Engineered microorganisms and enzymes for efficiently synthesizing plant natural products

doi:10.1016/j.cjche.2020.12.015

摘要/Abstract

摘要： Plant natural products are a kind of active substance widely used in pharmaceuticals and foods. However, the current production mode based on plant culture and extraction suffer complex processes and severe concerns for environmental and ecological. With the increasing awareness of environmental sustainability, engineered microbial cell factories have been an alternative approach to produce natural products. Many engineering strategies have been utilized in microbial biosynthesis of complex phytochemicals such as dynamic control and substructure engineering. Meanwhile, Enzyme engineering including directed evolution and rational design has been implemented to improve enzyme catalysis efficiency and stability as well as change promiscuity to expand product spectra. In this review, we discussed recent advances in microbial biosynthesis of complex phytochemicals from the following aspects, including pathway construction, strain engineering to boost the production.

关键词: Plant natural products, Microorganisms, Synthetic biology, Enzyme engineering

Abstract: Plant natural products are a kind of active substance widely used in pharmaceuticals and foods. However, the current production mode based on plant culture and extraction suffer complex processes and severe concerns for environmental and ecological. With the increasing awareness of environmental sustainability, engineered microbial cell factories have been an alternative approach to produce natural products. Many engineering strategies have been utilized in microbial biosynthesis of complex phytochemicals such as dynamic control and substructure engineering. Meanwhile, Enzyme engineering including directed evolution and rational design has been implemented to improve enzyme catalysis efficiency and stability as well as change promiscuity to expand product spectra. In this review, we discussed recent advances in microbial biosynthesis of complex phytochemicals from the following aspects, including pathway construction, strain engineering to boost the production.

Key words: Plant natural products, Microorganisms, Synthetic biology, Enzyme engineering

Wenqiang Li, Wentao Sun, Chun Li. Engineered microorganisms and enzymes for efficiently synthesizing plant natural products[J]. 中国化学工程学报, 2021, 29(2): 62-73.

Wenqiang Li, Wentao Sun, Chun Li. Engineered microorganisms and enzymes for efficiently synthesizing plant natural products[J]. Chinese Journal of Chemical Engineering, 2021, 29(2): 62-73.

参考文献

[1] M. Scognamiglio, B. D’Abrosca, V. Fiumano, A. Chambery, V. Severino, N. Tsafantakis, S. Pacifico, A. Esposito, A. Fiorentino, Oleanane saponins from Bellis sylvestris Cyr. and evaluation of their phytotoxicity on Aegilops geniculata Roth, Phytochemistry 84 (2012) 125–134.
[2] R. Thimmappa, K. Geisler, T. Louveau, P. O’Maille, A. Osbourn, Triterpene biosynthesis in plants, Annu. Rev. Plant Biol. 65 (2014) 225–257.
[3] W. Sun, Y.-J. Zhao, C. Li, De Novo Synthesis of Plant Natural Products in Yeast, Yeasts Biotechnology, Intech Open, London (2019).
[4] L. Wang, C.L. Weller, Recent advances in extraction of nutraceuticals from plants, Trends Food Sci. Tech. 17 (2006) 300–312.
[5] K. Thodey, S. Galanie, C.D. Smolke, A microbial biomanufacturing platform for natural and semisynthetic opioids, Nat. Chem. Biol. 10 (2014) 837–844.
[6] A.O. Zabala, R.A. Cacho, Y. Tang, Protein engineering towards natural product synthesis and diversification, J. Ind. Microbiol. Biot. 39 (2012) 227–241.
[7] C. Li, R. Zhang, J. Wang, L.M. Wilson, Y. Yan, Protein engineering for improving and diversifying natural product biosynthesis, Trends Biotechnol. 38 (2020) 729–744.
[8] E. Vranova, D. Coman, W. Gruissem, Network analysis of the MVA and MEP pathways for isoprenoid synthesis, Annu. Rev. Plant Biol. 64 (2013) 665–700.
[9] A. Disch, M. Rohmer, On the absence of the glyceraldehyde 3-phosphate/pyruvate pathway for isoprenoid biosynthesis in fungi and yeasts, FEMS Microbiol. Lett. 168 (1998) 201–208.
[10] W.J. Kovacs, L.M. Olivier, S.K. Krisans, Central role of peroxisomes in isoprenoid biosynthesis, Prog. Lipid Res. 41 (2002) 369–391.
[11] A. Smit, A. Mushegian, Biosynthesis of isoprenoids via mevalonate in Archaea: the lost pathway, Genome Res. 10 (2000) 1468–1484.
[12] B.M. Lange, M. Ghassemian, Genome organization in Arabidopsis thaliana: a survey for genes involved in isoprenoid and chlorophyll metabolism, Plant Mol. Biol. 51 (2003) 925–948.
[13] H. Cao, X. Chen, A.R. Jassbi, J. Xiao, Microbial biotransformation of bioactive flavonoids, Biotechnol. Adv. 33 (2015) 214–223.
[14] T.M. Kutchan, Expression of enzymatically active cloned strictosidine synthase from the higher plant Rauvolfia serpentina in Escherichia coli, FEBS Lett. 257 (1989) 127–130.
[15] M. Lopez-Meyer, C.L. Nessler, Tryptophan decarboxylase is encoded by two autonomously regulated genes in Camptotheca acuminata which are differentially expressed during development and stress, Plant J. 11 (2010) 1167–1175.
[16] P.F. Kraus, T.M. Kutchan, Molecular cloning and heterologous expression of a cDNA encoding berbamunine synthase, a C-O phenol-coupling cytochrome P450 from the higher plant Berberis stolonifera, Proc. Natl. Acad. Sci. USA 92 (1995) 2071–2075.
[17] X. Liu, J. Cheng, G. Zhang, W. Ding, L. Duan, J. Yang, L. Kui, X. Cheng, J. Ruan, W. Fan, J. Chen, G. Long, Y. Zhao, J. Cai, W. Wang, Y. Ma, Y. Dong, S. Yang, H. Jiang, Engineering yeast for the production of breviscapine by genomic analysis and synthetic biology approaches, Nat. Commun. 9 (2018) 448.
[18] C.L. Steele, M. Gijzen, D. Qutob, R.A. Dixon, Molecular characterization of the enzyme catalyzing the aryl migration reaction of isoflavonoid biosynthesis in soybean, Arch. Biochem. Biophys. 367 (1999) 146–150.
[19] C.J. Liu, D. Huhman, L.W. Sumner, R.A. Dixon, Regiospecific hydroxylation of isoflavones by cytochrome p450 81E enzymes from Medicago truncatula, Plant J. 36 (2003) 471–484.
[20] Q. Liu, Y. Liu, Y. Chen, J. Nielsen, Current state of aromatics production using yeast: achievements and challenges, Curr. Opin. Biotechnol. 65 (2020) 65–74.
[21] J. Ziegler, P.J. Facchini, Alkaloid biosynthesis: Metabolism and trafficking, Annu. Rev. Plant Biol. 59 (2008) 735–769.
[22] G. Schröder, E. Unterbusch, M. Kaltenbach, J. Schmidt, D. Strack, V. De Luca, J. Schröder, Light-induced cytochrome P450-dependent enzyme in indole alkaloid biosynthesis: tabersonine 16-hydroxylase, FEBS Lett. 458 (1999) 97–102.
[23] B.R. Lichman, The scaffold-forming steps of plant alkaloid biosynthesis, Nat. Prod. Rep. (2020), https://doi.org/10.1039/d0np0031k (Article in press).
[24] S.C. Farrow, J.M. Hagel, G.A. Beaudoin, D.C. Burns, P.J. Facchini, Stereochemical inversion of (S)-reticuline by a cytochrome P450 fusion in opium poppy, Nat. Chem. Biol. 11 (2015) 728–732.
[25] A. Gesell, M. Rolf, J. Ziegler, M.L. Diaz Chavez, F.C. Huang, T.M. Kutchan, CYP719B1 is salutaridine synthase, the C-C phenol-coupling enzyme of morphine biosynthesis in opium poppy, J. Biol. Chem. 284 (2009) 24432–24442.
[26] H. Seki, K. Ohyama, S. Sawai, M. Mizutani, T. Ohnishi, H. Sudo, T. Akashi, T. Aoki, K. Saito, T. Muranaka, Licorice beta-amyrin 11-oxidase, a cytochrome P450 with a key role in the biosynthesis of the triterpene sweetener glycyrrhizin, Proc. Natl. Acad. Sci. USA 105 (2008) 14204–14209.
[27] H. Seki, S. Sawai, K. Ohyama, M. Mizutani, T. Ohnishi, H. Sudo, E.O. Fukushima, T. Akashi, T. Aoki, K. Saito, T. Muranaka, Triterpene functional genomics in licorice for identification of CYP72A154 involved in the biosynthesis of glycyrrhizin, Plant Cell 23 (2011) 4112–4123.
[28] Y. Shang, Y. Ma, Y. Zhou, H. Zhang, L. Duan, H. Chen, J. Zeng, Q. Zhou, S. Wang, W. Gu, M. Liu, J. Ren, X. Gu, S. Zhang, Y. Wang, K. Yasukawa, H.J. Bouwmeester, X. Qi, Z. Zhang, W.J. Lucas, S. Huang, Plant science. Biosynthesis, regulation, and domestication of bitterness in cucumber, Science 346 (2014) 1084–1088.
[29] T. Morishige, E. Dubouzet, K.B. Choi, K. Yazaki, F. Sato, Molecular cloning of columbamine O-methyltransferase from cultured Coptis japonica cells, Eur. J. Biochem. 269 (2010) 5659–5667.
[30] A. Singh, I.M. Menéndez-Perdomo, P.J. Facchini, Benzylisoquinoline alkaloid biosynthesis in opium poppy: an update, Phytochem. Rev. 18 (2019) 1457–1482.
[31] J. Xiao, T.S. Muzashvili, M.I. Georgiev, Advances in the biotechnological glycosylation of valuable flavonoids, Biotechnol. Adv. 32 (2014) 1145–1156.
[32] L.V. Modolo, L. Li, H. Pan, J.W. Blount, R.A. Dixon, X. Wang, Crystal structures of glycosyltransferase UGT78G1 reveal the molecular basis for glycosylation and deglycosylation of (iso)flavonoids, J. Mol. Biol. 392 (2009) 1292–1302.
[33] L. Achnine, D. Huhman, M.A. Farag, L.W. Sumner, J. Blount, R.A. Dixon, Genomics-based selection and functional characterization of triterpene glycosyltransferases from the model legume Medicago truncatula, Plant J. 41 (2010) 875–887.
[34] L. Li, L.V. Modolo, L.L. Escamilla-Trevino, L. Achnine, R.A. Dixon, X. Wang, Crystal structure of Medicago truncatula UGT85H2–insights into the structural basis of a multifunctional (iso)flavonoid glycosyltransferase, J. Mol. Biol. 370 (2007) 951–963.
[35] C.M. Kramer, R.T. Prata, M.G. Willits, V. De Luca, J.C. Steffens, G. Graser, Cloning and regiospecificity studies of two flavonoid glucosyltransferases from Allium cepa, Phytochemistry 64 (2003) 1069–1076.
[36] C. Gosch, H. Halbwirth, B. Schneider, D. HöLscher, K. Stich, Cloning and heterologous expression of glycosyltransferases from Malus x domestica and Pyrus communis, which convert phloretin to phloretin 2’-O-glucoside (phloridzin), Plant Sci. 178 (2010) 299–306.
[37] N. Kovinich, A. Saleem, J.T. Arnason, B. Miki, Functional characterization of a UDP-glucose:flavonoid 3-O-glucosyltransferase from the seed coat of black soybean (Glycine max (L.) Merr.), Phytochemistry 71 (2010) 1253–1263.
[38] P. Arendt, K. Miettinen, J. Pollier, R. De Rycke, N. Callewaert, A. Goossens, An endoplasmic reticulum-engineered yeast platform for overproduction of triterpenoids, Metab. Eng. 40 (2017) 165–175.
[39] J.Y. Han, H.J. Kim, Y.S. Kwon, Y.E. Choi, The Cyt P450 enzyme CYP716A47 catalyzes the formation of protopanaxadiol from dammarenediol-II during ginsenoside biosynthesis in Panax ginseng, Plant Cell Physiol. 52 (2011) 2062–2073.
[40] J.Y. Han, H.S. Hwang, S.W. Choi, H.J. Kim, Y.E. Choi, Cytochrome P450 CYP716A53v2 catalyzes the formation of protopanaxatriol from protopanaxadiol during ginsenoside biosynthesis in Panax ginseng, Plant Cell Physiol. 53 (2012) 1535–1545.
[41] X. Yan, Y. Fan, W. Wei, P. Wang, Q. Liu, Y. Wei, L. Zhang, G. Zhao, J. Yue, Z. Zhou, Production of bioactive ginsenoside compound K in metabolically engineered yeast, Cell Res. 24 (2014) 770–773.
[42] S.C. Jung, W. Kim, S.C. Park, J. Jeong, M.K. Park, S. Lim, Y. Lee, W.T. Im, J.H. Lee, G. Choi, S.C. Kim, Two ginseng UDP-glycosyltransferases synthesize ginsenoside Rg3 and Rd, Plant Cell Physiol. 55 (2014) 2177–2188.
[43] P. Wang, Y. Wei, Y. Fan, Q. Liu, W. Wei, C. Yang, L. Zhang, G. Zhao, J. Yue, X. Yan, Z. Zhou, Production of bioactive ginsenosides Rh2 and Rg3 by metabolically engineered yeasts, Metab. Eng. 29 (2015) 97–105.
[44] Y. Hanasaki, S. Ogawa, S. Fukui, The correlation between active oxygens scavenging and antioxidative effects of flavonoids, Free Radic Biol. Med. 16 (1994) 845–850.
[45] Y. Katsuyama, N. Funa, I. Miyahisa, S. Horinouchi, Synthesis of unnatural flavonoids and stilbenes by exploiting the plant biosynthetic pathway in Escherichia coli, Chem. Biol. 14 (2007) 613–621.
[46] E. Leonard, Y. Yan, Z.L. Fowler, Z. Li, C.G. Lim, K.H. Lim, M.A.G. Koffas, Strain improvement of recombinant Escherichia coli for efficient production of plant flavonoids, Mol. Pharmaceut. 5 (2008) 257–265.
[47] R.P. Pandey, P. Parajuli, M.A.G. Koffas, J.K. Sohng, Microbial production of natural and non-natural flavonoids: Pathway engineering, directed evolution and systems/synthetic biology, Biotechnol. Adv. 34 (2016) 634–662.
[48] J.A. Chemler, Z.L. Fowler, K.P. McHugh, M.A. Koffas, Improving NADPH availability for natural product biosynthesis in Escherichia coli by metabolic engineering, Metab. Eng. 12 (2010) 96–104.
[49] X. Wang, X. Feng, B. Lv, A. Zhou, Y. Hou, C. Li, Enhanced yeast surface display of b-glucuronidase using dual anchor motifs for high-temperature glycyrrhizin hydrolysis, AIChE J. 65 (2019) e16629.
[50] L. Narcross, E. Fossati, L. Bourgeois, J.E. Dueber, V.J.J. Martin, Microbial factories for the production of benzylisoquinoline alkaloids, Trends Biotechnol. 34 (2016) 228–241.
[51] Y. Li, C.D. Smolke, Engineering biosynthesis of the anticancer alkaloid noscapine in yeast, Nat. Commun. 7 (2016) 12137.
[52] M. Zhu, C. Wang, W. Sun, A. Zhou, Y. Wang, G. Zhang, X. Zhou, Y. Huo, C. Li, Boosting 11-oxo-beta-amyrin and glycyrrhetinic acid synthesis in Saccharomyces cerevisiae via pairing novel oxidation and reduction system from legume plants, Metab. Eng. 45 (2018) 43–50.
[53] T. Moses, J.M. Thevelein, A. Goossens, J. Pollier, Comparative analysis of CYP93E proteins for improved microbial synthesis of plant triterpenoids, Phytochemistry 108 (2014) 47–56.
[54] Y. Yu, P. Chang, H. Yu, H. Ren, D. Hong, Z. Li, Y. Wang, H. Song, Y. Huo, C. Li, Productive amyrin synthases for efficient alpha-amyrin synthesis in engineered Saccharomyces cerevisiae, ACS Synth. Biol. 7 (2018) 2391–2402.
[55] C.J. Paddon, P.J. Westfall, D.J. Pitera, K. Benjamin, K. Fisher, D. McPhee, M.D. Leavell, A. Tai, A. Main, D. Eng, D.R. Polichuk, K.H. Teoh, D.W. Reed, T. Treynor, J. Lenihan, M. Fleck, S. Bajad, G. Dang, D. Dengrove, D. Diola, G. Dorin, K.W. Ellens, S. Fickes, J. Galazzo, S.P. Gaucher, T. Geistlinger, R. Henry, M. Hepp, T. Horning, T. Iqbal, H. Jiang, L. Kizer, B. Lieu, D. Melis, N. Moss, R. Regentin, S. Secrest, H. Tsuruta, R. Vazquez, L.F. Westblade, L. Xu, M. Yu, Y. Zhang, L. Zhao, J. Lievense, P.S. Covello, J.D. Keasling, K.K. Reiling, N.S. Renninger, J.D. Newman, High-level semi-synthetic production of the potent antimalarial artemisinin, Nature 496 (2013) 528–532.
[56] J. Li, Y. Zhang, Modulating betulinic acid production in Saccharomyces cerevisiae by managing the intracellular supplies of the co-factor NADPH and oxygen, J. Biosci. Bioeng. 119 (2015) 77–81.
[57] A. Rasool, M.S. Ahmed, C. Li, Overproduction of squalene synergistically downregulates ethanol production in Saccharomyces cerevisiae, Chem. Eng. Sci. 152 (2016) 370–380.
[58] Y. Zhao, B. Lv, X. Feng, C. Li, Perspective on biotransformation and De Novo biosynthesis of licorice constituents, J. Agric. Food Chem. 65 (2017) 11147–11156.
[59] Y.J. Zhao, C. Li, Biosynthesis of plant triterpenoid saponins in microbial cell factories, J. Agric. Food Chem. 66 (2018) 12155–12165.
[60] G. Zhang, Q. Cao, J. Liu, B. Liu, J. Li, C. Li, Refactoring b-amyrin synthesis in Saccharomyces cerevisiae, AIChE J. 61 (2015) 3172–3179.
[61] J. Alonso-Gutierrez, R. Chan, T.S. Batth, P.D. Adams, J.D. Keasling, C.J. Petzold, T.S. Lee, Metabolic engineering of Escherichia coli for limonene and perillyl alcohol production, Metab. Eng. 19 (2013) 33–41.
[62] Y. Zhao, J. Fan, C. Wang, X. Feng, C. Li, Enhancing oleanolic acid production in engineered Saccharomyces cerevisiae, Bioresour. Technol. 257 (2018) 339–343.
[63] S. Wattanachaisaereekul, A.E. Lantz, M.L. Nielsen, J. Nielsen, Production of the polyketide 6-MSA in yeast engineered for increased malonyl-CoA supply, Metab. Eng. 10 (2008) 246–254.
[64] B.F. Cress, O.D. Toparlak, S. Guleria, M. Lebovich, J.T. Stieglitz, J.A. Englaender, J.A. Jones, R.J. Linhardt, M.A. Koffas, CRISPathBrick: modular combinatorial assembly of type II-A CRISPR arrays for dCas9-mediated multiplex transcriptional repression in E. coli, ACS Synth. Biol. 4 (2015) 987–1000.
[65] Q. Liu, T. Yu, X. Li, Y. Chen, K. Campbell, J. Nielsen, Y. Chen, Rewiring carbon metabolism in yeast for high level production of aromatic chemicals, Nat. Commun. 10 (2019) 4976.
[66] H. Liu, J. Fan, C. Wang, C. Li, X. Zhou, Enhanced beta-amyrin synthesis in Saccharomyces cerevisiae by coupling an optimal acetyl-CoA supply pathway, J. Agric. Food Chem. 67 (2019) 3723–3732.
[67] A.O. Chatzivasileiou, V. Ward, S.M. Edgar, G. Stephanopoulos, Two-step pathway for isoprenoid synthesis, Proc. Natl. Acad. Sci. USA 116 (2019) 506–511.
[68] J. Kirby, D.W. Romanini, E.M. Paradise, J.D. Keasling, Engineering triterpene production in Saccharomyces cerevisiae-beta-amyrin synthase from Artemisia annua, FEBS J. 275 (2008) 1852–1859.
[69] J. Ni, G. Zhang, L. Qin, J. Li, C. Li, Simultaneously down-regulation of multiplex branch pathways using CRISPRi and fermentation optimization for enhancing beta-amyrin production in Saccharomyces cerevisiae, Synth. Syst. Biotechnol. 4 (2019) 79–85.
[70] G.S. Liu, T. Li, W. Zhou, M. Jiang, X.Y. Tao, M. Liu, M. Zhao, Y.H. Ren, B. Gao, F.Q. Wang, D.Z. Wei, The yeast peroxisome: a dynamic storage depot and subcellular factory for squalene overproduction, Metab. Eng. 57 (2020) 151–161.
[71] G. Daletos, C. Katsimpouras, G. Stephanopoulos, Novel strategies and platforms for industrial isoprenoid engineering, Trends Biotechnol. 38 (2020) 811–822.
[72] Y. Yu, A. Rasool, H. Liu, B. Lv, P. Chang, H. Song, Y. Wang, C. Li, Engineering Saccharomyces cerevisiae for high yield production of alpha-amyrin via synergistic remodeling of alpha-amyrin synthase and expanding the storage pool, Metab. Eng. 62 (2020) 72–83.
[73] C. Liang, X. Zhang, J. Wu, S. Mu, Z. Wu, J.M. Jin, S.Y. Tang, Dynamic control of toxic natural product biosynthesis by an artificial regulatory circuit, Metab. Eng. 57 (2020) 239–246.
[74] J. Yuan, C.B. Ching, Dynamic control of ERG9 expression for improved amorpha-4,11-diene production in Saccharomyces cerevisiae, Microb. Cell Fact. 14 (2015) 38.
[75] B. Peng, M.R. Plan, P. Chrysanthopoulos, M.P. Hodson, L.K. Nielsen, C.E. Vickers, A squalene synthase protein degradation method for improved sesquiterpene production in Saccharomyces cerevisiae, Metab. Eng. 39 (2017) 209–219.
[76] P. Xu, M. Marsafari, J. Zha, M. Koffas, Microbial coculture for flavonoid synthesis, Trends Biotechnol. 38 (2020) 686–688.
[77] A.E. Nixon, S.M. Firestine, Rational and “irrational” design of proteins and their use in biotechnology, IUBMB Life 49 (2000) 181–187.
[78] S. Li, Y. Li, C.D. Smolke, Strategies for microbial synthesis of high-value phytochemicals, Nat. Chem. 10 (2018) 395–404.
[79] W. Sun, L. Qin, H. Xue, Y. Yu, Y. Ma, Y. Wang, C. Li, Novel trends for producing plant triterpenoids in yeast, Cri. Rev. Biotechol. 39 (2019) 618–632.
[80] P. Wang, W. Wei, W. Ye, X. Li, W. Zhao, C. Yang, C. Li, X. Yan, Z. Zhou, Synthesizing ginsenoside Rh2 in Saccharomyces cerevisiae cell factory at highefficiency, Cell discov. 5 (2019) 1–14.
[81] I. Kozono, K. Mihara, K. Minagawa, M. Hibi, J. Ogawa, Engineering of the cytochrome P450 monooxygenase system for benzyl maltol hydroxylation, Appl. Microbiol. Biot. 101 (2017) 6651–6658.
[82] P. Zhou, Y. Du, N. Xu, C. Yue, L. Ye, Improved linalool production in Saccharomyces cerevisiae by combining directed evolution of linalool synthase and overexpression of the complete mevalonate pathway, Biochem. Eng. J. 161 (2020) 107655.
[83] W. Ma, L. Zhao, Y. Ma, Y. Li, S. Qin, B. He, Oriented efficient biosynthesis of rare ginsenoside Rh2 from PPD by compiling UGT-Yjic mutant with sucrose synthase, Int. J. Biol. Macromol. 146 (2020) 853–859.
[84] R.-J. Li, A. Li, J. Zhao, Q. Chen, N. Li, H.-L. Yu, J.-H. Xu, Engineering P450LaMO stereospecificity and product selectivity for selective C-H oxidation of tetralin-like alkylbenzenes, Catal. Sci. Technol. 8 (2018) 4638–4644.
[85] L. Zhang, S. Ren, X. Liu, X. Liu, F. Guo, W. Sun, X. Feng, C. Li, Mining of UDPglucosyltrfansferases in licorice for controllable glycosylation of pentacyclic triterpenoids, Biotechnol. Bioeng. 117 (12) (2020) 3651–3663.
[86] X. Liu, L. Zhang, X. Feng, B. Lv, C. Li, Biosynthesis of glycyrrhetinic acid-3-Omonoglucose using glycosyltransferase UGT73C11 from Barbarea vulgaris, Ind. Eng. Chem. Res. 56 (2017) 14949–14958.
[87] C.G. Acevedo-Rocha, C.G. Gamble, R. Lonsdale, A. Li, N. Nett, S. Hoebenreich, J. B. Lingnau, C. Wirtz, C. Fares, H. Hinrichs, A. Deege, A.J. Mulholland, Y. Nov, D. Leys, K.J. McLean, A.W. Munro, M.T. Reetz, P450-catalyzed regio- and diastereoselective steroid hydroxylation: Efficient directed evolution enabled by mutability landscaping, ACS Catal. 8 (2018) 3395–3410.
[88] J. Li, J. Yang, S. Mu, N. Shang, C. Liu, Y. Zhu, Y. Cai, P. Liu, J. Lin, W. Liu, Y. Sun, Y. Ma, Efficient O-glycosylation of triterpenes enabled by protein engineering of plant glycosyltransferase UGT74AC1, ACS Catal. 10 (2020) 3629–3639.
[89] S. Galanie, D. Entwistle, J. Lalonde, Engineering biosynthetic enzymes for industrial natural product synthesis, Nat. Prod. Rep. 37 (2020) 1122–1143.
[90] R. Lauchli, K.S. Rabe, K.Z. Kalbarczyk, A. Tata, T. Heel, R.Z. Kitto, F.H. Arnold, High-throughput screening for terpene-synthase-cyclization activity and directed evolution of a terpene synthase, Angew. Chem. Int. Ed. Engl. 52 (2013) 5571–5574.
[91] B.-L. Xu, M. Dai, Y. Chen, D. Meng, Y. Wang, N. Fang, X.F. Tang, B. Tang, Improving the thermostability and activity of a thermophilic subtilase by incorporating structural elements of its psychrophilic counterpart, Appl. Environ. Microb. 81 (2015) 6302–6313.
[92] P.C. Rathi, A. Fulton, K.E. Jaeger, H. Gohlke, Application of rigidity theory to the thermostabilization of lipase A from Bacillus subtilis, PLoS Comput. Biol. 12 (2016) 21.
[93] Z. Xu, Y.K. Cen, S.P. Zou, Y.P. Xue, Y.G. Zheng, Recent advances in the improvement of enzyme thermostability by structure modification, Crit. Rev. Biotechnol. 40 (2020) 83–98.
[94] M.Q. Styles, E.A. Nesbitt, S. Marr, M. Hutchby, D.J. Leak, Characterization of the first naturally thermostable terpene synthases and development of strategies to improve thermostability in this family of enzymes, FEBS J. 284 (2017) 1700–1711.
[95] J.E. Diaz, C.-S. Lin, K. Kunishiro, B.K. Feld, S.K. Avrantinis, J. Bronson, J. Greaves, J.G. Saven, G.A. Weiss, Computational design and selections for an engineered, thermostable terpene synthase, Protein Sci. 20 (2011) 1597–1606.
[96] Q. Li, T. Jiang, R. Liu, X. Feng, C. Li, Tuning the pH profile of beta-glucuronidase by rational site-directed mutagenesis for efficient transformation of glycyrrhizin, Appl. Microbiol. Biotechnol. 103 (2019) 4813–4823.
[97] X. Feng, H. Tang, B. Han, B. Lv, C. Li, Enhancing the thermostability of bglucuronidase by rationally redesigning the catalytic domain based on sequence alignment strategy, Ind. Eng. Chem. Res. 55 (2016) 5474–5483.
[98] Y. Xu, Y. Liu, A. Rasool, E. Wenwen, C. Li, Sequence editing strategy for improving performance of b-glucuronidase from Aspergillus terreus, Chem Eng Sci. 167 (2017) 145–153.
[99] B. Han, Y. Hou, T. Jiang, B. Lv, L. Zhao, X. Feng, C. Li, Computation-aided rational deletion Of C-terminal region improved the stability, activity, and expression level of GH2 b-glucuronidase, J. Agr. Food Chem. 66 (2018) 11380–11389.
[100] X. Feng, H. Tang, B. Han, L. Zhang, B. Lv, C. Li, Engineering the thermostability of beta-glucuronidase from Penicillium purpurogenum Li-3 by loop transplant, Appl. Microbiol. Biotechnol. 100 (2016) 9955–9966.
[101] X. Feng, X. Liu, J. Jia, X. Chen, T. Jiang, C. Li, Enhancing the thermostability of bglucuronidase from T. pinophilus enables the biotransformation of glycyrrhizin at elevated temperature, Chem. Eng. Sci. 204 (2019) 91–98.
[102] Y. Xu, X. Feng, J. Jia, X. Chen, T. Jiang, A. Rasool, B. Lv, L. Qu, C. Li, A novel betaglucuronidase from Talaromyces pinophilus Li-93 precisely hydrolyzes glycyrrhizin into glycyrrhetinic acid 3-O-mono-beta-d-glucuronide, Appl. Environ. Microbiol. 84 (19) (2018) 00755–00818.
[103] X. Feng, X. Wang, B. Han, C. Zou, Y. Hou, L. Zhao, C. Li, Design of glyco-linkers at multiple structural levels to modulate protein stability, J. Phys. Chem. Lett. 9 (2018) 4638–4645.
[104] B. Lv, H. Sun, S. Huang, X. Feng, T. Jiang, C. Li, Structure-guided engineering of the substrate specificity of a fungal beta-glucuronidase toward triterpenoid saponins, J. Biol. Chem. 293 (2018) 433–443.
[105] A. Biswas, M. Thattai, Promiscuity and specificity of eukaryotic glycosyltransferases, Biochem. Soc. Trans. 48 (2020) 891–900.
[106] O.F. Brandenberg, K. Chen, F.H. Arnold, Directed evolution of a cytochrome P450 carbene transferase for selective functionalization of cyclic compounds, J. Am. Chem. Soc. 141 (2019) 8989–8995.
[107] Y. Malbert, C. Moulis, Y. Brison, S. Morel, I. Andre, M. Remaud-Simeon, Engineering a branching sucrase for flavonoid glucoside diversification, Sci. Rep. 8 (2018) 15153.
[108] G.J. Williams, C. Zhang, J.S. Thorson, Expanding the promiscuity of a naturalproduct glycosyltransferase by directed evolution, Nat. Chem. Biol. 3 (2007) 657–662.
[109] T.R. Valentic, J.T. Payne, C.D. Smolke, Structure-guided engineering of a scoulerine 9-O-methyltransferase enables the biosynthesis of tetrahydropalmatrubine and tetrahydropalmatine in yeast, ACS Catal. 10 (2020) 4497–4509.
[110] M.J. Kschowak, F. Maier, H. Wortmann, M. Buchhaupt, Analyzing and engineering the product selectivity of a 2-methylenebornane synthase, ACS Synth. Biol. 9 (2020) 981–986.
[111] J.M. Klenk, P. Dubiel, M. Sharma, G. Grogan, B. Hauer, Characterization and structure-guided engineering of the novel versatile terpene monooxygenase CYP109Q5 from Chondromyces apiculatus DSM436, Microb. Biotechnol. 12 (2019) 377–391.
[112] A. Broom, R.V. Rakotoharisoa, M.C. Thompson, N. Zarifi, E. Nguyen, N. Mukhametzhanov, L. Liu, J.S. Fraser, R.A. Chica, Ensemble-based enzyme design can recapitulate the effects of laboratory directed evolution in silico, Nat. Commun. 11 (2020) 4808.
[113] D. De Raffele, S. Martí, V. Moliner, Understanding the directed evolution of De Novo retro-aldolases from QM/MM studies, ACS Catal. (2020) 7871–7883.