids in yeast. Synthetic and systems biotechnology 2020;5(3):179-86.  https://doi.org/10.1016/j.synbio.2020.06.005
  95. Jiao X, et al. Recent advances in construction and regulation of yeast cell factories. World J Microbiol Biotechnol 2022;38(4). 
  96. Moon SY, et al. Harnessing cellular organelles to bring new functionalities into yeast. Biotechnol Bioproc Eng 2023:1-13. 
  97. Moon SY, et al. Designing microbial cell factories for programmable control of cellular metabolism. Curr Opin Struct Biol 2023:100493. 
  98. Zhao C, et al. Enhancing biosynthesis of a ginsenoside precursor by self-assembly of two key enzymes in Pichia pastoris. J Agric Food Chem 2016;64(17):3380-5.  https://doi.org/10.1021/acs.jafc.6b00650
  99. Wei W, et al. Characterization of Panax ginseng UDP-glycosyltransferases catalyzing protopanaxatriol and biosyntheses of bioactive ginsenosides F1 and Rh1 in metabolically engineered yeasts. Mol Plant 2015;8(9):1412-24. https://doi.org/10.1016/j.molp.2015.05.010