Advances in engineering microbial biosynthesis of aromatic compounds and related compounds

Abstract

Aromatic compounds have broad applications and have been the target of biosynthetic processes for several decades. New biomolecular engineering strategies have been applied to improve production of aromatic compounds in recent years, some of which are expected to set the stage for the next wave of innovations. Here, we will briefly complement existing reviews on microbial production of aromatic compounds by focusing on a few recent trends where considerable work has been performed in the last 5 years. The trends we highlight are pathway modularization and compartmentalization, microbial co-culturing, non-traditional host engineering, aromatic polymer feedstock utilization, engineered ring cleavage, aldehyde stabilization, and biosynthesis of non-standard amino acids. Throughout this review article, we will also touch on unmet opportunities that future research could address.

Keywords

Metabolic engineering / Biocatalysis / Synthetic biology / Aromatic / Modular pathway design / Co-culture / Aldehydes / Lignin utilization / Plastic utilization / Non-standard amino acids

References

[1] Akdemir H, Silva A, Zha J, . Production of pyranoanthocyanins using Escherichia coli co-cultures. Metab Eng, 2019

[2] Alfonta L, Zhang Z, Uryu S, . Site-specific incorporation of a redox-active amino acid into proteins. J Am Chem Soc, 2003, 125: 14662-14663.

[3] Almhjell PJ, Boville CE, Arnold FH. Engineering enzymes for noncanonical amino acid synthesis. Chem Soc Rev, 2018, 47: 8980-8997.

[4] Al-Sabagh AM, Yehia FZ, Eshaq G, . Greener routes for recycling of polyethylene terephthalate. Egypt J Pet, 2016, 25: 53-64.

[5] Alvarez-Gonzalez G, Dixon N. Genetically encoded biosensors for lignocellulose valorization. Biotechnol Biofuels, 2019, 12: 246.

[6] Antonenkov VD, Sormunen RT, Hiltunen JK. The rat liver peroxisomal membrane forms a permeability barrier for cofactors but not for small metabolites in vitro. J Cell Sci, 2004, 117: 5633-5642.

[7] Austin HP, Allen MD, Donohoe BS, . Characterization and engineering of a plastic-degrading aromatic polyesterase. Proc Natl Acad Sci, 2018, 115: E4350LP-E4357.

[8] Ayer A, Sanwald J, Pillay BA, . Distinct redox regulation in sub-cellular compartments in response to various stress conditions in Saccharomycescerevisiae. PLoS ONE, 2013, 8: 65240.

[9] Bayer T, Milker S, Wiesinger T, . In vivo synthesis of polyhydroxylated compounds from a “hidden reservoir” of toxic aldehyde species. ChemCatChem, 2017, 9: 2919-2923.

[10] Berry A. Improving production of aromatic compounds in Escherichia coli by metabolic engineering. Trends Biotechnol, 1996, 14: 250-256.

[11] Blanc V, Gil P, Bamas-Jacques N, . Identification of analysis of genes from Streptomycespristinaespiralis encoding enzymes involved in the biosynthesis of the 4-dimethylamino-L-phenylalanine precursor of pristinamycin I. Mol Microbiol, 1997, 23: 191-202.

[12] Bose M, Groff D, Xie J, . The incorporation of a photoisomerizable amino acid into proteins in E. coli. J Am Chem Soc, 2006, 128: 388-389.

[13] Brey LF, Włodarczyk AJ, Bang Thøfner JF, . Metabolic engineering of Synechocystis sp. PCC 6803 for the production of aromatic amino acids and derived phenylpropanoids. Metab Eng, 2020, 57: 129-139.

[14] Bruder S, Boles E. Improvement of the yeast based (R)-phenylacetylcarbinol production process via reduction of by-product formation. Biochem Eng J, 2017, 120: 103-112.

[15] Bugg TDH, Williamson JJ, Rashid GMM. Bacterial enzymes for lignin depolymerisation: new biocatalysts for generation of renewable chemicals from biomass. Curr Opin Chem Biol, 2020, 55: 26-33.

[16] Bunzel M, Schüßler A, Tchetseubu Saha G. Chemical characterization of klason lignin preparations from plant-based foods. J Agric Food Chem, 2011, 59: 12506-12513.

[17] Butler N, Kunjapur AM. Carboxylic acid reductases in metabolic engineering. J Biotechnol, 2020, 307: 1-14.

[18] Cao M, Gao M, Suástegui M, . Building microbial factories for the production of aromatic amino acid pathway derivatives: from commodity chemicals to plant-sourced natural products. Metab Eng, 2020, 58: 94-132.

[19] Celińska E, Kubiak P, Białas W, . Yarrowia lipolytica: the novel and promising 2-phenylethanol producer. J Ind Microbiol Biotechnol, 2013, 40: 389-392.

[20] Chakar FS, Ragauskas AJ. Review of current and future softwood kraft lignin process chemistry. Ind Crops Prod, 2004, 20: 131-141.

[21] Chen Y, Loredo A, Gordon A, . A noncanonical amino acid-based relay system for site-specific protein labeling. Chem Commun, 2018, 54: 7187-7190.

[22] Chen Y, Tang J, Wang L, . Creation of bacterial cells with 5-hydroxytryptophan as a 21st amino acid building block. Chem, 2020

[23] Chen Y, Fu B, Xiao G, . Bioconversion of lignin-derived feedstocks to muconic acid by whole-cell biocatalysis. ACS Food Sci Technol, 2021, 1: 382-387.

[24] Chin JW, Santoro SW, Martin AB, . Addition of p-azido-L-phenylalanine to the genetic code of Escherichia coli. J Am Chem Soc, 2002, 124: 9026-9027.

[25] Chio C, Sain M, Qin W. Lignin utilization: a review of lignin depolymerization from various aspects. Renew Sustain Energy Rev, 2019, 107: 232-249.

[26] Clarkson SM, Giannone RJ, Kridelbaugh DM, . Construction and optimization of a heterologous pathway for protocatechuate catabolism in Escherichia coli enables bioconversion of model aromatic compou. Appl Environ Microbiol, 2017, 83: e01313-e1317.

[27] de la Torre D, Chin JW. Reprogramming the genetic code. Nat Rev Genet, 2020, 22: 169-184.

[28] Deiters A, Schultz PG. In vivo incorporation of an alkyne into proteins in Escherichia coli. Bioorg Med Chem Lett, 2005, 15: 1521-1524.

[29] DeLoache WC, Russ ZN, Dueber JE. Towards repurposing the yeast peroxisome for compartmentalizing heterologous metabolic pathways. Nat Commun, 2016

[30] Dı́az E, Ferrández A, Prieto MA, Garcı́a JL,. Biodegradation of aromatic compounds by Escherichia coli. Microbiol Mol Biol Rev, 2001, 65: 523-569.

[31] Dinh CV, Chen X, Prather KLJ. Development of a quorum-sensing based circuit for control of coculture population composition in a naringenin production system. ACS Synth Biol, 2020, 9: 590-597.

[32] Du Y, Yang B, Yi Z, . Engineering Saccharomyces cerevisiae coculture platform for the production of flavonoids. J Agric Food Chem, 2020, 68: 2146-2154.

[33] Dumas A, Lercher L, Spicer CD, Davis BG. Designing logical codon reassignment—expanding the chemistry in biology. Chem Sci, 2015, 6: 50-69.

[34] Eng T, Banerjee D, Lau AK, . Engineering Pseudomonas putida for efficient aromatic conversion to bioproduct using high throughput screening in a bioreactor. Metab Eng, 2021, 66: 1-33.

[35] EPA (2018) Advancing sustainable materials management. https://www.epa.gov/facts-and-figures-about-materials-waste-and-recycling/advancingsustainable-materials-management

[36] Eriksen MK, Christiansen JD, Daugaard AE, Astrup TF. Closing the loop for PET, PE and PP waste from households: influence of material properties and product design for plastic recycling. Waste Manag, 2019, 96: 75-85.

[37] Fang Z, Jones JA, Zhou J, Koffas MAG. Engineering Escherichia coli co-cultures for production of curcuminoids from glucose. Biotechnol J, 2018

[38] Fesko K. Threonine aldolases: perspectives in engineering and screening the enzymes with enhanced substrate and stereo specificities. Appl Microbiol Biotechnol, 2016, 100: 2579-2590.

[39] Fordjour E, Adipah FK, Zhou S, . Metabolic engineering of Escherichia coli BL21 (DE3) for de novo production of l-DOPA from d-glucose. Microb Cell Fact, 2019, 18: 74.

[40] Fujiwara R, Noda S, Tanaka T, Kondo A. Muconic acid production using gene-level fusion proteins in Escherichiacoli. ACS Synth Biol, 2018, 7: 2698-2705.

[41] Gatfield IL. Biotechnological production of natural flavor materials. Flavor chemistry, 1999, Berlin: Springer, 211-227.

[42] Grewal PS, Samson JA, Baker JJ, . Peroxisome compartmentalization of a toxic enzyme improves alkaloid production. Nat Chem Biol, 2021, 17: 96-103.

[43] Gu Y, Ma J, Zhu Y, . Engineering Yarrowia lipolytica as a Chassis for de novo synthesis of five aromatic-derived natural products and chemicals. ACS Synth Biol, 2020, 9: 2096-2106.

[44] Hammer SK, Avalos JL. Harnessing yeast organelles for metabolic engineering. Nat Chem Biol, 2017, 13: 823-832.

[45] Han H, Xu B, Zeng W, Zhou J. Regulating the biosynthesis of pyridoxal 5’-phosphate with riboswitch to enhance L-DOPA production by Escherichia coli whole-cell biotransformation. J Biotechnol, 2020, 321: 68-77.

[46] He A, Li T, Daniels L, . Nocardia sp. carboxylic acid reductase: cloning, expression, and characterization of a new aldehyde oxidoreductase family. Appl Environ Microbiol, 2004, 58: 2116-2122.

[47] Herrmann KM, Weaver LM. The shikimate pathway. Annu Rev Plant Physiol Plant Mol Biol, 1999, 50: 473-503.

[48] Hillman ET, Li M, Hooker CA, . Hydrolysis of lignocellulose by anaerobic fungi produces free sugars and organic acids for two-stage fine chemical production with Kluyveromycesmarxianus. Biotechnol Prog, 2021

[49] Hong M. Chemically recyclable polymers: a circular economy approach to sustainability. Green Chem, 2017

[50] Huccetogullari D, Luo ZW, Lee SY. Metabolic engineering of microorganisms for production of aromatic compounds. Microb Cell Fact, 2019, 18: 41.

[51] Jankauskaite V, Macijauskas G, Lygaitis R. Polyethylene terephthalate waste recycling and application possibilities: a review. Polym Compos, 2008, 14: 119-127.

[52] Jawed K, Yazdani SS, Koffas MAG. Advances in the development and application of microbial consortia for metabolic engineering. Metab Eng Commun, 2019, 9: e00095.

[53] Ji X-J, Liu Q, Xie X, . Metabolic engineering of the shikimate pathway for production of aromatics and derived compounds—present and future strain construction strategies. Bioeng Biotechnol, 2018, 6: 32.

[54] Jones JA, Vernacchio VR, Sinkoe AL, . Experimental and computational optimization of an Escherichia coli co-culture for the efficient production of flavonoids. Metab Eng, 2016, 35: 55-63.

[55] Jones JA, Vernacchio VR, Collins SM, . Complete biosynthesis of anthocyanins using E. coli polycultures. Mbio, 2017, 8: e00621-17.

[56] Kallscheuer N, Marienhagen J. Corynebacterium glutamicum as platform for the production of hydroxybenzoic acids. Microb Cell Fact, 2018, 17: 70.

[57] Kallscheuer N, Vogt M, Stenzel A, . Construction of a Corynebacteriumglutamicum platform strain for the production of stilbenes and (2S)-flavanones. Metab Eng, 2016, 38: 47-55.

[58] Kawai F, Kawabata T, Oda M. Current state and perspectives related to the polyethylene terephthalate hydrolases available for biorecycling. ACS Sustain Chem Eng, 2020, 8: 8894-8908.

[59] Kazimírová V, Rebroš M. Production of aldehydes by biocatalysis. Int J Mol Sci, 2021, 22: 4949.

[60] Kim TY, Lee SW, Oh MK. Biosynthesis of 2-phenylethanol from glucose with genetically engineered Kluyveromycesmarxianus. Enzyme Microb Technol, 2014, 61–62: 44-47.

[61] Kim JS, Lee YY, Kim TH. A review on alkaline pretreatment technology for bioconversion of lignocellulosic biomass. Bioresour Technol, 2016, 199: 42-48.

[62] Kim S, Sung BH, Kim SC, Lee HS. Genetic incorporation of l -dihydroxyphenylalanine (DOPA) biosynthesized by a tyrosine phenol-lyase. Chem Commun, 2018, 54: 3002-3005.

[63] Kim HT, Kim JK, Cha HG, . Biological valorization of poly(ethylene terephthalate) monomers for upcycling waste PET. ACS Sustain Chem Eng, 2019, 7: 19396-19406.

[64] Kim DH, Han DO, In Shim K, . One-Pot Chemo-bioprocess of PET depolymerization and recycling enabled by a biocompatible catalyst, betaine. ACS Catal, 2021, 11: 3996-4008.

[65] Knott BC, Erickson E, Allen MD, . Characterization and engineering of a two-enzyme system for plastics depolymerization. Proc Natl Acad Sci, 2020, 117: 25476LP-25485.

[66] Kohman RE, Kunjapur AM, Hysolli E, . From designing the molecules of life to designing life: future applications derived from advances in DNA technologies. Angew Chem Int Ed, 2018, 57: 4313-4328.

[67] Koshti R, Mehta L, Samarth N. Biological recycling of polyethylene terephthalate: a mini-review. J Polym Environ, 2018, 26: 3520-3529.

[68] Kuepper J, Dickler J, Biggel M, . Metabolic engineering of Pseudomonasputida KT2440 to produce anthranilate from glucose. Front Microbiol, 2015, 6: 1310.

[69] Kunjapur AM, Prather KLJ. Microbial engineering for aldehyde synthesis. Appl Environ Microbiol, 2015, 81: 1892-1901.

[70] Kunjapur AM, Prather KLJ. Development of a vanillate biosensor for the vanillin biosynthesis pathway in E. coli. ACS Synth Biol, 2019, 8: 1958-1967.

[71] Kunjapur AM, Tarasova Y, Prather KLJ. Synthesis and accumulation of aromatic aldehydes in an engineered strain of Escherichia coli. J Am Chem Soc, 2014, 136: 11644-11654.

[72] Kunjapur AM, Hyun JC, Prather KLJ. Deregulation of S-adenosylmethionine biosynthesis and regeneration improves methylation in the E. coli de novo vanillin biosynthesis pathway. Microb Cell Fact, 2016, 15: 1-17.

[73] Kunjapur AM, Stork DA, Kuru E, . Engineering posttranslational proofreading to discriminate nonstandard amino acids. Proc Natl Acad Sci USA, 2018, 115: 619-624.

[74] Kunjapur AM, Napolitano MG, Hysolli E, . Synthetic auxotrophy remains stable after continuous evolution and in coculture with mammalian cells. Sci Adv, 2021, 7: eabf5851.

[75] Lancefield CS, Rashid GMM, Bouxin F, . Investigation of the chemocatalytic and biocatalytic valorization of a range of different lignin preparations: the importance of β-o-4 content. ACS Sustain Chem Eng, 2016, 4: 6921-6930.

[76] Larroude M, Nicaud JM, Rossignol T. Yarrowia lipolytica chassis strains engineered to produce aromatic amino acids via the shikimate pathway. Microb Biotechnol, 2020

[77] Lee H, DeLoache WC, Dueber JE. Spatial organization of enzymes for metabolic engineering. Metab Eng, 2011

[78] Li Z, Wang X, Zhang H. Balancing the non-linear rosmarinic acid biosynthetic pathway by modular co-culture engineering. Metab Eng, 2019, 54: 1-11.

[79] Lin YJ, Chang JJ, Lin HY, . Metabolic engineering a yeast to produce astaxanthin. Bioresour Technol, 2017, 245: 899-905.

[80] Linger JG, Vardon DR, Guarnieri MT, . Lignin valorization through integrated biological funneling and chemical catalysis. Proc Natl Acad Sci, 2014, 111: 12013LP-12018.

[81] Liu L, Zhu Y, Chen Y, . One-pot cascade biotransformation for efficient synthesis of benzyl alcohol and its analogs. Chem an Asian J, 2020, 15: 1018-1021.

[82] Liu X, Bouxin FP, Fan J, . Recent advances in the catalytic depolymerization of lignin towards phenolic chemicals: a review. Chemsuschem, 2020, 13: 4296-4317.

[83] Ma B, Zhao C, Agrawal SR, Abu-Omar M. A synergistic biorefinery based on catalytic conversion of lignin prior to cellulose starting from lignocellulosic biomass. Green Chem, 2015

[84] Machas M, Kurgan G, Jha AK, . Emerging tools, enabling technologies, and future opportunities for the bioproduction of aromatic chemicals. J Chem Technol Biotechnol, 2019, 94: 38-52.

[85] Mandell DJ, Lajoie MJ, Mee MT, . Biocontainment of genetically modified organisms by synthetic protein design. Nature, 2015, 518: 55-60.

[86] Marchand JA, Neugebauer ME, Ing MC, . Discovery of a pathway for terminal-alkyne amino acid biosynthesis. Nature, 2019

[87] Masuo S, Zhou S, Kaneko T, Takaya N. Bacterial fermentation platform for producing artificial aromatic amines. Sci Rep, 2016, 6: 25764.

[88] Mehl RA, Christopher Anderson J, Santoro SW, . Generation of a bacterium with a 21 amino acid genetic code. J Am Chem Soc, 2003

[89] Meijnen JP, Verhoef S, Briedjlal AA, . Improved p-hydroxybenzoate production by engineered Pseudomonas putida S12 by using a mixed-substrate feeding strategy. Appl Microbiol Biotechnol, 2011, 90: 885-893.

[90] Mohammadi Nargesi B, Trachtmann N, Sprenger GA, Youn JW. Production of p-amino-l-phenylalanine (l-PAPA) from glycerol by metabolic grafting of Escherichiacoli. Microb Cell Fact, 2018, 17: 1-11.

[91] Müller R-J, Schrader H, Profe J, . Enzymatic degradation of poly(ethylene terephthalate): rapid hydrolyse using a hydrolase from T. fusca. Macromol Rapid Commun, 2005, 26: 1400-1405.

[92] Muñoz AJ, Hernández-Chávez G, de Anda R, . Metabolic engineering of Escherichiacoli for improving l-3,4-dihydroxyphenylalanine (l-DOPA) synthesis from glucose. J Ind Microbiol Biotechnol, 2011, 38: 1845-1852.

[93] Nagasawa T, Utagawa T, Goto J, . Syntheses of l-tyrosine-related amino acids by tyrosine phenol-lyase of Citrobacter intermedius. Eur J Biochem, 1981, 117: 33-40.

[94] Nakagawa A, Minami H, Kim J-S, . A bacterial platform for fermentative production of plant alkaloids. Nat Commun, 2011, 2: 326.

[95] Ni J, Gao YY, Tao F, . Temperature-directed biocatalysis for the sustainable production of aromatic aldehydes or alcohols. Angew Chem Int Ed, 2018, 57: 1214-1217.

[96] Nijkamp K, Van Luijk N, De Bont JAM, Wery J. The solvent-tolerant Pseudomonasputida S12 as host for the production of cinnamic acid from glucose. Appl Microbiol Biotechnol, 2005, 69: 170-177.

[97] Nijkamp K, Westerhof RGM, Ballerstedt H, . Optimization of the solvent-tolerant Pseudomonasputida S12 as host for the production of p-coumarate from glucose. Appl Microbiol Biotechnol, 2007, 74: 617-624.

[98] Niu W, Willett H, Mueller J, . Direct biosynthesis of adipic acid from lignin-derived aromatics using engineered Pseudomonasputida KT2440. Metab Eng, 2020, 59: 151-161.

[99] Noda S, Shirai T, Mori Y, . Engineering a synthetic pathway for maleate in Escherichiacoli. Nat Commun, 2017, 8: 1153.

[100] Obermeyer AC, Jarman JB, Netirojjanakul C, . Mild bioconjugation through the oxidative coupling of ortho-aminophenols and anilines with ferricyanide. Angew Chem Int Ed, 2014, 53: 1057-1061.

[101] Opgrande JL, Dobratz CJ, Brown E et al (2000) Benzaldehyde. In: Kirk-Othmer encyclopedia of chemical technology. Wiley

[102] Palmer CM, Miller KK, Nguyen A, Alper HS. Engineering 4-coumaroyl-CoA derived polyketide production in Yarrowia lipolytica through a β-oxidation mediated strategy. Metab Eng, 2020, 57: 174-181.

[103] Parker MT, Kunjapur AM. Deployment of engineered microbes: contributions to the bioeconomy and considerations for biosecurity. Health Secur, 2020, 18: 278-296.

[104] Peters FB, Brock A, Wang J, Schultz PG. Photocleavage of the polypeptide backbone by 2-nitrophenylalanine. Chem Biol, 2009, 16: 148-152.

[105] Picart P, Liu H, Grande PM, . Multi-step biocatalytic depolymerization of lignin. Appl Microbiol Biotechnol, 2017, 101: 6277-6287.

[106] Pinkert A, Marsh NK, Pang S, Staiger PM. Ionic liquids and their interaction with cellulose. Chem Rev, 2009, 109: 6712-6728.

[107] Pyne ME, Kevvai K, Grewal PS, . A yeast platform for high-level synthesis of tetrahydroisoquinoline alkaloids. Nat Commun, 2020, 11: 3337.

[108] Ragauskas AJ, Beckham GT, Biddy MJ, . Lignin valorization: improving lignin processing in the biorefinery. Science (80−), 2014, 344: 1246843.

[109] Raheem AB, Noor ZZ, Hassan A, . Current developments in chemical recycling of post-consumer polyethylene terephthalate wastes for new materials production: a review. J Clean Prod, 2019, 225: 1052-1064.

[110] Reifenrath M, Bauer M, Oreb M, Boles E. Bacterial bifunctional chorismate mutase-prephenate dehydratase PheA increases flux into the yeast phenylalanine pathway and improves mandelic acid production. Metab Eng Commun, 2018, 7: e00079.

[111] Reifenrath M, Oreb M, Boles E, Tripp J. Artificial ER-derived vesicles as synthetic organelles for in vivo compartmentalization of biochemical pathways. ACS Synth Biol, 2020, 9: 2909-2916.

[112] Rovner AJ, Haimovich AD, Katz SR, . Recoded organisms engineered to depend on synthetic amino acids. Nature, 2015, 518: 89-93.

[113] Rowles I, Groenendaal B, Binay B, . Engineering of phenylalanine ammonia lyase from Rhodotorula graminis for the enhanced synthesis of unnatural L-amino acids. Tetrahedron, 2016, 72: 7343-7347.

[114] Sadler JC, Wallace S. Microbial synthesis of vanillin from waste poly(ethylene terephthalate). Green Chem, 2021, 23: 4665-4672.

[115] Sáez-Sáez J, Wang G, Marella ER, . Engineering the oleaginous yeast Yarrowia lipolytica for high-level resveratrol production. Metab Eng, 2020, 62: 51-61.

[116] Salvachúa D, Rydzak T, Auwae R, . Metabolic engineering of Pseudomonas putida for increased polyhydroxyalkanoate production from lignin. Microb Biotechnol, 2020, 13: 290-298.

[117] Sampson EM, Bobik TA. Microcompartments for B₁₂-dependent 1,2-propanediol degradation provide protection from DNA and cellular damage by a reactive metabolic intermediate. J Bacteriol, 2008, 190: 2966LP-2971.

[118] Santos CNS, Koffas M, Stephanopoulos G. Optimization of a heterologous pathway for the production of flavonoids from glucose. Metab Eng, 2011, 13: 392-400.

[119] Schutyser W, Renders T, Van den Bosch S, . Chemicals from lignin: an interplay of lignocellulose fractionation, depolymerisation, and upgrading. Chem Soc Rev, 2018, 47: 852-908.

[120] Schwendenwein D, Fiume G, Weber H, . Selective enzymatic transformation to aldehydes in vivo by fungal carboxylate reductase from Neurospora crassa. Adv Synth Catal, 2016, 358: 3414-3421.

[121] Seitchik JL, Peeler JC, Taylor MT, . Genetically encoded tetrazine amino acid directs rapid site-specific in vivo bioorthogonal ligation with trans-cyclooctenes. J Am Chem Soc, 2012, 134: 2898-2901.

[122] Sengupta S, Jonnalagadda S, Goonewardena L, Juturu V. Metabolic engineering of a novel muconic acid biosynthesis pathway via 4-hydroxybenzoic acid in E. coli. Appl Environ Microbiol, 2015, 81: 8037LP-8043.

[123] Shen B. Leeper FJ, Vederas JC. Biosynthesis of aromatic polyketides. Biosynthesis—aromatic polyketides, isoprenoids, alkaloids, 2000, Berlin: Springer, 1-51.

[124] Sheng H, Jing Y, An N, . Extending the shikimate pathway for microbial production of maleate from glycerol in engineered Escherichiacoli. Biotechnol Bioeng, 2021

[125] Sulzbach M, Kunjapur AM. The pathway less traveled: engineering biosynthesis of nonstandard functional groups. Trends Biotechnol, 2020, 38: 532-545.

[126] Sun J, Ren Y, Raza M, . Microbial production of glutaconic acid via extradiol ring cleavage of catechol. J Chem Technol Biotechnol, 2018, 93: 1677-1683.

[127] Sun Z, Fridrich B, de Santi A, . Bright side of lignin depolymerization: toward new platform chemicals. Chem Rev, 2018, 118: 614-678.

[128] Sweeney WA, Bryan PF (2000) BTX processing. In: Kirk‐othmer encyclopedia of chemical technology. Wiley

[129] Taylor PP, Pantaleone DP, Senkpeil RF, Fotheringham IG. Novel biosynthetic approaches to the production of unnatural amino acids using transaminases. Trends Biotechnol, 1998, 16: 412-418.

[130] Thielemans W, Can E, Morye SS, Wool RP. Novel applications of lignin in composite materials. J Appl Polym Sci, 2002, 83: 323-331.

[131] Thompson B, Pugh S, Machas M, Nielsen DR. Muconic acid production via alternative pathways and a synthetic “metabolic funnel”. ACS Synth Biol, 2017, 7: 565-575.

[132] Thyer R, d’Oelsnitz S, Blevins MS, . Directed evolution of an improved aminoacyl-tRNA synthetase for incorporation of L-3,4-dihydroxyphenylalanine (L-DOPA). Angew Chem, 2021

[133] Tripathi CM, Agarwal SC, Basu SK. Production of l-phenylacetylcarbinol by fermentation. J Ferment Bioeng, 1997, 84: 487-492.

[134] Tsoi R, Wu F, Zhang C, . Metabolic division of labor in microbial systems. Proc Natl Acad Sci USA, 2018, 115: 2526-2531.

[135] Turner WJ, Dunlop MJ. Trade-offs in improving biofuel tolerance using combinations of efflux pumps. ACS Synth Biol, 2014, 4: 1056-1063.

[136] Tzin V, Galili G. New insights into the shikimate and aromatic amino acids biosynthesis pathways in plants. Mol Plant, 2010, 3: 956-972.

[137] Van Den Bosch S, Schutyser W, Vanholme R et al (2015) Open access article. | Energy Environ Sci 8:1748. https://doi.org/10.1039/c5ee00204d

[138] van Haveren J, Scott EL, Sanders J. Bulk chemicals from biomass. Biofuels Bioprod Biorefin, 2008, 2: 41-57.

[139] Venkitasubramanian P, Daniels L, Rosazza JPN. Patel R. Chapter 15 Biocatalytic reduction of carboxylic acids: mechanism and applications. Biocatalysis in the pharmaceutical and biotechnology industries, 2007, Boca Raton: CRC Press, 425-440.

[140] Verhoef S, Ruijssenaars HJ, de Bont JAM, Wery J. Bioproduction of p-hydroxybenzoate from renewable feedstock by solvent-tolerant Pseudomonas putida S12. J Biotechnol, 2007, 132: 49-56.

[141] Verhoef S, Wierckx N, Westerhof RGM, . Bioproduction of p-hydroxystyrene from glucose by the solvent-tolerant bacterium Pseudomonas putida S12 in a two-phase water-decanol fermentation. Appl Environ Microbiol, 2009, 75: 931-936.

[142] Vogt T. Phenylpropanoid Biosynthesis. Mol Plant, 2010, 3: 2-20.

[143] Völler J-S, Budisa N. Coupling genetic code expansion and metabolic engineering for synthetic cells. Curr Opin Biotechnol, 2017, 48: 1-7.

[144] Walton NJ, Mayer MJ, Narbad A. Vanillin. Phytochemistry, 2003, 63: 505-515.

[145] Wang L, Zhang Z, Brock A, Schultz PG. Addition of the keto functional group to the genetic code of Escherichia coli. Proc Natl Acad Sci USA, 2003, 100: 56-61.

[146] Wang X, Li Z, Policarpio L, . De novo biosynthesis of complex natural product sakuranetin using modular co-culture engineering. Appl Microbiol Biotechnol, 2020, 104: 4849-4861.

[147] Ward J, Wohlgemuth R (2010) High-yield biocatalytic amination reactions in organic synthesis. In: Current organic chemistry. Bentham Science Publishers, pp 1914–1927

[148] Wei T, Cheng B-Y, Liu J-Z. Genome engineering Escherichia coli for L-DOPA overproduction from glucose. Sci Rep, 2016, 6: 30080.

[149] Westermann B, Neupert W. Mitochondria-targeted green fluorescent proteins: convenient tools for the study of organelle biogenesis in Saccharomycescerevisiae. Yeast, 2000, 16: 1421-1427.

[150] Westlake DWS, Vining LC. Biosynthesis of chloramphenicol. Biotechnol Bioeng, 1969, 11: 1125-1134.

[151] Wierckx NJP, Ballerstedt H, De Bont JAM, Wery J. Engineering of solvent-tolerant Pseudomonas putida S12 for bioproduction of phenol from glucose. Appl Environ Microbiol, 2005, 71: 8221-8227.

[152] Wittmann C. Analysis and engineering of metabolic pathway fluxes in Corynebacterium glutamicum. Adv Biochem Eng Biotechnol, 2010, 120: 21-49.

[153] Xie J, Liu W, Schultz PG. A genetically encoded bidentate, metal-binding amino acid. Angew Chem, 2007, 119: 9399-9402.

[154] Xin J, Zhang Q, Huang J, . Progress in the catalytic glycolysis of polyethylene terephthalate. J Environ Manage, 2021, 296.

[155] Xu R, Zhang K, Liu P, . Lignin depolymerization and utilization by bacteria. Bioresour Technol, 2018, 269: 557-566.

[156] Xue Y, Zhang Y, Grace S, He Q. Functional expression of an Arabidopsis p450 enzyme, p-coumarate-3-hydroxylase, in the cyanobacterium Synechocystis PCC 6803 for the biosynthesis of caffeic acid. J Appl Phycol, 2014, 26: 219-226.

[157] Yadav VG, De Mey M, Giaw Lim C, . The future of metabolic engineering and synthetic biology: towards a systematic practice. Metab Eng, 2012, 14: 233-241.

[158] Yaguchi A, Franaszek N, O’Neill K, . Identification of oleaginous yeasts that metabolize aromatic compounds. J Ind Microbiol Biotechnol, 2020, 47: 801-813.

[159] Yoshida S, Hiraga K, Takehana T, . A bacterium that degrades and assimilates poly(ethylene terephthalate). Science (80−), 2016, 351: 1196-1199.

[160] Yuan SF, Yi X, Johnston TG, Alper HS. De novo resveratrol production through modular engineering of an Escherichia coli-Saccharomycescerevisiae co-culture. Microb Cell Fact, 2020, 19: 143.

[161] Zakzeski J, Bruijnincx PCA, Jongerius AL, Weckhuysen BM. The catalytic valorization of lignin for the production of renewable chemicals. Chem Rev, 2010, 110: 3552-3599.

[162] Zeng W, Xu B, Du G, . Integrating enzyme evolution and high-throughput screening for efficient biosynthesis of l -DOPA. J Ind Microbiol Biotechnol, 2019, 46: 1631-1641.

[163] Zhang C, Wang F. Catalytic lignin depolymerization to aromatic chemicals. Acc Chem Res, 2020, 53: 470-484.

[164] Zhao EM, Suek N, Wilson MZ, . Light-based control of metabolic flux through assembly of synthetic organelles. Nat Chem Biol, 2019, 15: 589-597.

[165] Zhao M, Tao Y, Wu X, Xiao Y. One-pot efficient biosynthesis of 4-hydroxyphenylacetic acid and its analogues from lignin-related p-coumaric and ferulic acids. ACS Sustain Chem Eng, 2021, 9: 6400-6409.

[166] Zhou K, Zou R, Stephanopoulos G, Too H-P. Metabolite profiling identified methylerythritol cyclodiphosphate efflux as a limiting step in microbial isoprenoid production. PLoS ONE, 2012, 7: e47513.

[167] Zhou J, Chen Z, Wang Y. Bioaldehydes and beyond: expanding the realm of bioderived chemicals using biogenic aldehydes as platforms. Curr Opin Chem Biol, 2020, 59: 37-46.

[168] Zhu Y, Yang T, Chen Y, . One-pot synthesis of aromatic amines from renewable feedstocks via whole-cell biocatalysis. ChemistrySelect, 2020, 5: 14292-14295.

Funding

Basic Energy Sciences(DE‐SC0021166)