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S41467-020-18833-7.Pdf ARTICLE https://doi.org/10.1038/s41467-020-18833-7 OPEN One-pot biocatalytic route from cycloalkanes to α,ω‐dicarboxylic acids by designed Escherichia coli consortia Fei Wang1,4, Jing Zhao1,4, Qian Li1,4, Jun Yang1, Renjie Li1, Jian Min1, Xiaojuan Yu1, Gao-Wei Zheng 2, ✉ Hui-Lei Yu2, Chao Zhai1, Carlos G. Acevedo-Rocha 3, Lixin Ma 1 & Aitao Li 1 α ω‐ 1234567890():,; Aliphatic , dicarboxylic acids (DCAs) are a class of useful chemicals that are currently produced by energy-intensive, multistage chemical oxidations that are hazardous to the environment. Therefore, the development of environmentally friendly, safe, neutral routes to DCAs is important. We report an in vivo artificially designed biocatalytic cascade process for biotransformation of cycloalkanes to DCAs. To reduce protein expression burden and redox constraints caused by multi-enzyme expression in a single microbe, the biocatalytic pathway is divided into three basic Escherichia coli cell modules. The modules possess either redox- neutral or redox-regeneration systems and are combined to form E. coli consortia for use in biotransformations. The designed consortia of E. coli containing the modules efficiently convert cycloalkanes or cycloalkanols to DCAs without addition of exogenous coenzymes. Thus, this developed biocatalytic process provides a promising alternative to the current industrial process for manufacturing DCAs. 1 State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, 430062 Wuhan, P. R. China. 2 State Key Laboratory of Bioreactor Engineering and Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, 200237 Shanghai, P. R. China. 3 Biosyntia ApS, 2100 Copenhagen, Denmark. 4These authors contributed equally: Fei Wang, Jing Zhao, Qian Li. ✉ email: [email protected] NATURE COMMUNICATIONS | (2020) 11:5035 | https://doi.org/10.1038/s41467-020-18833-7 | www.nature.com/naturecommunications 1 ARTICLE NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-020-18833-7 liphatic α,ω‐dicarboxylic acids (DCAs) are a class of Nevertheless, protein expression burden and redox balance chemicals extensively used in the preparation of perfumes, issues often arise when attempting to express multiple enzymes in A 1,2 polymers, adhesives, and macrolide antibiotics . Cur- a single microbe for the construction of in vivo whole-cell cata- rently, the majority of industrial DCAs are synthesized by energy- lysts23. To solve these problems, and inspired by the metabolic intensive, hazardous multistage oxidations. For example, adipic engineering concept of using microbial consortia through co- acid (AA) is the most industrially important DCA, with a global culture of engineered organisms to improve production of tar- market of about $6.3 billion per year3. The current industrial geted compounds23–26, we envisioned the design of microbial- production process for AA relies on a two-step chemical oxida- consortia-mediated in vivo biocatalytic cascades with these fol- tion under harsh conditions using cyclohexane (CH) as starting lowing advantages: (i) protein expression burden and redox material (Fig. 1a)4. This industrial process has low efficiency with constraints can be reduced by distributing the biocatalytic path- formation of succinic acid and glutaric acid as byproducts5.In way among different cell modules; (ii) each expression system or addition, this process generates almost 10% of global anthro- cell module can be constructed and optimized in parallel, sub- pogenic nitrous oxide N2O emissions because it uses a large stantially reducing development time; and (iii) the catalyst load- amount of nitric acid6. These emissions cause serious environ- ing of each cell module can be adjusted, allowing beneficial mental problems such as global warming and ozone depletion. interactions among cell modules to enhance productivity. In The alternative routes of directed oxidation of CH to AA with addition, to eliminate redox constraints and cross-contamination, hydrogen peroxide7 and carbonylation of 1,3-butadiene to adi- cofactor self-sufficiency-based modularization can be employed pate diester by a designed palladium catalyst8 produce no nitrous to ensure that each cell module is either redox neutral or coupled oxide waste and are more environmentally friendly. However, to redox regeneration27,28. This strategy of modularization is substrate prices and technical challenges (such as catalyst stabi- rarely used. lity, preparation of the catalyst, and heavy metal recovery) limit Here, we develop an in vivo, artificially designed biocatalytic their implementation9. cascade for the oxidation of cycloalkanes or cycloalkanols to To address these challenges, environmentally friendly, biobased DCAs using a designed biocatalytic Escherichia coli consortia approaches for DCA production have been recently developed3. system modularized for redox self-sufficiency. With the oxidation Biobased routes from renewable feedstocks such as glucose10 have of CH to AA as a model reaction, each basic cell module with been attempted. However, these routes require complex engi- assigned functions are engineered and optimized in parallel, fol- neering of production microbes by metabolic engineering and lowed by combinatorial optimization to achieve efficient pro- synthetic biology techniques, and many challenges remain duction of AA from CH (Fig. 1b). Finally, the substrates are including redox constraints, enzyme optimization, selection of expanded to cycloalkanes with different carbon numbers to suitable production hosts and metabolic pathways, and potential demonstrate the generality of the developed biocatalytic system. harm to cell growth11–13. In addition, these methods generate only a limited range of DCA products. Artificially designed multi-enzyme cascades are a useful tool Results for accomplishing challenging reactions that cannot be achieved Design and modularization of a biocatalytic cascade.To by one-pot chemical catalysis14. Among them, the construction of implement the targeted production of different DCAs 7a-d from an in vivo multi-enzymatic cascade offers many advantages over cycloalkanes 1a-d, we designed an artificial biosynthetic route in vitro approaches since the costly steps (e.g., enzyme purifica- based on biocatalytic retrosynthesis29 (Fig. 2). The cascade had tion, addition of expensive cofactors) can be avoided15. For these six enzymatic reactions and eight enzymes (Fig. 2). The ideal reasons, the de novo design of in vivo cascade reactions has in vivo cascade would be a single-cell biocatalyst harboring all gained attention16–22 with successful examples such as the oxy- necessary enzymes. Therefore, we first tried to construct E. coli and amino-functionalization of alkenes20 and synthesis of cells expressing all enzymes needed to produce AA 7b from α-functionalized organic acids from glycine and aldehydes17. cyclohexanol (CHOL) 2b or CH 1b (Supplementary Figs. 1a, 2a). a Greenhouse gas Industrial chemical process N O 2 Byproducts 830~960 kPa HNO3, Cu, NH4VO3 150~160 °C 100~900 kPa Conversion: 60~80°C 5–12% KA-oil Cell 3 Cyclohexane (CH) O2 Adipic acid (AA) H2O Cell 1 Ring-opening and further oxidations Inert C–H bond activation H O Cell 2 2 H O b 2 Alcohol and Present work Baeyer–Villiger oxidations O2 O2 Fig. 1 Industrial chemical and designed biocatalytic processes for adipic acid (AA) production. a Current industrial process for synthesis of AA by multistage chemical oxidation from cyclohexane (CH). b designed one-pot biocatalytic route for synthesis of AA from CH using an Escherichia coli consortium, composed of three E. coli cell modules. 2 NATURE COMMUNICATIONS | (2020) 11:5035 | https://doi.org/10.1038/s41467-020-18833-7 | www.nature.com/naturecommunications NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-020-18833-7 ARTICLE Module 3 Module 1 Module 2 OH O O O P450 ADH1 BVMO O Lactonase HO OH n n n n n H2O 1a-d 2a-d 3a-d 4a-d 5a-d + H O NAD(P)H NAD(P) NADPH 2 NAD+ Gluconolactone Glucose ADH2 GDH NADP+ NOX NADH O2 H O 1a-7a: n = 1 1b-7b: n = 2 O n OH 1c-7c: n = 3 H2O 6a-d 1d-7d: n = 4 NAD+ P450: cytochrome P450 monooxygenase ADH1: alcohol dehydrogenase NOX ALDH GDH: glucose dehydrogenase BVMO: Baeyer–Villiger monooxygenase NADH O Lactonase: lactone hydrolase 2 ADH2: alcohol dehydrogenase O O ALDH: aldehyde dehydrogenase HO OH NOX: NADH oxidase n 7a-d Fig. 2 Design and modularization of an artificial biocatalytic cascade. Modularization was developed based on the rule that each module would be either redox neutral or coupled with a redox-regeneration system: Module 1 involves P450-catalyzed hydroxylation of cycloalkanes 1a-d coupled to a glucose dehydrogenase (GDH) mediated cofactor NAD(P)H regeneration. Module 2 comprises of a redox neutral system consisting of an alcohol dehydrogenase (ADH1) and a Baeyer-Villiger monooxygenase (BVMO), which catalyzes oxidation of cycloalkanols 2a-d to corresponding lactones 4a-d. Module 3 contains lactonase-catalyzed hydrolysis of lactones to hydroxyl acids 5a-d, followed by consecutive oxidations to DCA 7a-d with an alcohol dehydrogenase (ADH2) and an aldehyde dehydrogenase (ALDH), in which NAD+ regeneration was achieved in presence of NADH oxidase (NOX). However, none showed satisfactory productivity with only trace Engineering of basic cell module catalysts. The three basic cell amounts of product AA (2-4
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