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Sokolova N, Peng B, Haslinger K. Design and engineering of artificial biosynthetic pathways-where do we stand and where do we go? FEBS Lett 2023; 597:2897-2907. [PMID: 37777818 DOI: 10.1002/1873-3468.14745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/29/2023] [Accepted: 09/12/2023] [Indexed: 10/02/2023]
Abstract
The production of commodity and specialty chemicals relies heavily on fossil fuels. The negative impact of this dependency on our environment and climate has spurred a rising demand for more sustainable methods to obtain such chemicals from renewable resources. Herein, biotransformations of these renewable resources facilitated by enzymes or (micro)organisms have gained significant attention, since they can occur under mild conditions and reduce waste. These biotransformations typically leverage natural metabolic processes, which limits the scope and production capacity of such processes. In this mini-review, we provide an overview of advancements made in the past 5 years to expand the repertoire of biotransformations in engineered microorganisms. This ranges from redesign of existing pathways driven by retrobiosynthesis and computational design to directed evolution of enzymes and de novo pathway design to unlock novel routes for the synthesis of desired chemicals. We highlight notable examples of pathway designs for the production of commodity and specialty chemicals, showcasing the potential of these approaches. Lastly, we provide an outlook on future pathway design approaches.
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Affiliation(s)
- Nika Sokolova
- Department of Chemical and Pharmaceutical Biology, University of Groningen, The Netherlands
| | - Bo Peng
- Department of Chemical and Pharmaceutical Biology, University of Groningen, The Netherlands
| | - Kristina Haslinger
- Department of Chemical and Pharmaceutical Biology, University of Groningen, The Netherlands
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2
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Zha J, Zhao Z, Xiao Z, Eng T, Mukhopadhyay A, Koffas MA, Tang YJ. Biosystem design of Corynebacterium glutamicum for bioproduction. Curr Opin Biotechnol 2023; 79:102870. [PMID: 36549106 DOI: 10.1016/j.copbio.2022.102870] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 11/13/2022] [Accepted: 11/24/2022] [Indexed: 12/24/2022]
Abstract
Corynebacterium glutamicum, a natural glutamate-producing bacterium adopted for industrial production of amino acids, has been extensively explored recently for high-level biosynthesis of amino acid derivatives, bulk chemicals such as organic acids and short-chain alcohols, aromatics, and natural products, including polyphenols and terpenoids. Here, we review the recent advances with a focus on biosystem design principles, metabolic characterization and modeling, omics analysis, utilization of nonmodel feedstock, emerging CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) tools for Corynebacterium strain engineering, biosensors, and novel strains of C. glutamicum. Future research directions for developing C. glutamicum cell factories are also discussed.
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Affiliation(s)
- Jian Zha
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, China
| | - Zhen Zhao
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, China
| | - Zhengyang Xiao
- Department of Energy, Environmental and Chemical Engineering, Washington University in Saint Louis, MO 63130, USA
| | - Thomas Eng
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Aindrila Mukhopadhyay
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mattheos Ag Koffas
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Yinjie J Tang
- Department of Energy, Environmental and Chemical Engineering, Washington University in Saint Louis, MO 63130, USA.
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3
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Freudenberg RA, Wittemeier L, Einhaus A, Baier T, Kruse O. Advanced pathway engineering for phototrophic putrescine production. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1968-1982. [PMID: 35748533 PMCID: PMC9491463 DOI: 10.1111/pbi.13879] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/13/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
The polyamine putrescine (1,4-diaminobutane) contributes to cellular fitness in most organisms, where it is derived from the amino acids ornithine or arginine. In the chemical industry, putrescine serves as a versatile building block for polyamide synthesis. The green microalga Chlamydomonas reinhardtii accumulates relatively high putrescine amounts, which, together with recent advances in genetic engineering, enables the generation of a powerful green cell factory to promote sustainable biotechnology for base chemical production. Here, we report a systematic investigation of the native putrescine metabolism in C. reinhardtii, leading to the first CO2 -based bio-production of putrescine, by employing modern synthetic biology and metabolic engineering strategies. A CRISPR/Cas9-based knockout of key enzymes of the polyamine biosynthesis pathway identified ornithine decarboxylase 1 (ODC1) as a gatekeeper for putrescine accumulation and demonstrated that the arginine decarboxylase (ADC) route is likely inactive and that amine oxidase 2 (AMX2) is mainly responsible for putrescine degradation in C. reinhardtii. A 4.5-fold increase in cellular putrescine levels was achieved by engineered overexpression of potent candidate ornithine decarboxylases (ODCs). We identified unexpected substrate promiscuity in two bacterial ODCs, which exhibited co-production of cadaverine and 4-aminobutanol. Final pathway engineering included overexpression of recombinant arginases for improved substrate availability as well as functional knockout of putrescine degradation, which resulted in a 10-fold increase in cellular putrescine titres and yielded 200 mg/L in phototrophic high cell density cultivations after 10 days.
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Affiliation(s)
- Robert A. Freudenberg
- Faculty of Biology, Center for Biotechnology (CeBiTec)Bielefeld UniversityBielefeldGermany
| | - Luisa Wittemeier
- Faculty of Biology, Center for Biotechnology (CeBiTec)Bielefeld UniversityBielefeldGermany
| | - Alexander Einhaus
- Faculty of Biology, Center for Biotechnology (CeBiTec)Bielefeld UniversityBielefeldGermany
| | - Thomas Baier
- Faculty of Biology, Center for Biotechnology (CeBiTec)Bielefeld UniversityBielefeldGermany
| | - Olaf Kruse
- Faculty of Biology, Center for Biotechnology (CeBiTec)Bielefeld UniversityBielefeldGermany
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4
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Cho JS, Kim GB, Eun H, Moon CW, Lee SY. Designing Microbial Cell Factories for the Production of Chemicals. JACS AU 2022; 2:1781-1799. [PMID: 36032533 PMCID: PMC9400054 DOI: 10.1021/jacsau.2c00344] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/26/2022] [Accepted: 07/26/2022] [Indexed: 05/24/2023]
Abstract
The sustainable production of chemicals from renewable, nonedible biomass has emerged as an essential alternative to address pressing environmental issues arising from our heavy dependence on fossil resources. Microbial cell factories are engineered microorganisms harboring biosynthetic pathways streamlined to produce chemicals of interests from renewable carbon sources. The biosynthetic pathways for the production of chemicals can be defined into three categories with reference to the microbial host selected for engineering: native-existing pathways, nonnative-existing pathways, and nonnative-created pathways. Recent trends in leveraging native-existing pathways, discovering nonnative-existing pathways, and designing de novo pathways (as nonnative-created pathways) are discussed in this Perspective. We highlight key approaches and successful case studies that exemplify these concepts. Once these pathways are designed and constructed in the microbial cell factory, systems metabolic engineering strategies can be used to improve the performance of the strain to meet industrial production standards. In the second part of the Perspective, current trends in design tools and strategies for systems metabolic engineering are discussed with an eye toward the future. Finally, we survey current and future challenges that need to be addressed to advance microbial cell factories for the sustainable production of chemicals.
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Affiliation(s)
- Jae Sung Cho
- Metabolic
and Biomolecular Engineering National Research Laboratory and Systems
Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative
Laboratory, Department of Chemical and Biomolecular Engineering (BK21
four), Korea Advanced Institute of Science
and Technology (KAIST), Daejeon 34141, Republic of Korea
- KAIST
Institute for the BioCentury and KAIST Institute for Artificial Intelligence, Korea Advanced Institute of Science and Technology
(KAIST), Daejeon 34141, Republic of Korea
- BioProcess
Engineering Research Center and BioInformatics Research Center, Korea Advanced Institute of Science and Technology
(KAIST), Daejeon 34141, Republic of Korea
| | - Gi Bae Kim
- Metabolic
and Biomolecular Engineering National Research Laboratory and Systems
Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative
Laboratory, Department of Chemical and Biomolecular Engineering (BK21
four), Korea Advanced Institute of Science
and Technology (KAIST), Daejeon 34141, Republic of Korea
- KAIST
Institute for the BioCentury and KAIST Institute for Artificial Intelligence, Korea Advanced Institute of Science and Technology
(KAIST), Daejeon 34141, Republic of Korea
| | - Hyunmin Eun
- Metabolic
and Biomolecular Engineering National Research Laboratory and Systems
Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative
Laboratory, Department of Chemical and Biomolecular Engineering (BK21
four), Korea Advanced Institute of Science
and Technology (KAIST), Daejeon 34141, Republic of Korea
- KAIST
Institute for the BioCentury and KAIST Institute for Artificial Intelligence, Korea Advanced Institute of Science and Technology
(KAIST), Daejeon 34141, Republic of Korea
| | - Cheon Woo Moon
- Metabolic
and Biomolecular Engineering National Research Laboratory and Systems
Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative
Laboratory, Department of Chemical and Biomolecular Engineering (BK21
four), Korea Advanced Institute of Science
and Technology (KAIST), Daejeon 34141, Republic of Korea
- KAIST
Institute for the BioCentury and KAIST Institute for Artificial Intelligence, Korea Advanced Institute of Science and Technology
(KAIST), Daejeon 34141, Republic of Korea
| | - Sang Yup Lee
- Metabolic
and Biomolecular Engineering National Research Laboratory and Systems
Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative
Laboratory, Department of Chemical and Biomolecular Engineering (BK21
four), Korea Advanced Institute of Science
and Technology (KAIST), Daejeon 34141, Republic of Korea
- KAIST
Institute for the BioCentury and KAIST Institute for Artificial Intelligence, Korea Advanced Institute of Science and Technology
(KAIST), Daejeon 34141, Republic of Korea
- BioProcess
Engineering Research Center and BioInformatics Research Center, Korea Advanced Institute of Science and Technology
(KAIST), Daejeon 34141, Republic of Korea
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Chai M, Deng C, Chen Q, Lu W, Liu Y, Li J, Du G, Lv X, Liu L. Synthetic Biology Toolkits and Metabolic Engineering Applied in Corynebacterium glutamicum for Biomanufacturing. ACS Synth Biol 2021; 10:3237-3250. [PMID: 34855356 DOI: 10.1021/acssynbio.1c00355] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Corynebacterium glutamicum is an important workhorse in industrial white biotechnology. It has been widely applied in the producing processes of amino acids, fuels, and diverse value-added chemicals. With the continuous disclosure of genetic regulation mechanisms, various strategies and technologies of synthetic biology were used to design and construct C. glutamicum cells for biomanufacturing and bioremediation. This study mainly aimed to summarize the design and construction strategies of C. glutamicum-engineered strains, which were based on genomic modification, synthetic biological device-assisted metabolic flux optimization, and directed evolution-based engineering. Then, taking two important bioproducts (N-acetylglucosamine and hyaluronic acid) as examples, the applications of C. glutamicum cell factories were introduced. Finally, we discussed the current challenges and future development trends of C. glutamicum-engineered strain construction.
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Affiliation(s)
- Meng Chai
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Chen Deng
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Qi Chen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Wei Lu
- Shandong Runde Biotechnology Co., Ltd., Tai’an 271000, China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
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Tsuge Y, Matsuzawa H. Recent progress in production of amino acid-derived chemicals using Corynebacterium glutamicum. World J Microbiol Biotechnol 2021; 37:49. [PMID: 33569648 DOI: 10.1007/s11274-021-03007-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/17/2021] [Indexed: 01/07/2023]
Abstract
Green chemical production by microbial processes is critical for the development of a sustainable society in the twenty-first century. Among the important industrial microorganisms, the gram-positive bacterium Corynebacterium glutamicum has been utilized for amino acid fermentation, which is one of the largest microbial-based industries. To date, several amino acids, including L-glutamic acid, L-lysine, and L-threonine, have been produced by C. glutamicum. The capability to produce substantial amounts of amino acids has gained immense attention because the amino acids can be used as a precursor to produce other high-value-added chemicals. Recent developments in metabolic engineering and synthetic biology technologies have enabled the extension of metabolic pathways from amino acids. The present review provides an overview of the recent progress in the microbial production of amino acid-derived bio-based monomers such as 1,4-diaminobutane, 1,5-diaminopentane, glutaric acid, 5-aminolevulinic acid, L-pipecolic acid, 4-amino-1-butanol, and 5-aminolevulinic acid, as well as building blocks for healthcare products and pharmaceuticals such as ectoine, L-theanine, and gamma-aminobutyric acid by metabolically engineered C. glutamicum.
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Affiliation(s)
- Yota Tsuge
- Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Ishikawa, 920-1192, Japan. .,Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Ishikawa, 920-1192, Japan.
| | - Hiroki Matsuzawa
- Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Ishikawa, 920-1192, Japan
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