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Peng W, Bao H, Wang Y, Cote E, Sagues WJ, Hagelin-Weaver H, Gao J, Xiao D, Tong Z. Selective Depolymerization of Lignin Towards Isolated Phenolic Acids Under Mild Conditions. CHEMSUSCHEM 2023; 16:e202300750. [PMID: 37419862 DOI: 10.1002/cssc.202300750] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/04/2023] [Accepted: 07/07/2023] [Indexed: 07/09/2023]
Abstract
The selective transformation of lignin to value-added biochemicals (e. g., phenolic acids) in high yields is incredibly challenging due to its structural complexity and many possible reaction pathways. Phenolic acids (PA) are key building blocks for various aromatic polymers, but the isolation of PAs from lignin is below 5 wt.% and requires harsh reaction conditions. Herein, we demonstrate an effective route to selectively convert lignin extracted from sweet sorghum and poplar into isolated PA in a high yield (up to 20 wt.% of lignin) using a low-cost graphene oxide-urea hydrogen peroxide (GO-UHP) catalyst under mild conditions (<120 °C). The lignin conversion yield is up to 95 %, and the remaining low molecular weight organic oils are ready for aviation fuel production to complete lignin utilization. Mechanistic studies demonstrate that pre-acetylation allows the selective depolymerization of lignin to aromatic aldehydes with a decent yield by GO through the Cα activation of β-O-4 cleavage. A urea-hydrogen peroxide (UHP) oxidative process is followed to transform aldehydes in the depolymerized product to PAs by avoiding the undesired Dakin side reaction due to the electron-withdrawing effect of the acetyl group. This study opens a new way to selectively cleave lignin side chains to isolated biochemicals under mild conditions.
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Affiliation(s)
- Wenbo Peng
- School of Chemical & Biomolecular Engineering Renewable Bioproduct Institute, Georgia Institute of Technology, Atlanta, GA 30318, USA
| | - Hanxi Bao
- Department of Agricultural and Biological Engineering, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Raleigh, NC 27695, USA
| | - Yigui Wang
- Center for Integrative Materials Discovery, Department of Chemistry and Chemical Engineering, University of New Haven, West Haven, CT 06516, USA
| | - Elizabeth Cote
- Center for Integrative Materials Discovery, Department of Chemistry and Chemical Engineering, University of New Haven, West Haven, CT 06516, USA
| | - William J Sagues
- Department of Biological & Agricultural Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Halena Hagelin-Weaver
- Department of Chemical Engineering, University of Florida, Gainesville, FL 32611, USA
| | - Ji Gao
- School of Chemical & Biomolecular Engineering Renewable Bioproduct Institute, Georgia Institute of Technology, Atlanta, GA 30318, USA
| | - Dequan Xiao
- Center for Integrative Materials Discovery, Department of Chemistry and Chemical Engineering, University of New Haven, West Haven, CT 06516, USA
| | - Zhaohui Tong
- School of Chemical & Biomolecular Engineering Renewable Bioproduct Institute, Georgia Institute of Technology, Atlanta, GA 30318, USA
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2
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Tan Z, Li J, Hou J, Gonzalez R. Designing artificial pathways for improving chemical production. Biotechnol Adv 2023; 64:108119. [PMID: 36764336 DOI: 10.1016/j.biotechadv.2023.108119] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023]
Abstract
Metabolic engineering exploits manipulation of catalytic and regulatory elements to improve a specific function of the host cell, often the synthesis of interesting chemicals. Although naturally occurring pathways are significant resources for metabolic engineering, these pathways are frequently inefficient and suffer from a series of inherent drawbacks. Designing artificial pathways in a rational manner provides a promising alternative for chemicals production. However, the entry barrier of designing artificial pathway is relatively high, which requires researchers a comprehensive and deep understanding of physical, chemical and biological principles. On the other hand, the designed artificial pathways frequently suffer from low efficiencies, which impair their further applications in host cells. Here, we illustrate the concept and basic workflow of retrobiosynthesis in designing artificial pathways, as well as the most currently used methods including the knowledge- and computer-based approaches. Then, we discuss how to obtain desired enzymes for novel biochemistries, and how to trim the initially designed artificial pathways for further improving their functionalities. Finally, we summarize the current applications of artificial pathways from feedstocks utilization to various products synthesis, as well as our future perspectives on designing artificial pathways.
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Affiliation(s)
- Zaigao Tan
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China; School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; Department of Bioengineering, Shanghai Jiao Tong University, Shanghai, China.
| | - Jian Li
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China; School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; Department of Bioengineering, Shanghai Jiao Tong University, Shanghai, China
| | - Jin Hou
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Ramon Gonzalez
- Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA.
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3
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Zhang P, Gao J, Zhang H, Wang Y, Liu Z, Lee SY, Mao X. Metabolic engineering of Escherichia coli for the production of an antifouling agent zosteric acid. Metab Eng 2023; 76:247-259. [PMID: 36822462 DOI: 10.1016/j.ymben.2023.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/13/2023] [Accepted: 02/19/2023] [Indexed: 02/23/2023]
Abstract
Zosteric acid (ZA) is a Zostera species-derived, sulfated phenolic acid compound with antifouling activity and has gained much attention due to its nontoxic and biodegradable characteristics. However, the yield of Zostera species available for ZA extraction is limited by natural factors, such as season, latitude, light, and temperature. Here we report the development of metabolically engineered Escherichia coli strains capable of producing ZA from glucose and glycerol. First, intracellular availability of the sulfur donor 3'-phosphoadenosine-5'-phosphosulfate (PAPS) was enhanced by knocking out the cysH gene responsible for PAPS consumption and overexpressing the genes required for PAPS biosynthesis. Co-overexpression of the genes encoding tyrosine ammonia-lyase, sulfotransferase 1A1, ATP sulfurylase, and adenosine 5'-phosphosulfate kinase constructed ZA producing strain with enhanced PAPS supply. Second, the feedback-resistant forms of aroG and tyrA genes (encoding 3-deoxy-d-arabinoheptulosonate 7-phosphate synthase and chorismate mutase, respectively) were overexpressed to relieve the feedback regulation of L-tyrosine biosynthesis. Third, the pykA gene involved in phosphoenolpyruvate-consuming reaction, the regulator gene tyrR, the competing pathway gene pheA, and the ptsHIcrr genes essential for the PEP:carbohydrate phosphotransferase system were deleted. Moreover, all genes involved in the shikimate pathway and the talA, tktA, and tktB genes in the pentose phosphate pathway were examined for ZA production. The PTS-independent glucose uptake system, the expression vector system, and the carbon source were also optimized. As a result, the best-performing strain successfully produced 1.52 g L-1 ZA and 1.30 g L-1p-hydroxycinnamic acid from glucose and glycerol in a 700 mL fed-batch bioreactor.
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Affiliation(s)
- Peichao Zhang
- Qingdao Key Laboratory of Food Biotechnology, College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Jing Gao
- Qingdao Key Laboratory of Food Biotechnology, College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Haiyang Zhang
- Qingdao Key Laboratory of Food Biotechnology, College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Yongzhen Wang
- Qingdao Key Laboratory of Food Biotechnology, College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Zhen Liu
- Qingdao Key Laboratory of Food Biotechnology, College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Four), BioProcess Engineering Research Center, Institute for the BioCentury, KAIST, Daejeon, Republic of Korea.
| | - Xiangzhao Mao
- Qingdao Key Laboratory of Food Biotechnology, College of Food Science and Engineering, Ocean University of China, Qingdao, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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4
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Laboratory evolution reveals general and specific tolerance mechanisms for commodity chemicals. Metab Eng 2023; 76:179-192. [PMID: 36738854 DOI: 10.1016/j.ymben.2023.01.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 01/06/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023]
Abstract
Although strain tolerance to high product concentrations is a barrier to the economically viable biomanufacturing of industrial chemicals, chemical tolerance mechanisms are often unknown. To reveal tolerance mechanisms, an automated platform was utilized to evolve Escherichia coli to grow optimally in the presence of 11 industrial chemicals (1,2-propanediol, 2,3-butanediol, glutarate, adipate, putrescine, hexamethylenediamine, butanol, isobutyrate, coumarate, octanoate, hexanoate), reaching tolerance at concentrations 60%-400% higher than initial toxic levels. Sequencing genomes of 223 isolates from 89 populations, reverse engineering, and cross-compound tolerance profiling were employed to uncover tolerance mechanisms. We show that: 1) cells are tolerized via frequent mutation of membrane transporters or cell wall-associated proteins (e.g., ProV, KgtP, SapB, NagA, NagC, MreB), transcription and translation machineries (e.g., RpoA, RpoB, RpoC, RpsA, RpsG, NusA, Rho), stress signaling proteins (e.g., RelA, SspA, SpoT, YobF), and for certain chemicals, regulators and enzymes in metabolism (e.g., MetJ, NadR, GudD, PurT); 2) osmotic stress plays a significant role in tolerance when chemical concentrations exceed a general threshold and mutated genes frequently overlap with those enabling chemical tolerance in membrane transporters and cell wall-associated proteins; 3) tolerization to a specific chemical generally improves tolerance to structurally similar compounds whereas a tradeoff can occur on dissimilar chemicals, and 4) using pre-tolerized starting isolates can hugely enhance the subsequent production of chemicals when a production pathway is inserted in many, but not all, evolved tolerized host strains, underpinning the need for evolving multiple parallel populations. Taken as a whole, this study provides a comprehensive genotype-phenotype map based on identified mutations and growth phenotypes for 223 chemical tolerant isolates.
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Effect of sequential or ternary starters-assisted fermentation on the phenolic and glucosinolate profiles of sauerkraut in comparison with spontaneous fermentation. Food Res Int 2022; 156:111116. [DOI: 10.1016/j.foodres.2022.111116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 03/06/2022] [Accepted: 03/08/2022] [Indexed: 11/23/2022]
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Oliver Huidobro M, Tica J, Wachter GKA, Isalan M. Synthetic spatial patterning in bacteria: advances based on novel diffusible signals. Microb Biotechnol 2022; 15:1685-1694. [PMID: 34843638 PMCID: PMC9151330 DOI: 10.1111/1751-7915.13979] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 11/14/2021] [Accepted: 11/14/2021] [Indexed: 12/22/2022] Open
Abstract
Engineering multicellular patterning may help in the understanding of some fundamental laws of pattern formation and thus may contribute to the field of developmental biology. Furthermore, advanced spatial control over gene expression may revolutionize fields such as medicine, through organoid or tissue engineering. To date, foundational advances in spatial synthetic biology have often been made in prokaryotes, using artificial gene circuits. In this review, engineered patterns are classified into four levels of increasing complexity, ranging from spatial systems with no diffusible signals to systems with complex multi-diffusor interactions. This classification highlights how the field was held back by a lack of diffusible components. Consequently, we provide a summary of both previously characterized and some new potential candidate small-molecule signals that can regulate gene expression in Escherichia coli. These diffusive signals will help synthetic biologists to successfully engineer increasingly intricate, robust and tuneable spatial structures.
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Affiliation(s)
| | - Jure Tica
- Department of Life SciencesImperial College LondonLondonSW7 2AZUK
| | | | - Mark Isalan
- Department of Life SciencesImperial College LondonLondonSW7 2AZUK
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7
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Dickey RM, Forti AM, Kunjapur AM. Advances in engineering microbial biosynthesis of aromatic compounds and related compounds. BIORESOUR BIOPROCESS 2021; 8:91. [PMID: 38650203 PMCID: PMC10992092 DOI: 10.1186/s40643-021-00434-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 08/18/2021] [Indexed: 01/14/2023] Open
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.
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Affiliation(s)
- Roman M Dickey
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, USA
| | - Amanda M Forti
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, USA
| | - Aditya M Kunjapur
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, USA.
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8
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Liu K, Li L, Yao W, Wang W, Huang Y, Wang R, Li P. Genetic engineering of Pseudomonas chlororaphis Lzh-T5 to enhance production of trans-2,3-dihydro-3-hydroxyanthranilic acid. Sci Rep 2021; 11:16451. [PMID: 34385485 PMCID: PMC8361184 DOI: 10.1038/s41598-021-94674-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 07/08/2021] [Indexed: 02/07/2023] Open
Abstract
Trans-2,3-dihydro-3-hydroxyanthranilic acid (DHHA) is a cyclic β-amino acid used for the synthesis of non-natural peptides and chiral materials. And it is an intermediate product of phenazine production in Pseudomonas spp. Lzh-T5 is a P. chlororaphis strain isolated from tomato rhizosphere found in China. It can synthesize three antifungal phenazine compounds. Disruption the phzF gene of P. chlororaphis Lzh-T5 results in DHHA accumulation. Several strategies were used to improve production of DHHA: enhancing the shikimate pathway by overexpression, knocking out negative regulatory genes, and adding metal ions to the medium. In this study, three regulatory genes (psrA, pykF, and rpeA) were disrupted in the genome of P. chlororaphis Lzh-T5, yielding 5.52 g/L of DHHA. When six key genes selected from the shikimate, pentose phosphate, and gluconeogenesis pathways were overexpressed, the yield of DHHA increased to 7.89 g/L. Lastly, a different concentration of Fe3+ was added to the medium for DHHA fermentation. This genetically engineered strain increased the DHHA production to 10.45 g/L. According to our result, P. chlororaphis Lzh-T5 could be modified as a microbial factory to produce DHHA. This study laid a good foundation for the future industrial production and application of DHHA.
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Affiliation(s)
- Kaiquan Liu
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
| | - Ling Li
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China.
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250103, People's Republic of China.
| | - Wentao Yao
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
| | - Wei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
| | - Yujie Huang
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250103, People's Republic of China
| | - Ruiming Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
| | - Piwu Li
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
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9
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Noda S, Mori Y, Fujiwara R, Shirai T, Tanaka T, Kondo A. Reprogramming Escherichia coli pyruvate-forming reaction towards chorismate derivatives production. Metab Eng 2021; 67:1-10. [PMID: 34044138 DOI: 10.1016/j.ymben.2021.05.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/30/2021] [Accepted: 05/13/2021] [Indexed: 11/18/2022]
Abstract
Microbial metabolic pathway engineering is a potent strategy used worldwide to produce aromatic compounds. We drastically rewired the primary metabolic pathway of Escherichia coli to produce aromatics and their derivatives. The metabolic pathway of E. coli was compartmentalized into the production and energy modules. We focused on the pyruvate-forming reaction in the biosynthesis pathway of some compounds as the reaction connecting those modules. E. coli strains were engineered to show no growth unless pyruvate was synthesized along with the compounds of interest production. Production of salicylate and maleate was demonstrated to confirm our strategy's versatility. In maleate production, the production, yield against the theoretical yield, and production rate reached 12.0 g L-1, 67%, and up to fourfold compared to that in previous reports, respectively; these are the highest values of maleate production in microbes to our knowledge. The results reveal that our strategy strongly promotes the production of aromatics and their derivatives.
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Affiliation(s)
- Shuhei Noda
- Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
| | - Yutaro Mori
- Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Ryosuke Fujiwara
- Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Tomokazu Shirai
- Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Tsutomu Tanaka
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Akihiko Kondo
- Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan; Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
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10
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Wang S, Cui J, Bilal M, Hu H, Wang W, Zhang X. Pseudomonas spp. as cell factories (MCFs) for value-added products: from rational design to industrial applications. Crit Rev Biotechnol 2020; 40:1232-1249. [PMID: 32907412 DOI: 10.1080/07388551.2020.1809990] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
In recent years, there has been increasing interest in microbial biotechnology for the production of value-added compounds from renewable resources. Pseudomonas species have been proposed as a suitable workhorse for high-value secondary metabolite production because of their unique characteristics for fast growth on sustainable carbon sources, a clear inherited background, versatile intrinsic metabolism with diverse enzymatic capacities, and their robustness in an extreme environment. It has also been demonstrated that metabolically engineered Pseudomonas strains can produce several industrially valuable aromatic chemicals and natural products such as phenazines, polyhydroxyalkanoates, rhamnolipids, and insecticidal proteins from renewable feedstocks with remarkably high yields suitable for commercial application. In this review, we summarize cell factory construction in Pseudomonas for the biosynthesis of native and non-native bioactive compounds in P. putida, P. chlororaphis, P. aeruginosa, as well as pharmaceutical proteins production by P. fluorescens. Additionally, some novel strategies together with metabolic engineering strategies in order to improve the biosynthetic abilities of Pseudomonas as an ideal chassis are discussed. Finally, we proposed emerging opportunities, challenges, and essential strategies to enable the successful development of Pseudomonas as versatile microbial cell factories for the bioproduction of diverse bioactive compounds.
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Affiliation(s)
- Songwei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiajia Cui
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, China
| | - Hongbo Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xuehong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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11
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Choi S, Lee HN, Park E, Lee SJ, Kim ES. Recent Advances in Microbial Production of cis,cis-Muconic Acid. Biomolecules 2020; 10:biom10091238. [PMID: 32854378 PMCID: PMC7564838 DOI: 10.3390/biom10091238] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 08/20/2020] [Accepted: 08/20/2020] [Indexed: 02/06/2023] Open
Abstract
cis,cis-Muconic acid (MA) is a valuable C6 dicarboxylic acid platform chemical that is used as a starting material for the production of various valuable polymers and drugs, including adipic acid and terephthalic acid. As an alternative to traditional chemical processes, bio-based MA production has progressed to the establishment of de novo MA pathways in several microorganisms, such as Escherichia coli, Corynebacterium glutamicum, Pseudomonas putida, and Saccharomyces cerevisiae. Redesign of the metabolic pathway, intermediate flux control, and culture process optimization were all pursued to maximize the microbial MA production yield. Recently, MA production from biomass, such as the aromatic polymer lignin, has also attracted attention from researchers focusing on microbes that are tolerant to aromatic compounds. This paper summarizes recent microbial MA production strategies that involve engineering the metabolic pathway genes as well as the heterologous expression of some foreign genes involved in MA biosynthesis. Microbial MA production will continue to play a vital role in the field of bio-refineries and a feasible way to complement various petrochemical-based chemical processes.
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Affiliation(s)
- Sisun Choi
- Department of Biological Engineering, Inha University, Incheon 22212, Korea; (S.C.); (H.-N.L.); (E.P.)
| | - Han-Na Lee
- Department of Biological Engineering, Inha University, Incheon 22212, Korea; (S.C.); (H.-N.L.); (E.P.)
- STR Biotech Co., Ltd., Chuncheon-si, Gangwon-do 24232, Korea;
| | - Eunhwi Park
- Department of Biological Engineering, Inha University, Incheon 22212, Korea; (S.C.); (H.-N.L.); (E.P.)
| | - Sang-Jong Lee
- STR Biotech Co., Ltd., Chuncheon-si, Gangwon-do 24232, Korea;
| | - Eung-Soo Kim
- Department of Biological Engineering, Inha University, Incheon 22212, Korea; (S.C.); (H.-N.L.); (E.P.)
- Correspondence: ; Tel.: +82-32-860-8318; Fax: +82-32-872-4046
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12
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Qian X, Chen L, Sui Y, Chen C, Zhang W, Zhou J, Dong W, Jiang M, Xin F, Ochsenreither K. Biotechnological potential and applications of microbial consortia. Biotechnol Adv 2020; 40:107500. [DOI: 10.1016/j.biotechadv.2019.107500] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 11/13/2019] [Accepted: 12/17/2019] [Indexed: 12/20/2022]
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13
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Wang G, Øzmerih S, Guerreiro R, Meireles AC, Carolas A, Milne N, Jensen MK, Ferreira BS, Borodina I. Improvement of cis, cis-Muconic Acid Production in Saccharomyces cerevisiae through Biosensor-Aided Genome Engineering. ACS Synth Biol 2020; 9:634-646. [PMID: 32058699 PMCID: PMC8457548 DOI: 10.1021/acssynbio.9b00477] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Muconic acid is a potential platform chemical for the production of nylon, polyurethanes, and terephthalic acid. It is also an attractive functional copolymer in plastics due to its two double bonds. At this time, no economically viable process for the production of muconic acid exists. To harness novel genetic targets for improved production of cis,cis-muconic acid (CCM) in the yeast Saccharomyces cerevisiae, we employed a CCM-biosensor coupled to GFP expression with a broad dynamic response to screen UV-mutagenesis libraries of CCM-producing yeast. Via fluorescence activated cell sorting we identified a clone Mut131 with a 49.7% higher CCM titer and 164% higher titer of biosynthetic intermediate-protocatechuic acid (PCA). Genome resequencing of the Mut131 and reverse engineering identified seven causal missense mutations of the native genes (PWP2, EST2, ATG1, DIT1, CDC15, CTS2, and MNE1) and a duplication of two CCM biosynthetic genes, encoding dehydroshikimate dehydratase and catechol 1,2-dioxygenase, which were not recognized as flux controlling before. The Mut131 strain was further rationally engineered by overexpression of the genes encoding for PCA decarboxylase and AROM protein without shikimate dehydrogenase domain (Aro1pΔE), and by restoring URA3 prototrophy. The resulting engineered strain produced 20.8 g/L CCM in controlled fed-batch fermentation, with a yield of 66.2 mg/g glucose and a productivity of 139 mg/L/h, representing the highest reported performance metrics in a yeast for de novo CCM production to date and the highest production of an aromatic compound in yeast. The study illustrates the benefit of biosensor-based selection and brings closer the prospect of biobased muconic acid.
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Affiliation(s)
- Guokun Wang
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, DK-2800 Kgs, Denmark
| | - Süleyman Øzmerih
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, DK-2800 Kgs, Denmark
| | - Rogério Guerreiro
- Biotrend-Inovação e Engenharia em Biotecnologia SA, Cantanhede, 3060-197, Portugal
| | - Ana C. Meireles
- Biotrend-Inovação e Engenharia em Biotecnologia SA, Cantanhede, 3060-197, Portugal
| | - Ana Carolas
- Biotrend-Inovação e Engenharia em Biotecnologia SA, Cantanhede, 3060-197, Portugal
| | - Nicholas Milne
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, DK-2800 Kgs, Denmark
| | - Michael K. Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, DK-2800 Kgs, Denmark
| | - Bruno S. Ferreira
- Biotrend-Inovação e Engenharia em Biotecnologia SA, Cantanhede, 3060-197, Portugal
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, DK-2800 Kgs, Denmark
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14
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Capelli S, Motta D, Evangelisti C, Dimitratos N, Prati L, Pirola C, Villa A. Effect of Carbon Support, Capping Agent Amount, and Pd NPs Size for Bio-Adipic Acid Production from Muconic Acid and Sodium Muconate. NANOMATERIALS 2020; 10:nano10030505. [PMID: 32168904 PMCID: PMC7153248 DOI: 10.3390/nano10030505] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/02/2020] [Accepted: 03/06/2020] [Indexed: 11/21/2022]
Abstract
The effect of support, stabilizing agent, and Pd nanoparticles (NPs) size was studied for sodium muconate and t,t-muconic acid hydrogenation to bio-adipic acid. Three different activated carbons (AC) were used (Norit, KB, and G60) and carbon morphology did not affect the substrate conversion, but it greatly influenced the adipic acid yield. 1% Pd/KB Darco catalyst, which has the highest surface area and Pd surface exposure, and the smallest NPs size displayed the highest activity. Furthermore, the effect of the amount of the protective agent was studied varying metal/protective agent weight ratios in the range of 1/0.00–1/1.20, using KB as the chosen support. For sodium muconate reduction 1% Pd/KB_1.2 catalyst gave the best results in terms of activity (0.73 s−1), conversion, and adipic acid yield (94.8%), while for t,t-muconic acid hydrogenation the best activity result (0.85 s−1) was obtained with 1% Pd/KB_0.0 catalyst. Correlating the results obtained from XPS and TEM analyses with catalytic results, we found that the amount of PVA (polyvinyl alcohol) influences mean Pd NPs size, Pd(0)/Pd(II) ratio, and Pd surface exposure. Pd(0)/Pd(II) ratio and Pd NPs size affected adipic acid yield and activity during sodium muconate hydrogenation, respectively, while adipic acid yield was related by exposed Pd amount during t,t-muconic acid hydrogenation. The synthesized catalysts showed higher activity than commercial 5% Pd/AC.
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Affiliation(s)
- Sofia Capelli
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milan, Italy; (L.P.); (C.P.)
- Correspondence: (S.C.); (A.V.); Tel.: +39-025-031-4365 (S.C.); +39-025-031-4361 (A.V.)
| | - Davide Motta
- School of Chemistry, Cardiff Catalysis Institute, Cardiff University, Park Place, Cardiff CF10 3AT, UK;
| | - Claudio Evangelisti
- National Council of the Research, CNR-Istituto di Chimica dei Composti Organometallici, Via G. Moruzzi 1, 20124 Pisa, Italy;
| | - Nikolaos Dimitratos
- Dipartimento di Chimica Industriale “Toso Montanari”, Università degli Studi di Bologna, Viale Risorgimento 4, 40136 Bologna, Italy;
| | - Laura Prati
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milan, Italy; (L.P.); (C.P.)
| | - Carlo Pirola
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milan, Italy; (L.P.); (C.P.)
| | - Alberto Villa
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milan, Italy; (L.P.); (C.P.)
- Correspondence: (S.C.); (A.V.); Tel.: +39-025-031-4365 (S.C.); +39-025-031-4361 (A.V.)
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15
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Cao M, Gao M, Suástegui M, Mei Y, Shao Z. 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. [DOI: 10.1016/j.ymben.2019.08.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 08/03/2019] [Accepted: 08/07/2019] [Indexed: 01/23/2023]
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16
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Metabolic engineering of Escherichia coli for shikimate pathway derivative production from glucose-xylose co-substrate. Nat Commun 2020; 11:279. [PMID: 31937786 PMCID: PMC6959354 DOI: 10.1038/s41467-019-14024-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 12/13/2019] [Indexed: 11/08/2022] Open
Abstract
Glucose and xylose are the major components of lignocellulose. Effective utilization of both sugars can improve the efficiency of bioproduction. Here, we report a method termed parallel metabolic pathway engineering (PMPE) for producing shikimate pathway derivatives from glucose–xylose co-substrate. In this method, we seek to use glucose mainly for target chemical production, and xylose for supplying essential metabolites for cell growth. Glycolysis and the pentose phosphate pathway are completely separated from the tricarboxylic acid (TCA) cycle. To recover cell growth, we introduce a xylose catabolic pathway that directly flows into the TCA cycle. As a result, we can produce 4.09 g L−1cis,cis-muconic acid using the PMPE Escherichia coli strain with high yield (0.31 g g−1 of glucose) and produce l-tyrosine with 64% of the theoretical yield. The PMPE strategy can contribute to the development of clean processes for producing various valuable chemicals from lignocellulosic resources. In lignocellulose biomass, microbes prefer consuming glucose over xylose, which affects target compound production. Here, the authors achieve simultaneous utilization of glucose and xylose for target chemical production and cell growth, respectively, and realize high-level production of shikimate pathway derivatives.
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17
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Choi SS, Seo SY, Park SO, Lee HN, Song JS, Kim JY, Park JH, Kim S, Lee SJ, Chun GT, Kim ES. Cell Factory Design and Culture Process Optimization for Dehydroshikimate Biosynthesis in Escherichia coli. Front Bioeng Biotechnol 2019; 7:241. [PMID: 31649923 PMCID: PMC6795058 DOI: 10.3389/fbioe.2019.00241] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 09/11/2019] [Indexed: 11/13/2022] Open
Abstract
3-Dehydroshikimate (DHS) is a useful starting metabolite for the biosynthesis of muconic acid (MA) and shikimic acid (SA), which are precursors of various valuable polymers and drugs. Although DHS biosynthesis has been previously reported in several bacteria, the engineered strains were far from satisfactory, due to their low DHS titers. Here, we created an engineered Escherichia coli cell factory to produce a high titer of DHS as well as an efficient system for the conversion DHS into MA. First, the genes showing negative effects on DHS accumulation in E. coli, such as tyrR (tyrosine dependent transcriptional regulator), ptsG (glucose specific sugar: phosphoenolpyruvate phosphotransferase), and pykA (pyruvate kinase 2), were disrupted. In addition, the genes involved in DHS biosynthesis, such as aroB (DHQ synthase), aroD (DHQ dehydratase), ppsA (phosphoenolpyruvate synthase), galP (D-galactose transporter), aroG (DAHP synthase), and aroF (DAHP synthase), were overexpressed to increase the glucose uptake and flux of intermediates. The redesigned DHS-overproducing E. coli strain grown in an optimized medium produced ~117 g/L DHS in 7-L fed-batch fermentation, which is the highest level of DHS production demonstrated in E. coli. To accomplish the DHS-to-MA conversion, which is originally absent in E. coli, a codon-optimized heterologous gene cassette containing asbF, aroY, and catA was expressed as a single operon under a strong promoter in a DHS-overproducing E. coli strain. This redesigned E. coli grown in an optimized medium produced about 64.5 g/L MA in 7-L fed-batch fermentation, suggesting that the rational cell factory design of DHS and MA biosynthesis could be a feasible way to complement petrochemical-based chemical processes.
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Affiliation(s)
- Si-Sun Choi
- Department of Biological Engineering, Inha University, Incheon, South Korea
| | - Seung-Yeul Seo
- STR Biotech Co., Ltd., Chuncheon-si, South Korea.,Department of Molecular Bio-Science, Kangwon National University, Chuncheon-si, South Korea
| | - Sun-Ok Park
- STR Biotech Co., Ltd., Chuncheon-si, South Korea
| | - Han-Na Lee
- Department of Biological Engineering, Inha University, Incheon, South Korea.,STR Biotech Co., Ltd., Chuncheon-si, South Korea
| | - Ji-Soo Song
- Department of Biological Engineering, Inha University, Incheon, South Korea
| | - Ji-Yeon Kim
- Department of Biological Engineering, Inha University, Incheon, South Korea
| | - Ji-Hoon Park
- Department of Biological Engineering, Inha University, Incheon, South Korea
| | - Sangyong Kim
- Green Chemistry and Materials Group, Korea Institute of Industrial Technology, Cheonan-si, South Korea.,Green Process and System Engineering Major, Korea University of Science and Technology (UST), Daejeon, South Korea
| | | | - Gie-Taek Chun
- Department of Molecular Bio-Science, Kangwon National University, Chuncheon-si, South Korea
| | - Eung-Soo Kim
- Department of Biological Engineering, Inha University, Incheon, South Korea
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18
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Bui LM, Geraldi A, Nguyen TT, Lee JH, Lee JY, Cho BK, Kim SC. mRNA Engineering for the Efficient Chaperone-Mediated Co-Translational Folding of Recombinant Proteins in Escherichia coli. Int J Mol Sci 2019; 20:ijms20133163. [PMID: 31261687 PMCID: PMC6651523 DOI: 10.3390/ijms20133163] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 06/18/2019] [Accepted: 06/21/2019] [Indexed: 12/22/2022] Open
Abstract
The production of soluble, functional recombinant proteins by engineered bacterial hosts is challenging. Natural molecular chaperone systems have been used to solubilize various recombinant proteins with limited success. Here, we attempted to facilitate chaperone-mediated folding by directing the molecular chaperones to their protein substrates before the co-translational folding process completed. To achieve this, we either anchored the bacterial chaperone DnaJ to the 3ʹ untranslated region of a target mRNA by fusing with an RNA-binding domain in the chaperone-recruiting mRNA scaffold (CRAS) system, or coupled the expression of DnaJ and a target recombinant protein using the overlapping stop-start codons 5ʹ-TAATG-3ʹ between the two genes in a chaperone-substrate co-localized expression (CLEX) system. By engineering the untranslated and intergenic sequences of the mRNA transcript, bacterial molecular chaperones are spatially constrained to the location of protein translation, expressing selected aggregation-prone proteins in their functionally active, soluble form. Our mRNA engineering methods surpassed the in-vivo solubilization efficiency of the simple DnaJ chaperone co-overexpression method, thus providing more effective tools for producing soluble therapeutic proteins and enzymes.
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Affiliation(s)
- Le Minh Bui
- KAIST Institute for BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
- NTT Hi-Tech Institute, Nguyen Tat Thanh University (NTTU), Ho Chi Minh City 700000, Vietnam
| | - Almando Geraldi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
- Biology Department, Science and Technology Faculty, Universitas Airlangga Mulyorejo, Surabaya 60115, Indonesia
| | - Thi Thuy Nguyen
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Jun Hyoung Lee
- KAIST Institute for BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Ju Young Lee
- Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), Ulsan 44429, Korea
| | - Byung-Kwan Cho
- KAIST Institute for BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
- Intelligent Synthetic Biology Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
| | - Sun Chang Kim
- KAIST Institute for BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
- Intelligent Synthetic Biology Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
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19
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Capelli S, Motta D, Evangelisti C, Dimitratos N, Prati L, Pirola C, Villa A. Bio Adipic Acid Production from Sodium Muconate and Muconic Acid: A Comparison of two Systems. ChemCatChem 2019. [DOI: 10.1002/cctc.201900343] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Sofia Capelli
- Dipartimento di ChimicaUniversità degli Studi di Milano Via C. Golgi 19 20133 Milan Italy
| | - Davide Motta
- Cardiff Catalysis Institute, School of ChemistryCardiff University Park Place CF10 3AT Cardiff UK
| | - Claudio Evangelisti
- National Council of the ResearchCNR-ISTM Via G. Fantoli, 16/15 20138 Milan Italy
| | - Nikolaos Dimitratos
- Dipartimento di Chimica “Toso Montanari”Università degli Studi di Bologna Viale Risorgimento 4 40136 Bologna Italy
| | - Laura Prati
- Dipartimento di ChimicaUniversità degli Studi di Milano Via C. Golgi 19 20133 Milan Italy
| | - Carlo Pirola
- Dipartimento di ChimicaUniversità degli Studi di Milano Via C. Golgi 19 20133 Milan Italy
| | - Alberto Villa
- Dipartimento di ChimicaUniversità degli Studi di Milano Via C. Golgi 19 20133 Milan Italy
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20
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Jha RK, Narayanan N, Pandey N, Bingen JM, Kern TL, Johnson CW, Strauss CEM, Beckham GT, Hennelly SP, Dale T. Sensor-Enabled Alleviation of Product Inhibition in Chorismate Pyruvate-Lyase. ACS Synth Biol 2019; 8:775-786. [PMID: 30861344 DOI: 10.1021/acssynbio.8b00465] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Product inhibition is a frequent bottleneck in industrial enzymes, and testing mutations to alleviate product inhibition via traditional methods remains challenging as many variants need to be tested against multiple substrate and product concentrations. Further, traditional screening methods are conducted in vitro, and resulting enzyme variants may perform differently in vivo in the context of whole-cell metabolism and regulation. In this study, we address these two problems by establishing a high-throughput screening method to alleviate product inhibition in an industrially relevant enzyme, chorismate pyruvate-lyase (UbiC). First, we engineered a highly specific, genetically encoded biosensor for 4-hydroxybenzoate (4HB) in an industrially relevant host, Pseudomonas putida KT2440. We subsequently applied the biosensor to detect the activity of a heterologously expressed UbiC that converts chorismate into 4HB and pyruvate. By using benzoate as a product surrogate that inhibits UbiC without activating the biosensor, we were able to efficiently create and screen a diversified library for UbiC variants with reduced product inhibition. Introduction of the improved UbiC enzyme variant into an experimental production strain for the industrial precursor cis,cis-muconic acid (muconate), enabled a >2-fold yield improvement for glucose to muconate conversion when the new UbiC variant was expressed from a plasmid and a 60% yield increase when the same UbiC variant was genomically integrated into the strain. Overall, this work demonstrates that by coupling a library of enzyme variants to whole-cell catalysis and biosensing, variants with reduced product inhibition can be identified, and that this improved enzyme can result in increased titers of a downstream molecule of interest.
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Affiliation(s)
- Ramesh K. Jha
- Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Niju Narayanan
- Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Naresh Pandey
- Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Jeremy M. Bingen
- Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Theresa L. Kern
- Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Christopher W. Johnson
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Charlie E. M. Strauss
- Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Gregg T. Beckham
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Scott P. Hennelly
- Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Taraka Dale
- Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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21
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Huccetogullari D, Luo ZW, Lee SY. Metabolic engineering of microorganisms for production of aromatic compounds. Microb Cell Fact 2019; 18:41. [PMID: 30808357 PMCID: PMC6390333 DOI: 10.1186/s12934-019-1090-4] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 02/19/2019] [Indexed: 01/09/2023] Open
Abstract
Metabolic engineering has been enabling development of high performance microbial strains for the efficient production of natural and non-natural compounds from renewable non-food biomass. Even though microbial production of various chemicals has successfully been conducted and commercialized, there are still numerous chemicals and materials that await their efficient bio-based production. Aromatic chemicals, which are typically derived from benzene, toluene and xylene in petroleum industry, have been used in large amounts in various industries. Over the last three decades, many metabolically engineered microorganisms have been developed for the bio-based production of aromatic chemicals, many of which are derived from aromatic amino acid pathways. This review highlights the latest metabolic engineering strategies and tools applied to the biosynthesis of aromatic chemicals, many derived from shikimate and aromatic amino acids, including L-phenylalanine, L-tyrosine and L-tryptophan. It is expected that more and more engineered microorganisms capable of efficiently producing aromatic chemicals will be developed toward their industrial-scale production from renewable biomass.
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Affiliation(s)
- Damla Huccetogullari
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program) and Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon, 34141, Republic of Korea
| | - Zi Wei Luo
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program) and Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon, 34141, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program) and Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
- Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon, 34141, Republic of Korea.
- BioProcess Engineering Research Center and Bioinformatics Research Center, KAIST, Daejeon, 34141, Republic of Korea.
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22
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Calero P, Nikel PI. Chasing bacterial chassis for metabolic engineering: a perspective review from classical to non-traditional microorganisms. Microb Biotechnol 2019; 12:98-124. [PMID: 29926529 PMCID: PMC6302729 DOI: 10.1111/1751-7915.13292] [Citation(s) in RCA: 150] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 05/28/2018] [Accepted: 05/29/2018] [Indexed: 12/27/2022] Open
Abstract
The last few years have witnessed an unprecedented increase in the number of novel bacterial species that hold potential to be used for metabolic engineering. Historically, however, only a handful of bacteria have attained the acceptance and widespread use that are needed to fulfil the needs of industrial bioproduction - and only for the synthesis of very few, structurally simple compounds. One of the reasons for this unfortunate circumstance has been the dearth of tools for targeted genome engineering of bacterial chassis, and, nowadays, synthetic biology is significantly helping to bridge such knowledge gap. Against this background, in this review, we discuss the state of the art in the rational design and construction of robust bacterial chassis for metabolic engineering, presenting key examples of bacterial species that have secured a place in industrial bioproduction. The emergence of novel bacterial chassis is also considered at the light of the unique properties of their physiology and metabolism, and the practical applications in which they are expected to outperform other microbial platforms. Emerging opportunities, essential strategies to enable successful development of industrial phenotypes, and major challenges in the field of bacterial chassis development are also discussed, outlining the solutions that contemporary synthetic biology-guided metabolic engineering offers to tackle these issues.
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Affiliation(s)
- Patricia Calero
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark2800Kongens LyngbyDenmark
| | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark2800Kongens LyngbyDenmark
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23
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Corynebacterium Cell Factory Design and Culture Process Optimization for Muconic Acid Biosynthesis. Sci Rep 2018; 8:18041. [PMID: 30575781 PMCID: PMC6303301 DOI: 10.1038/s41598-018-36320-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 11/13/2018] [Indexed: 12/03/2022] Open
Abstract
Muconic acid (MA) is a valuable compound for adipic acid production, which is a precursor for the synthesis of various polymers such as plastics, coatings, and nylons. Although MA biosynthesis has been previously reported in several bacteria, the engineered strains were not satisfactory owing to low MA titers. Here, we generated an engineered Corynebacterium cell factory to produce a high titer of MA through 3-dehydroshikimate (DHS) conversion to MA, with heterologous expression of foreign protocatechuate (PCA) decarboxylase genes. To accumulate key intermediates in the MA biosynthetic pathway, aroE (shikimate dehydrogenase gene), pcaG/H (PCA dioxygenase alpha/beta subunit genes) and catB (chloromuconate cycloisomerase gene) were disrupted. To accomplish the conversion of PCA to catechol (CA), a step that is absent in Corynebacterium, a codon-optimized heterologous PCA decarboxylase gene was expressed as a single operon under the strong promoter in a aroE-pcaG/H-catB triple knock-out Corynebacterium strain. This redesigned Corynebacterium, grown in an optimized medium, produced about 38 g/L MA and 54 g/L MA in 7-L and 50-L fed-batch fermentations, respectively. These results show highest levels of MA production demonstrated in Corynebacterium, suggesting that the rational cell factory design of MA biosynthesis could be an alternative way to complement petrochemical-based chemical processes.
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24
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Skoog E, Shin JH, Saez-Jimenez V, Mapelli V, Olsson L. Biobased adipic acid – The challenge of developing the production host. Biotechnol Adv 2018; 36:2248-2263. [DOI: 10.1016/j.biotechadv.2018.10.012] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 10/18/2018] [Accepted: 10/27/2018] [Indexed: 11/28/2022]
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25
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Fujiwara R, Noda S, Tanaka T, Kondo A. Muconic Acid Production Using Gene-Level Fusion Proteins in Escherichia coli. ACS Synth Biol 2018; 7:2698-2705. [PMID: 30350569 DOI: 10.1021/acssynbio.8b00380] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This study reports on the improving of muconic acid (MA) production by using metabolically engineered Escherichia coli. Three MA synthesis pathways separately were introduced into E. coli. After 72 h of cultivation, two of the three strains, i.e., one carrying the Pathway 1 (1.00 g/L) and the other carrying the Pathway 3 (1.34 g/L) produced MA. To increase MA production, the enzymes of the shikimate pathway (AroC and AroD) were overexpressed in these strains. Although the overexpression of AroC increased the MA production (1.59 g/L) by the Pathway 1, AroD overexpression decreased it by the Pathway 3. The metabolic channeling using gene-level fusion proteins additionally increased the MA production. In the pathway 1 and pH-controlled cultures, the overexpression of a fusion protein (AroC and MenF) increased the MA production from 20 g/L glucose to >3 and 4.45 g/L, respectively. These results suggest that the metabolic channeling approach is a promising strategy to increase the yield of the target compound.
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Affiliation(s)
- Ryosuke Fujiwara
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe 657-8501, Japan
| | - Shuhei Noda
- Center for Sustainable Resource Science, RIKEN, Wako, Saitama 351-0198, Japan
| | - Tsutomu Tanaka
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe 657-8501, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe 657-8501, Japan
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26
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Escherichia coli as a host for metabolic engineering. Metab Eng 2018; 50:16-46. [DOI: 10.1016/j.ymben.2018.04.008] [Citation(s) in RCA: 181] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 04/11/2018] [Accepted: 04/12/2018] [Indexed: 12/21/2022]
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27
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Luo ZW, Kim WJ, Lee SY. Metabolic Engineering of Escherichia coli for Efficient Production of 2-Pyrone-4,6-dicarboxylic Acid from Glucose. ACS Synth Biol 2018; 7:2296-2307. [PMID: 30096230 DOI: 10.1021/acssynbio.8b00281] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
2-Pyrone-4,6-dicarboxylic acid (PDC) is a pseudoaromatic dicarboxylic acid and is a promising biobased building block chemical that can be used to make diverse polyesters with novel functionalities. In this study, Escherichia coli was metabolically engineered to produce PDC from glucose. First, an efficient biosynthetic pathway for PDC production from glucose was suggested by in silico metabolic flux simulation. This best pathway employs a single-step biosynthetic route to protocatechuic acid (PCA), a metabolic precursor for PDC biosynthesis. On the basis of the selected PDC biosynthetic pathway, a shikimate dehydrogenase (encoded by aroE)-deficient E. coli strain was engineered by introducing heterologous genes of different microbial origin encoding enzymes responsible for converting 3-dehydroshikimate (DHS) to PDC, which allowed de novo biosynthesis of PDC from glucose. Next, production of PDC was further improved by applying stepwise rational metabolic engineering strategies. These include elimination of feedback inhibition on 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase (encoded by aroG) by overexpressing a feedback-resistant variant, enhancement of the precursor phosphoenolpyruvate supply by changing the native promoter of the ppsA gene with the strong trc promoter, and reducing accumulation of the major byproduct DHS by overexpression of a DHS importer (encoded by shiA). Furthermore, cofactor (NADP+/NADPH) utilization was manipulated through genetic modifications of the E. coli soluble pyridine nucleotide transhydrogenase (encoded by sthA), and the resultant impact on PDC production was investigated. Fed-batch fermentation of the final engineered E. coli strain allowed production of 16.72 g/L of PDC from glucose with the yield and productivity of 0.201 g/g and 0.172 g/L/h, respectively, representing the highest PDC production performance indices reported to date.
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Affiliation(s)
- Zi Wei Luo
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon 34141, Republic of Korea
| | - Won Jun Kim
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon 34141, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon 34141, Republic of Korea
- BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, Daejeon 34141, Republic of Korea
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Recent advances in metabolic engineering of Corynebacterium glutamicum for bioproduction of value-added aromatic chemicals and natural products. Appl Microbiol Biotechnol 2018; 102:8685-8705. [DOI: 10.1007/s00253-018-9289-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 07/30/2018] [Accepted: 07/31/2018] [Indexed: 02/06/2023]
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Biosynthesis of adipic acid via microaerobic hydrogenation of cis,cis-muconic acid by oxygen-sensitive enoate reductase. J Biotechnol 2018; 280:49-54. [DOI: 10.1016/j.jbiotec.2018.06.304] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 05/24/2018] [Accepted: 06/05/2018] [Indexed: 12/26/2022]
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Becker J, Kuhl M, Kohlstedt M, Starck S, Wittmann C. Metabolic engineering of Corynebacterium glutamicum for the production of cis, cis-muconic acid from lignin. Microb Cell Fact 2018; 17:115. [PMID: 30029656 PMCID: PMC6054733 DOI: 10.1186/s12934-018-0963-2] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 07/13/2018] [Indexed: 11/25/2022] Open
Abstract
Background Cis, cis-muconic acid (MA) is a dicarboxylic acid of recognized industrial value. It provides direct access to adipic acid and terephthalic acid, prominent monomers of commercial plastics. Results In the present work, we engineered the soil bacterium Corynebacterium glutamicum into a stable genome-based cell factory for high-level production of bio-based MA from aromatics and lignin hydrolysates. The elimination of muconate cycloisomerase (catB) in the catechol branch of the β-ketoadipate pathway provided a mutant, which accumulated MA at 100% molar yield from catechol, phenol, and benzoic acid, using glucose as additional growth substrate. The production of MA was optimized by constitutive overexpression of catA, which increased the activity of the encoded catechol 1,2-dioxygenase, forming MA from catechol, tenfold. Intracellular levels of catechol were more than 30-fold lower than extracellular levels, minimizing toxicity, but still saturating the high affinity CatA enzyme. In a fed-batch process, the created strain C. glutamicum MA-2 accumulated 85 g L−1 MA from catechol in 60 h and achieved a maximum volumetric productivity of 2.4 g L−1 h−1. The strain was furthermore used to demonstrate the production of MA from lignin in a cascade process. Following hydrothermal depolymerization of softwood lignin into small aromatics, the MA-2 strain accumulated 1.8 g L−1 MA from the obtained hydrolysate. Conclusions Our findings open the door to valorize lignin, the second most abundant polymer on earth, by metabolically engineered C. glutamicum for industrial production of MA and potentially other chemicals. Electronic supplementary material The online version of this article (10.1186/s12934-018-0963-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Judith Becker
- Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Martin Kuhl
- Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Michael Kohlstedt
- Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Sören Starck
- Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Campus A1.5, Saarbrücken, Germany.
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Wang S, Bilal M, Zong Y, Hu H, Wang W, Zhang X. Development of a Plasmid-Free Biosynthetic Pathway for Enhanced Muconic Acid Production in Pseudomonas chlororaphis HT66. ACS Synth Biol 2018; 7:1131-1142. [PMID: 29608278 DOI: 10.1021/acssynbio.8b00047] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Muconic acid is a platform chemical and an important intermediate in the degradation process of a series of aromatic compounds. Herein, a plasmid-free synthetic pathway in Pseudomonas chlororaphis HT66 is constructed for the enhanced biosynthesis of muconic acid by connecting endogenous ubiquinone biosynthesis pathway with protocatechuate degradation pathway using chromosomal integration. Instead of being plasmid and inducer dependent, the engineered strains could steadily produce the high muconic acid using glycerol as a carbon source. The engineered strain HT66-MA6 achieved a 3376 mg/L muconic acid production with a yield of 187.56 mg/g glycerol via the following strategies: (1) block muconic acid conversion and enhance muconic acid efflux pumping with phenazine biosynthesis cluster; (2) increase the muconic acid precursors supply through overexpressing the rate-limiting step, and (3) coexpress the "3-dehydroshikimate-derived" route in parallel with the "4-hydroxybenzoic acid-derived" route to create a synthetic "metabolic funnel". Finally, on the basis of the glycerol feeding strategies, the muconic acid yield reached 0.122 mol/mol glycerol. The results suggest that the construction of synthetic pathway with a plasmid-free strategy in P. chlororaphis displays a high biotechnological perspective.
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Averesch NJH, Krömer JO. Metabolic Engineering of the Shikimate Pathway for Production of Aromatics and Derived Compounds-Present and Future Strain Construction Strategies. Front Bioeng Biotechnol 2018; 6:32. [PMID: 29632862 PMCID: PMC5879953 DOI: 10.3389/fbioe.2018.00032] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 03/12/2018] [Indexed: 11/25/2022] Open
Abstract
The aromatic nature of shikimate pathway intermediates gives rise to a wealth of potential bio-replacements for commonly fossil fuel-derived aromatics, as well as naturally produced secondary metabolites. Through metabolic engineering, the abundance of certain intermediates may be increased, while draining flux from other branches off the pathway. Often targets for genetic engineering lie beyond the shikimate pathway, altering flux deep in central metabolism. This has been extensively used to develop microbial production systems for a variety of compounds valuable in chemical industry, including aromatic and non-aromatic acids like muconic acid, para-hydroxybenzoic acid, and para-coumaric acid, as well as aminobenzoic acids and aromatic α-amino acids. Further, many natural products and secondary metabolites that are valuable in food- and pharma-industry are formed outgoing from shikimate pathway intermediates. (Re)construction of such routes has been shown by de novo production of resveratrol, reticuline, opioids, and vanillin. In this review, strain construction strategies are compared across organisms and put into perspective with requirements by industry for commercial viability. Focus is put on enhancing flux to and through shikimate pathway, and engineering strategies are assessed in order to provide a guideline for future optimizations.
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Affiliation(s)
- Nils J H Averesch
- Universities Space Research Association at NASA Ames Research Center, Moffett Field, CA, United States
| | - Jens O Krömer
- Department of Solar Materials, Helmholtz Centre for Environmental Research, Leipzig, Germany
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Wang S, Bilal M, Hu H, Wang W, Zhang X. 4-Hydroxybenzoic acid-a versatile platform intermediate for value-added compounds. Appl Microbiol Biotechnol 2018. [PMID: 29516141 DOI: 10.1007/s00253-018-8815-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
4-Hydroxybenzoic acid (4-HBA) has recently emerged as a promising intermediate for several value-added bioproducts with potential biotechnological applications in food, cosmetics, pharmacy, fungicides, etc. Over the past years, a variety of biosynthetic techniques have been developed for producing the 4-HBA and 4-HBA-based products. At this juncture, synthetic biology and metabolic engineering approaches enabled the biosynthesis of 4-HBA to address the increasing demand for high-value bioproducts. This review summarizes the biosynthesis of a variety of industrially pertinent compounds such as resveratrol, muconic acid, gastrodin, xiamenmycin, and vanillyl alcohol using 4-HBA as the starting feedstock. Moreover, potential research activities with a close-up look at the future perspectives to produce new compounds using 4-HBA have also been discussed.
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Affiliation(s)
- Songwei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Muhammad Bilal
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hongbo Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xuehong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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34
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Thompson B, Pugh S, Machas M, Nielsen DR. Muconic Acid Production via Alternative Pathways and a Synthetic "Metabolic Funnel". ACS Synth Biol 2018; 7:565-575. [PMID: 29053259 DOI: 10.1021/acssynbio.7b00331] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Muconic acid is a promising platform biochemical and precursor to adipic acid, which can be used to synthesize various plastics and polymers. In this study, the systematic construction and comparative evaluation of a modular network of non-natural pathways for muconic acid biosynthesis was investigated in Escherichia coli, including via three distinct and novel pathways proceeding via phenol as a common intermediate. However, poor recombinant activity and high promiscuity of phenol hydroxylase ultimately limited "phenol-dependent" muconic acid production. A fourth pathway proceeding via p-hydroxybenzoate, protocatechuate, and catechol was accordingly developed, though with muconic acid titers by this route reaching just 819 mg/L, its performance lagged behind that of the established, "3-dehydroshikimiate-derived" route. Finally, these two most promising pathways were coexpressed in parallel to create a synthetic "metabolic funnel" that, by enabling maximal net precursor assimilation and flux while preserving native chorismate biosynthesis, nearly doubled muconic acid production to up to >3.1 g/L at a glucose yield of 158 mg/g while introducing only a single auxotrophy. This generalizable, "funneling" strategy is expected to have broad applications in metabolic engineering for further enhancing production of muconic acid, as well as other important bioproducts of interest.
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Affiliation(s)
- Brian Thompson
- Chemical Engineering, School for Engineering
of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287, United States
| | - Shawn Pugh
- Chemical Engineering, School for Engineering
of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287, United States
| | - Michael Machas
- Chemical Engineering, School for Engineering
of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287, United States
| | - David R. Nielsen
- Chemical Engineering, School for Engineering
of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287, United States
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35
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Averesch NJH, Martínez VS, Nielsen LK, Krömer JO. Toward Synthetic Biology Strategies for Adipic Acid Production: An in Silico Tool for Combined Thermodynamics and Stoichiometric Analysis of Metabolic Networks. ACS Synth Biol 2018; 7:490-509. [PMID: 29237121 DOI: 10.1021/acssynbio.7b00304] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Adipic acid, a nylon-6,6 precursor, has recently gained popularity in synthetic biology. Here, 16 different production routes to adipic acid were evaluated using a novel tool for network-embedded thermodynamic analysis of elementary flux modes. The tool distinguishes between thermodynamically feasible and infeasible modes under determined metabolite concentrations, allowing the thermodynamic feasibility of theoretical yields to be assessed. Further, patterns that always caused infeasible flux distributions were identified, which will aid the development of tailored strain design. A review of cellular efflux mechanisms revealed that significant accumulation of extracellular product is only possible if coupled with ATP hydrolysis. A stoichiometric analysis demonstrated that the maximum theoretical product carbon yield heavily depends on the metabolic route, ranging from 32 to 99% on glucose and/or palmitate in Escherichia coli and Saccharomyces cerevisiae metabolic models. Equally important, metabolite concentrations appeared to be thermodynamically restricted in several pathways. Consequently, the number of thermodynamically feasible flux distributions was reduced, in some cases even rendering whole pathways infeasible, highlighting the importance of pathway choice. Only routes based on the shikimate pathway were thermodynamically favorable over a large concentration and pH range. The low pH capability of S. cerevisiae shifted the thermodynamic equilibrium of some pathways toward product formation. One identified infeasible-pattern revealed that the reversibility of the mitochondrial malate dehydrogenase contradicted the current state of knowledge, which imposes a major restriction on the metabolism of S. cerevisiae. Finally, the evaluation of industrially relevant constraints revealed that two shikimate pathway-based routes in E. coli were the most robust.
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Affiliation(s)
- Nils J. H. Averesch
- Centre
for Microbial Electrochemical Systems (CEMES), Advanced Water Management
Centre (AWMC), The University of Queensland, Brisbane 4072, Australia
- Universities Space Research Association at NASA Ames Research Center, Moffett Field, California 94035, United States
| | - Verónica S. Martínez
- Systems
and Synthetic Biology Group, Australian Institute for Bioengineering
and Nanotechnology (AIBN), The University of Queensland, Brisbane 4072, Australia
- ARC
Training Centre for Biopharmaceutical Innovation (CBI), Australian
Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane 4072, Australia
| | - Lars K. Nielsen
- Systems
and Synthetic Biology Group, Australian Institute for Bioengineering
and Nanotechnology (AIBN), The University of Queensland, Brisbane 4072, Australia
- DTU
BIOSUSTAIN, Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Jens O. Krömer
- Centre
for Microbial Electrochemical Systems (CEMES), Advanced Water Management
Centre (AWMC), The University of Queensland, Brisbane 4072, Australia
- Department
for Solar Materials, Helmholtz Centre of Environmental Research−UFZ, 04318 Leipzig, Germany
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36
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Li SY, Ng IS, Chen PT, Chiang CJ, Chao YP. Biorefining of protein waste for production of sustainable fuels and chemicals. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:256. [PMID: 30250508 PMCID: PMC6146663 DOI: 10.1186/s13068-018-1234-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 08/22/2018] [Indexed: 05/21/2023]
Abstract
To mitigate the climate change caused by CO2 emission, the global incentive to the low-carbon alternatives as replacement of fossil fuel-derived products continuously expands the need for renewable feedstock. There will be accompanied by the generation of enormous protein waste as a result. The economical viability of the biorefinery platform can be realized once the surplus protein waste is recycled in a circular economy scenario. In this context, the present review focuses on the current development of biotechnology with the emphasis on biotransformation and metabolic engineering to refine protein-derived amino acids for production of fuels and chemicals. Its scope starts with the explosion of potential feedstock sources rich in protein waste. The availability of techniques is applied for purification and hydrolysis of various feedstock proteins to amino acids. Useful lessons are leaned from the microbial catabolism of amino acids and lay a foundation for the development of the protein-based biotechnology. At last, the future perspective of the biorefinery scheme based on protein waste is discussed associated with remarks on possible solutions to overcome the technical bottlenecks.
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Affiliation(s)
- Si-Yu Li
- Department of Chemical Engineering, National Chung Hsing University, Taichung, 402 Taiwan
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan, 70101 Taiwan
| | - Po Ting Chen
- Department of Biotechnology, Southern Taiwan University of Science and Technology, Tainan, 710 Taiwan
| | - Chung-Jen Chiang
- Department of Medical Laboratory Science and Biotechnology, China Medical University, No. 91, Hsueh-Shih Road, Taichung, 40402 Taiwan
| | - Yun-Peng Chao
- Department of Chemical Engineering, Feng Chia University, 100 Wenhwa Road, Taichung, 40724 Taiwan
- Department of Health and Nutrition Biotechnology, Asia University, Taichung, 41354 Taiwan
- Department of Medical Research, China Medical University Hospital, Taichung, 40447 Taiwan
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37
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Matsumoto T, Tanaka T, Kondo A. Engineering metabolic pathways in Escherichia coli for constructing a "microbial chassis" for biochemical production. BIORESOURCE TECHNOLOGY 2017; 245:1362-1368. [PMID: 28522199 DOI: 10.1016/j.biortech.2017.05.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 04/28/2017] [Accepted: 05/01/2017] [Indexed: 06/07/2023]
Abstract
The present work reviews literature describing the re-design of the metabolic pathways of a microbial host using sophisticated genetic tools, yielding strains for producing value-added chemicals including fuels, building-block chemicals, pharmaceuticals, and derivatives. This work employed Escherichia coli, a well-studied microorganism that has been successfully engineered to produce various chemicals. E. coli has several advantages compared with other microorganisms, including robustness, and handling. To achieve efficient productivities of target compounds, an engineered E. coli should accumulate metabolic precursors of target compounds. Multiple researchers have reported the use of pathway engineering to generate strains capable of accumulating various metabolic precursors, including pyruvate, acetyl-CoA, malonyl-CoA, mevalonate and shikimate. The aim of this review provides a promising guideline for designing E. coli strains capable of producing a variety of useful chemicals. Herein, the present work reviews their common and unique strategies, treating metabolically engineered E. coli as a "microbial chassis".
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Affiliation(s)
- Takuya Matsumoto
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodaicho, Nada, Kobe 657-8501, Japan
| | - Tsutomu Tanaka
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada, Kobe 657-8501, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodaicho, Nada, Kobe 657-8501, Japan; Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada, Kobe 657-8501, Japan.
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38
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Biotechnological production of aromatic compounds of the extended shikimate pathway from renewable biomass. J Biotechnol 2017; 257:211-221. [DOI: 10.1016/j.jbiotec.2016.11.016] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/17/2016] [Accepted: 11/17/2016] [Indexed: 01/17/2023]
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39
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Production of trans-2,3-dihydro-3-hydroxyanthranilic acid by engineered Pseudomonas chlororaphis GP72. Appl Microbiol Biotechnol 2017; 101:6607-6613. [DOI: 10.1007/s00253-017-8408-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 06/02/2017] [Accepted: 06/27/2017] [Indexed: 12/11/2022]
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40
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Abstract
Along with the development of metabolic engineering and synthetic biology tools, various microbes are being used to produce aromatic chemicals. In microbes, aromatics are mainly produced via a common important precursor, chorismate, in the shikimate pathway. Natural or non-natural aromatics have been produced by engineering metabolic pathways involving chorismate. In the past decade, novel approaches have appeared to produce various aromatics or to increase their productivity, whereas previously, the targets were mainly aromatic amino acids and the strategy was deregulating feedback inhibition. In this review, we summarize recent studies of microbial production of aromatics based on metabolic engineering approaches. In addition, future perspectives and challenges in this research area are discussed.
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Affiliation(s)
- Shuhei Noda
- Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Akihiko Kondo
- Center for Sustainable Resource Science, RIKEN, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Department of Chemical Science and Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan.
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41
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Milker S, Fink MJ, Rudroff F, Mihovilovic MD. Non-hazardous biocatalytic oxidation in Nylon-9 monomer synthesis on a 40 g scale with efficient downstream processing. Biotechnol Bioeng 2017; 114:1670-1678. [PMID: 28409822 DOI: 10.1002/bit.26312] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 04/03/2017] [Accepted: 04/09/2017] [Indexed: 11/11/2022]
Abstract
This paper describes the development of a biocatalytic process on the multi-dozen gram scale for the synthesis of a precursor to Nylon-9, a specialty polyamide. Such materials are growing in demand, but their corresponding monomers are often difficult to synthesize, giving rise to biocatalytic approaches. Here, we implemented cyclopentadecanone monooxygenase as an Escherichia coli whole-cell biocatalyst in a defined medium, together with a substrate feeding-product removal concept, and an optimized downstream processing (DSP). A previously described hazardous peracid-mediated oxidation was thus replaced with a safe and scalable protocol, using aerial oxygen as oxidant, and water as reaction solvent. The engineered process converted 42 g (0.28 mol) starting material ketone to the corresponding lactone with an isolated yield of 70% (33 g), after highly efficient DSP with 95% recovery of the converted material, translating to a volumetric yield of 8 g pure product per liter. Biotechnol. Bioeng. 2017;114: 1670-1678. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Sofia Milker
- Institute of Applied Synthetic Chemistry, Vienna University of Technology, Getreidemarkt 9/163, Vienna, 1060, Austria
| | - Michael J Fink
- Institute of Applied Synthetic Chemistry, Vienna University of Technology, Getreidemarkt 9/163, Vienna, 1060, Austria.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts
| | - Florian Rudroff
- Institute of Applied Synthetic Chemistry, Vienna University of Technology, Getreidemarkt 9/163, Vienna, 1060, Austria
| | - Marko D Mihovilovic
- Institute of Applied Synthetic Chemistry, Vienna University of Technology, Getreidemarkt 9/163, Vienna, 1060, Austria
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42
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Purdy HM, Reed JL. Evaluating the capabilities of microbial chemical production using genome-scale metabolic models. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.coisb.2017.01.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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43
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Metabolic engineering strategies to bio-adipic acid production. Curr Opin Biotechnol 2017; 45:136-143. [PMID: 28365404 DOI: 10.1016/j.copbio.2017.03.006] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 03/08/2017] [Accepted: 03/09/2017] [Indexed: 11/21/2022]
Abstract
Adipic acid is the most industrially important dicarboxylic acid as it is a key monomer in the synthesis of nylon. Today, adipic acid is obtained via a chemical process that relies on petrochemical precursors and releases large quantities of greenhouse gases. In the last two years, significant progress has been made in engineering microbes for the production of adipic acid and its immediate precursors, muconic acid and glucaric acid. Not only have the microbial substrates expanded beyond glucose and glycerol to include lignin monomers and hemicellulose components, but the number of microbial chassis now goes further than Escherichia coli and Saccharomyces cerevisiae to include microbes proficient in aromatic degradation, cellulose secretion and degradation of multiple carbon sources. Here, we review the metabolic engineering and nascent protein engineering strategies undertaken in each of these chassis to convert different feedstocks to adipic, muconic and glucaric acid. We also highlight near term prospects and challenges for each of the metabolic routes discussed.
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