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Chen Z, Yu S, Liu J, Guo L, Wu T, Duan P, Yan D, Huang C, Huo YX. Concentration Recognition-Based Auto-Dynamic Regulation System (CRUISE) Enabling Efficient Production of Higher Alcohols. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2310215. [PMID: 38626358 DOI: 10.1002/advs.202310215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 03/12/2024] [Indexed: 04/18/2024]
Abstract
Microbial factories lacking the ability of dynamically regulating the pathway enzymes overexpression, according to in situ metabolite concentrations, are suboptimal, especially when the metabolic intermediates are competed by growth and chemical production. The production of higher alcohols (HAs), which hijacks the amino acids (AAs) from protein biosynthesis, minimizes the intracellular concentration of AAs and thus inhibits the host growth. To balance the resource allocation and maintain stable AA flux, this work utilizes AA-responsive transcriptional attenuator ivbL and HA-responsive transcriptional activator BmoR to establish a concentration recognition-based auto-dynamic regulation system (CRUISE). This system ultimately maintains the intracellular homeostasis of AA and maximizes the production of HA. It is demonstrated that ivbL-driven enzymes overexpression can dynamically regulate the AA-to-HA conversion while BmoR-driven enzymes overexpression can accelerate the AA biosynthesis during the HA production in a feedback activation mode. The AA flux in biosynthesis and conversion pathways is balanced via the intracellular AA concentration, which is vice versa stabilized by the competition between AA biosynthesis and conversion. The CRUISE, further aided by scaffold-based self-assembly, enables 40.4 g L-1 of isobutanol production in a bioreactor. Taken together, CRUISE realizes robust HA production and sheds new light on the dynamic flux control during the process of chemical production.
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Affiliation(s)
- Zhenya Chen
- Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Haidian District, No. 5 South Zhongguancun Street, Beijing, 100081, China
- Tangshan Research Institute, Beijing Institute of Technology, No. 57, South Jianshe Road, Lubei District, Tangshan, Hebei, 063000, China
| | - Shengzhu Yu
- Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Haidian District, No. 5 South Zhongguancun Street, Beijing, 100081, China
| | - Jing Liu
- Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Haidian District, No. 5 South Zhongguancun Street, Beijing, 100081, China
| | - Liwei Guo
- Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Haidian District, No. 5 South Zhongguancun Street, Beijing, 100081, China
| | - Tong Wu
- Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Haidian District, No. 5 South Zhongguancun Street, Beijing, 100081, China
| | - Peifeng Duan
- Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Haidian District, No. 5 South Zhongguancun Street, Beijing, 100081, China
| | - Dongli Yan
- Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Haidian District, No. 5 South Zhongguancun Street, Beijing, 100081, China
| | - Chaoyong Huang
- Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Haidian District, No. 5 South Zhongguancun Street, Beijing, 100081, China
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Haidian District, No. 5 South Zhongguancun Street, Beijing, 100081, China
- Tangshan Research Institute, Beijing Institute of Technology, No. 57, South Jianshe Road, Lubei District, Tangshan, Hebei, 063000, China
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Huang J, Liu J, Dong H, Shi J, You X, Zhang Y. Engineering of a Substrate Affinity Reduced S-Adenosyl-methionine Synthetase as a Novel Biosensor for Growth-Coupling Selection of L-Methionine Overproducers. Appl Biochem Biotechnol 2023:10.1007/s12010-023-04807-0. [PMID: 38150159 DOI: 10.1007/s12010-023-04807-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2023] [Indexed: 12/28/2023]
Abstract
Biosensors are powerful tools for monitoring specific metabolites or controlling metabolic flux towards the products in a single cell, which play important roles in microbial cell factory construction. Despite their potential role in metabolic flux monitoring, the development of biosensors for small molecules is still limited. Reported biosensors often exhibit bottlenecks of poor specificity and a narrow dynamic range. Moreover, fine-tuning the substrate binding affinity of a crucial enzyme can decrease its catalytic activity, which ultimately results in the repression of the corresponding essential metabolite biosynthesis and impairs cell growth. However, increasing intracellular substrate concentration can elevate the availability of the essential metabolite and may lead to restore cellular growth. Herein, a new strategy was proposed for constructing whole-cell biosensors based on enzyme encoded by essential gene that offer inherent specificity and universality. Specifically, S-adenosyl-methionine synthetase (MetK) in E. coli was chosen as the crucial enzyme, and a series of MetK variants were identified that were sensitive to L-methionine concentration. This occurrence enabled the engineered cell to sense L-methionine and exhibit L-methionine dose-dependent cell growth. To improve the biosensor's dynamic range, an S-adenosyl-methionine catabolic enzyme was overexpressed to reduce the intracellular availability of S-adenosyl-methionine. The resulting whole-cell biosensor effectively coupled the intracellular concentration of L-methionine with growth and was successfully applied to select strains with enhanced L-methionine biosynthesis from random mutagenesis libraries. Overall, our study presents a universal strategy for designing and constructing growth-coupled biosensors based on crucial enzyme, which can be applied to select strains overproducing high value-added metabolites in cellular metabolism.
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Affiliation(s)
- Jianfeng Huang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, People's Republic of China
| | - Jinhui Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
- Henan Engineering Research Center of Food Microbiology, College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, 471023, People's Republic of China
| | - Huaming Dong
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, 430205, People's Republic of China
| | - Jingjing Shi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, People's Republic of China
| | - Xiaoyan You
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.
- Henan Engineering Research Center of Food Microbiology, College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, 471023, People's Republic of China.
| | - Yanfei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, People's Republic of China.
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Halle L, Hollmann N, Tenhaef N, Mbengi L, Glitz C, Wiechert W, Polen T, Baumgart M, Bott M, Noack S. Robotic workflows for automated long-term adaptive laboratory evolution: improving ethanol utilization by Corynebacterium glutamicum. Microb Cell Fact 2023; 22:175. [PMID: 37679814 PMCID: PMC10483779 DOI: 10.1186/s12934-023-02180-5] [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: 08/15/2023] [Indexed: 09/09/2023] Open
Abstract
BACKGROUND Adaptive laboratory evolution (ALE) is known as a powerful tool for untargeted engineering of microbial strains and genomics research. It is particularly well suited for the adaptation of microorganisms to new environmental conditions, such as alternative substrate sources. Since the probability of generating beneficial mutations increases with the frequency of DNA replication, ALE experiments are ideally free of constraints on the required duration of cell proliferation. RESULTS Here, we present an extended robotic workflow for performing long-term evolution experiments based on fully automated repetitive batch cultures (rbALE) in a well-controlled microbioreactor environment. Using a microtiter plate recycling approach, the number of batches and thus cell generations is technically unlimited. By applying the validated workflow in three parallel rbALE runs, ethanol utilization by Corynebacterium glutamicum ATCC 13032 (WT) was significantly improved. The evolved mutant strain WT_EtOH-Evo showed a specific ethanol uptake rate of 8.45 ± 0.12 mmolEtOH gCDW-1 h-1 and a growth rate of 0.15 ± 0.01 h-1 in lab-scale bioreactors. Genome sequencing of this strain revealed a striking single nucleotide variation (SNV) upstream of the ald gene (NCgl2698, cg3096) encoding acetaldehyde dehydrogenase (ALDH). The mutated basepair was previously predicted to be part of the binding site for the global transcriptional regulator GlxR, and re-engineering demonstrated that the identified SNV is key for enhanced ethanol assimilation. Decreased binding of GlxR leads to increased synthesis of the rate-limiting enzyme ALDH, which was confirmed by proteomics measurements. CONCLUSIONS The established rbALE technology is generally applicable to any microbial strain and selection pressure that fits the small-scale cultivation format. In addition, our specific results will enable improved production processes with C. glutamicum from ethanol, which is of particular interest for acetyl-CoA-derived products.
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Affiliation(s)
- Lars Halle
- Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, 52425, Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Niels Hollmann
- Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, 52425, Jülich, Germany
| | - Niklas Tenhaef
- Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, 52425, Jülich, Germany
| | - Lea Mbengi
- Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, 52425, Jülich, Germany
| | - Christiane Glitz
- Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, 52425, Jülich, Germany
| | - Wolfgang Wiechert
- Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, 52425, Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Tino Polen
- Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, 52425, Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Meike Baumgart
- Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, 52425, Jülich, Germany
| | - Michael Bott
- Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, 52425, Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Stephan Noack
- Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, IBG-1: Biotechnology, 52425, Jülich, Germany.
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.
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Qian J, Fan L, Yang J, Feng J, Gao N, Cheng G, Pu W, Zhou W, Cai T, Li S, Zheng P, Sun J, Wang D, Wang Y. Directed evolution of a neutrophilic and mesophilic methanol dehydrogenase based on high-throughput and accurate measurement of formaldehyde. Synth Syst Biotechnol 2023; 8:386-395. [PMID: 37342805 PMCID: PMC10277290 DOI: 10.1016/j.synbio.2023.05.004] [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: 03/20/2023] [Revised: 05/01/2023] [Accepted: 05/21/2023] [Indexed: 06/23/2023] Open
Abstract
Methanol is a promising one-carbon feedstock for biomanufacturing, which can be sustainably produced from carbon dioxide and natural gas. However, the efficiency of methanol bioconversion is limited by the poor catalytic properties of nicotinamide adenine dinucleotide (NAD+)-dependent methanol dehydrogenase (Mdh) that oxidizes methanol to formaldehyde. Herein, the neutrophilic and mesophilic NAD+-dependent Mdh from Bacillus stearothermophilus DSM 2334 (MdhBs) was subjected to directed evolution for enhancing the catalytic activity. The combination of formaldehyde biosensor and Nash assay allowed high-throughput and accurate measurement of formaldehyde and facilitated efficient selection of desired variants. MdhBs variants with up to 6.5-fold higher Kcat/KM value for methanol were screened from random mutation libraries. The T153 residue that is spatially proximal to the substrate binding pocket has significant influence on enzyme activity. The beneficial T153P mutation changes the interaction network of this residue and breaks the α-helix important for substrate binding into two short α-helices. Reconstructing the interaction network of T153 with surrounding residues may represent a promising strategy to further improve MdhBs, and this study provides an efficient strategy for directed evolution of Mdh.
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Affiliation(s)
- Jin Qian
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300222, China
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Liwen Fan
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Jinxing Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Jinhui Feng
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Ning Gao
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guimin Cheng
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300222, China
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Wei Pu
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Wenjuan Zhou
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Tao Cai
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Shuang Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Ping Zheng
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jibin Sun
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Depei Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300222, China
| | - Yu Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300222, China
- Haihe Laboratory of Synthetic Biology, Tianjin, 300308, China
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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5
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Zuchowski R, Schito S, Neuheuser F, Menke P, Berger D, Hollmann N, Gujar S, Sundermeyer L, Mack C, Wirtz A, Weiergräber OH, Polen T, Bott M, Noack S, Baumgart M. Discovery of novel amino acid production traits by evolution of synthetic co-cultures. Microb Cell Fact 2023; 22:71. [PMID: 37061714 PMCID: PMC10105947 DOI: 10.1186/s12934-023-02078-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 04/02/2023] [Indexed: 04/17/2023] Open
Abstract
BACKGROUND Amino acid production features of Corynebacterium glutamicum were extensively studied in the last two decades. Many metabolic pathways, regulatory and transport principles are known, but purely rational approaches often provide only limited progress in production optimization. We recently generated stable synthetic co-cultures, termed Communities of Niche-optimized Strains (CoNoS), that rely on cross-feeding of amino acids for growth. This setup has the potential to evolve strains with improved production by selection of faster growing communities. RESULTS Here we performed adaptive laboratory evolution (ALE) with a CoNoS to identify mutations that are relevant for amino acid production both in mono- and co-cultures. During ALE with the CoNoS composed of strains auxotrophic for either L-leucine or L-arginine, we obtained a 23% growth rate increase. Via whole-genome sequencing and reverse engineering, we identified several mutations involved in amino acid transport that are beneficial for CoNoS growth. The L-leucine auxotrophic strain carried an expression-promoting mutation in the promoter region of brnQ (cg2537), encoding a branched-chain amino acid transporter in combination with mutations in the genes for the Na+/H+-antiporter Mrp1 (cg0326-cg0321). This suggested an unexpected link of Mrp1 to L-leucine transport. The L-arginine auxotrophic partner evolved expression-promoting mutations near the transcriptional start site of the yet uncharacterized operon argTUV (cg1504-02). By mutation studies and ITC, we characterized ArgTUV as the only L-arginine uptake system of C. glutamicum with an affinity of KD = 30 nM. Finally, deletion of argTUV in an L-arginine producer strain resulted in a faster and 24% higher L-arginine production in comparison to the parental strain. CONCLUSION Our work demonstrates the power of the CoNoS-approach for evolution-guided identification of non-obvious production traits, which can also advance amino acid production in monocultures. Further rounds of evolution with import-optimized strains can potentially reveal beneficial mutations also in metabolic pathway enzymes. The approach can easily be extended to all kinds of metabolite cross-feeding pairings of different organisms or different strains of the same organism, thereby enabling the identification of relevant transport systems and other favorable mutations.
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Affiliation(s)
- Rico Zuchowski
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Simone Schito
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Friederike Neuheuser
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Philipp Menke
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Daniel Berger
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Niels Hollmann
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Srushti Gujar
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
- Institute of Biological Information Processing, IBI-7: Structural Biochemistry, Forschungszentrum Jülich, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Lea Sundermeyer
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Christina Mack
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Astrid Wirtz
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Oliver H Weiergräber
- Institute of Biological Information Processing, IBI-7: Structural Biochemistry, Forschungszentrum Jülich, Jülich, Germany
| | - Tino Polen
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Michael Bott
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Stephan Noack
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Meike Baumgart
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany.
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Jiang S, Wang R, Wang D, Zhao C, Ma Q, Wu H, Xie X. Metabolic reprogramming and biosensor-assisted mutagenesis screening for high-level production of L-arginine in Escherichia coli. Metab Eng 2023; 76:146-157. [PMID: 36758663 DOI: 10.1016/j.ymben.2023.02.003] [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: 11/10/2022] [Revised: 01/14/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023]
Abstract
L-arginine is a value-added amino acid with promising applications in the pharmaceutical and nutraceutical industries. Further unleashing the potential of microbial cell factories to make L-arginine production more competitive remains challenging due to the sophisticated intracellular interaction networks and the insufficient knowledge of global metabolic regulation. Here, we combined multilevel rational metabolic engineering with biosensor-assisted mutagenesis screening to exploit the L-arginine production potential of Escherichia coli. First, multiple metabolic pathways were systematically reprogrammed to redirect the metabolic flux into L-arginine synthesis, including the L-arginine biosynthesis, TCA cycle, and L-arginine export. Specifically, a toggle switch responding to special cellular physiological conditions was designed to dynamically control the expression of sucA and pull more carbon flux from the TCA cycle toward L-arginine biosynthesis. Subsequently, a biosensor-assisted high-throughput screening platform was designed and applied to further exploit the L-arginine production potential. The best-engineered ARG28 strain produced 132 g/L L-arginine in a 5-L bioreactor with a yield of 0.51 g/g glucose and productivity of 2.75 g/(L ⋅ h), which were the highest values reported so far. Through whole genome sequencing and reverse engineering, Frc frameshift mutant, PqiB A78P mutant, and RpoB P564T mutant were revealed for enhancing the L-arginine biosynthesis. Our study exhibited the power of coupling rational metabolic reprogramming and biosensor-assisted mutagenesis screening to unleash the cellular potential for value-added metabolite production.
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Affiliation(s)
- Shuai Jiang
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science & Technology, Tianjin, 300457, PR China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, PR China
| | - Ruirui Wang
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science & Technology, Tianjin, 300457, PR China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, PR China
| | - Dehu Wang
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science & Technology, Tianjin, 300457, PR China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, PR China
| | - Chunguang Zhao
- Ningxia Eppen Biotech Co., Ltd, Ningxia, 750000, PR China
| | - Qian Ma
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science & Technology, Tianjin, 300457, PR China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, PR China
| | - Heyun Wu
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science & Technology, Tianjin, 300457, PR China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, PR China.
| | - Xixian Xie
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin University of Science & Technology, Tianjin, 300457, PR China; College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, PR China.
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7
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Yim SS, Choi JW, Lee YJ, Jeong KJ. Rapid combinatorial rewiring of metabolic networks for enhanced poly(3-hydroxybutyrate) production in Corynebacterium glutamicum. Microb Cell Fact 2023; 22:29. [PMID: 36803485 PMCID: PMC9936768 DOI: 10.1186/s12934-023-02037-x] [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: 10/07/2022] [Accepted: 02/07/2023] [Indexed: 02/19/2023] Open
Abstract
BACKGROUND The disposal of plastic waste is a major environmental challenge. With recent advances in microbial genetic and metabolic engineering technologies, microbial polyhydroxyalkanoates (PHAs) are being used as next-generation biomaterials to replace petroleum-based synthetic plastics in a sustainable future. However, the relatively high production cost of bioprocesses hinders the production and application of microbial PHAs on an industrial scale. RESULTS Here, we describe a rapid strategy to rewire metabolic networks in an industrial microorganism, Corynebacterium glutamicum, for the enhanced production of poly(3-hydroxybutyrate) (PHB). A three-gene PHB biosynthetic pathway in Rasltonia eutropha was refactored for high-level gene expression. A fluorescence-based quantification assay for cellular PHB content using BODIPY was devised for the rapid fluorescence-activated cell sorting (FACS)-based screening of a large combinatorial metabolic network library constructed in C. glutamicum. Rewiring metabolic networks across the central carbon metabolism enabled highly efficient production of PHB up to 29% of dry cell weight with the highest cellular PHB productivity ever reported in C. glutamicum using a sole carbon source. CONCLUSIONS We successfully constructed a heterologous PHB biosynthetic pathway and rapidly optimized metabolic networks across central metabolism in C. glutamicum for enhanced production of PHB using glucose or fructose as a sole carbon source in minimal media. We expect that this FACS-based metabolic rewiring framework will accelerate strain engineering processes for the production of diverse biochemicals and biopolymers.
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Affiliation(s)
- Sung Sun Yim
- grid.37172.300000 0001 2292 0500Department of Biological Sciences, KAIST, Daejeon, Republic of Korea ,grid.37172.300000 0001 2292 0500Institute for BioCentury, KAIST, Daejeon, Republic of Korea
| | - Jae Woong Choi
- grid.418974.70000 0001 0573 0246Traditional Food Research Group, Korea Food Research Institute, Jeonju, Republic of Korea
| | - Yong Jae Lee
- grid.249967.70000 0004 0636 3099Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141 Korea ,grid.412786.e0000 0004 1791 8264Major of Environmental Biotechnology, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), Daejeon, Korea
| | - Ki Jun Jeong
- Department of Chemical and Biomolecular Engineering, KAIST, Daejeon, Republic of Korea. .,Institute for BioCentury, KAIST, Daejeon, Republic of Korea.
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Stability, robustness, and containment: preparing synthetic biology for real-world deployment. Curr Opin Biotechnol 2023; 79:102880. [PMID: 36621221 DOI: 10.1016/j.copbio.2022.102880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/23/2022] [Accepted: 12/07/2022] [Indexed: 01/07/2023]
Abstract
As engineered microbes are used in increasingly diverse applications across human health and bioproduction, the field of synthetic biology will need to focus on strategies that stabilize and contain the function of these populations within target environments. To this end, recent advancements have created layered sensing circuits that can compute cell survival, genetic contexts that are less susceptible to mutation, burden, and resource control circuits, and methods for population variability reduction. These tools expand the potential for real-world deployment of complex microbial systems by enhancing their environmental robustness and functional stability in the face of unpredictable host response and evolutionary pressure.
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Wang Y, Zhao D, Sun L, Wang J, Fan L, Cheng G, Zhang Z, Ni X, Feng J, Wang M, Zheng P, Bi C, Zhang X, Sun J. Engineering of the Translesion DNA Synthesis Pathway Enables Controllable C-to-G and C-to-A Base Editing in Corynebacterium glutamicum. ACS Synth Biol 2022; 11:3368-3378. [PMID: 36099191 DOI: 10.1021/acssynbio.2c00265] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Expanding the base conversion type is expected to largely broaden the application of base editing, whereas it requires decipherment of the machinery controlling the editing outcome. Here, we discovered that the DNA polymerase V-mediated translesion DNA synthesis (TLS) pathway controlled the C-to-A editing by a glycosylase base editor (GBE) in Escherichia coli. However, C-to-G conversion was surprisingly found to be the main product of the GBE in Corynebacterium glutamicum and subsequent gene inactivation identified the decisive TLS enzymes. Introduction of the E. coli TLS pathway into a TLS-deficient C. glutamicum mutant completely changed the GBE outcome from C-to-G to C-to-A. Combining the canonical C-to-T editor, a pioneering C-to-N base editing toolbox was established in C. glutamicum. The expanded base conversion capability produces greater genetic diversity and promotes the application of base editing in gene inactivation and protein evolution. This study demonstrates the possibility of engineering TLS systems to develop advanced genome editing tools.
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Affiliation(s)
- Yu Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Dongdong Zhao
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Letian Sun
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Liwen Fan
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Guimin Cheng
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China.,College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300222, China
| | - Zhihui Zhang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaomeng Ni
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Jinhui Feng
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Meng Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Ping Zheng
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Changhao Bi
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Xueli Zhang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Jibin Sun
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
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10
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Physiological Responses of Ribosomal Protein S12 K43 Mutants of Corynebacterium glutamicum. Curr Microbiol 2022; 79:94. [PMID: 35142919 DOI: 10.1007/s00284-022-02795-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 01/31/2022] [Indexed: 11/03/2022]
Abstract
Bacterial resistance to streptomycin is often acquired as a consequence of mutations in rpsL, the gene encoding ribosomal protein S12. Corynebacterium glutamicum is a non-pathogenic Gram-positive soil bacterium that has been widely used in industry. In a previous study, we screened several streptomycin-resistant rpsL K43 mutants of C. glutamicum, and surprisingly found that two of them also confer chloramphenicol and/or kanamycin resistance. In order to understand whether or not a single mutation of rpsLK43 could confer resistance to multiple antibiotics, in this study we attempted to construct saturation mutagenesis of rpsL K43 by rational genetic manipulation. Despite many efforts had been made, only nine mutants were successfully constructed. They were indeed resistant to streptomycin, but not to other antibiotics. This suggested that other mutations should be acquired, contributing to multiple antibiotics in the screened strains. The growth and enhanced green fluorescent protein (eGFP) expression of these nine mutants were then investigated. The results showed that they grew differently in CGXII minimal medium, but not in BHI medium. When cultured in the absence of streptomycin, the expression of eGFP was positively proportional to the growth, approximately, while in the presence of streptomycin, the expression of eGFP was proportional to the ability of streptomycin resistance.
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