1
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Zhang K, Qin M, Hou Y, Zhang W, Wang Z, Wang H. Efficient production of guanosine in Escherichia coli by combinatorial metabolic engineering. Microb Cell Fact 2024; 23:182. [PMID: 38898430 PMCID: PMC11186194 DOI: 10.1186/s12934-024-02452-8] [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: 04/22/2024] [Accepted: 06/06/2024] [Indexed: 06/21/2024] Open
Abstract
BACKGROUND Guanosine is a purine nucleoside that is widely used as a raw material for food additives and pharmaceutical products. Microbial fermentation is the main production method of guanosine. However, the guanosine-producing strains possess multiple metabolic pathway interactions and complex regulatory mechanisms. The lack of strains with efficiently producing-guanosine greatly limited industrial application. RESULTS We attempted to efficiently produce guanosine in Escherichia coli using systematic metabolic engineering. First, we overexpressed the purine synthesis pathway from Bacillus subtilis and the prs gene, and deleted three genes involved in guanosine catabolism to increase guanosine accumulation. Subsequently, we attenuated purA expression and eliminated feedback and transcription dual inhibition. Then, we modified the metabolic flux of the glycolysis and Entner-Doudoroff (ED) pathways and performed redox cofactors rebalancing. Finally, transporter engineering and enhancing the guanosine synthesis pathway further increased the guanosine titre to 134.9 mg/L. After 72 h of the fed-batch fermentation in shake-flask, the guanosine titre achieved 289.8 mg/L. CONCLUSIONS Our results reveal that the guanosine synthesis pathway was successfully optimized by combinatorial metabolic engineering, which could be applicable to the efficient synthesis of other nucleoside products.
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Affiliation(s)
- Kun Zhang
- Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Mengxing Qin
- Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Yu Hou
- Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Wenwen Zhang
- Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Zhenyu Wang
- Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Hailei Wang
- Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China.
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2
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Curry E, Muir G, Qu J, Kis Z, Hulley M, Brown A. Engineering an Escherichia coli based in vivo mRNA manufacturing platform. Biotechnol Bioeng 2024; 121:1912-1926. [PMID: 38419526 DOI: 10.1002/bit.28684] [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: 11/03/2023] [Revised: 01/31/2024] [Accepted: 02/15/2024] [Indexed: 03/02/2024]
Abstract
Synthetic mRNA is currently produced in standardized in vitro transcription systems. However, this one-size-fits-all approach has associated drawbacks in supply chain shortages, high reagent costs, complex product-related impurity profiles, and limited design options for molecule-specific optimization of product yield and quality. Herein, we describe for the first time development of an in vivo mRNA manufacturing platform, utilizing an Escherichia coli cell chassis. Coordinated mRNA, DNA, cell and media engineering, primarily focussed on disrupting interactions between synthetic mRNA molecules and host cell RNA degradation machinery, increased product yields >40-fold compared to standard "unengineered" E. coli expression systems. Mechanistic dissection of cell factory performance showed that product mRNA accumulation levels approached theoretical limits, accounting for ~30% of intracellular total RNA mass, and that this was achieved via host-cell's reallocating biosynthetic capacity away from endogenous RNA and cell biomass generation activities. We demonstrate that varying sized functional mRNA molecules can be produced in this system and subsequently purified. Accordingly, this study introduces a new mRNA production technology, expanding the solution space available for mRNA manufacturing.
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Affiliation(s)
- Edward Curry
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | - George Muir
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | - Jixin Qu
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | - Zoltán Kis
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | | | - Adam Brown
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
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3
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Wu T, Jiang J, Zhang H, Liu J, Ruan H. Transcending membrane barriers: advances in membrane engineering to enhance the production capacity of microbial cell factories. Microb Cell Fact 2024; 23:154. [PMID: 38796463 PMCID: PMC11128114 DOI: 10.1186/s12934-024-02436-8] [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: 03/15/2024] [Accepted: 05/21/2024] [Indexed: 05/28/2024] Open
Abstract
Microbial cell factories serve as pivotal platforms for the production of high-value natural products, which tend to accumulate on the cell membrane due to their hydrophobic properties. However, the limited space of the cell membrane presents a bottleneck for the accumulation of these products. To enhance the production of intracellular natural products and alleviate the burden on the cell membrane caused by product accumulation, researchers have implemented various membrane engineering strategies. These strategies involve modifying the membrane components and structures of microbial cell factories to achieve efficient accumulation of target products. This review summarizes recent advances in the application of membrane engineering technologies in microbial cell factories, providing case studies involving Escherichia coli and yeast. Through these strategies, researchers have not only improved the tolerance of cells but also optimized intracellular storage space, significantly enhancing the production efficiency of natural products. This article aims to provide scientific evidence and references for further enhancing the efficiency of similar cell factories.
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Affiliation(s)
- Tao Wu
- Tianjin Key Laboratory of Food Science and Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China.
| | - Jingjing Jiang
- Tianjin Key Laboratory of Food Science and Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
| | - Hongyang Zhang
- Tianjin Key Laboratory of Food Science and Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
| | - Jiazhi Liu
- Tianjin Key Laboratory of Food Science and Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
| | - Haihua Ruan
- Tianjin Key Laboratory of Food Science and Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China.
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4
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Yu L, Gao Y, He Y, Liu Y, Shen J, Liang H, Gong R, Duan H, Price NPJ, Song X, Deng Z, Chen W. Developing the E. coli platform for efficient production of UMP-derived chemicals. Metab Eng 2024; 83:61-74. [PMID: 38522576 DOI: 10.1016/j.ymben.2024.03.004] [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: 11/03/2023] [Revised: 03/10/2024] [Accepted: 03/21/2024] [Indexed: 03/26/2024]
Abstract
5-Methyluridine (5-MU) is a prominent intermediate for industrial synthesis of several antiviral-drugs, however, its availability over the past decades has overwhelmingly relied on chemical and enzymatic strategies. Here, we have realized efficient production of 5-MU in E. coli, for the first time, via a designer artificial pathway consisting of a two-enzyme cascade (UMP 5-methylase and phosphatase). More importantly, we have engineered the E. coli cell factory to boost 5-MU production by systematic evaluation of multiple strategies, and as a proof of concept, we have further developed an antibiotic-free fermentation strategy to realize 5-MU production (10.71 g/L) in E. coli MB229 (a ΔthyA strain). Remarkably, we have also established a versatile and robust platform with exploitation of the engineered E. coli for efficient production of diversified UMP-derived chemicals. This study paves the way for future engineering of E. coli as a synthetic biology platform for acceleratively accessing UMP-derived chemical diversities.
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Affiliation(s)
- Le Yu
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Yaojie Gao
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Yuanyuan He
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Yang Liu
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Jianning Shen
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Han Liang
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Rong Gong
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - He Duan
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Neil P J Price
- US Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Peoria, IL, USA
| | - Xuemin Song
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Zixin Deng
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Wenqing Chen
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430071, China; Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China.
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5
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Padilla-Vaca F, de la Mora J, García-Contreras R, Ramírez-Prado JH, Vicente-Gómez M, Vargas-Gasca F, Anaya-Velázquez F, Páramo-Pérez I, Rangel-Serrano Á, Cuéllar-Mata P, Vargas-Maya NI, Franco B. Theoretical study of ArcB and its dimerization, interaction with anaerobic metabolites, and activation of ArcA. PeerJ 2023; 11:e16309. [PMID: 37849831 PMCID: PMC10578306 DOI: 10.7717/peerj.16309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 09/27/2023] [Indexed: 10/19/2023] Open
Abstract
The complex metabolism of Escherichia coli has been extensively studied, including its response to oxygen availability. The ArcA/B two-component system (TCS) is the key regulator for the transition between these two environmental conditions and has been thoroughly characterized using genetic and biochemical approaches. Still, to date, limited structural data is available. The breakthrough provided by AlphaFold2 in 2021 has brought a reliable tool to the scientific community for assessing the structural features of complex proteins. In this report, we analyzed the structural aspects of the ArcA/B TCS using AlphaFold2 models. The models are consistent with the experimentally determined structures of ArcB kinase. The predicted structure of the dimeric form of ArcB is consistent with the extensive genetic and biochemical data available regarding mechanistic signal perception and regulation. The predicted interaction of the dimeric form of ArcB with its cognate response regulator (ArcA) is also consistent with both the forward and reverse phosphotransfer mechanisms. The ArcB model was used to detect putative binding cavities to anaerobic metabolites, encouraging testing of these predictions experimentally. Finally, the highly accurate models of other ArcB homologs suggest that different experimental approaches are needed to determine signal perception in kinases lacking the PAS domain. Overall, ArcB is a kinase with features that need further testing, especially in determining its crystal structure under different conditions.
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Affiliation(s)
| | - Javier de la Mora
- Genética Molecular, Instituto de Fisiología Celular, Mexico City, Mexico City, México
| | | | | | | | | | | | | | | | | | | | - Bernardo Franco
- Biology, Universidad de Guanajuato, Guanajuato, Guanajuato, México
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6
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Yang Z, Li Z, Li B, Bu R, Tan GY, Wang Z, Yan H, Xin Z, Zhang G, Li M, Xiang H, Zhang L, Wang W. A thermostable type I-B CRISPR-Cas system for orthogonal and multiplexed genetic engineering. Nat Commun 2023; 14:6193. [PMID: 37794017 PMCID: PMC10551041 DOI: 10.1038/s41467-023-41973-5] [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: 04/19/2023] [Accepted: 09/26/2023] [Indexed: 10/06/2023] Open
Abstract
Thermophilic cell factories have remarkably broad potential for industrial applications, but are limited by a lack of genetic manipulation tools and recalcitrance to transformation. Here, we identify a thermophilic type I-B CRISPR-Cas system from Parageobacillus thermoglucosidasius and find it displays highly efficient transcriptional repression or DNA cleavage activity that can be switched by adjusting crRNA length to less than or greater than 26 bp, respectively, without ablating Cas3 nuclease. We then develop an orthogonal tool for genome editing and transcriptional repression using this type I-B system in both thermophile and mesophile hosts. Empowered by this tool, we design a strategy to screen the genome-scale targets involved in transformation efficiency and established dynamically controlled supercompetent P. thermoglucosidasius cells with high efficiency ( ~ 108 CFU/μg DNA) by temporal multiplexed repression. We also demonstrate the construction of thermophilic riboflavin cell factory with hitherto highest titers in high temperature fermentation by genome-scale identification and combinatorial manipulation of multiple targets. This work enables diverse high-efficiency genetic manipulation in P. thermoglucosidasius and facilitates the engineering of thermophilic cell factories.
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Affiliation(s)
- Zhiheng Yang
- State Key Laboratory of Bioreactor Engineering, and School of Biotechnology, East China University of Science and Technology (ECUST), 200237, Shanghai, China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Zilong Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Bixiao Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Ruihong Bu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
- School of Medicine and Pharmacy, Ocean University of China, 266003, Qingdao, China
| | - Gao-Yi Tan
- State Key Laboratory of Bioreactor Engineering, and School of Biotechnology, East China University of Science and Technology (ECUST), 200237, Shanghai, China
| | - Zhengduo Wang
- State Key Laboratory of Bioreactor Engineering, and School of Biotechnology, East China University of Science and Technology (ECUST), 200237, Shanghai, China
| | - Hao Yan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Zhenguo Xin
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Guojian Zhang
- School of Medicine and Pharmacy, Ocean University of China, 266003, Qingdao, China
| | - Ming Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering, and School of Biotechnology, East China University of Science and Technology (ECUST), 200237, Shanghai, China.
| | - Weishan Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
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7
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Sajid S, Mashkoor M, Jørgensen MG, Christensen LP, Hansen PR, Franzyk H, Mirza O, Prabhala BK. The Y-ome Conundrum: Insights into Uncharacterized Genes and Approaches for Functional Annotation. Mol Cell Biochem 2023:10.1007/s11010-023-04827-8. [PMID: 37610616 DOI: 10.1007/s11010-023-04827-8] [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: 07/07/2023] [Accepted: 08/09/2023] [Indexed: 08/24/2023]
Abstract
The ever-increasing availability of genome sequencing data has revealed a substantial number of uncharacterized genes without known functions across various organisms. The first comprehensive genome sequencing of E. coli K12 revealed that more than 50% of its open reading frames corresponded to transcripts with no known functions. The group of protein-coding genes without a functional description and/or a recognized pathway, beginning with the letter "Y", is classified as the "y-ome". Several efforts have been made to elucidate the functions of these genes and to recognize their role in biological processes. This review provides a brief update on various strategies employed when studying the y-ome, such as high-throughput experimental approaches, comparative omics, metabolic engineering, gene expression analysis, and data integration techniques. Additionally, we highlight recent advancements in functional annotation methods, including the use of machine learning, network analysis, and functional genomics approaches. Novel approaches are required to produce more precise functional annotations across the genome to reduce the number of genes with unknown functions.
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Affiliation(s)
- Salvia Sajid
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen Ø, Denmark
- Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Maliha Mashkoor
- Department of Surgery, Center for Surgical Sciences, Zealand University Hospital, Lykkebækvej 1, 4600, Køge, Denmark
| | - Mikkel Girke Jørgensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Lars Porskjær Christensen
- Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Paul Robert Hansen
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen Ø, Denmark
| | - Henrik Franzyk
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen Ø, Denmark
| | - Osman Mirza
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen Ø, Denmark
| | - Bala Krishna Prabhala
- Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark.
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8
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Carreón-Rodríguez OE, Gosset G, Escalante A, Bolívar F. Glucose Transport in Escherichia coli: From Basics to Transport Engineering. Microorganisms 2023; 11:1588. [PMID: 37375089 DOI: 10.3390/microorganisms11061588] [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: 05/04/2023] [Revised: 06/08/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Escherichia coli is the best-known model for the biotechnological production of many biotechnological products, including housekeeping and heterologous primary and secondary metabolites and recombinant proteins, and is an efficient biofactory model to produce biofuels to nanomaterials. Glucose is the primary substrate used as the carbon source for laboratory and industrial cultivation of E. coli for production purposes. Efficient growth and associated production and yield of desired products depend on the efficient sugar transport capabilities, sugar catabolism through the central carbon catabolism, and the efficient carbon flux through specific biosynthetic pathways. The genome of E. coli MG1655 is 4,641,642 bp, corresponding to 4702 genes encoding 4328 proteins. The EcoCyc database describes 532 transport reactions, 480 transporters, and 97 proteins involved in sugar transport. Nevertheless, due to the high number of sugar transporters, E. coli uses preferentially few systems to grow in glucose as the sole carbon source. E. coli nonspecifically transports glucose from the extracellular medium into the periplasmic space through the outer membrane porins. Once in periplasmic space, glucose is transported into the cytoplasm by several systems, including the phosphoenolpyruvate-dependent phosphotransferase system (PTS), the ATP-dependent cassette (ABC) transporters, and the major facilitator (MFS) superfamily proton symporters. In this contribution, we review the structures and mechanisms of the E. coli central glucose transport systems, including the regulatory circuits recruiting the specific use of these transport systems under specific growing conditions. Finally, we describe several successful examples of transport engineering, including introducing heterologous and non-sugar transport systems for producing several valuable metabolites.
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Affiliation(s)
- Ofelia E Carreón-Rodríguez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Cuernavaca 62210, Morelos, Mexico
| | - Guillermo Gosset
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Cuernavaca 62210, Morelos, Mexico
| | - Adelfo Escalante
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Cuernavaca 62210, Morelos, Mexico
| | - Francisco Bolívar
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Cuernavaca 62210, Morelos, Mexico
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9
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Ding Q, Ye C. Recent advances in producing food additive L-malate: Chassis, substrate, pathway, fermentation regulation and application. Microb Biotechnol 2023; 16:709-725. [PMID: 36604311 PMCID: PMC10034640 DOI: 10.1111/1751-7915.14206] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 12/22/2022] [Indexed: 01/07/2023] Open
Abstract
In addition to being an important intermediate in the TCA cycle, L-malate is also widely used in the chemical and beverage industries. Due to the resulting high demand, numerous studies investigated chemical methods to synthesize L-malate from petrochemical resources, but such approaches are hampered by complex downstream processing and environmental pollution. Accordingly, there is an urgent need to develop microbial methods for environmentally-friendly and economical L-malate biosynthesis. The rapid progress and understanding of DNA manipulation, cell physiology, and cell metabolism can improve industrial L-malate biosynthesis by applying intelligent biochemical strategies and advanced synthetic biology tools. In this paper, we mainly focused on biotechnological approaches for enhancing L-malate synthesis, encompassing the microbial chassis, substrate utilization, synthesis pathway, fermentation regulation, and industrial application. This review emphasizes the application of novel metabolic engineering strategies and synthetic biology tools combined with a deep understanding of microbial physiology to improve industrial L-malate biosynthesis in the future.
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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, China
- Anhui Key Laboratory of Modern Biomanufacturing, Hefei, China
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
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10
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Thuan NH, Tatipamula VB, Trung NT, Van Giang N. Metabolic engineering and optimization of Escherichia coli co-culture for the de novo synthesis of genkwanin. J Ind Microbiol Biotechnol 2023; 50:kuad030. [PMID: 37738435 PMCID: PMC10565888 DOI: 10.1093/jimb/kuad030] [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: 08/04/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023]
Abstract
Genkwanin has various significant roles in nutrition, biomedicine, and pharmaceutical biology. Previously, this compound was chiefly produced by plant-originated extraction or chemical synthesis. However, due to increasing concern and demand for safe food and environmental issues, the biotechnological production of genkwanin and other bioactive compounds based on safe, cheap, and renewable substrates has gained much interest. This paper described recombinant Escherichia coli-based co-culture engineering that was reconstructed for the de novo production of genkwanin from d-glucose. The artificial genkwanin biosynthetic chain was divided into 2 modules in which the upstream strain contained the genes for synthesizing p-coumaric acid from d-glucose, and the downstream module contained a gene cluster that produced the precursor apigenin and the final product, genkwanin. The Box-Behnken design, a response surface methodology, was used to empirically model the production of genkwanin and optimize its productivity. As a result, the application of the designed co-culture improved the genkwanin production by 48.8 ± 1.3 mg/L or 1.7-fold compared to the monoculture. In addition, the scale-up of genkwanin bioproduction by a bioreactor resulted in 68.5 ± 1.9 mg/L at a 48 hr time point. The combination of metabolic engineering and fermentation technology was therefore a very efficient and applicable approach to enhance the production of other bioactive compounds.
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Affiliation(s)
- Nguyen Huy Thuan
- Center for Pharmaceutical Biotechnology, Duy Tan University, Da Nang 550000, Vietnam
| | | | - Nguyen Thanh Trung
- Center for Pharmaceutical Biotechnology, Duy Tan University, Da Nang 550000, Vietnam
| | - Nguyen Van Giang
- Faculty of Biotechnology, Vietnam National University of Agriculture, Trau Quy, Hanoi 100000, Vietnam
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11
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Microorganisms for Ginsenosides Biosynthesis: Recent Progress, Challenges, and Perspectives. Molecules 2023; 28:molecules28031437. [PMID: 36771109 PMCID: PMC9921939 DOI: 10.3390/molecules28031437] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/24/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
Ginsenosides are major bioactive compounds present in the Panax species. Ginsenosides exhibit various pharmaceutical properties, including anticancer, anti-inflammatory, antimetastatic, hypertension, and neurodegenerative disorder activities. Although several commercial products have been presented on the market, most of the current chemical processes have an unfriendly environment and a high cost of downstream processing. Compared to plant extraction, microbial production exhibits high efficiency, high selectivity, and saves time for the manufacturing of industrial products. To reach the full potential of the pharmaceutical resource of ginsenoside, a suitable microorganism has been developed as a novel approach. In this review, cell biological mechanisms in anticancer activities and the present state of research on the production of ginsenosides are summarized. Microbial hosts, including native endophytes and engineered microbes, have been used as novel and promising approaches. Furthermore, the present challenges and perspectives of using microbial hosts to produce ginsenosides have been discussed.
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Pan X, Tang M, You J, Hao Y, Zhang X, Yang T, Rao Z. A Novel Method to Screen Strong Constitutive Promoters in Escherichia coli and Serratia marcescens for Industrial Applications. BIOLOGY 2022; 12:biology12010071. [PMID: 36671763 PMCID: PMC9855843 DOI: 10.3390/biology12010071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/18/2022] [Accepted: 12/28/2022] [Indexed: 01/04/2023]
Abstract
Promoters serve as the switch of gene transcription, playing an important role in regulating gene expression and metabolites production. However, the approach to screening strong constitutive promoters in microorganisms is still limited. In this study, a novel method was designed to identify strong constitutive promoters in E. coli and S. marcescens based on random genomic interruption and fluorescence-activated cell sorting (FACS) technology. First, genomes of E. coli, Bacillus subtilis, and Corynebacterium glutamicum were randomly interrupted and inserted into the upstream of reporter gene gfp to construct three promoter libraries, and a potential strong constitutive promoter (PBS) suitable for E. coli was screened via FACS technology. Second, the core promoter sequence (PBS76) of the screened promoter was identified by sequence truncation. Third, a promoter library of PBS76 was constructed by installing degenerate bases via chemical synthesis for further improving its strength, and the intensity of the produced promoter PBS76-100 was 59.56 times higher than that of the promoter PBBa_J23118. Subsequently, promoters PBBa_J23118, PBS76, PBS76-50, PBS76-75, PBS76-85, and PBS76-100 with different strengths were applied to enhance the metabolic flux of L-valine synthesis, and the L-valine yield was significantly improved. Finally, a strong constitutive promoter suitable for S. marcescens was screened by a similar method and applied to enhance prodigiosin production by 34.81%. Taken together, the construction of a promoter library based on random genomic interruption was effective to screen the strong constitutive promoters for fine-tuning gene expression and reprogramming metabolic flux in various microorganisms.
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Affiliation(s)
- 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
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Mi Tang
- 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
| | - 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
| | - Xian 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
| | - Taowei Yang
- 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
- Correspondence: ; Tel.: +86-510-85916881
| | - 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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Cheng J, Luo Z, Wang B, Yan L, Zhang S, Zhang J, Lu Y, Wang W. An artificial pathway for trans-4-hydroxy-L-pipecolic acid production from L-lysine in Escherichia coli. Biosci Biotechnol Biochem 2022; 86:1476-1481. [PMID: 35998310 DOI: 10.1093/bbb/zbac118] [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: 06/01/2022] [Accepted: 07/06/2022] [Indexed: 11/14/2022]
Abstract
Trans-4-hydroxy-L-pipecolic acid (Trans-4-HyPip) is a hydroxylated product of L-pipecolic acid, and which is widely used in pharmaceutical and chemical industry. Here, a trans-4-HyPip biosynthesis module was designed and constructed in Escherichia coli by overexpressing lysine α-oxidase, Δ1-piperideine-2-carboxylase reductase, glucose dehydrogenase, lysine permease, catalase and L-pipecolic acid trans-4-hydroxylase for expanding the lysine catabolism pathway. 4.89 g/L of trans-4-HyPip was generated in shake flasks from 8 g/L of L-pipecolic acid. By this approach, 14.86 g/L of trans-4-HyPip was produced from lysine after 48 h in a 5-L bioreactor. As far as we know, this is the first multi-enzyme cascade catalytic system for the production of trans-4-HyPip using Escherichia coli from L-lysine. Therefore, it can be considered as a potential candidate for industrial production of trans-4-HyPip in microorganisms.
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Affiliation(s)
- Jie Cheng
- Meat Processing Key Laboratory of Sichuan Province, College of Food and Biological Engineering, Chengdu University, Chengdu, P.R. China
| | - Zhou Luo
- Meat Processing Key Laboratory of Sichuan Province, College of Food and Biological Engineering, Chengdu University, Chengdu, P.R. China
| | - Bangxu Wang
- Meat Processing Key Laboratory of Sichuan Province, College of Food and Biological Engineering, Chengdu University, Chengdu, P.R. China.,College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, P.R. China
| | - Lixiu Yan
- Chongqing Academy of Metrology and Quality Inspection, Chongqing, P.R. China
| | - Suyi Zhang
- Luzhou Laojiao Co., Ltd., Luzhou, Sichuan, P.R. China
| | - Jiamin Zhang
- Meat Processing Key Laboratory of Sichuan Province, College of Food and Biological Engineering, Chengdu University, Chengdu, P.R. China
| | - Yao Lu
- College of Biological and Chemical Engineering, Guangxi University of Science and Technology, Liuzhou, P.R. China
| | - Wei Wang
- Meat Processing Key Laboratory of Sichuan Province, College of Food and Biological Engineering, Chengdu University, Chengdu, P.R. China
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14
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Thuan NH, Tatipamula VB, Canh NX, Van Giang N. Recent advances in microbial co-culture for production of value-added compounds. 3 Biotech 2022; 12:115. [PMID: 35547018 PMCID: PMC9018925 DOI: 10.1007/s13205-022-03177-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 03/31/2022] [Indexed: 02/06/2023] Open
Abstract
Micro-organisms have often been used to produce bioactive compounds as antibiotics, antifungals, and anti-tumors, etc. due to their easy and applicable culture, genetic manipulation, and extraction, etc. Mainly, microbial mono-cultures have been applied to produce value-added compounds and gotten numerous valuable results. However, mono-culture also has several complicated problems, such as metabolic burdens affecting the growth and development of the host, leading to a decrease in titer of the target compound. To circumvent those limitations, microbial co-culture has been technically developed and gained much interest compared to mono-culture. For example, co-culture simplifies the design of artificial biosynthetic pathways and restricts the recombinant host's metabolic burden, causing increased titer of desired compounds. This paper summarizes the recent advanced progress in applying microbial platform co-culture to produce natural products, such as flavonoid, terpenoid, alkaloid, etc. Furthermore, importantly different strategies for enhancing production, overcoming the metabolic burdens, building autonomous modulation of cell growth rate and culture composition in response to a quorum-sensing signal, etc., were also described in detail.
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Affiliation(s)
- Nguyen Huy Thuan
- Center for Molecular Biology, Duy Tan University, Da Nang, 550000 Vietnam
| | | | - Nguyen Xuan Canh
- Faculty of Biotechnology, Vietnam National University of Agriculture, Gialam, Hanoi Vietnam
| | - Nguyen Van Giang
- Faculty of Biotechnology, Vietnam National University of Agriculture, Gialam, Hanoi Vietnam
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15
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Meng S, Wang Y, Mu J, Pang Z, Wang F, Liao Y. Biological preparation and characterization of surfactant‐like peptides. J SURFACTANTS DETERG 2022. [DOI: 10.1002/jsde.12590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Shujuan Meng
- School of Light Industry Beijing Technology and Business University (BTBU) Beijing China
| | - Yadong Wang
- School of Light Industry Beijing Technology and Business University (BTBU) Beijing China
| | - Jing Mu
- School of Light Industry Beijing Technology and Business University (BTBU) Beijing China
| | - Zhengjun Pang
- School of Light Industry Beijing Technology and Business University (BTBU) Beijing China
| | - Fenghuan Wang
- School of Light Industry Beijing Technology and Business University (BTBU) Beijing China
| | - Yonghong Liao
- School of Light Industry Beijing Technology and Business University (BTBU) Beijing China
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16
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Dong H, Cui Y, Zhang D. CRISPR/Cas Technologies and Their Applications in Escherichia coli. Front Bioeng Biotechnol 2021; 9:762676. [PMID: 34858961 PMCID: PMC8632213 DOI: 10.3389/fbioe.2021.762676] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 10/20/2021] [Indexed: 11/22/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) systems have revolutionized genome editing and greatly promoted the development of biotechnology. However, these systems unfortunately have not been developed and applied in bacteria as extensively as in eukaryotic organism. Here, the research progress on the most widely used CRISPR/Cas tools and their applications in Escherichia coli is summarized. Genome editing based on homologous recombination, non-homologous DNA end-joining, transposons, and base editors are discussed. Finally, the state of the art of transcriptional regulation using CRISPRi is briefly reviewed. This review provides a useful reference for the application of CRISPR/Cas systems in other bacterial species.
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Affiliation(s)
- Huina Dong
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Yali Cui
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,University of Chinese Academy of Sciences, Beijing, China
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Microbial cell factories: a biotechnology journey across species. Essays Biochem 2021. [DOI: 10.1042/ebc20210037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Abstract
An increasingly large number of microbial species with potential for synthetic biology and metabolic engineering has been introduced over the last few years, adding huge variety to the opportunities of biotechnology. Historically, however, only a handful of microbes have attained the acceptance and widespread use that are needed to fulfil the needs of industrial bioproduction. Synthetic biology is setting out to standardise the methods, parts and platform organisms for bioproduction. These platform organisms, or chassis cells, derive from what has been termed microbial cell factories since the 1990s. In this collection of reviews, 18 microbial cell factories are featured, which belong to one of these three groups: (i) microbes already used before modern biotechnology was introduced; (ii) the first generation of engineered microbes; and (iii) promising new host organisms. The reviews are intended to provide readers with an overview of the current state of methodology and application of these cell factories, and with guidelines of how to use them for bioproduction.
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