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Chen F, Fang H, Zhao J, Jiang P, Dong H, Zhao Y, Wang H, Zhang T, Zhang D. Multivariate modular metabolic engineering and medium optimization for vitamin B 12 production by Escherichia coli. Synth Syst Biotechnol 2024; 9:453-461. [PMID: 38634001 PMCID: PMC11021867 DOI: 10.1016/j.synbio.2024.03.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 03/24/2024] [Accepted: 03/29/2024] [Indexed: 04/19/2024] Open
Abstract
Vitamin B12 is a complex compound synthesized by microorganisms. The industrial production of vitamin B12 relies on specific microbial fermentation processes. E. coli has been utilized as a host for the de novo biosynthesis of vitamin B12, incorporating approximately 30 heterologous genes. However, a metabolic imbalance in the intricate pathway significantly limits vitamin B12 production. In this study, we employed multivariate modular metabolic engineering to enhance vitamin B12 production in E. coli by manipulating two modules comprising a total of 10 genes within the vitamin B12 biosynthetic pathway. These two modules were integrated into the chromosome of a chassis cell, regulated by T7, J23119, and J23106 promoters to achieve combinatorial pathway optimization. The highest vitamin B12 titer was attained by engineering the two modules controlled by J23119 and T7 promoters. The inclusion of yeast powder to the fermentation medium increased the vitamin B12 titer to 1.52 mg/L. This enhancement was attributed to the effect of yeast powder on elevating the oxygen transfer rate and augmenting the strain's isopropyl-β-d-1-thiogalactopyranoside (IPTG) tolerance. Ultimately, vitamin B12 titer of 2.89 mg/L was achieved through scaled-up fermentation in a 5-liter fermenter. The strategies reported herein will expedite the development of industry-scale vitamin B12 production utilizing E. coli.
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Affiliation(s)
- Feitao Chen
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Huan Fang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- University of Chinese Academy of Science, Beijing, 100049, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Jianghua Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- University of Chinese Academy of Science, Beijing, 100049, China
| | - Pingtao Jiang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Huina Dong
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- University of Chinese Academy of Science, Beijing, 100049, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Ying Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Huiying Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Tongcun Zhang
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- University of Chinese Academy of Science, Beijing, 100049, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
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2
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Ding Q, Liu L. Reprogramming cellular metabolism to increase the efficiency of microbial cell factories. Crit Rev Biotechnol 2024; 44:892-909. [PMID: 37380349 DOI: 10.1080/07388551.2023.2208286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 04/11/2023] [Indexed: 06/30/2023]
Abstract
Recent studies are increasingly focusing on advanced biotechnological tools, self-adjusting smart microorganisms, and artificial intelligent networks, to engineer microorganisms with various functions. Microbial cell factories are a vital platform for improving the bioproduction of medicines, biofuels, and biomaterials from renewable carbon sources. However, these processes are significantly affected by cellular metabolism, and boosting the efficiency of microbial cell factories remains a challenge. In this review, we present a strategy for reprogramming cellular metabolism to enhance the efficiency of microbial cell factories for chemical biosynthesis, which improves our understanding of microbial physiology and metabolic control. Current methods are mainly focused on synthetic pathways, metabolic resources, and cell performance. This review highlights the potential biotechnological strategy to reprogram cellular metabolism and provide novel guidance for designing more intelligent industrial microbes with broader applications in this growing field.
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Affiliation(s)
- Qiang Ding
- School of Life Sciences, Anhui University, Hefei, China
- Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei, Anhui, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, Anhui, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
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3
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Chen YC, Destouches L, Cook A, Fedorec AJH. Synthetic microbial ecology: engineering habitats for modular consortia. J Appl Microbiol 2024; 135:lxae158. [PMID: 38936824 DOI: 10.1093/jambio/lxae158] [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: 04/27/2024] [Revised: 06/13/2024] [Accepted: 06/26/2024] [Indexed: 06/29/2024]
Abstract
Microbiomes, the complex networks of micro-organisms and the molecules through which they interact, play a crucial role in health and ecology. Over at least the past two decades, engineering biology has made significant progress, impacting the bio-based industry, health, and environmental sectors; but has only recently begun to explore the engineering of microbial ecosystems. The creation of synthetic microbial communities presents opportunities to help us understand the dynamics of wild ecosystems, learn how to manipulate and interact with existing microbiomes for therapeutic and other purposes, and to create entirely new microbial communities capable of undertaking tasks for industrial biology. Here, we describe how synthetic ecosystems can be constructed and controlled, focusing on how the available methods and interaction mechanisms facilitate the regulation of community composition and output. While experimental decisions are dictated by intended applications, the vast number of tools available suggests great opportunity for researchers to develop a diverse array of novel microbial ecosystems.
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Affiliation(s)
- Yue Casey Chen
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Louie Destouches
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Alice Cook
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Alex J H Fedorec
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
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4
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Liang J, Xiao K, Wang X, Hou T, Zeng C, Gao X, Wang B, Zhong C. Revisiting Solar Energy Flow in Nanomaterial-Microorganism Hybrid Systems. Chem Rev 2024. [PMID: 38900019 DOI: 10.1021/acs.chemrev.3c00831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Nanomaterial-microorganism hybrid systems (NMHSs), integrating semiconductor nanomaterials with microorganisms, present a promising platform for broadband solar energy harvesting, high-efficiency carbon reduction, and sustainable chemical production. While studies underscore its potential in diverse solar-to-chemical energy conversions, prevailing NMHSs grapple with suboptimal energy conversion efficiency. Such limitations stem predominantly from an insufficient systematic exploration of the mechanisms dictating solar energy flow. This review provides a systematic overview of the notable advancements in this nascent field, with a particular focus on the discussion of three pivotal steps of energy flow: solar energy capture, cross-membrane energy transport, and energy conversion into chemicals. While key challenges faced in each stage are independently identified and discussed, viable solutions are correspondingly postulated. In view of the interplay of the three steps in affecting the overall efficiency of solar-to-chemical energy conversion, subsequent discussions thus take an integrative and systematic viewpoint to comprehend, analyze and improve the solar energy flow in the current NMHSs of different configurations, and highlighting the contemporary techniques that can be employed to investigate various aspects of energy flow within NMHSs. Finally, a concluding section summarizes opportunities for future research, providing a roadmap for the continued development and optimization of NMHSs.
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Affiliation(s)
- Jun Liang
- Key Laboratory of Quantitative Synthetic Biology, Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Kemeng Xiao
- Key Laboratory of Quantitative Synthetic Biology, Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xinyu Wang
- Key Laboratory of Quantitative Synthetic Biology, Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Tianfeng Hou
- Key Laboratory of Quantitative Synthetic Biology, Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Cuiping Zeng
- Key Laboratory of Quantitative Synthetic Biology, Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xiang Gao
- Key Laboratory of Quantitative Synthetic Biology, Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Bo Wang
- Key Laboratory of Quantitative Synthetic Biology, Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Chao Zhong
- Key Laboratory of Quantitative Synthetic Biology, Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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Xue M, Huang R, Liu W, Cheng J, Liu Y, Zhang J, Wang L, Liu D, Jiang H. Identification and characterization of a potential strain for the production of polyhydroxyalkanoate from glycerol. Front Microbiol 2024; 15:1413120. [PMID: 38966388 PMCID: PMC11223650 DOI: 10.3389/fmicb.2024.1413120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 05/20/2024] [Indexed: 07/06/2024] Open
Abstract
While poly (3-hydroxybutyrate) (PHB) holds promise as a bioplastic, its commercial utilization has been hampered by the high cost of raw materials. However, glycerol emerges as a viable feedstock for PHB production, offering a sustainable production approach and substantial cost reduction potential. Glycerol stands out as a promising feedstock for PHB production, offering a pathway toward sustainable manufacturing and considerable cost savings. The identification and characterization of strains capable of converting glycerol into PHB represent a pivotal strategy in advancing PHB production research. In this study, we isolated a strain, Ralstonia sp. RRA (RRA). The strain exhibits remarkable proficiency in synthesizing PHB from glycerol. With glycerol as the carbon source, RRA achieved a specific growth rate of 0.19 h-1, attaining a PHB content of approximately 50% within 30 h. Through third-generation genome and transcriptome sequencing, we elucidated the genome composition and identified a total of eight genes (glpR, glpD, glpS, glpT, glpP, glpQ, glpV, and glpK) involved in the glycerol metabolism pathway. Leveraging these findings, the strain RRA demonstrates significant promise in producing PHB from low-cost renewable carbon sources.
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Affiliation(s)
- Mengheng Xue
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Rong Huang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Wei Liu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Jian Cheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Yuwan Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Jie Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Limei Wang
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
| | - Dingyu Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Huifeng Jiang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
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Ebrahimzadeh Kouchesfahani M, Bahrami A, Babaeipour V. Poly-γ-glutamic acid overproduction of Bacillus licheniformis ATCC 9945 a by developing a novel optimum culture medium and glutamate pulse feeding using different experimental design approaches. Biotechnol Appl Biochem 2024; 71:565-583. [PMID: 38246886 DOI: 10.1002/bab.2559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 12/31/2023] [Indexed: 01/23/2024]
Abstract
The commercial production of multifunctional, biocompatible, and biodegradable biopolymers such as poly-γ-glutamic acid via microbial fermentation requires the development of simple and cheap methods for mass production. This study optimized the poly-γ-glutamic acid production of Bacillus licheniformis ATCC 9945a in several steps. At first, the most critical components of the culture medium, including l-glutamic acid, citric acid, and glycerol, were selected by screening nine factors through the Plackett-Burman experimental design and then were optimized using the response surface method and the central composite design algorithm. Under optimal conditions, the production of poly-γ-glutamic acid increased by more than 4.2 times from 11.2 to 47.2 g/L. This is one of the highest production rates of this strain in submerged batch fermentation reported so far using the optimized medium compared to the conventional base medium. A novel and efficient sudden pulse feeding strategy (achieved by a novel one-factorial statistical technique) of l-glutamic acid to the optimized medium increased biopolymer production from 47.2 to 66.1 g/L, the highest value reported in published literature with this strain. This simple, reproducible, and cheap fermentation process can considerably enhance the commercial applications of the poly-γ-glutamic acid synthesized by B. licheniformis ATCC 9945a.
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Affiliation(s)
| | - Ali Bahrami
- Faculty of Chemistry and Chemical Engineering, Malek Ashtar University of Technology, Tehran, Iran
| | - Valiollah Babaeipour
- Faculty of Chemistry and Chemical Engineering, Malek Ashtar University of Technology, Tehran, Iran
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Ruan Z, Chen K, Cao W, Meng L, Yang B, Xu M, Xing Y, Li P, Freilich S, Chen C, Gao Y, Jiang J, Xu X. Engineering natural microbiomes toward enhanced bioremediation by microbiome modeling. Nat Commun 2024; 15:4694. [PMID: 38824157 PMCID: PMC11144243 DOI: 10.1038/s41467-024-49098-z] [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: 03/26/2022] [Accepted: 05/21/2024] [Indexed: 06/03/2024] Open
Abstract
Engineering natural microbiomes for biotechnological applications remains challenging, as metabolic interactions within microbiomes are largely unknown, and practical principles and tools for microbiome engineering are still lacking. Here, we present a combinatory top-down and bottom-up framework to engineer natural microbiomes for the construction of function-enhanced synthetic microbiomes. We show that application of herbicide and herbicide-degrader inoculation drives a convergent succession of different natural microbiomes toward functional microbiomes (e.g., enhanced bioremediation of herbicide-contaminated soils). We develop a metabolic modeling pipeline, SuperCC, that can be used to document metabolic interactions within microbiomes and to simulate the performances of different microbiomes. Using SuperCC, we construct bioremediation-enhanced synthetic microbiomes based on 18 keystone species identified from natural microbiomes. Our results highlight the importance of metabolic interactions in shaping microbiome functions and provide practical guidance for engineering natural microbiomes.
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Affiliation(s)
- Zhepu Ruan
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China
| | - Kai Chen
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Weimiao Cao
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Lei Meng
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Bingang Yang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Mengjun Xu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Youwen Xing
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Pengfa Li
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Shiri Freilich
- Newe Ya'ar Research Center, Agricultural Research Organization, P.O. Box 1021, Ramat Yishay, 30095, Israel
| | - Chen Chen
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China
| | - Yanzheng Gao
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Jiandong Jiang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China.
| | - Xihui Xu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing, 210095, China.
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Zhang YM, Qiao B, Shang W, Ding MZ, Xu QM, Duan TX, Cheng JS. Improving salt-tolerant artificial consortium of Bacillus amyloliquefaciens for bioconverting food waste to lipopeptides. WASTE MANAGEMENT (NEW YORK, N.Y.) 2024; 181:89-100. [PMID: 38598883 DOI: 10.1016/j.wasman.2024.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/20/2024] [Accepted: 04/03/2024] [Indexed: 04/12/2024]
Abstract
High-salt content in food waste (FW) affects its resource utilization during biotransformation. In this study, adaptive laboratory evolution (ALE), gene editing, and artificial consortia were performed out to improve the salt-tolerance of Bacillus amyloliquefaciens for producing lipopeptide under FW and seawater. High-salt stress significantly decreased lipopeptide production in the B. amyloliquefaciens HM618 and ALE strains. The total lipopeptide production in the recombinant B. amyloliquefaciens HM-4KSMSO after overexpressing the ion transportor gene ktrA and proline transporter gene opuE and replacing the promoter of gene mrp was 1.34 times higher than that in the strain HM618 in medium containing 30 g/L NaCl. Lipopeptide production under salt-tolerant consortia containing two strains (HM-4KSMSO and Corynebacterium glutamicum) and three-strains (HM-4KSMSO, salt-tolerant C. glutamicum, and Yarrowia lipolytica) was 1.81- and 2.28-fold higher than that under pure culture in a medium containing FW or both FW and seawater, respectively. These findings provide a new strategy for using high-salt FW and seawater to produce value-added chemicals.
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Affiliation(s)
- Yu-Miao Zhang
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, People's Republic of China
| | - Bin Qiao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, People's Republic of China
| | - Wei Shang
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, People's Republic of China
| | - Ming-Zhu Ding
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, People's Republic of China
| | - Qiu-Man Xu
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Science, Tianjin Normal University, Binshuixi Road 393, Xiqing District, Tianjin 300387, People's Republic of China
| | - Tian-Xu Duan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, People's Republic of China
| | - Jing-Sheng Cheng
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, People's Republic of China.
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Beck SW, Ye DY, Hwang HG, Jung GY. Stepwise Flux Optimization for Enhanced GABA Production from Acetate in Escherichia coli. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:10420-10427. [PMID: 38657224 DOI: 10.1021/acs.jafc.4c01198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Strategic allocation of metabolic flux is essential for achieving a higher production performance in genetically engineered organisms. Flux optimization between cell growth and chemical production has led to the establishment of cost-effective chemical production methods in microbial cell factories. This effect is amplified when utilizing a low-cost carbon source. γ-Aminobutyric acid (GABA), crucial in pharmaceuticals and biodegradable polymers, can be efficiently produced from acetate, a cost-effective substrate. However, a balanced distribution of acetate-derived flux is essential for optimizing the production without hindering growth. In this study, we demonstrated GABA production from acetate using Escherichia coli by focusing on optimizing the metabolic flux at isocitrate and α-ketoglutarate nodes. Through a series of flux optimizations, the final strain produced 2.54 g/L GABA from 5.91 g/L acetate in 24 h (0.43 g/g yield). These findings suggest that delicate flux balancing with the application of a cheap substrate can contribute to cost-effective production of GABA.
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Affiliation(s)
- Sun Woo Beck
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Dae-Yeol Ye
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Hyun Gyu Hwang
- Institute of Environmental and Energy Technology, Pohang University of Science and Technology, 77 Cheongam - Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Gyoo Yeol Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Republic of Korea
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10
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Zhang C, Wu J, Sun Q, Ding S, Tao H, He Y, Qiu H, Shu B, Zhu D, Zhu H, Hong K. De novo production of bioactive sesterterpenoid ophiobolins in Saccharomyces cerevisiae cell factories. Microb Cell Fact 2024; 23:129. [PMID: 38711040 DOI: 10.1186/s12934-024-02406-0] [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: 01/15/2024] [Accepted: 04/25/2024] [Indexed: 05/08/2024] Open
Abstract
BACKGROUND Sesterterpenoids are rare species among the terpenoids family. Ophiobolins are sesterterpenes with a 5-8-5 tricyclic skeleton. The oxidized ophiobolins exhibit significant cytotoxic activity and potential medicinal value. There is an urgent need for large amounts of ophiobolins supplication for drug development. The synthetic biology approach has been successfully employed in lots of terpene compound production and inspired us to develop a cell factory for ophiobolin biosynthesis. RESULTS We developed a systematic metabolic engineering strategy to construct an ophiobolin biosynthesis chassis based on Saccharomyces cerevisiae. The whole-cell biotransformation methods were further combined with metabolic engineering to enhance the expression of key ophiobolin biosynthetic genes and improve the supply of precursors and cofactors. A high yield of 5.1 g/L of ophiobolin F was reached using ethanol and fatty acids as substrates. To accumulate oxidized ophiobolins, we optimized the sources and expression conditions for P450-CPR and alleviated the toxicity of bioactive compounds to cells through PDR engineering. We unexpectedly obtained a novel ophiobolin intermediate with potent cytotoxicity, 5-hydroxy-21-formyl-ophiobolin F, and the known bioactive compound ophiobolin U. Finally, we achieved the ophiobolin U titer of 128.9 mg/L. CONCLUSIONS We established efficient cell factories based on S. cerevisiae, enabling de novo biosynthesis of the ophiobolin skeleton ophiobolin F and oxidized ophiobolins derivatives. This work has filled the gap in the heterologous biosynthesis of sesterterpenoids in S. cerevisiae and provided valuable solutions for new drug development based on sesterterpenoids.
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Affiliation(s)
- Caizhe Zhang
- Department of Radiation and Medical Oncology, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Zhongnan Hospital, Ministry of Education, Wuhan University, Wuhan, 430071, China
| | - Jun Wu
- Department of Radiation and Medical Oncology, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Zhongnan Hospital, Ministry of Education, Wuhan University, Wuhan, 430071, China
| | - Qing Sun
- Department of Radiation and Medical Oncology, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Zhongnan Hospital, Ministry of Education, Wuhan University, Wuhan, 430071, China
| | - Shuaishuai Ding
- Department of Radiation and Medical Oncology, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Zhongnan Hospital, Ministry of Education, Wuhan University, Wuhan, 430071, China
| | - Hua Tao
- Department of Radiation and Medical Oncology, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Zhongnan Hospital, Ministry of Education, Wuhan University, Wuhan, 430071, China
| | - Yuhua He
- Department of Radiation and Medical Oncology, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Zhongnan Hospital, Ministry of Education, Wuhan University, Wuhan, 430071, China
| | - Hui Qiu
- Department of Radiation and Medical Oncology, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Zhongnan Hospital, Ministry of Education, Wuhan University, Wuhan, 430071, China
| | - Bei Shu
- Department of Radiation and Medical Oncology, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Zhongnan Hospital, Ministry of Education, Wuhan University, Wuhan, 430071, China
| | - Dongqing Zhu
- Department of Radiation and Medical Oncology, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Zhongnan Hospital, Ministry of Education, Wuhan University, Wuhan, 430071, China
| | - Hengcheng Zhu
- Department of Urology, Renmin Hospital of Wuhan University, No. 238 Jie-Fang Avenue, Wuhan, 430060, China
| | - Kui Hong
- Department of Radiation and Medical Oncology, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Zhongnan Hospital, Ministry of Education, Wuhan University, Wuhan, 430071, China.
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11
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Chaisupa P, Wright RC. State-of-the-art in engineering small molecule biosensors and their applications in metabolic engineering. SLAS Technol 2024; 29:100113. [PMID: 37918525 DOI: 10.1016/j.slast.2023.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/18/2023] [Accepted: 10/25/2023] [Indexed: 11/04/2023]
Abstract
Genetically encoded biosensors are crucial for enhancing our understanding of how molecules regulate biological systems. Small molecule biosensors, in particular, help us understand the interaction between chemicals and biological processes. They also accelerate metabolic engineering by increasing screening throughput and eliminating the need for sample preparation through traditional chemical analysis. Additionally, they offer significantly higher spatial and temporal resolution in cellular analyte measurements. In this review, we discuss recent progress in in vivo biosensors and control systems-biosensor-based controllers-for metabolic engineering. We also specifically explore protein-based biosensors that utilize less commonly exploited signaling mechanisms, such as protein stability and induced degradation, compared to more prevalent transcription factor and allosteric regulation mechanism. We propose that these lesser-used mechanisms will be significant for engineering eukaryotic systems and slower-growing prokaryotic systems where protein turnover may facilitate more rapid and reliable measurement and regulation of the current cellular state. Lastly, we emphasize the utilization of cutting-edge and state-of-the-art techniques in the development of protein-based biosensors, achieved through rational design, directed evolution, and collaborative approaches.
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Affiliation(s)
- Patarasuda Chaisupa
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA 24061, United States
| | - R Clay Wright
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA 24061, United States; Translational Plant Sciences Center (TPSC), Virginia Tech, Blacksburg, VA 24061, United States.
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12
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Hao Y, Pan X, You J, Li G, Xu M, Rao Z. Microbial production of branched chain amino acids: Advances and perspectives. BIORESOURCE TECHNOLOGY 2024; 397:130502. [PMID: 38417463 DOI: 10.1016/j.biortech.2024.130502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 02/23/2024] [Accepted: 02/25/2024] [Indexed: 03/01/2024]
Abstract
Branched-chain amino acids (BCAAs) such as L-valine, L-leucine, and L-isoleucine are widely used in food and feed. To comply with sustainable development goals, commercial production of BCAAs has been completely replaced with microbial fermentation. However, the efficient production of BCAAs by microorganisms remains a serious challenge due to their staggered metabolic networks and cell growth. To overcome these difficulties, systemic metabolic engineering has emerged as an effective and feasible strategy for the biosynthesis of BCAA. This review firstly summarizes the research advances in the microbial synthesis of BCAAs and representative engineering strategies. Second, systematic methods, such as high-throughput screening, adaptive laboratory evolution, and omics analysis, can be used to analyses the synthesis of BCAAs at the whole-cell level and further improve the titer of target chemicals. Finally, new tools and engineering strategies that may increase the production output and development direction of the microbial production of BCAAs are discussed.
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Affiliation(s)
- Yanan Hao
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xuewei Pan
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jiajia You
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Guomin Li
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Meijuan Xu
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zhiming Rao
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi 214122, China.
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13
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Kong X, Gui Q, Liu H, Qian F, Wang P. Efficient Synthesis of Chiral Aryl Alcohol with a Novel Kosakonia radicincitans Isolate in Tween 20/L-carnitine: Lysine-Containing Synergistic Reaction System. Appl Biochem Biotechnol 2024; 196:1509-1526. [PMID: 37428385 DOI: 10.1007/s12010-023-04641-4] [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] [Accepted: 07/01/2023] [Indexed: 07/11/2023]
Abstract
Chiral trifluoromethyl alcohols as vital intermediates are of great interest in fine chemicals and especially in pharmaceutical synthesis. In this work, a novel isolate Kosakonia radicincitans ZJPH202011 was firstly employed as biocatalyst for the synthesis of (R)-1-(4-bromophenyl)-2,2,2-trifluoroethanol ((R)-BPFL) with good enantioselectivity. By optimizing fermentation conditions and bioreduction parameters in aqueous buffer system, the substrate concentration of 1-(4-bromophenyl)-2,2,2-trifluoroethanone (BPFO) was doubled from 10 to 20 mM, and the enantiomeric excess (ee) value for (R)-BPFL increased from 88.8 to 96.4%. To improve biocatalytic efficiency by strengthening the mass-transfer rate, natural deep-eutectic solvents, surfactants and cyclodextrins (CDs) were introduced separately in the reaction system as cosolvent. Among them, L-carnitine: lysine (C: Lys, molar ratio 1:2), Tween 20 and γ-CD manifested higher (R)-BPFL yield compared with other same kind of cosolvents. Furthermore, based on the excellent performance of both Tween 20 and C: Lys (1:2) in enhancing BPFO solubility and ameliorating cell permeability, a Tween 20/C: Lys (1:2)-containing integrated reaction system was then established for efficient bioproduction of (R)-BPFL. After optimizing the critical factors involved in BPFO bioreduction in this synergistic reaction system, BPFO loading increased up to 45 mM and the yield reached 90.0% within 9 h, comparatively only 37.6% yield was acquired in neat aqueous buffer. This is the first report on K. radicincitans cells as new biocatalyst applied in (R)-BPFL preparation, and the developed Tween 20/C: Lys-containing synergistic reaction system has great potential for the synthesis of various chiral alcohols.
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Affiliation(s)
- Xiangxin Kong
- Key Laboratory of Pharmaceutical Engineering of Zhejiang Province, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
- Key Laboratory for Green Pharmaceutical Technologies and Related Equipment of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Qian Gui
- Key Laboratory of Pharmaceutical Engineering of Zhejiang Province, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
- Key Laboratory for Green Pharmaceutical Technologies and Related Equipment of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Hanyu Liu
- Key Laboratory of Pharmaceutical Engineering of Zhejiang Province, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
- Key Laboratory for Green Pharmaceutical Technologies and Related Equipment of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Feng Qian
- Key Laboratory of Pharmaceutical Engineering of Zhejiang Province, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
- Key Laboratory for Green Pharmaceutical Technologies and Related Equipment of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Pu Wang
- Key Laboratory of Pharmaceutical Engineering of Zhejiang Province, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.
- Key Laboratory for Green Pharmaceutical Technologies and Related Equipment of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.
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14
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Zou Y, Li X, Xin X, Xu H, Zhao G. Microbial-Driven Synthesis and Hydrolysis of Neohesperidin Dihydrochalcone: Biotransformation Process and Feasibility Investigation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:4246-4256. [PMID: 38317352 DOI: 10.1021/acs.jafc.3c08339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
A novel yeast-mediated hydrogenation was developed for the synthesis of neohesperidin dihydrochalcone (NHDC) in high yields (over 83%). Moreover, whole-cell catalytic hydrolysis was also designed to hydrolyze NHDC into potential sweeteners, hesperetin dihydrochalcone-7-O-glucoside (HDC-G) and hesperetin dihydrochalcone (HDC). The biohydrogenation was further combined with whole-cell hydrolysis to achieve a one-pot two-step biosynthesis, utilizing yeast to hydrogenate C═C in the structure, while Aspergillus niger cells hydrolyze glycosides. The conversion of NHDC and the proportion of hydrolysis products could be controlled by adjusting the catalysts, the components of the reaction system, and the addition of glucose. Furthermore, yeast-mediated biotransformation demonstrated superior reaction stability and enhanced safety and employed more cost-effective catalysts compared to the traditional chemical hydrogenation of NHDC synthesis. This research not only provides a new route for NHDC production but also offers a safe and flexible one-pot cascade biosynthetic platform for the production of high-value compounds from citrus processing wastes.
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Affiliation(s)
- Yucong Zou
- School of Food Science and Engineering, South China University of Technology, Wushan Road 381, Guangzhou, Guangdong 510640, China
| | - Xiaofeng Li
- School of Food Science and Engineering, South China University of Technology, Wushan Road 381, Guangzhou, Guangdong 510640, China
| | - Xuan Xin
- College of Light Industry and Food Technology, Zhongkai University of Agriculture and Engineering, Dongsha Street 24, Guangzhou, Guangdong 510225, China
| | - Haixia Xu
- Jiangxi Key Laboratory National Products and Functional Food, College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi 3300045, China
| | - Guanglei Zhao
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou, Guangdong 510641, China
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15
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Hassani L, Moosavi MR, Setoodeh P, Zare H. FastKnock: an efficient next-generation approach to identify all knockout strategies for strain optimization. Microb Cell Fact 2024; 23:37. [PMID: 38287320 PMCID: PMC10823710 DOI: 10.1186/s12934-023-02277-x] [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: 06/30/2023] [Accepted: 12/15/2023] [Indexed: 01/31/2024] Open
Abstract
Overproduction of desired native or nonnative biochemical(s) in (micro)organisms can be achieved through metabolic engineering. Appropriate rewiring of cell metabolism is performed by making rational changes such as insertion, up-/down-regulation and knockout of genes and consequently metabolic reactions. Finding appropriate targets (including proper sets of reactions to be knocked out) for metabolic engineering to design optimal production strains has been the goal of a number of computational algorithms. We developed FastKnock, an efficient next-generation algorithm for identifying all possible knockout strategies (with a predefined maximum number of reaction deletions) for the growth-coupled overproduction of biochemical(s) of interest. We achieve this by developing a special depth-first traversal algorithm that allows us to prune the search space significantly. This leads to a drastic reduction in execution time. We evaluate the performance of the FastKnock algorithm using various Escherichia coli genome-scale metabolic models in different conditions (minimal and rich mediums) for the overproduction of a number of desired metabolites. FastKnock efficiently prunes the search space to less than 0.2% for quadruple- and 0.02% for quintuple-reaction knockouts. Compared to the classic approaches such as OptKnock and the state-of-the-art techniques such as MCSEnumerator methods, FastKnock found many more beneficial and important practical solutions. The availability of all the solutions provides the opportunity to further characterize, rank and select the most appropriate intervention strategy based on any desired evaluation index. Our implementation of the FastKnock method in Python is publicly available at https://github.com/leilahsn/FastKnock .
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Affiliation(s)
- Leila Hassani
- Department of Computer Science and Engineering and IT, School of Electrical and Computer Engineering, Shiraz University, Shiraz, Iran
| | - Mohammad R Moosavi
- Department of Computer Science and Engineering and IT, School of Electrical and Computer Engineering, Shiraz University, Shiraz, Iran.
| | - Payam Setoodeh
- Department of Chemical Engineering, School of Chemical, Petroleum and Gas Engineering, Shiraz University, Shiraz, Iran
- Booth School of Engineering Practice and Technology, McMaster University, Hamilton, ON, Canada
| | - Habil Zare
- Department of Cell Systems and Anatomy, University of Texas Health Science Center, San Antonio, TX, USA.
- Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas Health Science Center, San Antonio, USA.
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16
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Hooe S, Thakur M, Lasarte-Aragonés G, Breger JC, Walper SA, Medintz IL, Ellis GA. Exploration of the In Vitro Violacein Synthetic Pathway with Substrate Analogues. ACS OMEGA 2024; 9:3894-3904. [PMID: 38284012 PMCID: PMC10809250 DOI: 10.1021/acsomega.3c08233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/21/2023] [Accepted: 12/26/2023] [Indexed: 01/30/2024]
Abstract
Evolution has gifted enzymes with the ability to synthesize an abundance of small molecules with incredible control over efficiency and selectivity. Central to an enzyme's role is the ability to selectively catalyze reactions in the milieu of chemicals within a cell. However, for chemists it is often desirable to extend the substrate scope of reactions to produce analogue(s) of a desired product and therefore some degree of enzyme promiscuity is often desired. Herein, we examine this dichotomy in the context of the violacein biosynthetic pathway. Importantly, we chose to interrogate this pathway with tryptophan analogues in vitro, to mitigate possible interference from cellular components and endogenous tryptophan. A total of nine tryptophan analogues were screened for by analyzing the substrate promiscuity of the initial enzyme, VioA, and compared to the substrate tryptophan. These results suggested that for VioA, substitutions at either the 2- or 4-position of tryptophan were not viable. The seven analogues that showed successful substrate conversion by VioA were then applied to the five enzyme cascade (VioABEDC) for the production of violacein, where l-tryptophan and 6-fluoro-l-tryptophan were the only substrates which were successfully converted to the corresponding violacein derivative(s). However, many of the other tryptophan analogues did convert to various substituted intermediaries. Overall, our results show substrate promiscuity with the initial enzyme, VioA, but much less for the full pathway. This work demonstrates the complexity involved when attempting to analyze substrate analogues within multienzymatic cascades, where each enzyme involved within the cascade possesses its own inherent promiscuity, which must be compatible with the remaining enzymes in the cascade for successful formation of a desired product.
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Affiliation(s)
- Shelby
L. Hooe
- National
Research Council, Washington, D.C. 20001, United States
- Center
for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Meghna Thakur
- Center
for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College
of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Guillermo Lasarte-Aragonés
- Center
for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College
of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Joyce C. Breger
- Center
for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Scott A. Walper
- Center
for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Igor L. Medintz
- Center
for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Gregory A. Ellis
- Center
for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
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17
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Lu P, Bai R, Gao T, Chen J, Jiang K, Zhu Y, Lu Y, Zhang S, Xu F, Zhao H. Systemic metabolic engineering of Enterobacter aerogenes for efficient 2,3-butanediol production. Appl Microbiol Biotechnol 2024; 108:146. [PMID: 38240862 PMCID: PMC10798932 DOI: 10.1007/s00253-023-12911-8] [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: 07/18/2023] [Revised: 11/05/2023] [Accepted: 11/14/2023] [Indexed: 01/22/2024]
Abstract
2,3-Butanediol (2,3-BDO) is an important gateway molecule for many chemical derivatives. Currently, microbial production is gradually being recognized as a green and sustainable alternative to petrochemical synthesis, but the titer, yield, and productivity of microbial 2,3-BDO remain suboptimal. Here, we used systemic metabolic engineering strategies to debottleneck the 2,3-BDO production in Enterobacter aerogenes. Firstly, the pyruvate metabolic network was reconstructed by deleting genes for by-product synthesis to improve the flux toward 2,3-BDO synthesis, which resulted in a 90% increase of the product titer. Secondly, the 2,3-BDO productivity of the IAM1183-LPCT/D was increased by 55% due to the heterologous expression of DR1558 which boosted cell resistance to abiotic stress. Thirdly, carbon sources were optimized to further improve the yield of target products. The IAM1183-LPCT/D showed the highest titer of 2,3-BDO from sucrose, 20% higher than that from glucose, and the yield of 2,3-BDO reached 0.49 g/g. Finally, the titer of 2,3-BDO of IAM1183-LPCT/D in a 5-L fermenter reached 22.93 g/L, 85% higher than the wild-type strain, and the titer of by-products except ethanol was very low. KEY POINTS: Deletion of five key genes in E. aerogenes improved 2,3-BDO production The titer of 2,3-BDO was increased by 90% by regulating metabolic flux Response regulator DR1558 was expressed to increase 2,3-BDO productivity.
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Affiliation(s)
- Ping Lu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Ruoxuan Bai
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Ting Gao
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Jiale Chen
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Ke Jiang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Yalun Zhu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Ye Lu
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Shuting Zhang
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Fangxu Xu
- Liaoning Province Key Laboratory of Cordyceps Militaris With Functional Value, Experimental Teaching Center, Shenyang Normal University, Shenyang, 110034, China
| | - Hongxin Zhao
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
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18
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Verma S, Paliwal S. Recent Developments and Applications of Biocatalytic and Chemoenzymatic Synthesis for the Generation of Diverse Classes of Drugs. Curr Pharm Biotechnol 2024; 25:448-467. [PMID: 37885105 DOI: 10.2174/0113892010238984231019085154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 08/26/2023] [Accepted: 09/19/2023] [Indexed: 10/28/2023]
Abstract
Biocatalytic and chemoenzymatic biosynthesis are powerful methods of organic chemistry that use enzymes to execute selective reactions and allow the efficient production of organic compounds. The advantages of these approaches include high selectivity, mild reaction conditions, and the ability to work with complex substrates. The utilization of chemoenzymatic techniques for the synthesis of complicated compounds has lately increased dramatically in the area of organic chemistry. Biocatalytic technologies and modern synthetic methods are utilized synergistically in a multi-step approach to a target molecule under this paradigm. Chemoenzymatic techniques are promising for simplifying access to essential bioactive compounds because of the remarkable regio- and stereoselectivity of enzymatic transformations and the reaction diversity of modern organic chemistry. Enzyme kits may include ready-to-use, reproducible biocatalysts. Its use opens up new avenues for the synthesis of active therapeutic compounds and aids in drug development by synthesizing active components to construct scaffolds in a targeted and preparative manner. This study summarizes current breakthroughs as well as notable instances of biocatalytic and chemoenzymatic synthesis. To assist organic chemists in the use of enzymes for synthetic applications, it also provides some basic guidelines for selecting the most appropriate enzyme for a targeted reaction while keeping aspects like cofactor requirement, solvent tolerance, use of whole cell or isolated enzymes, and commercial availability in mind.
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Affiliation(s)
- Swati Verma
- Department of Pharmacy, ITS College of Pharmacy, Muradnagar, Ghaziabad, India
- Department of Pharmacy, Banasthali Vidyapith, Banasthali, 304022, Rajasthan, India
| | - Sarvesh Paliwal
- Department of Pharmacy, Banasthali Vidyapith, Banasthali, 304022, Rajasthan, India
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19
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Wang S, Jiang W, Jin X, Qi Q, Liang Q. Genetically encoded ATP and NAD(P)H biosensors: potential tools in metabolic engineering. Crit Rev Biotechnol 2023; 43:1211-1225. [PMID: 36130803 DOI: 10.1080/07388551.2022.2103394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 05/08/2022] [Indexed: 11/03/2022]
Abstract
To date, many metabolic engineering tools and strategies have been developed, including tools for cofactor engineering, which is a common strategy for bioproduct synthesis. Cofactor engineering is used for the regulation of pyridine nucleotides, including NADH/NAD+ and NADPH/NADP+, and adenosine triphosphate/adenosine diphosphate (ATP/ADP), which is crucial for maintaining redox and energy balance. However, the intracellular levels of NADH/NAD+, NADPH/NADP+, and ATP/ADP cannot be monitored in real time using traditional methods. Recently, many biosensors for detecting, monitoring, and regulating the intracellular levels of NADH/NAD+, NADPH/NADP+, and ATP/ADP have been developed. Although cofactor biosensors have been mainly developed for use in mammalian cells, the potential application of cofactor biosensors in metabolic engineering in bacterial and yeast cells has received recent attention. Coupling cofactor biosensors with genetic circuits is a promising strategy in metabolic engineering for optimizing the production of biochemicals. In this review, we focus on the development of biosensors for NADH/NAD+, NADPH/NADP+, and ATP/ADP and the potential application of these biosensors in metabolic engineering. We also provide critical perspectives, identify current research challenges, and provide guidance for future research in this promising field.
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Affiliation(s)
- Sumeng Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Wei Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xin Jin
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Quanfeng Liang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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20
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Cai M, Liu Z, Zhao Z, Wu H, Xu M, Rao Z. Microbial production of L-methionine and its precursors using systems metabolic engineering. Biotechnol Adv 2023; 69:108260. [PMID: 37739275 DOI: 10.1016/j.biotechadv.2023.108260] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/11/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023]
Abstract
L-methionine is an essential amino acid with versatile applications in food, feed, cosmetics and pharmaceuticals. At present, the production of L-methionine mainly relies on chemical synthesis, which conflicts with the concern over serious environmental problems and sustainable development goals. In recent years, microbial production of natural products has been amply rewarded with the emergence and rapid development of system metabolic engineering. However, efficient L-methionine production by microbial fermentation remains a great challenge due to its complicated biosynthetic pathway and strict regulatory mechanism. Additionally, the engineered production of L-methionine precursors, L-homoserine, O-succinyl-L-homoserine (OSH) and O-acetyl-L-homoserine (OAH), has also received widespread attention because they can be catalyzed to L-methionine via a high-efficiently enzymatic reaction in vitro, which is also a promising alternative to chemical route. This review provides a comprehensive overview on the recent advances in the microbial production of L-methionine and its precursors, highlighting the challenges and potential solutions for developing L-methionine microbial cell factories from the perspective of systems metabolic engineering, aiming to offer guidance for future engineering.
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Affiliation(s)
- Mengmeng Cai
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Zhifei Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Zhenqiang Zhao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Hongxuan Wu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Meijuan Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China
| | - Zhiming Rao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing 214200, China.
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21
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Liu Y, Chen L, Liu P, Yuan Q, Ma C, Wang W, Zhang C, Ma H, Zeng A. Design, Evaluation, and Implementation of Synthetic Isopentyldiol Pathways in Escherichia coli. ACS Synth Biol 2023; 12:3381-3392. [PMID: 37870756 DOI: 10.1021/acssynbio.3c00394] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
Isopentyldiol (IPDO) is an important raw material in the cosmetic industry. So far, IPDO is exclusively produced through chemical synthesis. Growing interest in natural personal care products has inspired the quest to develop a biobased process. We previously reported a biosynthetic route that produces IPDO via extending the leucine catabolism (route A), the efficiency of which, however, is not satisfactory. To address this issue, we computationally designed a novel non-natural IPDO synthesis pathway (route B) using RetroPath RL, the state-of-the-art tool for bioretrosynthesis based on artificial intelligence methods. We compared this new pathway with route A and two other intuitively designed routes for IPDO biosynthesis from various perspectives. Route B, which exhibits the highest thermodynamic driving force, least non-native reaction steps, and lowest energy requirements, appeared to hold the greatest potential for IPDO production. All three newly designed routes were then implemented in the Escherichia coli BL21(DE3) strain. Results show that the computationally designed route B can produce 2.2 mg/L IPDO from glucose but no IPDO production from routes C and D. These results highlight the importance and usefulness of in silico design and comprehensive evaluation of the potential efficiencies of candidate pathways in constructing novel non-natural pathways for the production of biochemicals.
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Affiliation(s)
- Yongfei Liu
- Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, Hangzhou, Zhejiang 310024, China
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Denickestr. 15, Hamburg 21073, Germany
| | - Lin Chen
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Denickestr. 15, Hamburg 21073, Germany
| | - Pi Liu
- Biodesign Center, Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Qianqian Yuan
- Biodesign Center, Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Chengwei Ma
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Denickestr. 15, Hamburg 21073, Germany
| | - Wei Wang
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Denickestr. 15, Hamburg 21073, Germany
| | - Chijian Zhang
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Denickestr. 15, Hamburg 21073, Germany
- Hua An Tang Biotech Group Co., Ltd, Guangzhou 511434, China
| | - Hongwu Ma
- Biodesign Center, Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - AnPing Zeng
- Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, Hangzhou, Zhejiang 310024, China
- Institute of Bioprocess and Biosystems Engineering, Hamburg University of Technology, Denickestr. 15, Hamburg 21073, Germany
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22
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Kim J, Lee TS. Enhancing isoprenol production by systematically tuning metabolic pathways using CRISPR interference in E. coli. Front Bioeng Biotechnol 2023; 11:1296132. [PMID: 38026852 PMCID: PMC10659101 DOI: 10.3389/fbioe.2023.1296132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Regulation of metabolic gene expression is crucial for maximizing bioproduction titers. Recent engineering tools including CRISPR/Cas9, CRISPR interference (CRISPRi), and CRISPR activation (CRISPRa) have enabled effective knock-out, knock-down, and overexpression of endogenous pathway genes, respectively, for advanced strain engineering. CRISPRi in particular has emerged as a powerful tool for gene repression through the use of a deactivated Cas9 (dCas9) protein and target guide RNA (gRNA). By constructing gRNA arrays, CRISPRi has the capacity for multiplexed gene downregulation across multiple orthogonal pathways for enhanced bioproduction titers. In this study, we harnessed CRISPRi to downregulate 32 essential and non-essential genes in E. coli strains heterologously expressing either the original mevalonate pathway or isopentenyl diphosphate (IPP) bypass pathway for isoprenol biosynthesis. Isoprenol remains a candidate bioproduct both as a drop-in blend additive and as a precursor for the high-performance sustainable aviation fuel, 1,4-dimethylcyclooctane (DMCO). Of the 32 gRNAs targeting genes associated with isoprenol biosynthesis, a subset was found to vastly improve product titers. Construction of a multiplexed gRNA library based on single guide RNA (sgRNA) performance enabled simultaneous gene repression, yielding a 3 to 4.5-fold increase in isoprenol titer (1.82 ± 0.19 g/L) on M9-MOPS minimal medium. We then scaled the best performing CRISPRi strain to 2-L fed-batch cultivation and demonstrated translatable titer improvements, ultimately obtaining 12.4 ± 1.3 g/L isoprenol. Our strategy further establishes CRISPRi as a powerful tool for tuning metabolic flux in production hosts and that titer improvements are readily scalable with potential for applications in industrial bioproduction.
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Affiliation(s)
- Jinho Kim
- Joint BioEnergy Institute, Emeryville, CA, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Taek Soon Lee
- Joint BioEnergy Institute, Emeryville, CA, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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23
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Liu J, Ou Y, Xu JZ, Rao ZM, Zhang WG. L-lysine production by systems metabolic engineering of an NADPH auto-regulated Corynebacterium glutamicum. BIORESOURCE TECHNOLOGY 2023; 387:129701. [PMID: 37604260 DOI: 10.1016/j.biortech.2023.129701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 08/23/2023]
Abstract
Here, the systems metabolic engineering of L-lysine-overproducing Corynebacterium glutamicum is described to create a highly efficient microorganism producer. The key chromosomal mutations associated with L-lysine synthesis were identified based on whole-genome sequencing. The carbon flux was subsequently redirected into the L-lysine synthesis pathway and increased the availability of energy and product transport systems required for L-lysine synthesis. In addition, a promoter library sensitive to intracellular L-lysine concentration was constructed and applied to regulate the NADPH pool dynamically. In the fed-batch fermentation experiment, the L-lysine titer of the final engineered strain was 223.4 ± 6.5 g/L. This study is the first to improve L-lysine production by enhancing ATP supply and NADPH self-regulation to improve the intracellular environment.
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Affiliation(s)
- Jie Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800(#) Lihu Road, WuXi 214122, People's Republic of China
| | - Ying Ou
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800(#) Lihu Road, WuXi 214122, People's Republic of China
| | - Jian-Zhong Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800(#) Lihu Road, WuXi 214122, People's Republic of China
| | - Zhi-Ming Rao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800(#) Lihu Road, WuXi 214122, People's Republic of China; National Engineering Laboratory for Cereal Fermentation Technology, School of Biotechnology, Jiangnan University, 1800(#) Lihu Road, WuXi 214122, People's Republic of China
| | - Wei-Guo Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800(#) Lihu Road, WuXi 214122, People's Republic of China.
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24
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Orsi E, Nikel PI, Nielsen LK, Donati S. Synergistic investigation of natural and synthetic C1-trophic microorganisms to foster a circular carbon economy. Nat Commun 2023; 14:6673. [PMID: 37865689 PMCID: PMC10590403 DOI: 10.1038/s41467-023-42166-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/02/2023] [Indexed: 10/23/2023] Open
Abstract
A true circular carbon economy must upgrade waste greenhouse gases. C1-based biomanufacturing is an attractive solution, in which one carbon (C1) molecules (e.g. CO2, formate, methanol, etc.) are converted by microbial cell factories into value-added goods (i.e. food, feed, and chemicals). To render C1-based biomanufacturing cost-competitive, we must adapt microbial metabolism to perform chemical conversions at high rates and yields. To this end, the biotechnology community has undertaken two (seemingly opposing) paths: optimizing natural C1-trophic microorganisms versus engineering synthetic C1-assimilation de novo in model microorganisms. Here, we pose how these approaches can instead create synergies for strengthening the competitiveness of C1-based biomanufacturing as a whole.
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Affiliation(s)
- Enrico Orsi
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Pablo Ivan Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Lars Keld Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072, Brisbane, QLD, Australia
| | - Stefano Donati
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark.
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25
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Hao Y, Pan X, Li G, You J, Zhang H, Yan S, Xu M, Rao Z. Construction of a plasmid-free L-leucine overproducing Escherichia coli strain through reprogramming of the metabolic flux. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:145. [PMID: 37775757 PMCID: PMC10541719 DOI: 10.1186/s13068-023-02397-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 09/18/2023] [Indexed: 10/01/2023]
Abstract
BACKGROUND L-Leucine is a high-value amino acid with promising applications in the medicine and feed industries. However, the complex metabolic network and intracellular redox imbalance in fermentative microbes limit their efficient biosynthesis of L-leucine. RESULTS In this study, we applied rational metabolic engineering and a dynamic regulation strategy to construct a plasmid-free, non-auxotrophic Escherichia coli strain that overproduces L-leucine. First, the L-leucine biosynthesis pathway was strengthened through multi-step rational metabolic engineering. Then, a cooperative cofactor utilization strategy was designed to ensure redox balance for L-leucine production. Finally, to further improve the L-leucine yield, a toggle switch for dynamically controlling sucAB expression was applied to accurately regulate the tricarboxylic acid cycle and the carbon flux toward L-leucine biosynthesis. Strain LEU27 produced up to 55 g/L of L-leucine, with a yield of 0.23 g/g glucose. CONCLUSIONS The combination of strategies can be applied to the development of microbial platforms that produce L-leucine and its derivatives.
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Affiliation(s)
- Yanan Hao
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, China
| | - Xuewei Pan
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, China
| | - Guomin Li
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, China
| | - Jiajia You
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, China
| | - Hengwei Zhang
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, China
| | - Sihan Yan
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, China
| | - Meijuan Xu
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, China
| | - Zhiming Rao
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
- Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, China.
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26
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Lv X, Jin K, Yi Y, Song L, Xiu X, Liu Y, Li J, Du G, Chen J, Liu L. Analysis of acid-tolerance mechanism based on membrane microdomains in Saccharomyces cerevisiae. Microb Cell Fact 2023; 22:180. [PMID: 37700284 PMCID: PMC10498586 DOI: 10.1186/s12934-023-02195-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 09/05/2023] [Indexed: 09/14/2023] Open
Abstract
BACKGROUND Saccharomyces cerevisiae has been used in the biosynthesis of acid products such as organic acids owing to its acid tolerance. Improving the acid tolerance of S. cerevisiae is beneficial for expanding its application range. Our previous study isolated the TAMC strain that was tolerant to a pH 2.3 through adaptive laboratory evolution; however, its mechanism underlying tolerance to low pH environment remains unclear. RESULTS In this study, through visual observation and order analysis of plasma membrane and membrane microdomains, we revealed that the membrane microdomains of TAMC strain play an indispensable role in acid tolerance. Transcriptomic analysis showed an increase in the expression of genes related to key components of membrane microdomains in TAMC strain. Furthermore, an obvious reduction was observed in the acid tolerance of the strain with sterol C-24 methyltransferase encoding gene ERG6 knockout for inhibiting membrane microdomain formation. Finally, colocalization analysis of H+-ATPase PMA1 and plasma membrane protein PMP1 showed that disruption of membrane microdomains could inhibit the formation of the H+-ATPase complex. CONCLUSIONS Membrane microdomains could provide a platform for forming H+-ATPase complexes to facilitate intracellular H+ homeostasis, and thereby improve cell acid resistance. This study proposed a novel acid tolerance mechanism, providing a new direction for the rational engineering of acid-tolerant strains.
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Affiliation(s)
- 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
- Yixing Institute of Food Biotechnology Co., Ltd, Yixing, 214200, China
| | - Ke Jin
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- Yixing Institute of Food Biotechnology Co., Ltd, Yixing, 214200, China
| | - Yu Yi
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Lingang Song
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Xiang Xiu
- 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
| | - 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
| | - Jian 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
- Yixing Institute of Food Biotechnology Co., Ltd, Yixing, 214200, 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.
- Yixing Institute of Food Biotechnology Co., Ltd, Yixing, 214200, China.
- Food Laboratory of Zhongyuan, Jiangnan University, Wuxi, 214122, China.
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27
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Baumann PT, Dal Molin M, Aring H, Krumbach K, Müller MF, Vroling B, van Summeren-Wesenhagen PV, Noack S, Marienhagen J. Beyond rational-biosensor-guided isolation of 100 independently evolved bacterial strain variants and comparative analysis of their genomes. BMC Biol 2023; 21:183. [PMID: 37667306 PMCID: PMC10478468 DOI: 10.1186/s12915-023-01688-x] [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: 02/13/2023] [Accepted: 08/23/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND In contrast to modern rational metabolic engineering, classical strain development strongly relies on random mutagenesis and screening for the desired production phenotype. Nowadays, with the availability of biosensor-based FACS screening strategies, these random approaches are coming back into fashion. In this study, we employ this technology in combination with comparative genome analyses to identify novel mutations contributing to product formation in the genome of a Corynebacterium glutamicum L-histidine producer. Since all known genetic targets contributing to L-histidine production have been already rationally engineered in this strain, identification of novel beneficial mutations can be regarded as challenging, as they might not be intuitively linkable to L-histidine biosynthesis. RESULTS In order to identify 100 improved strain variants that had each arisen independently, we performed > 600 chemical mutagenesis experiments, > 200 biosensor-based FACS screenings, isolated > 50,000 variants with increased fluorescence, and characterized > 4500 variants with regard to biomass formation and L-histidine production. Based on comparative genome analyses of these 100 variants accumulating 10-80% more L-histidine, we discovered several beneficial mutations. Combination of selected genetic modifications allowed for the construction of a strain variant characterized by a doubled L-histidine titer (29 mM) and product yield (0.13 C-mol C-mol-1) in comparison to the starting variant. CONCLUSIONS This study may serve as a blueprint for the identification of novel beneficial mutations in microbial producers in a more systematic manner. This way, also previously unexplored genes or genes with previously unknown contribution to the respective production phenotype can be identified. We believe that this technology has a great potential to push industrial production strains towards maximum performance.
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Affiliation(s)
- Philipp T Baumann
- Institute of Bio- and Geosciences, Forschungszentrum Jülich, IBG-1: Biotechnology, 52425, Jülich, Germany
| | - Michael Dal Molin
- Institute of Bio- and Geosciences, Forschungszentrum Jülich, IBG-1: Biotechnology, 52425, Jülich, Germany
- Department I of Internal Medicine, University of Cologne, 50937, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931, Cologne, Germany
| | - Hannah Aring
- Institute of Bio- and Geosciences, Forschungszentrum Jülich, IBG-1: Biotechnology, 52425, Jülich, Germany
| | - Karin Krumbach
- Institute of Bio- and Geosciences, Forschungszentrum Jülich, IBG-1: Biotechnology, 52425, Jülich, Germany
| | - Moritz-Fabian Müller
- Institute of Bio- and Geosciences, Forschungszentrum Jülich, IBG-1: Biotechnology, 52425, Jülich, Germany
| | - Bas Vroling
- Bioprodict GmbH, Nieuwe Marktstraat 54E, 6511AA, Nijmegen, The Netherlands
| | | | - Stephan Noack
- Institute of Bio- and Geosciences, Forschungszentrum Jülich, IBG-1: Biotechnology, 52425, Jülich, Germany
| | - Jan Marienhagen
- Institute of Bio- and Geosciences, Forschungszentrum Jülich, IBG-1: Biotechnology, 52425, Jülich, Germany.
- Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, 52074, Aachen, Germany.
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28
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Collas F, Dronsella BB, Kubis A, Schann K, Binder S, Arto N, Claassens NJ, Kensy F, Orsi E. Engineering the biological conversion of formate into crotonate in Cupriavidus necator. Metab Eng 2023; 79:49-65. [PMID: 37414134 DOI: 10.1016/j.ymben.2023.06.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/08/2023] [Accepted: 06/29/2023] [Indexed: 07/08/2023]
Abstract
To advance the sustainability of the biobased economy, our society needs to develop novel bioprocesses based on truly renewable resources. The C1-molecule formate is increasingly proposed as carbon and energy source for microbial fermentations, as it can be efficiently generated electrochemically from CO2 and renewable energy. Yet, its biotechnological conversion into value-added compounds has been limited to a handful of examples. In this work, we engineered the natural formatotrophic bacterium C. necator as cell factory to enable biological conversion of formate into crotonate, a platform short-chain unsaturated carboxylic acid of biotechnological relevance. First, we developed a small-scale (150-mL working volume) cultivation setup for growing C. necator in minimal medium using formate as only carbon and energy source. By using a fed-batch strategy with automatic feeding of formic acid, we could increase final biomass concentrations 15-fold compared to batch cultivations in flasks. Then, we engineered a heterologous crotonate pathway in the bacterium via a modular approach, where each pathway section was assessed using multiple candidates. The best performing modules included a malonyl-CoA bypass for increasing the thermodynamic drive towards the intermediate acetoacetyl-CoA and subsequent conversion to crotonyl-CoA through partial reverse β-oxidation. This pathway architecture was then tested for formate-based biosynthesis in our fed-batch setup, resulting in a two-fold higher titer, three-fold higher productivity, and five-fold higher yield compared to the strain not harboring the bypass. Eventually, we reached a maximum product titer of 148.0 ± 6.8 mg/L. Altogether, this work consists in a proof-of-principle integrating bioprocess and metabolic engineering approaches for the biological upgrading of formate into a value-added platform chemical.
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Affiliation(s)
| | - Beau B Dronsella
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | - Karin Schann
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | | | - Nico J Claassens
- Laboratory of Microbiology, Wageningen University, Wageningen, the Netherlands
| | | | - Enrico Orsi
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
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29
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Bezold F, Scheffer J, Wendering P, Razaghi-Moghadam Z, Trauth J, Pook B, Nußhär H, Hasenjäger S, Nikoloski Z, Essen LO, Taxis C. Optogenetic control of Cdc48 for dynamic metabolic engineering in yeast. Metab Eng 2023; 79:97-107. [PMID: 37422133 DOI: 10.1016/j.ymben.2023.06.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 06/25/2023] [Accepted: 06/26/2023] [Indexed: 07/10/2023]
Abstract
Dynamic metabolic engineering is a strategy to switch key metabolic pathways in microbial cell factories from biomass generation to accumulation of target products. Here, we demonstrate that optogenetic intervention in the cell cycle of budding yeast can be used to increase production of valuable chemicals, such as the terpenoid β-carotene or the nucleoside analog cordycepin. We achieved optogenetic cell-cycle arrest in the G2/M phase by controlling activity of the ubiquitin-proteasome system hub Cdc48. To analyze the metabolic capacities in the cell cycle arrested yeast strain, we studied their proteomes by timsTOF mass spectrometry. This revealed widespread, but highly distinct abundance changes of metabolic key enzymes. Integration of the proteomics data in protein-constrained metabolic models demonstrated modulation of fluxes directly associated with terpenoid production as well as metabolic subsystems involved in protein biosynthesis, cell wall synthesis, and cofactor biosynthesis. These results demonstrate that optogenetically triggered cell cycle intervention is an option to increase the yields of compounds synthesized in a cellular factory by reallocation of metabolic resources.
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Affiliation(s)
- Filipp Bezold
- Unit for Structural Biochemistry, Department of Chemistry, Philipps-University Marburg, 35032, Marburg, Germany
| | - Johannes Scheffer
- Unit for Structural Biochemistry, Department of Chemistry, Philipps-University Marburg, 35032, Marburg, Germany
| | - Philipp Wendering
- Systems Biology and Mathematical Modeling, Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany; Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Zahra Razaghi-Moghadam
- Systems Biology and Mathematical Modeling, Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany; Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Jonathan Trauth
- Unit for Structural Biochemistry, Department of Chemistry, Philipps-University Marburg, 35032, Marburg, Germany
| | - Bastian Pook
- Unit for Structural Biochemistry, Department of Chemistry, Philipps-University Marburg, 35032, Marburg, Germany
| | - Hagen Nußhär
- Unit for Structural Biochemistry, Department of Chemistry, Philipps-University Marburg, 35032, Marburg, Germany
| | - Sophia Hasenjäger
- Unit for Structural Biochemistry, Department of Chemistry, Philipps-University Marburg, 35032, Marburg, Germany
| | - Zoran Nikoloski
- Systems Biology and Mathematical Modeling, Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany; Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Lars-Oliver Essen
- Unit for Structural Biochemistry, Department of Chemistry, Philipps-University Marburg, 35032, Marburg, Germany.
| | - Christof Taxis
- Department of Biology/Genetics, Philipps-University Marburg, 35032, Marburg, Germany; School of Science and Technology, University Siegen, 57076, Siegen, Germany.
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30
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Bragdon MDJ, Patel N, Chuang J, Levien E, Bashor CJ, Khalil AS. Cooperative assembly confers regulatory specificity and long-term genetic circuit stability. Cell 2023; 186:3810-3825.e18. [PMID: 37552983 PMCID: PMC10528910 DOI: 10.1016/j.cell.2023.07.012] [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: 05/16/2022] [Revised: 05/17/2023] [Accepted: 07/10/2023] [Indexed: 08/10/2023]
Abstract
A ubiquitous feature of eukaryotic transcriptional regulation is cooperative self-assembly between transcription factors (TFs) and DNA cis-regulatory motifs. It is thought that this strategy enables specific regulatory connections to be formed in gene networks between otherwise weakly interacting, low-specificity molecular components. Here, using synthetic gene circuits constructed in yeast, we find that high regulatory specificity can emerge from cooperative, multivalent interactions among artificial zinc-finger-based TFs. We show that circuits "wired" using the strategy of cooperative TF assembly are effectively insulated from aberrant misregulation of the host cell genome. As we demonstrate in experiments and mathematical models, this mechanism is sufficient to rescue circuit-driven fitness defects, resulting in genetic and functional stability of circuits in long-term continuous culture. Our naturally inspired approach offers a simple, generalizable means for building high-fidelity, evolutionarily robust gene circuits that can be scaled to a wide range of host organisms and applications.
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Affiliation(s)
- Meghan D J Bragdon
- Biological Design Center, Boston University, Boston, MA 02215, USA; Program in Molecular Biology, Cell Biology and Biochemistry, Boston University, Boston, MA 02215, USA
| | - Nikit Patel
- Biological Design Center, Boston University, Boston, MA 02215, USA; Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - James Chuang
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Ethan Levien
- Department of Mathematics, Dartmouth College, Hanover, NH 03755, USA
| | - Caleb J Bashor
- Department of Bioengineering, Rice University, Houston, TX 77030, USA; Department of Biosciences, Rice University, Houston, TX 77030, USA
| | - Ahmad S Khalil
- Biological Design Center, Boston University, Boston, MA 02215, USA; Program in Molecular Biology, Cell Biology and Biochemistry, Boston University, Boston, MA 02215, USA; Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.
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31
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Aspacio D, Zhang Y, Cui Y, King E, Black WB, Perea S, Luu E, Siegel JB, Li H. Shifting Redox Reaction Equilibria on Demand Using an Orthogonal Redox Cofactor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.29.555398. [PMID: 37693387 PMCID: PMC10491207 DOI: 10.1101/2023.08.29.555398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Natural metabolism relies on chemical compartmentalization of two redox cofactors, NAD+ and NADP+, to orchestrate life-essential redox reaction directions. However, in whole cells the reliance on these canonical cofactors limits flexible control of redox reaction direction as these reactions are permanently tied to catabolism or anabolism. In cell-free systems, NADP+ is too expensive in large scale. We have previously reported the use of nicotinamide mononucleotide, (NMN+) as a low-cost, noncanonical redox cofactor capable of specific electron delivery to diverse chemistries. Here, we present Nox Ortho, an NMNH-specific water-forming oxidase, that completes the toolkit to modulate NMNH/NMN+ ratio. This work uncovers an enzyme design principle that succeeds in parallel engineering of six butanediol dehydrogenases as NMN(H)-orthogonal biocatalysts consistently with a 103 - 106 -fold cofactor specificity switch from NAD(P)+ to NMN+. We combine these to produce chiral-pure 2,3-butanediol (Bdo) isomers without interference from NAD(H) or NADP(H) in vitro and in E. coli cells. We establish that NMN(H) can be held at a distinct redox ratio on demand, decoupled from both NAD(H) and NADP(H) redox ratios in vitro and in vivo.
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Affiliation(s)
- Derek Aspacio
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Yulai Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Youtian Cui
- Genome Center, University of California, Davis, Davis, California 95616, United States
| | - Edward King
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California 92697-3900, United States
| | - William B. Black
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Sean Perea
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Emma Luu
- Genome Center, University of California, Davis, Davis, California 95616, United States
| | - Justin B. Siegel
- Genome Center, University of California, Davis, Davis, California 95616, United States
- Department of Chemistry, University of California, Davis, Davis, California 95616, United States
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, California 95616, United States
| | - Han Li
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697-3900, United States
- Department of Biomedical Engineering, University of California, Irvine, Irvine, California 92697-3900, United States
- Department of Biological Chemistry, University of California, Irvine, Irvine, California 92697-3900, United States
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32
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Hassani L, Moosavi MR, Setoodeh P, Zare H. FastKnock: An efficient next-generation approach to identify all knockout strategies for strain optimization. RESEARCH SQUARE 2023:rs.3.rs-3126389. [PMID: 37503204 PMCID: PMC10371132 DOI: 10.21203/rs.3.rs-3126389/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Overproduction of desired native or nonnative biochemical(s) in (micro)organisms can be achieved through metabolic engineering. Appropriate rewiring of cell metabolism is performed making rational changes such as insertion, up-/down-regulation and knockout of genes and consequently metabolic reactions. Finding appropriate targets (including proper sets of reactions to be knocked out) for metabolic engineering to design optimal production strains has been the goal of a number of computational algorithms. We developed FastKnock, an efficient next-generation algorithm for identifying all possible knockout strategies for the growth-coupled overproduction of biochemical(s) of interest. We achieve this by developing a special depth-first traversal algorithm that allows us to prune the search space significantly. This leads to a drastic reduction in execution time. We evaluate the performance of the FastKnock algorithm using three Escherichia coli genome-scale metabolic models in different conditions (minimal and rich mediums) for the overproduction of a number of desired metabolites. FastKnock efficiently prunes the search space to less than 0.2% for quadruple and 0.02% for quintuple-reaction knockouts. Compared to the classic approaches such as OptKnock and the state-of-the-art techniques such as MCSEnumerator methods, FastKnock found many more useful and important practical solutions. The availability of all the solutions provides the opportunity to further characterize and select the most appropriate intervention strategy based on any desired evaluation index. Our implementation of the FastKnock method in Python is publicly available at https://github.com/leilahsn/FastKnock.
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Affiliation(s)
| | | | | | - Habil Zare
- University of Texas Health Science Center
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33
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Li Z, Liu Q, Sun J, Sun J, Li M, Zhang Y, Deng A, Liu S, Wen T. Multivariate modular metabolic engineering for enhanced L-methionine biosynthesis in Escherichia coli. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:101. [PMID: 37312226 DOI: 10.1186/s13068-023-02347-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/23/2023] [Indexed: 06/15/2023]
Abstract
BACKGROUND L-Methionine is the only bulk amino acid that has not been industrially produced by the fermentation method. Due to highly complex and strictly regulated biosynthesis, the development of microbial strains for high-level L-methionine production has remained challenging in recent years. RESULTS By strengthening the L-methionine terminal synthetic module via site-directed mutation of L-homoserine O-succinyltransferase (MetA) and overexpression of metAfbr, metC, and yjeH, L-methionine production was increased to 1.93 g/L in shake flask fermentation. Deletion of the pykA and pykF genes further improved L-methionine production to 2.51 g/L in shake flask fermentation. Computer simulation and auxotrophic experiments verified that during the synthesis of L-methionine, equimolar amounts of L-isoleucine were accumulated via the elimination reaction of cystathionine γ-synthetase MetB due to the insufficient supply of L-cysteine. To increase the supply of L-cysteine, the L-cysteine synthetic module was strengthened by overexpression of cysEfbr, serAfbr, and cysDN, which further increased the production of L-methionine by 52.9% and significantly reduced the accumulation of the byproduct L-isoleucine by 29.1%. After optimizing the addition of ammonium thiosulfate, the final metabolically engineered strain MET17 produced 21.28 g/L L-methionine in 64 h with glucose as the carbon source in a 5 L fermenter, representing the highest L-methionine titer reported to date. CONCLUSIONS In this study, a high-efficiency strain for L-methionine production was derived from wild-type Escherichia coli W3110 by rational metabolic engineering strategies, providing an efficient platform for the industrial production of L-methionine.
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Affiliation(s)
- Zhongcai Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qian Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jiahui Sun
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, Hebei University, Baoding, 071002, China
| | - Jianjian Sun
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Mingjie Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yun Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Aihua Deng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shuwen Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Tingyi Wen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China.
- China Innovation Academy for Green Manufacture, Chinese Academy of Sciences, Beijing, 100049, China.
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Sosa-Carrillo S, Galez H, Napolitano S, Bertaux F, Batt G. Maximizing protein production by keeping cells at optimal secretory stress levels using real-time control approaches. Nat Commun 2023; 14:3028. [PMID: 37231013 DOI: 10.1038/s41467-023-38807-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 05/17/2023] [Indexed: 05/27/2023] Open
Abstract
Optimizing the production of recombinant proteins is a problem of major industrial and pharmaceutical importance. Secretion of the protein by the host cell considerably simplifies downstream purification processes. However, for many proteins, this is also the limiting production step. Current solutions involve extensive engineering of the chassis cell to facilitate protein trafficking and limit protein degradation triggered by excessive secretion-associated stress. Here, we propose instead a regulation-based strategy in which induction is dynamically adjusted to an optimal strength based on the current stress level of the cells. Using a small collection of hard-to-secrete proteins, a bioreactor-based platform with automated cytometry measurements, and a systematic assay to quantify secreted protein levels, we demonstrate that the secretion sweet spot is indicated by the appearance of a subpopulation of cells that accumulate high amounts of proteins, decrease growth, and face significant stress, that is, experience a secretion burnout. In these cells, adaptations capabilities are overwhelmed by a too strong production. Using these notions, we show for a single-chain antibody variable fragment that secretion levels can be improved by 70% by dynamically keeping the cell population at optimal stress levels using real-time closed-loop control.
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Affiliation(s)
| | - Henri Galez
- Institut Pasteur, Inria, Université Paris Cité, 75015, Paris, France
| | - Sara Napolitano
- Institut Pasteur, Inria, Université Paris Cité, 75015, Paris, France
| | - François Bertaux
- Institut Pasteur, Inria, Université Paris Cité, 75015, Paris, France
- Lesaffre International, 101 rue de Menin, Marcq-en-Baroeul, France
| | - Gregory Batt
- Institut Pasteur, Inria, Université Paris Cité, 75015, Paris, France.
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Laval F, Coppin G, Twizere JC, Vidal M. Homo cerevisiae-Leveraging Yeast for Investigating Protein-Protein Interactions and Their Role in Human Disease. Int J Mol Sci 2023; 24:9179. [PMID: 37298131 PMCID: PMC10252790 DOI: 10.3390/ijms24119179] [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: 05/01/2023] [Revised: 05/20/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023] Open
Abstract
Understanding how genetic variation affects phenotypes represents a major challenge, particularly in the context of human disease. Although numerous disease-associated genes have been identified, the clinical significance of most human variants remains unknown. Despite unparalleled advances in genomics, functional assays often lack sufficient throughput, hindering efficient variant functionalization. There is a critical need for the development of more potent, high-throughput methods for characterizing human genetic variants. Here, we review how yeast helps tackle this challenge, both as a valuable model organism and as an experimental tool for investigating the molecular basis of phenotypic perturbation upon genetic variation. In systems biology, yeast has played a pivotal role as a highly scalable platform which has allowed us to gain extensive genetic and molecular knowledge, including the construction of comprehensive interactome maps at the proteome scale for various organisms. By leveraging interactome networks, one can view biology from a systems perspective, unravel the molecular mechanisms underlying genetic diseases, and identify therapeutic targets. The use of yeast to assess the molecular impacts of genetic variants, including those associated with viral interactions, cancer, and rare and complex diseases, has the potential to bridge the gap between genotype and phenotype, opening the door for precision medicine approaches and therapeutic development.
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Affiliation(s)
- Florent Laval
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, USA; (F.L.); (G.C.)
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- TERRA Teaching and Research Centre, University of Liège, 5030 Gembloux, Belgium
- Laboratory of Viral Interactomes, GIGA Institute, University of Liège, 4000 Liège, Belgium
| | - Georges Coppin
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, USA; (F.L.); (G.C.)
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Laboratory of Viral Interactomes, GIGA Institute, University of Liège, 4000 Liège, Belgium
| | - Jean-Claude Twizere
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, USA; (F.L.); (G.C.)
- TERRA Teaching and Research Centre, University of Liège, 5030 Gembloux, Belgium
- Laboratory of Viral Interactomes, GIGA Institute, University of Liège, 4000 Liège, Belgium
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, USA; (F.L.); (G.C.)
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
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36
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Liu J, Zhang H, Xu Y, Meng H, Zeng AP. Turn air-captured CO 2 with methanol into amino acid and pyruvate in an ATP/NAD(P)H-free chemoenzymatic system. Nat Commun 2023; 14:2772. [PMID: 37188719 DOI: 10.1038/s41467-023-38490-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 04/27/2023] [Indexed: 05/17/2023] Open
Abstract
The use of gaseous and air-captured CO2 for technical biosynthesis is highly desired, but elusive so far due to several obstacles including high energy (ATP, NADPH) demand, low thermodynamic driving force and limited biosynthesis rate. Here, we present an ATP and NAD(P)H-free chemoenzymatic system for amino acid and pyruvate biosynthesis by coupling methanol with CO2. It relies on a re-engineered glycine cleavage system with the NAD(P)H-dependent L protein replaced by biocompatible chemical reduction of protein H with dithiothreitol. The latter provides a higher thermodynamic driving force, determines the reaction direction, and avoids protein polymerization of the rate-limiting enzyme carboxylase. Engineering of H protein to effectively release the lipoamide arm from a protected state further enhanced the system performance, achieving the synthesis of glycine, serine and pyruvate at g/L level from methanol and air-captured CO2. This work opens up the door for biosynthesis of amino acids and derived products from air.
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Affiliation(s)
- Jianming Liu
- Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, 600 Dunyu Road, Xihu District, Hangzhou, 310024, Zhejiang Province, China
| | - Han Zhang
- Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, 600 Dunyu Road, Xihu District, Hangzhou, 310024, Zhejiang Province, China
| | - Yingying Xu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China
| | - Hao Meng
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China
| | - An-Ping Zeng
- Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, 600 Dunyu Road, Xihu District, Hangzhou, 310024, Zhejiang Province, China.
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37
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Tian KK, Qian ZG, Xia XX. Synthetic biology-guided design and biosynthesis of protein polymers for delivery. Adv Drug Deliv Rev 2023; 194:114728. [PMID: 36791475 DOI: 10.1016/j.addr.2023.114728] [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: 07/23/2022] [Revised: 12/28/2022] [Accepted: 02/06/2023] [Indexed: 02/15/2023]
Abstract
Vehicles derived from genetically engineered protein polymers have gained momentum in the field of biomedical engineering due to their unique designability, remarkable biocompatibility and excellent biodegradability. However, the design and production of these protein polymers with on-demand sequences and supramolecular architectures remain underexplored, particularly from a synthetic biology perspective. In this review, we summarize the state-of-the art strategies for constructing the highly repetitive genes encoding the protein polymers, and highlight the advanced approaches for metabolically engineering expression hosts towards high-level biosynthesis of the target protein polymers. Finally, we showcase the typical protein polymers utilized to fabricate delivery vehicles.
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Affiliation(s)
- Kai-Kai Tian
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Zhi-Gang Qian
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Xiao-Xia Xia
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China.
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38
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Luo ZW, Choi KR, Lee SY. Improved terephthalic acid production from p-xylene using metabolically engineered Pseudomonas putida. Metab Eng 2023; 76:75-86. [PMID: 36693471 DOI: 10.1016/j.ymben.2023.01.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/10/2023] [Accepted: 01/20/2023] [Indexed: 01/22/2023]
Abstract
Terephthalic acid (TPA) is an important commodity chemical used as a monomer of polyethylene terephthalate (PET). Since a large quantity of PET is routinely manufactured and consumed worldwide, the development of sustainable biomanufacturing processes for its monomers (i.e. TPA and ethylene glycol) has recently gained much attention. In a previous study, we reported the development of a metabolically engineered Escherichia coli strain producing 6.7 g/L of TPA from p-xylene (pX) with a productivity and molar conversion yield of 0.278 g/L/h and 96.7 mol%, respectively. Here, we report metabolic engineering of Pseudomonas putida KT2440, a microbial chassis particularly suitable for the synthesis of aromatic compounds, for improved biocatalytic conversion of pX to TPA. To develop a plasmid-free, antibiotic-free, and inducer-free biocatalytic process for cost-competitive TPA production, all heterologous genes required for the synthetic pX-to-TPA bioconversion pathway were integrated into the chromosome of P. putida KT2440 by RecET-based markerless recombineering and overexpressed under the control of constitutive promoters. Next, TPA production was enhanced by integrating multiple copies of the heterologous genes to the ribosomal RNA genes through iteration of recombineering-based random integration and subsequent screening of high-performance strains. Finally, fed-batch fermentation process was optimized to further improve the performance of the engineered P. putida strain. As a result, 38.25 ± 0.11 g/L of TPA was produced from pX with a molar conversion yield of 99.6 ± 0.6%, which is equivalent to conversion of 99.3 ± 0.8 g pX to 154.6 ± 0.5 g TPA. This superior pX-to-TPA biotransformation process based on the engineered P. putida strain will pave the way to the commercial biomanufacturing of TPA in an industrial scale.
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Affiliation(s)
- Zi Wei Luo
- 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; BioProcess Engineering Research Center, KAIST, Daejeon, 34141, Republic of Korea
| | - Kyeong Rok Choi
- 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; BioProcess Engineering Research Center, 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; BioProcess Engineering Research Center, KAIST, Daejeon, 34141, Republic of Korea; BioInformatics Research Center, KAIST Institute for the BioCentury, and KAIST Institute for Artificial Intelligence, KAIST, Daejeon, 34141, Republic of Korea.
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Kim GB, Choi SY, Cho IJ, Ahn DH, Lee SY. Metabolic engineering for sustainability and health. Trends Biotechnol 2023; 41:425-451. [PMID: 36635195 DOI: 10.1016/j.tibtech.2022.12.014] [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: 11/09/2022] [Revised: 12/17/2022] [Accepted: 12/21/2022] [Indexed: 01/12/2023]
Abstract
Bio-based production of chemicals and materials has attracted much attention due to the urgent need to establish sustainability and enhance human health. Metabolic engineering (ME) allows purposeful modification of cellular metabolic, regulatory, and signaling networks to achieve enhanced production of desired chemicals and degradation of environmentally harmful chemicals. ME has significantly progressed over the past 30 years through further integration of the strategies of synthetic biology, systems biology, evolutionary engineering, and data science aided by artificial intelligence. Here we review the field of ME from its emergence to the current state-of-the-art, highlighting its contribution to sustainable production of chemicals, health, and the environment through representative examples. Future challenges of ME and perspectives are also discussed.
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Affiliation(s)
- Gi Bae Kim
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - So Young Choi
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - In Jin Cho
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Da-Hee Ahn
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
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40
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Kramer L, Sarkar A, Foderaro T, Markley AL, Lee J, Edstrom H, Sharma S, Gill E, Traylor MJ, Fox JM. Genetically Encoded Detection of Biosynthetic Protease Inhibitors. ACS Synth Biol 2023; 12:83-94. [PMID: 36574400 PMCID: PMC10072156 DOI: 10.1021/acssynbio.2c00384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Proteases are an important class of drug targets that continue to drive inhibitor discovery. These enzymes are prone to resistance mutations, yet their promise for treating viral diseases and other disorders continues to grow. This study develops a general approach for detecting microbially synthesized protease inhibitors and uses it to screen terpenoid pathways for inhibitory compounds. The detection scheme relies on a bacterial two-hybrid (B2H) system that links protease inactivation to the transcription of a swappable reporter gene. This system, which can accomodate multiple biochemical outputs (i.e., luminescence and antibiotic resistance), permitted the facile incorporation of four disease-relevant proteases. A B2H designed to detect the inactivation of the main protease of severe acute respiratory syndrome coronavirus 2 enabled the identification of a terpenoid inhibitor of modest potency. An analysis of multiple pathways that make this terpenoid, however, suggested that its production was necessary but not sufficient to confer a survival advantage in growth-coupled assays. This finding highlights an important challenge associated with the use of genetic selection to search for inhibitors─notably, the influence of pathway toxicity─and underlines the value of including multiple pathways with overlapping product profiles in pathway screens. This study provides a detailed experimental framework for using microbes to screen libraries of biosynthetic pathways for targeted protease inhibitors.
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Affiliation(s)
- Levi Kramer
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, 3415 Colorado Avenue, Boulder, Colorado80303, United States
| | - Ankur Sarkar
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, 3415 Colorado Avenue, Boulder, Colorado80303, United States
| | - Tom Foderaro
- Think Bioscience, Inc., 1945 Colorado Avenue, Boulder, Colorado80309, United States
| | - Andrew L Markley
- Think Bioscience, Inc., 1945 Colorado Avenue, Boulder, Colorado80309, United States
| | - Jessica Lee
- Think Bioscience, Inc., 1945 Colorado Avenue, Boulder, Colorado80309, United States
| | - Hannah Edstrom
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, 3415 Colorado Avenue, Boulder, Colorado80303, United States
| | - Shajesh Sharma
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, 3415 Colorado Avenue, Boulder, Colorado80303, United States
| | - Eden Gill
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, 3415 Colorado Avenue, Boulder, Colorado80303, United States
| | - Matthew J Traylor
- Think Bioscience, Inc., 1945 Colorado Avenue, Boulder, Colorado80309, United States
| | - Jerome M Fox
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, 3415 Colorado Avenue, Boulder, Colorado80303, United States
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41
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Dias MAM, Nitschke M. Bacterial-derived surfactants: an update on general aspects and forthcoming applications. Braz J Microbiol 2023; 54:103-123. [PMID: 36662441 PMCID: PMC9857925 DOI: 10.1007/s42770-023-00905-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 01/10/2023] [Indexed: 01/21/2023] Open
Abstract
The search for sustainable alternatives to the production of chemicals using renewable substrates and natural processes has been widely encouraged. Microbial surfactants or biosurfactants are surface-active compounds synthesized by fungi, yeasts, and bacteria. Due to their great metabolic versatility, bacteria are the most traditional and well-known microbial surfactant producers, being Bacillus and Pseudomonas species their typical representatives. To be successfully applied in industry, surfactants need to maintain stability under the harsh environmental conditions present in manufacturing processes; thus, the prospection of biosurfactants derived from extremophiles is a promising strategy to the discovery of novel and useful molecules. Bacterial surfactants show interesting properties suitable for a range of applications in the oil industry, food, agriculture, pharmaceuticals, cosmetics, bioremediation, and more recently, nanotechnology. In addition, they can be synthesized using renewable resources as substrates, contributing to the circular economy and sustainability. The article presents a general and updated review of bacterial-derived biosurfactants, focusing on the potential of some groups that are still underexploited, as well as, recent trends and contributions of these versatile biomolecules to circular bioeconomy and nanotechnology.
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Affiliation(s)
- Marcos André Moura Dias
- grid.11899.380000 0004 1937 0722Departamento de Físico-Química, Instituto de Química de São Carlos, Universidade de São Paulo-USP, Av Trabalhador São Carlense 400, CP 780, CEP 13560-970 São Carlos, SP Brasil
| | - Marcia Nitschke
- Departamento de Físico-Química, Instituto de Química de São Carlos, Universidade de São Paulo-USP, Av Trabalhador São Carlense 400, CP 780, CEP 13560-970, São Carlos, SP, Brasil.
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42
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Humphreys JR, Debebe BJ, Diggle SP, Winzer K. Clostridium beijerinckii strain degeneration is driven by the loss of Spo0A activity. Front Microbiol 2023; 13:1075609. [PMID: 36704551 PMCID: PMC9871927 DOI: 10.3389/fmicb.2022.1075609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/12/2022] [Indexed: 01/12/2023] Open
Abstract
Solventogenic clostridia represent a diverse group of anaerobic, spore-forming bacteria capable of producing acetone, butanol and ethanol through their unique biphasic metabolism. An intrinsic problem with these organisms however is their tendency to degenerate when repeatedly subcultured or when grown continuously. This phenomenon sees cells lose their ability to produce solvents and spores, posing a significant problem for industrial applications. To investigate the mechanistic and evolutionary basis of degeneration we combined comparative genomics, ultra-deep sequencing, and concepts of sociomicrobiology using Clostridium beijerinckii NCIMB 8052 as our model organism. These approaches revealed spo0A, the master regulator gene involved in spore and solvent formation, to be key to the degeneration process in this strain. Comparative genomics of 71 degenerate variants revealed four distinct hotspot regions that contained considerably more mutations than the rest of the genome. These included spo0A as well as genes suspected to regulate its expression and activity. Ultra-deep sequencing of populations during the subculturing process showed transient increases in mutations we believe linked to the spo0A network, however, these were ultimately dominated by mutations in the master regulator itself. Through frequency-dependent fitness assays, we found that spo0A mutants gained a fitness advantage, relative to the wild type, presumably allowing for propagation throughout the culture. Combined, our data provides new insights into the phenomenon of clostridial strain degeneration and the C. beijerinckii NCIMB 8052 solvent and spore regulation network.
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Affiliation(s)
- Jonathan R. Humphreys
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University Park, The University of Nottingham, Nottingham, United Kingdom
| | - Bisrat J. Debebe
- DeepSeq, Centre for Genetics and Genomics, The University of Nottingham, Nottingham, United Kingdom
| | - Stephen P. Diggle
- Center for Microbial Dynamics and Infection, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | - Klaus Winzer
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University Park, The University of Nottingham, Nottingham, United Kingdom,*Correspondence: Klaus Winzer, ✉
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Yoshimoto S, Aoki S, Ohara Y, Ishikawa M, Suzuki A, Linke D, Lupas AN, Hori K. Identification of the adhesive domain of AtaA from Acinetobacter sp. Tol 5 and its application in immobilizing Escherichia coli. Front Bioeng Biotechnol 2023; 10:1095057. [PMID: 36698637 PMCID: PMC9868564 DOI: 10.3389/fbioe.2022.1095057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/21/2022] [Indexed: 01/11/2023] Open
Abstract
Cell immobilization is an important technique for efficiently utilizing whole-cell biocatalysts. We previously invented a method for bacterial cell immobilization using AtaA, a trimeric autotransporter adhesin from the highly sticky bacterium Acinetobacter sp. Tol 5. However, except for Acinetobacter species, only one bacterium has been successfully immobilized using AtaA. This is probably because the heterologous expression of large AtaA (1 MDa), that is a homotrimer of polypeptide chains composed of 3,630 amino acids, is difficult. In this study, we identified the adhesive domain of AtaA and constructed a miniaturized AtaA (mini-AtaA) to improve the heterologous expression of ataA. In-frame deletion mutants were used to perform functional mapping, revealing that the N-terminal head domain is essential for the adhesive feature of AtaA. The mini-AtaA, which contains a homotrimer of polypeptide chains from 775 amino acids and lacks the unnecessary part for its adhesion, was properly expressed in E. coli, and a larger amount of molecules was displayed on the cell surface than that of full-length AtaA (FL-AtaA). The immobilization ratio of E. coli cells expressing mini-AtaA on a polyurethane foam support was significantly higher compared to the cells with or without FL-AtaA expression, respectively. The expression of mini-AtaA in E. coli had little effect on the cell growth and the activity of another enzyme reflecting the production level, and the immobilized E. coli cells could be used for repetitive enzymatic reactions as a whole-cell catalyst.
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Affiliation(s)
- Shogo Yoshimoto
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Sota Aoki
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Yuki Ohara
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Masahito Ishikawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Atsuo Suzuki
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Dirk Linke
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Andrei N. Lupas
- Department of Protein Evolution, Max Planck Institute for Biology, Tübingen, Germany
| | - Katsutoshi Hori
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan,*Correspondence: Katsutoshi Hori,
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44
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Su R, Wang T, Bo T, Cai N, Yuan M, Wu C, Jiang H, Peng H, Chen N, Li Y. Enhanced production of D-pantothenic acid in Corynebacterium glutamicum using an efficient CRISPR-Cpf1 genome editing method. Microb Cell Fact 2023; 22:3. [PMID: 36609377 PMCID: PMC9817396 DOI: 10.1186/s12934-023-02017-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 01/02/2023] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Corynebacterium glutamicum has industrial track records for producing a variety of valuable products such as amino acids. Although CRISPR-based genome editing technologies have undergone immense developments in recent years, the suicide-plasmid-based approaches are still predominant for C. glutamicum genome manipulation. It is crucial to develop a simple and efficient CRISPR genome editing method for C. glutamicum. RESULTS In this study, we developed a RecombinAtion Prior to Induced Double-strand-break (RAPID) genome editing technology for C. glutamicum, as Cpf1 cleavage was found to disrupt RecET-mediated homologous recombination (HR) of the donor template into the genome. The RAPID toolbox enabled highly efficient gene deletion and insertion, and notably, a linear DNA template was sufficient for gene deletion. Due to the simplified procedure and iterative operation ability, this methodology could be widely applied in C. glutamicum genetic manipulations. As a proof of concept, a high-yield D-pantothenic acid (vitamin B5)-producing strain was constructed, which, to the best of our knowledge, achieved the highest reported titer of 18.62 g/L from glucose only. CONCLUSIONS We developed a RecET-assisted CRISPR-Cpf1 genome editing technology for C. glutamicum that harnessed CRISPR-induced DSBs as a counterselection. This method is of great importance to C. glutamicum genome editing in terms of its practical applications, which also guides the development of CRISPR genome editing tools for other microorganisms.
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Affiliation(s)
- Rui Su
- grid.413109.e0000 0000 9735 6249College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457 China
| | - Ting Wang
- grid.413109.e0000 0000 9735 6249College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457 China
| | - Taidong Bo
- grid.413109.e0000 0000 9735 6249College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457 China
| | - Ningyun Cai
- grid.413109.e0000 0000 9735 6249College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457 China
| | - Meng Yuan
- grid.413109.e0000 0000 9735 6249College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457 China
| | - Chen Wu
- grid.413109.e0000 0000 9735 6249College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457 China
| | - Hao Jiang
- grid.413109.e0000 0000 9735 6249College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457 China
| | - Huadong Peng
- grid.5170.30000 0001 2181 8870The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Ning Chen
- grid.413109.e0000 0000 9735 6249College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457 China ,grid.413109.e0000 0000 9735 6249Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, 300457 China
| | - Yanjun Li
- grid.413109.e0000 0000 9735 6249College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457 China ,grid.413109.e0000 0000 9735 6249Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, 300457 China
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45
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Sheng Q, Yi L, Zhong B, Wu X, Liu L, Zhang B. Shikimic acid biosynthesis in microorganisms: Current status and future direction. Biotechnol Adv 2023; 62:108073. [PMID: 36464143 DOI: 10.1016/j.biotechadv.2022.108073] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 11/03/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022]
Abstract
Shikimic acid (SA), a hydroaromatic natural product, is used as a chiral precursor for organic synthesis of oseltamivir (Tamiflu®, an antiviral drug). The process of microbial production of SA has recently undergone vigorous development. Particularly, the sustainable construction of recombinant Corynebacterium glutamicum (141.2 g/L) and Escherichia coli (87 g/L) laid a solid foundation for the microbial fermentation production of SA. However, its industrial application is restricted by limitations such as the lack of fermentation tests for industrial-scale and the requirement of growth-limiting factors, antibiotics, and inducers. Therefore, the development of SA biosensors and dynamic molecular switches, as well as genetic modification strategies and optimization of the fermentation process based on omics technology could improve the performance of SA-producing strains. In this review, recent advances in the development of SA-producing strains, including genetic modification strategies, metabolic pathway construction, and biosensor-assisted evolution, are discussed and critically reviewed. Finally, future challenges and perspectives for further reinforcing the development of robust SA-producing strains are predicted, providing theoretical guidance for the industrial production of SA.
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Affiliation(s)
- Qi Sheng
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, China; Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Lingxin Yi
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, China; Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Bin Zhong
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, China; Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Xiaoyu Wu
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, China; Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
| | - Bin Zhang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, China; Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China.
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46
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Hu B, Zhao X, Zhou J, Li J, Chen J, Du G. Efficient hydroxylation of flavonoids by using whole-cell P450 sca-2 biocatalyst in Escherichia coli. Front Bioeng Biotechnol 2023; 11:1138376. [PMID: 36873357 PMCID: PMC9977193 DOI: 10.3389/fbioe.2023.1138376] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 02/03/2023] [Indexed: 02/17/2023] Open
Abstract
The hydroxylation is an important way to generate the functionalized derivatives of flavonoids. However, the efficient hydroxylation of flavonoids by bacterial P450 enzymes is rarely reported. Here, a bacterial P450 sca-2mut whole-cell biocatalyst with an outstanding 3'-hydroxylation activity for the efficient hydroxylation of a variety of flavonoids was first reported. The whole-cell activity of sca-2mut was enhanced using a novel combination of flavodoxin Fld and flavodoxin reductase Fpr from Escherichia coli. In addition, the double mutant of sca-2mut (R88A/S96A) exhibited an improved hydroxylation performance for flavonoids through the enzymatic engineering. Moreover, the whole-cell activity of sca-2mut (R88A/S96A) was further enhanced by the optimization of whole-cell biocatalytic conditions. Finally, eriodictyol, dihydroquercetin, luteolin, and 7,3',4'-trihydroxyisoflavone, as examples of flavanone, flavanonol, flavone, and isoflavone, were produced by whole-cell biocatalysis using naringenin, dihydrokaempferol, apigenin, and daidzein as the substrates, with the conversion yield of 77%, 66%, 32%, and 75%, respectively. The strategy used in this study provided an effective method for the further hydroxylation of other high value-added compounds.
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Affiliation(s)
- Baodong Hu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China.,Science Center for Future Foods, Jiangnan University, Wuxi, Jiangsu, China.,Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi, Jiangsu, China.,Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Xinrui Zhao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China.,Science Center for Future Foods, Jiangnan University, Wuxi, Jiangsu, China.,Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi, Jiangsu, China.,Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Jingwen Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China.,Science Center for Future Foods, Jiangnan University, Wuxi, Jiangsu, China.,Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi, Jiangsu, China.,Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Jianghua Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China.,Science Center for Future Foods, Jiangnan University, Wuxi, Jiangsu, China.,Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi, Jiangsu, China.,Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Jian Chen
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China.,Science Center for Future Foods, Jiangnan University, Wuxi, Jiangsu, China.,Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi, Jiangsu, China.,Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Guocheng Du
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China.,Science Center for Future Foods, Jiangnan University, Wuxi, Jiangsu, China.,Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi, Jiangsu, China.,Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, Wuxi, Jiangsu, China.,Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
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47
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Daboussi F, Lindley ND. Challenges to Ensure a Better Translation of Metabolic Engineering for Industrial Applications. Methods Mol Biol 2023; 2553:1-20. [PMID: 36227536 DOI: 10.1007/978-1-0716-2617-7_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Metabolic engineering has evolved towards creating cell factories with increasingly complex pathways as economic criteria push biotechnology to higher value products to provide a sustainable source of speciality chemicals. Optimization of such pathways often requires high combinatory exploration of best pathway balance, and this has led to increasing use of high-throughput automated strain construction platforms or novel optimization techniques. In addition, the low catalytic efficiency of such pathways has shifted emphasis from gene expression strategies towards novel protein engineering to increase specific activity of the enzymes involved so as to limit the metabolic burden associated with excessively high pressure on ribosomal machinery when using massive overexpression systems. Metabolic burden is now generally recognized as a major hurdle to be overcome with consequences on genetic stability but also on the intensified performance needed industrially to attain the economic targets for successful product launch. Increasing awareness of the need to integrate novel genetic information into specific sites within the genome which not only enhance genetic stability (safe harbors) but also enable maximum expression profiles has led to genome-wide assessment of best integration sites, and bioinformatics will facilitate the identification of most probable landing pads within the genome.To facilitate the transfer of novel biotechnological potential to industrial-scale production, more attention, however, has to be paid to engineering metabolic fitness adapted to the specific stress conditions inherent to large-scale fermentation and the inevitable heterogeneity that will occur due to mass transfer limitations and the resulting deviation away from ideal conditions as seen in laboratory-scale validation of the engineered cells. To ensure smooth and rapid transfer of novel cell lines to industry with an accelerated passage through scale-up, better coordination is required form the onset between the biochemical engineers involved in process technology and the genetic engineers building the new strain so as to have an overall strategy able to maximize innovation at all levels. This should be one of our key objectives when building fermentation-friendly chassis organisms.
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Affiliation(s)
- Fayza Daboussi
- Toulouse White Biotechnology, Toulouse cedex 4, France
- Toulouse Biotechnology Institute, Toulouse cedex 4, France
| | - Nic D Lindley
- Toulouse White Biotechnology, Toulouse cedex 4, France.
- Toulouse Biotechnology Institute, Toulouse cedex 4, France.
- ASTAR Singapore Institute of Food and Biotechnology Innovation (SIFBI), Singapore, Singapore.
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48
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Markova EA, Shaw RE, Reynolds CR. Prediction of strain engineerings that amplify recombinant protein secretion through the machine learning approach MaLPHAS. ENGINEERING BIOLOGY 2022; 6:82-90. [PMID: 36968340 PMCID: PMC9995161 DOI: 10.1049/enb2.12025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/01/2022] [Accepted: 09/05/2022] [Indexed: 11/19/2022] Open
Abstract
This article presents a discussion of the process of precision fermentation (PF), describing the history of the space, the expected 70% growth over the next 5 years, various applications of precision fermented products, and the markets available to be disrupted by the technology. A range of prokaryotic and eukaryotic host organisms used for PF are described, with the advantages, disadvantages and applications of each. The process of setting up PF and strain engineering is described, as well as various ways that computational analysis and design techniques can be employed to assist PF engineering. The article then describes the design and implementation of a machine learning method, machine learning predictions having amplified secretion (MaLPHAS) to predict strain engineerings, which optimise the secretion of a recombinant protein. This approach showed an in silico cross-validated R 2 accuracy on the training data of up to 46.6% and in an in vitro test on a Komagataella phaffii strain, identified one gene engineering out of five predicted, which was shown to double the secretion of a heterologous protein and outperform three of the best-known edits from the literature for improving secretion in K. phaffii.
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49
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Gao S, Lu J, Wang T, Xu S, Wang X, Chen K, Ouyang P. A novel co-production of cadaverine and succinic acid based on a thermal switch system in recombinant Escherichia coli. Microb Cell Fact 2022; 21:248. [DOI: 10.1186/s12934-022-01965-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 11/07/2022] [Indexed: 11/25/2022] Open
Abstract
Abstract
Background
Polyamide (nylon) is an important material, which has aroused plenty of attention from all aspects. PA 5.4 is one kind of nylon with excellent property, which consists of cadaverine and succinic acid. Due to the environmental pollution, bio-production of cadaverine and succinic acid has been more attractive due to the less pollution and environmental friendliness. Microbes, like Escherichia coli, has been employed as cell factory to produce cadaverine and succinic acid. However, the accumulation of cadaverine will cause severe damage on cells resulting in inhibition on cell growth and cadaverine production. Herein, a novel two stage co-production of succinic acid and cadaverine was designed based on an efficient thermos-regulated switch to avoid the inhibitory brought by cadaverine.
Results
The fermentation process was divided into two phase, one for cell growth and lysine production and the other for cadaverine and succinic acid synthesis. The genes of ldhA and ackA were deleted to construct succinic acid pathway in cadaverine producer strain. Then, a thermal switch system based on pR/pL promoter and CI857 was established and optimized. The fermentation conditions were investigated that the optimal temperature for the first stage was determined as 33 ℃ and the optimal temperature for the second stage was 39 ℃. Additionally, the time to shifting temperature was identified as the fermentation anaphase. For further enhance cadaverine and succinic acid production, a scale-up fermentation in 5 L bioreactor was operated. As a result, the titer, yield and productivity of cadaverine was 55.58 g/L, 0.38 g/g glucose and 1.74 g/(L·h), respectively. 28.39 g/L of succinic acid was also obtained with yield of 0.19 g/g glucose.
Conclusion
The succinic acid metabolic pathway was constructed into cadaverine producer strain to realize the co-production of succinic acid and cadaverine. This study provided a novel craft for industrial co-production of cadaverine and succinic acid.
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50
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Li M, Luo Y, Hu M, Li C, Liu Z, Zhang T. Module-Guided Metabolic Rewiring for Fucosyllactose Biosynthesis in Engineered Escherichia coli with Lactose De Novo Pathway. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:14761-14770. [PMID: 36375030 DOI: 10.1021/acs.jafc.2c05909] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Fucosyllactose (FL) has garnered considerable attention for its benefits on infant health. In this study, we report an efficient E. coli cell factory to produce 2'/3-fucosyllactose (2'/3-FL) with lactose de novo pathway through metabolic network remodeling, including (1) modification of the PTSGlc system to enhance glucose internalization efficiency; (2) screening for β-1,4-galactosyltransferase (β-1,4-GalT) and introduction of lactose synthesis pathway; (3) eliminating inhibition of byproduct pathways; (4) constructing antibiotic-free and inducer-free FL strains; and (5) up-regulating the expression of genes in the GDP-l-fucose module. The final engineered strains BP10-3 and BP11-3 produced 4.36 g/L for 2'-FL and 3.23 g/L for 3-FL in shake flasks. In 3 L bioreactors, fed-batch cultivations of the two strains produced 40.44 g/L for 2'-FL and 30.42 g/L for 3-FL, yielding 0.63 and 0.69 g/g glucose, respectively. The strategy described in this work will help to engineer E. coli as a safe chassis for other lactose-independent HMOs production.
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Affiliation(s)
- Mengli Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yejiao Luo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Miaomiao Hu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Chenchen Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Zhu Liu
- Zhejiang Institute for Food and Drug Control, Hangzhou 310052, China
| | - Tao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
- International Joint Laboratory on Food Science and Safety, Jiangnan University, Wuxi, Jiangsu 214122, China
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