Strategies for the Biosynthesis of Pharmaceuticals and Nutraceuticals in Microbes from Renewable Feedstock

Author(s): Congqiang Zhang*, Heng-Phon Too*

Journal Name: Current Medicinal Chemistry

Volume 27 , Issue 28 , 2020

  Journal Home
Translate in Chinese
Become EABM
Become Reviewer
Call for Editor


Backgrounds: Abundant and renewable biomaterials serve as ideal substrates for the sustainable production of various chemicals, including natural products (e.g., pharmaceuticals and nutraceuticals). For decades, researchers have been focusing on how to engineer microorganisms and developing effective fermentation processes to overproduce these molecules from biomaterials. Despite many laboratory achievements, it remains a challenge to transform some of these into successful industrial applications.

Results: Here, we review recent progress in strategies and applications in metabolic engineering for the production of natural products. Modular engineering methods, such as a multidimensional heuristic process markedly improve efficiencies in the optimization of long and complex biosynthetic pathways. Dynamic pathway regulation realizes autonomous adjustment and can redirect metabolic carbon fluxes to avoid the accumulation of toxic intermediate metabolites. Microbial co-cultivation bolsters the identification and overproduction of natural products by introducing competition or cooperation of different species. Efflux engineering is applied to reduce product toxicity or to overcome storage limitation and thus improves product titers and productivities.

Conclusion: Without dispute, many of the innovative methods and strategies developed are gradually catalyzing this transformation from the laboratory into the industry in the biosynthesis of natural products. Sometimes, it is necessary to combine two or more strategies to acquire additive or synergistic benefits. As such, we foresee a bright future of the biosynthesis of pharmaceuticals and nutraceuticals in microbes from renewable biomaterials.

Keywords: Natural products, secondary metabolites, metabolic engineering, synthetic biology, modular engineering, dynamic regulation, microbial co-cultivation, efflux engineering.

Newman, D.J.; Cragg, G.M. Natural products as sources of new drugs from 1981 to 2014. J. Nat. Prod., 2016, 79(3), 629-661.
[] [PMID: 26852623]
Procópio, R.E.; Silva, I.R.; Martins, M.K.; Azevedo, J.L.; Araújo, J.M. Antibiotics produced by Streptomyces. Braz. J. Infect. Dis., 2012, 16(5), 466-471.
[] [PMID: 22975171]
Nielsen, J.C.; Grijseels, S.; Prigent, S.; Ji, B.; Dainat, J.; Nielsen, K.F.; Frisvad, J.C.; Workman, M.; Nielsen, J. Global analysis of biosynthetic gene clusters reveals vast potential of secondary metabolite production in Penicillium species. Nat. Microbiol., 2017, 2, 17044.
[] [PMID: 28368369]
Zhang, C.; Too, HP. Revalorizing lignocellulose for the production of natural pharmaceuticals and other high value bioproducts. Curr. Med. Chem., 2019, 26(14), 2475-2484.
[] [PMID: 28901274]
Clomburg, J.M.; Crumbley, A.M.; Gonzalez, R. Industrial biomanufacturing: The future of chemical production. Science, 2017, 355(6320) aag0804
[] [PMID: 28059717]
Belasco, J.G. All things must pass: contrasts and commonalities in eukaryotic and bacterial mRNA decay. Nat. Rev. Mol. Cell Biol., 2010, 11(7), 467-478.
[] [PMID: 20520623]
Rape, M. Ubiquitylation at the crossroads of development and disease. Nat. Rev. Mol. Cell Biol., 2018, 19(1), 59-70.
[] [PMID: 28928488]
Joint Genome Institute (JGI). Genomes Online Database (GOD). Available at: . (Accessed date: 1st March, 2018)
Fleischmann, R.D.; Adams, M.D.; White, O.; Clayton, R.A.; Kirkness, E.F.; Kerlavage, A.R.; Bult, C.J.; Tomb, J.F.; Dougherty, B.A.; Merrick, J.M. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science, 1995, 269(5223), 496-512.
[] [PMID: 7542800]
Jain, M.; Koren, S.; Miga, K.H.; Quick, J.; Rand, A.C.; Sasani, T.A.; Tyson, J.R.; Beggs, A.D.; Dilthey, A.T.; Fiddes, I.T.; Malla, S.; Marriott, H.; Nieto, T.; O’Grady, J.; Olsen, H.E.; Pedersen, B.S.; Rhie, A.; Richardson, H.; Quinlan, A.R.; Snutch, T.P.; Tee, L.; Paten, B.; Phillippy, A.M.; Simpson, J.T.; Loman, N.J.; Loose, M. Nanopore sequencing and assembly of a human genome with ultra-long reads. Nat. Biotechnol., 2018, 36(4), 338-345.
[] [PMID: 29431738]
Ma, S.; Tang, N.; Tian, J.; Synthesis, D.N.A. DNA synthesis, assembly and applications in synthetic biology. Curr. Opin. Chem. Biol., 2012, 16(3-4), 260-267.
[] [PMID: 22633067]
Ajikumar, P.K.; Xiao, W-H.; Tyo, K.E.; Wang, Y.; Simeon, F.; Leonard, E.; Mucha, O.; Phon, T.H.; Pfeifer, B.; Stephanopoulos, G. Isoprenoid pathway optimization for Taxol precursor overproduction in Escherichia coli. Science, 2010, 330(6000), 70-74.
[] [PMID: 20929806]
Zhou, K.; Qiao, K.; Edgar, S.; Stephanopoulos, G. Distributing a metabolic pathway among a microbial consortium enhances production of natural products. Nat. Biotechnol., 2015, 33(4), 377-383.
[] [PMID: 25558867]
Thodey, K.; Galanie, S.; Smolke, C.D. A microbial biomanufacturing platform for natural and semisynthetic opioids. Nat. Chem. Biol., 2014, 10(10), 837-844.
[] [PMID: 25151135]
Nakagawa, A.; Matsumura, E.; Koyanagi, T.; Katayama, T.; Kawano, N.; Yoshimatsu, K.; Yamamoto, K.; Kumagai, H.; Sato, F.; Minami, H. Total biosynthesis of opiates by stepwise fermentation using engineered Escherichia coli. Nat. Commun., 2016, 7, 10390.
[] [PMID: 26847395]
Galanie, S.; Thodey, K.; Trenchard, I.J.; Filsinger Interrante, M.; Smolke, C.D. Complete biosynthesis of opioids in yeast. Science, 2015, 349(6252), 1095-1100.
[] [PMID: 26272907]
Zhang, C.; Seow, V.Y.; Chen, X.; Too, HP. Multidimensional heuristic process for high-yield production of astaxanthin and fragrance molecules in Escherichia coli. Nat. Commun., 2018, 9(1), 1858.
[] [PMID: 29752432]
Zhang, C.; Chen, X.; Zou, R.; Zhou, K.; Stephanopoulos, G.; Too, H-P. Combining genotype improvement and statistical media optimization for isoprenoid production in E. coli. PLoS One, 2013, 8(10) e75164
[] [PMID: 24124471]
Zhang, C.; Chen, X.; Lindley, N.D.; Too, H.P.A. A “plug-n-play” modular metabolic system for the production of apocarotenoids. Biotechnol. Bioeng., 2018, 115(1), 174-183.
[] [PMID: 29077207]
Paddon, C.J.; Westfall, P.J.; Pitera, D.J.; Benjamin, K.; Fisher, K.; McPhee, D.; Leavell, M.D.; Tai, A.; Main, A.; Eng, D.; Polichuk, D.R.; Teoh, K.H.; Reed, D.W.; Treynor, T.; Lenihan, J.; Fleck, M.; Bajad, S.; Dang, G.; Dengrove, D.; Diola, D.; Dorin, G.; Ellens, K.W.; Fickes, S.; Galazzo, J.; Gaucher, S.P.; Geistlinger, T.; Henry, R.; Hepp, M.; Horning, T.; Iqbal, T.; Jiang, H.; Kizer, L.; Lieu, B.; Melis, D.; Moss, N.; Regentin, R.; Secrest, S.; Tsuruta, H.; Vazquez, R.; Westblade, L.F.; Xu, L.; Yu, M.; Zhang, Y.; Zhao, L.; Lievense, J.; Covello, P.S.; Keasling, J.D.; Reiling, K.K.; Renninger, N.S.; Newman, J.D. High-level semi synthetic production of the potent antimalarial artemisinin. Nature, 2013, 496(7446), 528-532.
[] [PMID: 23575629]
Dahl, R.H.; Zhang, F.; Alonso-Gutierrez, J.; Baidoo, E.; Batth, T.S.; Redding-Johanson, A.M.; Petzold, C.J.; Mukhopadhyay, A.; Lee, T.S.; Adams, P.D.; Keasling, J.D. Engineering dynamic pathway regulation using stress-response promoters. Nat. Biotechnol., 2013, 31(11), 1039-1046.
[] [PMID: 24142050]
Zhang, C.; Zou, R.; Chen, X.; Stephanopoulos, G.; Too, HP. Experimental design-aided systematic pathway optimization of glucose uptake and deoxyxylulose phosphate pathway for improved amorphadiene production. Appl. Microbiol. Biotechnol., 2015, 99(9), 3825-3837.
[] [PMID: 25715782]
Zhang, C.; Chen, X.; Stephanopoulos, G.; Too, HP. Efflux transporter engineering markedly improves amorphadiene production in Escherichia coli. Biotechnol. Bioeng., 2016, 113(8), 1755-1763.
[] [PMID: 26804325]
Chen, X.; Zhang, C.; Zou, R.; Stephanopoulos, G.; Too, HP. In vitro metabolic engineering of amorpha-4,11-diene biosynthesis at enhanced rate and specific yield of production. ACS Synth. Biol., 2017, 6(9), 1691-1700.
[] [PMID: 28520394]
Jin, E.; Wong, L.; Jiao, Y.; Engel, J.; Holdridge, B.; Xu, P. Rapid evolution of regulatory element libraries for tunable transcriptional and translational control of gene expression. Synth Syst Biotechnol, 2017, 2(4), 295-301.
[] [PMID: 29552654]
Vasilakou, E.; Machado, D.; Theorell, A.; Rocha, I.; Nöh, K.; Oldiges, M.; Wahl, S.A. Current state and challenges for dynamic metabolic modeling. Curr. Opin. Microbiol., 2016, 33, 97-104.
[] [PMID: 27472025]
Smanski, M.J.; Bhatia, S.; Zhao, D.; Park, Y.; B A Woodruff, L.; Giannoukos, G.; Ciulla, D.; Busby, M.; Calderon, J.; Nicol, R.; Gordon, D.B.; Densmore, D.; Voigt, C.A. Functional optimization of gene clusters by combinatorial design and assembly. Nat. Biotechnol., 2014, 32(12), 1241-1249.
[] [PMID: 25419741]
Farmer, W.R.; Liao, J.C. Improving lycopene production in Escherichia coli by engineering metabolic control. Nat. Biotechnol., 2000, 18(5), 533-537.
[] [PMID: 10802621]
Martin, V.J.; Pitera, D.J.; Withers, S.T.; Newman, J.D.; Keasling, J.D. Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nat. Biotechnol., 2003, 21(7), 796-802.
[] [PMID: 12778056]
Xu, P.; Li, L.; Zhang, F.; Stephanopoulos, G.; Koffas, M. Improving fatty acids production by engineering dynamic pathway regulation and metabolic control. Proc. Natl. Acad. Sci. USA, 2014, 111(31), 11299-11304.
[] [PMID: 25049420]
Xu, P.; Bhan, N.; Koffas, M.A.G. Engineering plant metabolism into microbes: from systems biology to synthetic biology. Curr. Opin. Biotechnol., 2013, 24(2), 291-299.
[] [PMID: 22985679]
Gupta, A.; Reizman, I.M.; Reisch, C.R.; Prather, K.L. Dynamic regulation of metabolic flux in engineered bacteria using a pathway-independent quorum-sensing circuit. Nat. Biotechnol., 2017, 35(3), 273-279.
[] [PMID: 28191902]
Xu, P. Production of chemicals using dynamic control of metabolic fluxes. Curr. Opin. Biotechnol., 2018, 53, 12-19.
[] [PMID: 29145021]
Xu, P.; Rizzoni, E.A.; Sul, S.Y.; Stephanopoulos, G. Improving metabolic pathway efficiency by statistical model-based multivariate regulatory metabolic engineering. ACS Synth. Biol., 2017, 6(1), 148-158.
[] [PMID: 27490704]
Faust, K.; Raes, J. Microbial interactions: from networks to models. Nat. Rev. Microbiol., 2012, 10(8), 538-550.
[] [PMID: 22796884]
Netzker, T.; Fischer, J.; Weber, J.; Mattern, D.J.; König, C.C.; Valiante, V.; Schroeckh, V.; Brakhage, A.A. Microbial communication leading to the activation of silent fungal secondary metabolite gene clusters. Front. Microbiol., 2015, 6, 299.
[] [PMID: 25941517]
Nützmann, H.W.; Reyes-Dominguez, Y.; Scherlach, K.; Schroeckh, V.; Horn, F.; Gacek, A.; Schümann, J.; Hertweck, C.; Strauss, J.; Brakhage, A.A. Bacteria-induced natural product formation in the fungus Aspergillus nidulans requires Saga/Ada-mediated histone acetylation. Proc. Natl. Acad. Sci. USA, 2011, 108(34), 14282-14287.
[] [PMID: 21825172]
Park, H.B.; Kwon, H.C.; Lee, C.H.; Yang, H.O. Glionitrin A, an antibiotic-antitumor metabolite derived from competitive interaction between abandoned mine microbes. J. Nat. Prod., 2009, 72(2), 248-252.
[] [PMID: 19159274]
Ola, A.R.; Thomy, D.; Lai, D.; Brötz-Oesterhelt, H.; Proksch, P. Inducing secondary metabolite production by the endophytic fungus Fusarium tricinctum through coculture with Bacillus subtilis. J. Nat. Prod., 2013, 76(11), 2094-2099.
[] [PMID: 24175613]
Zhang, H.; Pereira, B.; Li, Z.; Stephanopoulos, G. Engineering Escherichia coli coculture systems for the production of biochemical products. Proc. Natl. Acad. Sci. USA, 2015, 112(27), 8266-8271.
[] [PMID: 26111796]
Minty, J.J.; Singer, M.E.; Scholz, S.A.; Bae, C.H.; Ahn, J.H.; Foster, C.E.; Liao, J.C.; Lin, X.N. Design and characterization of synthetic fungal-bacterial consortia for direct production of isobutanol from cellulosic biomass. Proc. Natl. Acad. Sci. USA, 2013, 110(36), 14592-14597.
[] [PMID: 23959872]
Jones, J.A.; Vernacchio, V.R.; Collins, S.M.; Shirke, A.N.; Xiu, Y.; Englaender, J.A.; Cress, B.F.; McCutcheon, C.C.; Linhardt, R.J.; Gross, R.A.; Koffas, M.A.G. complete biosynthesis of anthocyanins using E. coli polycultures. MBio, 2017, 8(3), e00621-e17.
[] [PMID: 28588129]
Brohée, S.; Barriot, R.; Moreau, Y.; André, B. YTPdb: a wiki database of yeast membrane transporters. Biochim. Biophys. Acta, 2010, 1798(10), 1908-1912.
[] [PMID: 20599686]
Daley, D.O.; Rapp, M.; Granseth, E.; Melén, K.; Drew, D.; von Heijne, G. Global topology analysis of the Escherichia coli inner membrane proteome. Science, 2005, 308(5726), 1321-1323.
[] [PMID: 15919996]
Piddock, L.J. Multidrug-resistance efflux pumps - not just for resistance. Nat. Rev. Microbiol., 2006, 4(8), 629-636.
[] [PMID: 16845433]
Dunlop, M.J.; Dossani, Z.Y.; Szmidt, H.L.; Chu, H.C.; Lee, T.S.; Keasling, J.D.; Hadi, M.Z.; Mukhopadhyay, A. Engineering microbial biofuel tolerance and export using efflux pumps. Mol. Syst. Biol., 2011, 7, 487.
[] [PMID: 21556065]
Foo, J.L.; Leong, S.S.J. Directed evolution of an E. coli inner membrane transporter for improved efflux of biofuel molecules. Biotechnol. Biofuels, 2013, 6(1), 81.
[] [PMID: 23693002]
Wang, J-F.; Xiong, Z-Q.; Li, S-Y.; Wang, Y. Enhancing isoprenoid production through systematically assembling and modulating efflux pumps in Escherichia coli. Appl. Microbiol. Biotechnol., 2013, 97(18), 8057-8067.
[] [PMID: 23864262]
Foo, J.L.; Jensen, H.M.; Dahl, R.H.; George, K.; Keasling, J.D.; Lee, T.S.; Leong, S.; Mukhopadhyay, A. Improving microbial biogasoline production in Escherichia coli using tolerance engineering. MBio, 2014, 5(6), e01932-e01914.
[] [PMID: 25370492]
Verhoef, S.; Ballerstedt, H.; Volkers, R.J.M.; de Winde, J.H.; Ruijssenaars, H.J. Comparative transcriptomics and proteomics of p-hydroxybenzoate producing Pseudomonas putida S12: novel responses and implications for strain improvement. Appl. Microbiol. Biotechnol., 2010, 87(2), 679-690.
[] [PMID: 20449741]
Ling, H.; Chen, B.; Kang, A.; Lee, J.M.; Chang, M.W. Transcriptome response to alkane biofuels in Saccharomyces cerevisiae: identification of efflux pumps involved in alkane tolerance. Biotechnol. Biofuels, 2013, 6(1), 95.
[] [PMID: 23826995]
Doshi, R.; Nguyen, T.; Chang, G. Transporter-mediated biofuel secretion. Proc. Natl. Acad. Sci. USA, 2013, 110(19), 7642-7647.
[] [PMID: 23613592]
Alvizo, O.; Nguyen, L.J.; Savile, C.K.; Bresson, J.A.; Lakhapatri, S.L.; Solis, E.O.; Fox, R.J.; Broering, J.M.; Benoit, M.R.; Zimmerman, S.A.; Novick, S.J.; Liang, J.; Lalonde, J.J. Directed evolution of an ultrastable carbonic anhydrase for highly efficient carbon capture from flue gas. Proc. Natl. Acad. Sci. USA, 2014, 111(46), 16436-16441.
[] [PMID: 25368146]
Gupta, R.D.; Goldsmith, M.; Ashani, Y.; Simo, Y.; Mullokandov, G.; Bar, H.; Ben-David, M.; Leader, H.; Margalit, R.; Silman, I.; Sussman, J.L.; Tawfik, D.S. Directed evolution of hydrolases for prevention of G-type nerve agent intoxication. Nat. Chem. Biol., 2011, 7(2), 120-125.
[] [PMID: 21217689]
Leonard, E.; Ajikumar, P.K.; Thayer, K.; Xiao, W-H.; Mo, J.D.; Tidor, B.; Stephanopoulos, G.; Prather, K.L. Combining metabolic and protein engineering of a terpenoid biosynthetic pathway for overproduction and selectivity control. Proc. Natl. Acad. Sci. USA, 2010, 107(31), 13654-13659.
[] [PMID: 20643967]
Schwander, T.; Schada von Borzyskowski, L.; Burgener, S.; Cortina, N.S.; Erb, T.J. A synthetic pathway for the fixation of carbon dioxide in vitro. Science, 2016, 354(6314), 900-904.
[] [PMID: 27856910]
Meadows, A.L.; Hawkins, K.M.; Tsegaye, Y.; Antipov, E.; Kim, Y.; Raetz, L.; Dahl, R.H.; Tai, A.; Mahatdejkul-Meadows, T.; Xu, L.; Zhao, L.; Dasika, M.S.; Murarka, A.; Lenihan, J.; Eng, D.; Leng, J.S.; Liu, C.L.; Wenger, J.W.; Jiang, H.; Chao, L.; Westfall, P.; Lai, J.; Ganesan, S.; Jackson, P.; Mans, R.; Platt, D.; Reeves, C.D.; Saija, P.R.; Wichmann, G.; Holmes, V.F.; Benjamin, K.; Hill, P.W.; Gardner, T.S.; Tsong, A.E. Rewriting yeast central carbon metabolism for industrial isoprenoid production. Nature, 2016, 537(7622), 694-697.
[] [PMID: 27654918]
Shaw, A.J.; Lam, F.H.; Hamilton, M.; Consiglio, A.; MacEwen, K.; Brevnova, E.E.; Greenhagen, E.; LaTouf, W.G.; South, C.R.; van Dijken, H.; Stephanopoulos, G. Metabolic engineering of microbial competitive advantage for industrial fermentation processes. Science, 2016, 353(6299), 583-586.
[] [PMID: 27493184]

Rights & PermissionsPrintExport Cite as

Article Details

Year: 2020
Published on: 06 August, 2020
Page: [4613 - 4621]
Pages: 9
DOI: 10.2174/0929867327666200212121047
Price: $65

Article Metrics

PDF: 23