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Chang CW, Truong VA, Pham NN, Hu YC. RNA-guided genome engineering: paradigm shift towards transposons. Trends Biotechnol 2024; 42:970-985. [PMID: 38443218 DOI: 10.1016/j.tibtech.2024.02.006] [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: 10/14/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 03/07/2024]
Abstract
CRISPR-Cas systems revolutionized the genome engineering field but need to induce double-strand breaks (DSBs) and may be difficult to deliver due to their large protein size. Tn7-like transposons such as CRISPR-associated transposons (CASTs) can be repurposed for RNA-guided DSB-free integration, and obligate mobile element guided activity (OMEGA) proteins of the IS200/IS605 transposon family have been developed as hypercompact RNA-guided genome editing tools. CASTs and OMEGA are exciting, innovative genome engineering tools that can improve the precision and efficiency of editing. This review explores the recent developments and uses of CASTs and OMEGA in genome editing across prokaryotic and eukaryotic cells. The pros and cons of these transposon-based systems are deliberated in comparison to other CRISPR systems.
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Affiliation(s)
- Chin-Wei Chang
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Vy Anh Truong
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Nam Ngoc Pham
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Yu-Chen Hu
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu 300, Taiwan; Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu 300, Taiwan.
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2
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Yang Y, Zou Y, Chen X, Sun H, Hua X, Johnston L, Zeng X, Qiao S, Ye C. Metabolic engineering of Escherichia coli for the production of 5-aminolevulinic acid based on combined metabolic pathway modification and reporter-guided mutant selection (RGMS). BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:82. [PMID: 38886801 PMCID: PMC11184883 DOI: 10.1186/s13068-024-02530-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 06/10/2024] [Indexed: 06/20/2024]
Abstract
BACKGROUND 5-Aminolevulinic acid (ALA) recently received much attention due to its potential application in many fields such as medicine, nutrition and agriculture. Metabolic engineering is an efficient strategy to improve microbial production of 5-ALA. RESULTS In this study, an ALA production strain of Escherichia coli was constructed by rational metabolic engineering and stepwise improvement. A metabolic strategy to produce ALA directly from glucose in this recombinant E. coli via both C4 and C5 pathways was applied herein. The expression of a modified hemARS gene and rational metabolic engineering by gene knockouts significantly improved ALA production from 765.9 to 2056.1 mg/L. Next, we tried to improve ALA production by RGMS-directed evolution of eamA gene. After RGMS, the ALA yield of strain A2-ASK reached 2471.3 mg/L in flask. Then, we aimed to improve the oxidation resistance of cells by overexpressing sodB and katE genes and ALA yield reached 2703.8 mg/L. A final attempt is to replace original promoter of hemB gene in genome with a weaker one to decrease its expression. After 24 h cultivation, a high ALA yield of 19.02 g/L was achieved by 108-ASK in a 5 L fermenter. CONCLUSIONS These results suggested that an industrially competitive strain can be efficiently developed by metabolic engineering based on combined rational modification and optimization of gene expression.
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Affiliation(s)
- Yuting Yang
- State Key Laboratory of Animal Nutrition and Feeding, Ministry of Agriculture Feed Industry Centre, China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Bio-Feed Additives, Beijing, 100193, China
| | - Yuhong Zou
- State Key Laboratory of Animal Nutrition and Feeding, Ministry of Agriculture Feed Industry Centre, China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Bio-Feed Additives, Beijing, 100193, China
| | - Xi Chen
- State Key Laboratory for Agro-Biotechnology, Ministry of Agriculture and Rural Affairs, Key Laboratory for Pest Monitoring and Green Management, Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Haidong Sun
- National Feed Engineering Technology Research Centre, Beijing, 100193, China
| | - Xia Hua
- State Key Laboratory for Agro-Biotechnology, Ministry of Agriculture and Rural Affairs, Key Laboratory for Pest Monitoring and Green Management, Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Lee Johnston
- Swine Nutrition and Production, West Central Research and Outreach Center, University of Minnesota, Morris, MN, 56267, USA
| | - Xiangfang Zeng
- State Key Laboratory of Animal Nutrition and Feeding, Ministry of Agriculture Feed Industry Centre, China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Bio-Feed Additives, Beijing, 100193, China
| | - Shiyan Qiao
- State Key Laboratory of Animal Nutrition and Feeding, Ministry of Agriculture Feed Industry Centre, China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Bio-Feed Additives, Beijing, 100193, China
| | - Changchuan Ye
- State Key Laboratory of Animal Nutrition and Feeding, Ministry of Agriculture Feed Industry Centre, China Agricultural University, Beijing, 100193, China.
- Department of Animal Science, College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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3
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Rafiq MS, Shabbir MA, Raza A, Irshad S, Asghar A, Maan MK, Gondal MA, Hao H. CRISPR-Cas System: A New Dawn to Combat Antibiotic Resistance. BioDrugs 2024; 38:387-404. [PMID: 38605260 DOI: 10.1007/s40259-024-00656-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2024] [Indexed: 04/13/2024]
Abstract
Antimicrobial resistance (AMR) can potentially harm global public health. Horizontal gene transfer (HGT), which speeds up the emergence of AMR and increases the burden of drug resistance in mobile genetic elements (MGEs), is the primary method by which AMR genes are transferred across bacterial pathogens. New approaches are urgently needed to halt the spread of bacterial diseases and antibiotic resistance. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), an RNA-guided adaptive immune system, protects prokaryotes from foreign DNA like plasmids and phages. This approach may be essential in limiting horizontal gene transfer and halting the spread of antibiotic resistance. The CRISPR-Cas system has been crucial in identifying and understanding resistance mechanisms and developing novel therapeutic approaches. This review article investigates the CRISPR-Cas system's potential as a tool to combat bacterial AMR. Antibiotic-resistant bacteria can be targeted and eliminated by the CRISPR-Cas system. It has been proven to be an efficient method for removing carbapenem-resistant plasmids and regaining antibiotic susceptibility. The CRISPR-Cas system has enormous potential as a weapon against bacterial AMR. It precisely targets and eliminates antibiotic-resistant bacteria, facilitates resistance mechanism identification, and offers new possibilities in diagnostics and therapeutics.
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Affiliation(s)
- Muhammad Shahzad Rafiq
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070, China
| | | | - Ahmed Raza
- Livestock and Dairy Development Department, Punjab, Pakistan
| | - Shoaib Irshad
- Livestock and Dairy Development Department, Punjab, Pakistan
| | - Andleeb Asghar
- Institute of Pharmaceutical Sciences, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Muhammad Kashif Maan
- Department of Veterinary Surgery and Pet Sciences, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Mushtaq Ahmed Gondal
- Institute of Continuing Education and Extension, Cholistan University of Veterinary and Animal Sciences, Bahawalpur, Pakistan
| | - Haihong Hao
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070, China.
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4
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Kumar V, Barwal A, Sharma N, Mir DS, Kumar P, Kumar V. Therapeutic proteins: developments, progress, challenges, and future perspectives. 3 Biotech 2024; 14:112. [PMID: 38510462 PMCID: PMC10948735 DOI: 10.1007/s13205-024-03958-z] [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: 06/03/2023] [Accepted: 02/13/2024] [Indexed: 03/22/2024] Open
Abstract
Proteins are considered magic molecules due to their enormous applications in the health sector. Over the past few decades, therapeutic proteins have emerged as a promising treatment option for various diseases, particularly cancer, cardiovascular disease, diabetes, and others. The formulation of protein-based therapies is a major area of research, however, a few factors still hinder the large-scale production of these therapeutic products, such as stability, heterogenicity, immunogenicity, high cost of production, etc. This review provides comprehensive information on various sources and production of therapeutic proteins. The review also summarizes the challenges currently faced by scientists while developing protein-based therapeutics, along with possible solutions. It can be concluded that these proteins can be used in combination with small molecular drugs to give synergistic benefits in the future.
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Affiliation(s)
- Vimal Kumar
- University Institute of Biotechnology, Chandigarh University, Gharuan, Mohali, Punjab 140413 India
| | - Arti Barwal
- Department of Microbial Biotechnology, Panjab University, South Campus, Sector-25, Chandigarh, 160014 India
| | - Nitin Sharma
- Department of Biotechnology, Chandigarh Group of Colleges, Mohali, Punjab 140307 India
| | - Danish Shafi Mir
- University Institute of Biotechnology, Chandigarh University, Gharuan, Mohali, Punjab 140413 India
| | - Pradeep Kumar
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, 173229 India
| | - Vikas Kumar
- University Institute of Biotechnology, Chandigarh University, Gharuan, Mohali, Punjab 140413 India
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5
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Junaid M, Thirapanmethee K, Khuntayaporn P, Chomnawang MT. CRISPR-Based Gene Editing in Acinetobacter baumannii to Combat Antimicrobial Resistance. Pharmaceuticals (Basel) 2023; 16:920. [PMID: 37513832 PMCID: PMC10384873 DOI: 10.3390/ph16070920] [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: 05/25/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023] Open
Abstract
Antimicrobial resistance (AMR) poses a significant threat to the health, social, environment, and economic sectors on a global scale and requires serious attention to addressing this issue. Acinetobacter baumannii was given top priority among infectious bacteria because of its extensive resistance to nearly all antibiotic classes and treatment options. Carbapenem-resistant A. baumannii is classified as one of the critical-priority pathogens on the World Health Organization (WHO) priority list of antibiotic-resistant bacteria for effective drug development. Although available genetic manipulation approaches are successful in A. baumannii laboratory strains, they are limited when employed on newly acquired clinical strains since such strains have higher levels of AMR than those used to select them for genetic manipulation. Recently, the CRISPR-Cas (Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein) system has emerged as one of the most effective, efficient, and precise methods of genome editing and offers target-specific gene editing of AMR genes in a specific bacterial strain. CRISPR-based genome editing has been successfully applied in various bacterial strains to combat AMR; however, this strategy has not yet been extensively explored in A. baumannii. This review provides detailed insight into the progress, current scenario, and future potential of CRISPR-Cas usage for AMR-related gene manipulation in A. baumannii.
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Affiliation(s)
- Muhammad Junaid
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
| | - Krit Thirapanmethee
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
| | - Piyatip Khuntayaporn
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
| | - Mullika Traidej Chomnawang
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
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6
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Luelf UJ, Böhmer LM, Li S, Urlacher VB. Effect of chromosomal integration on catalytic performance of a multi-component P450 system in Escherichia coli. Biotechnol Bioeng 2023. [PMID: 37186287 DOI: 10.1002/bit.28404] [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: 02/07/2023] [Revised: 04/04/2023] [Accepted: 04/09/2023] [Indexed: 05/17/2023]
Abstract
Cytochromes P450 are useful biocatalysts in synthetic chemistry and important bio-bricks in synthetic biology. Almost all bacterial P450s require separate redox partners for their activity, which are often expressed in recombinant Escherichia coli using multiple plasmids. However, the application of CRISPR/Cas recombineering facilitated chromosomal integration of heterologous genes which enables more stable and tunable expression of multi-component P450 systems for whole-cell biotransformations. Herein, we compared three E. coli strains W3110, JM109, and BL21(DE3) harboring three heterologous genes encoding a P450 and two redox partners either on plasmids or after chromosomal integration in two genomic loci. Both loci proved to be reliable and comparable for the model regio- and stereoselective two-step oxidation of (S)-ketamine. Furthermore, the CRISPR/Cas-assisted integration of the T7 RNA polymerase gene enabled an easy extension of T7 expression strains. Higher titers of soluble active P450 were achieved in E. coli harboring a single chromosomal copy of the P450 gene compared to E. coli carrying a medium copy pET plasmid. In addition, improved expression of both redox partners after chromosomal integration resulted in up to 80% higher (S)-ketamine conversion and more than fourfold increase in total turnover numbers.
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Affiliation(s)
- U Joost Luelf
- Institute of Biochemistry, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Lisa M Böhmer
- Institute of Biochemistry, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Shengying Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China
| | - Vlada B Urlacher
- Institute of Biochemistry, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
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7
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Zhang K, Zhang W, Qin M, Li Y, Wang H. Characterization and Application of the Sugar Transporter Zmo0293 from Zymomonas mobilis. Int J Mol Sci 2023; 24:ijms24065888. [PMID: 36982961 PMCID: PMC10055971 DOI: 10.3390/ijms24065888] [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: 02/03/2023] [Revised: 03/15/2023] [Accepted: 03/19/2023] [Indexed: 03/30/2023] Open
Abstract
Zymomonas mobilis is a natural ethanologen with many desirable characteristics, which makes it an ideal industrial microbial biocatalyst for the commercial production of desirable bioproducts. Sugar transporters are responsible for the import of substrate sugars and the conversion of ethanol and other products. Glucose-facilitated diffusion protein Glf is responsible for facilitating the diffusion of glucose uptake in Z. mobilis. However, another sugar transporter-encoded gene, ZMO0293, is poorly characterized. We employed gene deletion and heterologous expression mediated by the CRISPR/Cas method to investigate the role of ZMO0293. The results showed that deletion of the ZMO0293 gene slowed growth and reduced ethanol production and the activities of key enzymes involved in glucose metabolism in the presence of high concentrations of glucose. Moreover, ZMO0293 deletion caused different transcriptional changes in some genes of the Entner Doudoroff (ED) pathway in the ZM4-ΔZM0293 strain but not in ZM4 cells. The integrated expression of ZMO0293 restored the growth of the glucose uptake-defective strain Escherichia coli BL21(DE3)-ΔptsG. This study reveals the function of the ZMO0293 gene in Z. mobilis in response to high concentrations of glucose and provides a new biological part for synthetic biology.
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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
| | - Wenwen 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
| | - Yi Li
- 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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8
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Metabolic engineering of Escherichia coli to enhance protein production by coupling ShCAST-based optimized transposon system and CRISPR interference. J Taiwan Inst Chem Eng 2023. [DOI: 10.1016/j.jtice.2023.104746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
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9
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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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10
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Efficiency of CRISPR-Cas9 genetic engineering in Escherichia coli BL21 is impaired by lack of Lon protease. J Microbiol Methods 2023; 204:106648. [PMID: 36470413 DOI: 10.1016/j.mimet.2022.106648] [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: 10/24/2022] [Revised: 12/01/2022] [Accepted: 12/01/2022] [Indexed: 12/11/2022]
Abstract
The efficiency with which E.coli BL21 can be modified using CRISPR-Cas9 genetic engineering is several orders of magnitude lower than that of E. coli W3110. We show that the lack of Lon protease is responsible, and demonstrate that restoration of the Lon protease or knock-out of sulA improves CRISPR-Cas9 engineering efficiency of BL21 to levels comparable to E. coli W3110.
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11
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Takamori S, Cicuta P, Takeuchi S, Di Michele L. DNA-assisted selective electrofusion (DASE) of Escherichia coli and giant lipid vesicles. NANOSCALE 2022; 14:14255-14267. [PMID: 36129323 PMCID: PMC9536516 DOI: 10.1039/d2nr03105a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 08/24/2022] [Indexed: 05/27/2023]
Abstract
Synthetic biology and cellular engineering require chemical and physical alterations, which are typically achieved by fusing target cells with each other or with payload-carrying vectors. On one hand, electrofusion can efficiently induce the merging of biological cells and/or synthetic analogues via the application of intense DC pulses, but it lacks selectivity and often leads to uncontrolled fusion. On the other hand, synthetic DNA-based constructs, inspired by natural fusogenic proteins, have been shown to induce a selective fusion between membranes, albeit with low efficiency. Here we introduce DNA-assisted selective electrofusion (DASE) which relies on membrane-anchored DNA constructs to bring together the objects one seeks to merge, and applying an electric impulse to trigger their fusion. The DASE process combines the efficiency of standard electrofusion and the selectivity of fusogenic nanostructures, as we demonstrate by inducing and characterizing the fusion of spheroplasts derived from Escherichia coli bacteria with cargo-carrying giant lipid vesicles.
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Affiliation(s)
- Sho Takamori
- Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK.
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8505, Japan.
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa 213-0012, Japan
| | - Pietro Cicuta
- Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK.
| | - Shoji Takeuchi
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8505, Japan.
- Artificial Cell Membrane Systems Group, Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa 213-0012, Japan
- Department of Mechano-Informatics, Graduate School of Information Science and Technology, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8654, Japan
- International Research Center for Neurointelligence (IRCN), The University of Tokyo Institutes for Advanced Study (UTIAS), The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8654, Japan
| | - Lorenzo Di Michele
- Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK.
- Department of Chemistry, Imperial College London, London W12 0BZ, UK.
- fabriCELL, Imperial College London, London W12 0BZ, UK
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12
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Bubnov DM, Yuzbashev TV, Khozov AA, Melkina OE, Vybornaya TV, Stan GB, Sineoky SP. Robust counterselection and advanced λRed recombineering enable markerless chromosomal integration of large heterologous constructs. Nucleic Acids Res 2022; 50:8947-8960. [PMID: 35920321 PMCID: PMC9410887 DOI: 10.1093/nar/gkac649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 07/07/2022] [Accepted: 07/20/2022] [Indexed: 11/17/2022] Open
Abstract
Despite advances in bacterial genome engineering, delivery of large synthetic constructs remains challenging in practice. In this study, we propose a straightforward and robust approach for the markerless integration of DNA fragments encoding whole metabolic pathways into the genome. This approach relies on the replacement of a counterselection marker with cargo DNA cassettes via λRed recombineering. We employed a counterselection strategy involving a genetic circuit based on the CI repressor of λ phage. Our design ensures elimination of most spontaneous mutants, and thus provides a counterselection stringency close to the maximum possible. We improved the efficiency of integrating long PCR-generated cassettes by exploiting the Ocr antirestriction function of T7 phage, which completely prevents degradation of unmethylated DNA by restriction endonucleases in wild-type bacteria. The employment of highly restrictive counterselection and ocr-assisted λRed recombineering allowed markerless integration of operon-sized cassettes into arbitrary genomic loci of four enterobacterial species with an efficiency of 50–100%. In the case of Escherichia coli, our strategy ensures simple combination of markerless mutations in a single strain via P1 transduction. Overall, the proposed approach can serve as a general tool for synthetic biology and metabolic engineering in a range of bacterial hosts.
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Affiliation(s)
- Dmitrii M Bubnov
- Bioresource Center Russian National Collection of Industrial Microorganisms (BRC VKPM), State Research Institute for Genetics and Selection of Industrial Microorganisms of National Research Center 'Kurchatov Institute' (NRC 'Kurchatov Institute' - GosNIIgenetika), 1-st Dorozhny pr., 1, Moscow 117545, Russia.,Kurchatov Complex of Genetic Research, NRC 'Kurchatov Institute', Kurchatov Square, 1, Moscow 123098, Russia
| | - Tigran V Yuzbashev
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Andrey A Khozov
- Bioresource Center Russian National Collection of Industrial Microorganisms (BRC VKPM), State Research Institute for Genetics and Selection of Industrial Microorganisms of National Research Center 'Kurchatov Institute' (NRC 'Kurchatov Institute' - GosNIIgenetika), 1-st Dorozhny pr., 1, Moscow 117545, Russia.,Kurchatov Complex of Genetic Research, NRC 'Kurchatov Institute', Kurchatov Square, 1, Moscow 123098, Russia.,Department of Microbiology, Faculty of Biology, Lomonosov Moscow State University, Lenin's Hills 1-12, Moscow 119234, Russia
| | - Olga E Melkina
- Kurchatov Complex of Genetic Research, NRC 'Kurchatov Institute', Kurchatov Square, 1, Moscow 123098, Russia.,Laboratory of Bacterial Genetics, NRC 'Kurchatov Institute' - GosNIIgenetika, 1-st Dorozhny pr., 1, Moscow 117545, Russia
| | - Tatiana V Vybornaya
- Bioresource Center Russian National Collection of Industrial Microorganisms (BRC VKPM), State Research Institute for Genetics and Selection of Industrial Microorganisms of National Research Center 'Kurchatov Institute' (NRC 'Kurchatov Institute' - GosNIIgenetika), 1-st Dorozhny pr., 1, Moscow 117545, Russia.,Kurchatov Genomic Center, NRC 'Kurchatov Institute' - GosNIIgenetika, 1-st Dorozhny pr., 1, Moscow 117545, Russia
| | - Guy-Bart Stan
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Sergey P Sineoky
- Bioresource Center Russian National Collection of Industrial Microorganisms (BRC VKPM), State Research Institute for Genetics and Selection of Industrial Microorganisms of National Research Center 'Kurchatov Institute' (NRC 'Kurchatov Institute' - GosNIIgenetika), 1-st Dorozhny pr., 1, Moscow 117545, Russia.,Kurchatov Complex of Genetic Research, NRC 'Kurchatov Institute', Kurchatov Square, 1, Moscow 123098, Russia
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13
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Whole Genome Sequencing and CRISPR/Cas9 Gene Editing of Enterotoxigenic Escherichia coli BE311 for Fluorescence Labeling and Enterotoxin Analyses. Int J Mol Sci 2022; 23:ijms23147502. [PMID: 35886856 PMCID: PMC9321511 DOI: 10.3390/ijms23147502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/04/2022] [Accepted: 07/05/2022] [Indexed: 01/07/2023] Open
Abstract
Some prevention strategies, including vaccines and antibiotic alternatives, have been developed to reduce enterotoxigenic Escherichia coli proliferation in animal production. In this study, a wild-type strain of BE311 with a virulent heat-stable enterotoxin gene identical to E. coli K99 was isolated for its high potential for gene expression ability. The whole genome of E. coli BE311 was sequenced for gene analyses and editing. Subsequently, the fluorescent gene mCherry was successfully knocked into the genome of E. coli BE311 by CRISPR/Cas9. The E. coli BE311−mCherry strain was precisely quantified through the fluorescence intensity and red colony counting. The inflammatory factors in different intestinal tissues all increased significantly after an E. coli BE311−mCherry challenge in Sprague−Dawley rats (p < 0.05). The heat-stable enterotoxin gene of E. coli BE311 was knocked out, and an attenuated vaccine host E. coli BE311-STKO was constructed. Flow cytometry showed apoptotic cell numbers were lower following a challenge of IPEC-J2 cells with E. coli BE311-STKO than with E. coli BE311. Therefore, the E. coli BE311−mCherry and E. coli BE311-STKO strains that were successfully constructed based on the gene knock-in and knock-out technology could be used as ideal candidates in ETEC challenge models and for the development of attenuated vaccines.
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14
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Cheng ZH, Wu J, Liu JQ, Min D, Liu DF, Li WW, Yu HQ. Repurposing CRISPR RNA-guided integrases system for one-step, efficient genomic integration of ultra-long DNA sequences. Nucleic Acids Res 2022; 50:7739-7750. [PMID: 35776123 PMCID: PMC9303307 DOI: 10.1093/nar/gkac554] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 06/14/2022] [Accepted: 06/16/2022] [Indexed: 01/26/2023] Open
Abstract
Genomic integration techniques offer opportunities for generation of engineered microorganisms with improved or even entirely new functions but are currently limited by inability for efficient insertion of long genetic payloads due to multiplexing. Herein, using Shewanella oneidensis MR-1 as a model, we developed an optimized CRISPR-associated transposase from cyanobacteria Scytonema hofmanni (ShCAST system), which enables programmable, RNA-guided transposition of ultra-long DNA sequences (30 kb) onto bacterial chromosomes at ∼100% efficiency in a single orientation. In this system, a crRNA (CRISPR RNA) was used to target multicopy loci like insertion-sequence elements or combining I-SceI endonuclease, thereby allowing efficient single-step multiplexed or iterative DNA insertions. The engineered strain exhibited drastically improved substrate diversity and extracellular electron transfer ability, verifying the success of this system. Our work greatly expands the application range and flexibility of genetic engineering techniques and may be readily extended to other bacteria for better controlling various microbial processes.
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Affiliation(s)
- Zhou-Hua Cheng
- School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
| | - Jie Wu
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Jia-Qi Liu
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Di Min
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Dong-Feng Liu
- School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China.,Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Wen-Wei Li
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Han-Qing Yu
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
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15
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Li H, Pham NN, Shen CR, Chang CW, Tu Y, Chang YH, Tu J, Nguyen MTT, Hu YC. Combinatorial CRISPR Interference Library for Enhancing 2,3-BDO Production and Elucidating Key Genes in Cyanobacteria. Front Bioeng Biotechnol 2022; 10:913820. [PMID: 35800335 PMCID: PMC9253771 DOI: 10.3389/fbioe.2022.913820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/16/2022] [Indexed: 12/23/2022] Open
Abstract
Cyanobacteria can convert CO2 to chemicals such as 2,3-butanediol (2,3-BDO), rendering them promising for renewable production and carbon neutralization, but their applications are limited by low titers. To enhance cyanobacterial 2,3-BDO production, we developed a combinatorial CRISPR interference (CRISPRi) library strategy. We integrated the 2,3-BDO pathway genes and a CRISPRi library into the cyanobacterium PCC7942 using the orthogonal CRISPR system to overexpress pathway genes and attenuate genes that inhibit 2,3-BDO formation. The combinatorial CRISPRi library strategy allowed us to inhibit fbp, pdh, ppc, and sps (which catalyzes the synthesis of fructose-6-phosphate, acetyl-coenzyme A, oxaloacetate, and sucrose, respectively) at different levels, thereby allowing for rapid screening of a strain that enhances 2,3-BDO production by almost 2-fold to 1583.8 mg/L. Coupled with a statistical model, we elucidated that differentially inhibiting all the four genes enhances 2,3-BDO synthesis to varying degrees. fbp and pdh suppression exerted more profound effects on 2,3-BDO production than ppc and sps suppression, and these four genes can be repressed simultaneously without mutual interference. The CRISPRi library approach paves a new avenue to combinatorial metabolic engineering of cyanobacteria.
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Affiliation(s)
- Hung Li
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Nam Ngoc Pham
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Claire R. Shen
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Chin-Wei Chang
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Yi Tu
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Yi-Hao Chang
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Jui Tu
- Department of Chemical Engineering, National Taiwan University, Taipei, Taiwan
| | - Mai Thanh Thi Nguyen
- Faculty of Chemistry, University of Science, Vietnam National University Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Yu-Chen Hu
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
- Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu, Taiwan
- *Correspondence: Yu-Chen Hu, , orcid.org/0000-0002-9997-4467
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16
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Rangarajan AA, Yilmaz C, Schnetz K. Deletion of FRT-sites by no-SCAR recombineering in Escherichia coli. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35411846 DOI: 10.1099/mic.0.001173] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Lambda-Red recombineering is the most commonly used method to create point mutations, insertions or deletions in Escherichia coli and other bacteria, but usually an Flp recognition target (FRT) scar-site is retained in the genome. Alternative scarless recombineering methods, including CRISPR/Cas9-assisted methods, generally require cloning steps and/or complex PCR schemes for specific targeting of the genome. Here we describe the deletion of FRT scar-sites by the scarless Cas9-assisted recombineering method no-SCAR using an FRT-specific guide RNA, sgRNAFRT, and locus-specific ssDNA oligonucleotides. We applied this method to construct a scarless E. coli strain suitable for gradual induction by l-arabinose. Genome sequencing of the resulting strain and its parent strains demonstrated that no additional mutations were introduced along with the simultaneous deletion of two FRT scar-sites. The FRT-specific no-SCAR selection by sgRNAFRT/Cas9 may be generally applicable to cure FRT scar-sites of E. coli strains constructed by classical λ-Red recombineering.
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Affiliation(s)
- Aathmaja Anandhi Rangarajan
- Institute for Genetics, University of Cologne, Zülpicher Str. 47a, 50674 Cologne, Germany.,Present address: Department of Microbiology and Molecular Genetics, 5180 Biomedical and Physical Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Cihan Yilmaz
- Institute for Genetics, University of Cologne, Zülpicher Str. 47a, 50674 Cologne, Germany
| | - Karin Schnetz
- Institute for Genetics, University of Cologne, Zülpicher Str. 47a, 50674 Cologne, Germany
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17
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Fu D, Wu J, Gu Y, Li Q, Shao Y, Feng H, Song X, Tu J, Qi K. The response regulator OmpR contributes to the pathogenicity of avian pathogenic Escherichia coli. Poult Sci 2022; 101:101757. [PMID: 35240350 PMCID: PMC8892008 DOI: 10.1016/j.psj.2022.101757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/23/2022] [Accepted: 01/25/2022] [Indexed: 11/03/2022] Open
Abstract
Avian colibacillosis is a serious systemic infectious disease in poultry and caused by avian pathogenic Escherichia coli (APEC). Previous studies have shown that 2-component systems (TCSs) are involved in the pathogenicity of APEC. OmpR, a response regulator of OmpR/EnvZ TCS, plays an important role in E. coli K-12. However, whether OmpR correlates with APEC pathogenesis has not been established. In this study, we constructed an ompR gene mutant and complement strains by using the CRISPR-Cas9 system and found that the inactivation of the ompR gene attenuated bacterial motility, biofilm formation, and the production of curli. The resistance to environmental stress, serum sensitivity, adhesion, and invasion of DF-1 cells, and pathogenicity in chicks were all significantly reduced in the mutant strain AE17ΔompR. These phenotypes were restored in the complement strain AE17C-ompR. The qRT-PCR results showed that OmpR influences the expression of genes associated with the flagellum, biofilm formation, and virulence. These findings indicate that the regulator OmpR contributes to APEC pathogenicity by affecting the expression and function of virulence factors.
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18
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Paul Alphy M, Hakkim Hazeena S, Binoop M, Madhavan A, Arun KB, Vivek N, Sindhu R, Kumar Awasthi M, Binod P. Synthesis of C2-C4 diols from bioresources: Pathways and metabolic intervention strategies. BIORESOURCE TECHNOLOGY 2022; 346:126410. [PMID: 34838635 DOI: 10.1016/j.biortech.2021.126410] [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: 10/10/2021] [Revised: 11/17/2021] [Accepted: 11/19/2021] [Indexed: 06/13/2023]
Abstract
Diols are important platform chemicals with extensive industrial applications in biopolymer synthesis, cosmetics, and fuels. The increased dependence on non-renewable sources to meet the energy requirement of the population raised issues regarding fossil fuel depletion and environmental impacts. The utilization of biological methods for the synthesis of diols by utilizing renewable resources such as glycerol and agro-residual wastes gained attention worldwide because of its advantages. Among these, biotransformation of 1,3-propanediol (1,3-PDO) and 2,3-butanediol (2,3-BDO) were extensively studied and at present, these diols are produced commercially in large scale with high yield. Many important isomers of C2-C4 diols lack natural synthetic pathways and development of chassis strains for the synthesis can be accomplished by adopting synthetic biology approaches. This current review depicts an overall idea about the pathways involved in C2-C4 diol production, metabolic intervention strategies and technologies in recent years.
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Affiliation(s)
- Maria Paul Alphy
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum 695 019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sulfath Hakkim Hazeena
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum 695 019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Mohan Binoop
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum 695 019, Kerala, India
| | - Aravind Madhavan
- Rajiv Gandhi Center for Biotechnology, Jagathy, Thiruvananthapuram 695 014, Kerala, India
| | - K B Arun
- Rajiv Gandhi Center for Biotechnology, Jagathy, Thiruvananthapuram 695 014, Kerala, India
| | - Narisetty Vivek
- Centre for Climate and Environmental Protection, School of Water, Energy and Environment, Cranfield University, Cranfield MK43 0AL, UK
| | - Raveendran Sindhu
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum 695 019, Kerala, India
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi 712 100, China
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Trivandrum 695 019, Kerala, India.
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19
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Xue C, Ng IS. Sustainable production of 4-aminobutyric acid (GABA) and cultivation of Chlorella sorokiniana and Chlorella vulgaris as circular economy. BIORESOURCE TECHNOLOGY 2022; 343:126089. [PMID: 34624471 DOI: 10.1016/j.biortech.2021.126089] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/29/2021] [Accepted: 10/01/2021] [Indexed: 06/13/2023]
Abstract
The 4-aminobutyric acid (GABA) is important to produce bio-nylon 4 in biorefineries. First, a glutamate decarboxylase (GAD) was propagated in three different Escherichia coli strains to achieve 100% conversion from 1 M monosodium glutamate after optimization of the process. To make the process greener and more efficient, in situ CO2 adaptation and citrate feeding strategies to maintain the optimal pH value and 498 g/L of GABA was obtained. However, the process releases the equivalent amount of CO2. Therefore, CO2 generated from GABA production was completely sequestered in sodium hydroxide to form bicarbonate and applied in a coupling culture of Chlorella sorokiniana (CS) or Chlorella vulgaris (CV) to increase the biomass when combined with sodium bicarbonate and carbonic anhydrase. Further improvement of 1.65-fold biomass and 1.43-fold lipid content were occurred when supplying GABA to the culture. This integrative process provided the highest GABA production rate without CO2 release, forming an eco-friendly and carbon-neutral technology.
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Affiliation(s)
- Chengfeng Xue
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan.
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20
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Backes N, Phillips GJ. Repurposing CRISPR-Cas Systems as Genetic Tools for the Enterobacteriales. EcoSal Plus 2021; 9:eESP00062020. [PMID: 34125584 PMCID: PMC11163844 DOI: 10.1128/ecosalplus.esp-0006-2020] [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: 03/15/2021] [Accepted: 03/22/2021] [Indexed: 11/20/2022]
Abstract
Over the last decade, the study of CRISPR-Cas systems has progressed from a newly discovered bacterial defense mechanism to a diverse suite of genetic tools that have been applied across all domains of life. While the initial applications of CRISPR-Cas technology fulfilled a need to more precisely edit eukaryotic genomes, creative "repurposing" of this adaptive immune system has led to new approaches for genetic analysis of microorganisms, including improved gene editing, conditional gene regulation, plasmid curing and manipulation, and other novel uses. The main objective of this review is to describe the development and current state-of-the-art use of CRISPR-Cas techniques specifically as it is applied to members of the Enterobacteriales. While many of the applications covered have been initially developed in Escherichia coli, we also highlight the potential, along with the limitations, of this technology for expanding the availability of genetic tools in less-well-characterized non-model species, including bacterial pathogens.
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Affiliation(s)
- Nicholas Backes
- Department of Veterinary Microbiology, Iowa State University, Ames, Iowa, USA
| | - Gregory J. Phillips
- Department of Veterinary Microbiology, Iowa State University, Ames, Iowa, USA
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21
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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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22
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Cen YK, Gong H, Xue YP, Zheng YG. Biosynthesis of l-phosphinothricin with enzymes from chromosomal integrated expression in E. coli. 3 Biotech 2021; 11:477. [PMID: 34777934 DOI: 10.1007/s13205-021-03037-7] [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: 05/24/2021] [Accepted: 10/18/2021] [Indexed: 11/25/2022] Open
Abstract
Phosphinothricin (PPT) is one of the most prevalently using herbicides. The commercial phosphinothricin products are generally in the form of a racemic mixture, of which only the l-phosphinothricin (L-PPT) gives herbicidal function. Synthesis of optically pure L-PPT by deracemization of D/L-PPT is a promising way to cut down the environmental burden and manufacturing cost. To convert D/L-PPT to L-PPT, we expressed the catalytic enzymes by genomic integration in E. coli. The whole production was implemented in two steps in one pot using four catalytic enzymes, namely d-amino acid oxidase, catalase, glutamate dehydrogenase, and glucose dehydrogenase. Finally, after a series of process optimization, the results showed that with our system the overall L-PPT yield reached 86%. Our study demonstrated a new strategy for L-PPT synthesis, based on enzymes from chromosomal integrated expression, which does not depend on antibiotic selection, and shows a high potential for future industrial application.
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Affiliation(s)
- Yu-Ke Cen
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014 China
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014 People's Republic of China
| | - Huo Gong
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014 China
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014 People's Republic of China
| | - Ya-Ping Xue
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014 China
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014 People's Republic of China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014 China
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014 People's Republic of China
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23
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Ye C, Chen X, Yang M, Zeng X, Qiao S. CRISPR/Cas9 mediated T7 RNA polymerase gene knock-in in E. coli BW25113 makes T7 expression system work efficiently. J Biol Eng 2021; 15:22. [PMID: 34384456 PMCID: PMC8359068 DOI: 10.1186/s13036-021-00270-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 06/07/2021] [Indexed: 01/16/2023] Open
Abstract
T7 Expression System is a common method of ensuring tight control and high-level induced expression. However, this system can only work in some bacterial strains in which the T7 RNA Polymerase gene resides in the chromosome. In this study, we successfully introduced a chromosomal copy of the T7 RNA Polymerase gene under control of the lacUV5 promoter into Escherichia coli BW25113. The T7 Expression System worked efficiently in this mutant strain named BW25113-T7. We demonstrated that this mutant strain could satisfactorily produce 5-Aminolevulinic Acid via C5 pathway. A final study was designed to enhance the controllability of T7 Expression System in this mutant strain by constructing a T7 Promoter Variants Library. These efforts advanced E. coli BW25113-T7 to be a practical host for future metabolic engineering efforts.
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Affiliation(s)
- Changchuan Ye
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Centre, China Agricultural University, 100193, Beijing, China.,Beijing Key Laboratory of Bio-feed Additives, 100193, Beijing, China
| | - Xi Chen
- State Key Laboratory for Agro-Biotechnology, and Ministry of Agriculture and Rural Affairs, Key Laboratory for Pest Monitoring and Green Management, Department of Plant Pathology, China Agricultural University, 100193, Beijing, China
| | - Mengjie Yang
- National Feed Engineering Technology Research Centre, 100193, Beijing, China
| | - Xiangfang Zeng
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Centre, China Agricultural University, 100193, Beijing, China.,Beijing Key Laboratory of Bio-feed Additives, 100193, Beijing, China
| | - Shiyan Qiao
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Centre, China Agricultural University, 100193, Beijing, China. .,Beijing Key Laboratory of Bio-feed Additives, 100193, Beijing, China.
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24
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Ji X, Lu P, Hu Y, Xue J, Wu J, Zhang B, Zhang Y, Dong L, Lv H, Wang S. Function Characterization of Endogenous Plasmids in Cronobacter sakazakii and Identification of p-Coumaric Acid as Plasmid-Curing Agent. Front Microbiol 2021; 12:687243. [PMID: 34248908 PMCID: PMC8267800 DOI: 10.3389/fmicb.2021.687243] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 05/25/2021] [Indexed: 11/13/2022] Open
Abstract
Virulence traits and antibiotic resistance are frequently provided by genes located on plasmids. However, experimental verification of the functions of these genes is often lacking due to a lack of related experimental technology. In the present study, an integrated suicide vector was used to efficiently and specifically delete a bacterial endogenous plasmid in Cronobacter sakazakii. The pESA3 plasmid was removed from C. sakazakii BAA-894, and we confirmed that this plasmid contributes to the invasion and virulence of this strain. In addition, the pGW1 plasmid was expunged from C. sakazakii GZcsf-1, and we confirmed that this plasmid confers multidrug resistance. We further screened plasmid-curing agents and found that p-coumaric acid had a remarkable effect on the curing of pESA3 and pGW1 at sub-inhibitory concentrations. Our study investigated the contribution of endogenous plasmids pESA3 and pGW1 by constructing plasmid-cured strains using suicide vectors and suggested that p-coumaric acid can be a safe and effective plasmid-curing agent for C. sakazakii.
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Affiliation(s)
- Xuemeng Ji
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin, China
| | - Ping Lu
- Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical Collage, Tianjin, China
| | - Yaozhong Hu
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin, China
| | - Juan Xue
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Jing Wu
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin, China
| | - Bowei Zhang
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin, China
| | - Yan Zhang
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin, China
| | - Lu Dong
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin, China
| | - Huan Lv
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin, China
| | - Shuo Wang
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin, China
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25
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Alam K, Hao J, Zhang Y, Li A. Synthetic biology-inspired strategies and tools for engineering of microbial natural product biosynthetic pathways. Biotechnol Adv 2021; 49:107759. [PMID: 33930523 DOI: 10.1016/j.biotechadv.2021.107759] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 03/28/2021] [Accepted: 04/23/2021] [Indexed: 02/08/2023]
Abstract
Microbial-derived natural products (NPs) and their derivative products are of great importance and used widely in many fields, especially in pharmaceutical industries. However, there is an immediate need to establish innovative approaches, strategies, and techniques to discover new NPs with novel or enhanced biological properties, due to the less productivity and higher cost on traditional drug discovery pipelines from natural bioresources. Revealing of untapped microbial cryptic biosynthetic gene clusters (BGCs) using DNA sequencing technology and bioinformatics tools makes genome mining possible for NP discovery from microorganisms. Meanwhile, new approaches and strategies in the area of synthetic biology offer great potentials for generation of new NPs by engineering or creating synthetic systems with improved and desired functions. Development of approaches, strategies and tools in synthetic biology can facilitate not only exploration and enhancement in supply, and also in the structural diversification of NPs. Here, we discussed recent advances in synthetic biology-inspired strategies, including bioinformatics and genetic engineering tools and approaches for identification, cloning, editing/refactoring of candidate biosynthetic pathways, construction of heterologous expression hosts, fitness optimization between target pathways and hosts and detection of NP production.
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Affiliation(s)
- Khorshed Alam
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China.
| | - Jinfang Hao
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China.
| | - Aiying Li
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China.
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Benler S, Koonin EV. Phage lysis‐lysogeny switches and programmed cell death: Danse macabre. Bioessays 2020; 42:e2000114. [DOI: 10.1002/bies.202000114] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 08/25/2020] [Indexed: 01/04/2023]
Affiliation(s)
- Sean Benler
- National Center for Biotechnology Information National Library of Medicine National Institutes of Health Bethesda Maryland USA
| | - Eugene V. Koonin
- National Center for Biotechnology Information National Library of Medicine National Institutes of Health Bethesda Maryland USA
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Gurung D, Blumenthal RM. Distribution of RecBCD and AddAB recombination-associated genes among bacteria in 33 phyla. MICROBIOLOGY-SGM 2020; 166:1047-1064. [PMID: 33085588 DOI: 10.1099/mic.0.000980] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Homologous recombination plays key roles in fundamental processes such as recovery from DNA damage and in bacterial horizontal gene transfer, yet there are still open questions about the distribution of recognized components of recombination machinery among bacteria and archaea. RecBCD helicase-nuclease plays a central role in recombination among Gammaproteobacteria like Escherichia coli; while bacteria in other phyla, like the Firmicute Bacillus subtilis, use the related AddAB complex. The activity of at least some of these complexes is controlled by short DNA sequences called crossover hotspot instigator (Chi) sites. When RecBCD or AddAB complexes encounter an autologous Chi site during unwinding, they introduce a nick such that ssDNA with a free end is available to invade another duplex. If homologous DNA is present, RecA-dependent homologous recombination is promoted; if not (or if no autologous Chi site is present) the RecBCD/AddAB complex eventually degrades the DNA. We examined the distribution of recBCD and addAB genes among bacteria, and sought ways to distinguish them unambiguously. We examined bacterial species among 33 phyla, finding some unexpected distribution patterns. RecBCD and addAB are less conserved than recA, with the orthologous recB and addA genes more conserved than the recC or addB genes. We were able to classify RecB vs. AddA and RecC vs. AddB in some bacteria where this had not previously been done. We used logo analysis to identify sequence segments that are conserved, but differ between the RecBC and AddAB proteins, to help future differentiation between members of these two families.
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Affiliation(s)
- Deepti Gurung
- Present address: Department of Cancer Biology, College of Medicine & Life Sciences, The University of Toledo, Toledo OH 43614-1021, USA.,Department of Medical Microbiology & Immunology, and Program in Bioinformatics, College of Medicine & Life Sciences, The University of Toledo, Toledo OH 43614-1021, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology & Immunology, and Program in Bioinformatics, College of Medicine & Life Sciences, The University of Toledo, Toledo OH 43614-1021, USA
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Ting WW, Tan SI, Ng IS. Development of chromosome-based T7 RNA polymerase and orthogonal T7 promoter circuit in Escherichia coli W3110 as a cell factory. BIORESOUR BIOPROCESS 2020. [DOI: 10.1186/s40643-020-00342-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Abstract
Background
Orthogonal T7 RNA polymerase (T7RNAP) and T7 promoter is a powerful genetic element to mediate protein expression in different cells. Among all, Escherichia coli possess advantages of fast growth rate, easy for culture and comprehensive elements for genetic engineering. As E. coli W3110 owns the benefits of more heat shock proteins and higher tolerance to toxic chemicals, further execution of T7-based system in W3110 as cell factory is a conceivable strategy.
Results
Three novel W3110 strains, i.e., W3110:IL5, W3110::L5 and W3110::pI, were accomplished by chromosome-equipped T7RNAP. At first, the LacZ and T7RNAP with isopropyl-β-D-thiogalactopyranoside (IPTG) induction showed higher expression levels in W3110 derivatives than that in BL21(DE3). The plasmids with and without lacI/lacO repression were used to investigate the protein expression of super-fold green fluorescence protein (sfGFP), carbonic anhydrase (CA) for carbon dioxide uptake and lysine decarboxylase (CadA) to produce a toxic chemical cadaverine (DAP). All the proteins showed better expression in W3110::L5 and W3110::pI, respectively. As a result, the highest cadaverine production of 36.9 g/L, lysine consumption of 43.8 g/L and up to 100% yield were obtained in W3110::pI(−) with plasmid pSU-T7-CadA constitutively.
Conclusion
Effect of IPTG and lacI/lacO regulator has been investigated in three chromosome-based T7RNAP E. coli strains. The newly engineered W3110 strains possessed similar protein expression compared to commercial BL21(DE3). Furthermore, W3110::pI displays higher production of sfGFP, CA and CadA, due to it having the highest sensitivity to IPTG, thus it represents the greatest potential as a cell factory.
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Liu Z, Dong H, Cui Y, Cong L, Zhang D. Application of different types of CRISPR/Cas-based systems in bacteria. Microb Cell Fact 2020; 19:172. [PMID: 32883277 PMCID: PMC7470686 DOI: 10.1186/s12934-020-01431-z] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 08/25/2020] [Indexed: 12/26/2022] Open
Abstract
As important genome editing tools, CRISPR/Cas systems, especially those based on type II Cas9 and type V Cas12a, are widely used in genetic and metabolic engineering of bacteria. However, the intrinsic toxicity of Cas9 and Cas12a-mediated CRISPR/Cas tools can lead to cell death in some strains, which led to the development of endogenous type I and III CRISPR/Cas systems. However, these systems are hindered by complicated development and limited applications. Thus, further development and optimization of CRISPR/Cas systems is needed. Here, we briefly summarize the mechanisms of different types of CRISPR/Cas systems as genetic manipulation tools and compare their features to provide a reference for selecting different CRISPR/Cas tools. Then, we show the use of CRISPR/Cas technology for bacterial strain evolution and metabolic engineering, including genome editing, gene expression regulation and the base editor tool. Finally, we offer a view of future directions for bacterial CRISPR/Cas technology.
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Affiliation(s)
- Zhenquan Liu
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, People's Republic of China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
| | - Huina Dong
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
| | - Yali Cui
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
| | - Lina Cong
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, People's Republic of China.
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Huang C, Guo L, Wang J, Wang N, Huo YX. Efficient long fragment editing technique enables large-scale and scarless bacterial genome engineering. Appl Microbiol Biotechnol 2020; 104:7943-7956. [PMID: 32794018 DOI: 10.1007/s00253-020-10819-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 07/20/2020] [Accepted: 08/05/2020] [Indexed: 11/24/2022]
Abstract
Bacteria are versatile living systems that enhance our understanding of nature and enable biosynthesis of valuable chemicals. Long fragment editing techniques are of great importance for accelerating bacterial genome engineering to obtain desirable and genetically stable strains. However, the existing genome editing methods cannot meet the needs of engineers. We herein report an efficient long fragment editing method for large-scale and scarless genome engineering in Escherichia coli. The method enabled us to insert DNA fragments up to 12 kb into the genome and to delete DNA fragments up to 186.7 kb from the genome, with positive rates over 95%. We applied this method for E. coli genome simplification, resulting in 12 individual deletion mutants and four cumulative deletion mutants. The simplest genome lost a total of 370.6 kb of DNA sequence containing 364 open reading frames. Additionally, we applied this technique to metabolic engineering and obtained a genetically stable plasmid-independent isobutanol production strain that produced 1.3 g/L isobutanol via shake-flask fermentation. These results suggest that the method is a powerful genome engineering tool, highlighting its potential to be applied in synthetic biology and metabolic engineering. KEY POINTS: • This article reports an efficient genome engineering tool for E. coli. • The tool is advantageous for the manipulations of long DNA fragments. • The tool has been successfully applied for genome simplification. • The tool has been successfully applied for metabolic engineering.
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Affiliation(s)
- Chaoyong Huang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China.,SIP-UCLA Institute for Technology Advancement, Suzhou, 215123, China
| | - Liwei Guo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Jingge Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Ning Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China. .,SIP-UCLA Institute for Technology Advancement, Suzhou, 215123, China.
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Zhang F, Cheng D, Wang S, Zhu J. Crispr/Cas9-mediated cleavages facilitate homologous recombination during genetic engineering of a large chromosomal region. Biotechnol Bioeng 2020; 117:2816-2826. [PMID: 32449788 DOI: 10.1002/bit.27441] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 04/26/2020] [Accepted: 05/18/2020] [Indexed: 02/06/2023]
Abstract
Homologous recombination over large genomic regions is difficult to achieve due to low efficiencies. Here, we report the successful engineering of a humanized mTert allele, hmTert, in the mouse genome by replacing an 18.1-kb genomic region around the mTert gene with a recombinant fragment of over 45.5 kb, using homologous recombination facilitated by the Crispr/Cas9 technology, in mouse embryonic stem cells (mESCs). In our experiments, with DNA double-strand breaks (DSBs) generated by Crispr/Cas9 system, the homologous recombination efficiency was up to 11% and 16% in two mESC lines TC1 and v6.5, respectively. Overall, we obtained a total of 27 mESC clones with heterozygous hmTert/mTert alleles and three clones with homozygous hmTert alleles. DSBs induced by Crispr/Cas9 cleavages also caused high rates of genomic DNA deletions and mutations at single-guide RNA target sites. Our results indicated that the Crispr/Cas9 system significantly increased the efficiency of homologous recombination-mediated gene editing over a large genomic region in mammalian cells, and also caused frequent mutations at unedited target sites. Overall, this strategy provides an efficient and feasible way for manipulating large chromosomal regions.
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Affiliation(s)
- Fan Zhang
- Department of Pharmaceutical Sciences, Washington State University College of Pharmacy, Spokane, Washington
| | - De Cheng
- Department of Pharmaceutical Sciences, Washington State University College of Pharmacy, Spokane, Washington
| | - Shuwen Wang
- Department of Pharmaceutical Sciences, Washington State University College of Pharmacy, Spokane, Washington
| | - Jiyue Zhu
- Department of Pharmaceutical Sciences, Washington State University College of Pharmacy, Spokane, Washington
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Su B, Song D, Zhu H. Homology-dependent recombination of large synthetic pathways into E. coli genome via λ-Red and CRISPR/Cas9 dependent selection methodology. Microb Cell Fact 2020; 19:108. [PMID: 32448328 PMCID: PMC7245811 DOI: 10.1186/s12934-020-01360-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 04/30/2020] [Indexed: 01/01/2023] Open
Abstract
Background Metabolic engineering frequently needs genomic integration of many heterologous genes for biosynthetic pathway assembly. Despite great progresses in genome editing for the model microorganism Escherichia coli, the integration of large pathway into genome for stabilized chemical production is still challenging compared with small DNA integration. Results We have developed a λ-Red assisted homology-dependent recombination for large synthetic pathway integration in E. coli. With this approach, we can integrate as large as 12 kb DNA module into the chromosome of E. coli W3110 in a single step. The efficiency of this method can reach 100%, thus markedly improve the integration efficiency and overcome the limitation of the integration size adopted the common method. Furthermore, the limiting step in the methylerythritol 4-phosphate (MEP) pathway and lycopene synthetic pathway were integrated into the W3110 genome using our system. Subsequently, the yields of the final strain were increased 106 and 4.4-fold compared to the initial strain and the reference strain, respectively. Conclusions In addition to pre-existing method, our system presents an optional strategy for avoiding using plasmids and a valuable tool for large synthetic pathway assembly in E. coli.
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Affiliation(s)
- Buli Su
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Dandan Song
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Honghui Zhu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China.
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Pham NN, Chen CY, Li H, Nguyen MTT, Nguyen PKP, Tsai SL, Chou JY, Ramli TC, Hu YC. Engineering Stable Pseudomonas putida S12 by CRISPR for 2,5-Furandicarboxylic Acid (FDCA) Production. ACS Synth Biol 2020; 9:1138-1149. [PMID: 32298581 DOI: 10.1021/acssynbio.0c00006] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
FDCA (2,5-furandicarboxylic acid) can be enzymatically converted from HMF (5-hydroxymethylfurfural). Pseudomonas putida S12 is promising for FDCA production, but generating stable P. putida S12 is difficult due to its polyploidy and lack of genome engineering tools. Here we showed that coupling CRISPR and λ-Red recombineering enabled one-step gene integration with high efficiency and frequency, and simultaneously replaced endogenous genes in all chromosomes. Using this approach, we generated two stable P. putida S12 strains expressing HMF/furfural oxidoreductase (HMFH) and HMF oxidase (HMFO), both being able to convert 50 mM HMF to ≈42-43 mM FDCA in 24 h. Cosupplementation of MnO2 and CaCO3 to the medium drastically improved the cell tolerance to HMF and enhanced FDCA production. Cointegrating HMFH and HMFT1 (HMF transporter) genes further improved FDCA production, enabling the cells to convert 250 mM HMF to 196 mM (30.6 g/L) FDCA in 24 h. This study implicates the potentials of CRISPR for generating stable P. putida S12 strains for FDCA production.
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Affiliation(s)
- Nam Ngoc Pham
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Cho-Yi Chen
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Hung Li
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Mai Thanh Thi Nguyen
- Faculty of Chemistry, University of Science, Vietnam National University Ho Chi Minh City, Ho Chi Minh City 72711, Vietnam
| | - Phung Kim Phi Nguyen
- Faculty of Chemistry, University of Science, Vietnam National University Ho Chi Minh City, Ho Chi Minh City 72711, Vietnam
| | - Shen-Long Tsai
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 10607, Taiwan
| | - June-Yen Chou
- Innovation and R&D Division, Chang Chun Group, Taipei 10483, Taiwan
| | - Theresia Cecylia Ramli
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Yu-Chen Hu
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
- Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu 30013, Taiwan
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Cen YK, Lin JG, Wang YL, Wang JY, Liu ZQ, Zheng YG. The Gibberellin Producer Fusarium fujikuroi: Methods and Technologies in the Current Toolkit. Front Bioeng Biotechnol 2020; 8:232. [PMID: 32292777 PMCID: PMC7118215 DOI: 10.3389/fbioe.2020.00232] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 03/06/2020] [Indexed: 12/18/2022] Open
Abstract
In recent years, there has been a noticeable increase in research interests on the Fusarium species, which includes prevalent plant pathogens and human pathogens, common microbial food contaminants and industrial microbes. Taken the advantage of gibberellin synthesis, Fusarium fujikuroi succeed in being a prevalent plant pathogen. At the meanwhile, F. fujikuroi was utilized for industrial production of gibberellins, a group of extensively applied phytohormone. F. fujikuroi has been known for its outstanding performance in gibberellin production for almost 100 years. Research activities relate to this species has lasted for a very long period. The slow development in biological investigation of F. fujikuroi is largely due to the lack of efficient research technologies and molecular tools. During the past decade, technologies to analyze the molecular basis of host-pathogen interactions and metabolic regulations have been developed rapidly, especially on the aspects of genetic manipulation. At the meanwhile, the industrial fermentation technologies kept sustained development. In this article, we reviewed the currently available research tools/methods for F. fujikuroi research, focusing on the topics about genetic engineering and gibberellin production.
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Affiliation(s)
- Yu-Ke Cen
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Jian-Guang Lin
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - You-Liang Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Jun-You Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Zhi-Qiang Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
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Choudhury A, Fenster JA, Fankhauser RG, Kaar JL, Tenaillon O, Gill RT. CRISPR/Cas9 recombineering-mediated deep mutational scanning of essential genes in Escherichia coli. Mol Syst Biol 2020; 16:e9265. [PMID: 32175691 PMCID: PMC7073797 DOI: 10.15252/msb.20199265] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 01/14/2023] Open
Abstract
Deep mutational scanning can provide significant insights into the function of essential genes in bacteria. Here, we developed a high-throughput method for mutating essential genes of Escherichia coli in their native genetic context. We used Cas9-mediated recombineering to introduce a library of mutations, created by error-prone PCR, within a gene fragment on the genome using a single gRNA pre-validated for high efficiency. Tracking mutation frequency through deep sequencing revealed biases in the position and the number of the introduced mutations. We overcame these biases by increasing the homology arm length and blocking mismatch repair to achieve a mutation efficiency of 85% for non-essential genes and 55% for essential genes. These experiments also improved our understanding of poorly characterized recombineering process using dsDNA donors with single nucleotide changes. Finally, we applied our technology to target rpoB, the beta subunit of RNA polymerase, to study resistance against rifampicin. In a single experiment, we validate multiple biochemical and clinical observations made in the previous decades and provide insights into resistance compensation with the study of double mutants.
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Affiliation(s)
- Alaksh Choudhury
- Department of Chemical and Biological EngineeringUniversity of ColoradoBoulderCOUSA
- IAMEINSERMUniversité de ParisParisFrance
| | - Jacob A Fenster
- Department of Chemical and Biological EngineeringUniversity of ColoradoBoulderCOUSA
| | | | - Joel L Kaar
- Department of Chemical and Biological EngineeringUniversity of ColoradoBoulderCOUSA
| | | | - Ryan T Gill
- Department of Chemical and Biological EngineeringUniversity of ColoradoBoulderCOUSA
- Renewable & Sustainable Energy InstituteUniversity of ColoradoBoulderCOUSA
- Novo Nordisk Foundation Center for BiosustainabilityDanish Technical UniversityCopenhagenDenmark
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36
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Hao M, Wang Z, Qiao H, Yin P, Qiao J, Qi H. Dynamic Genome Editing Using In Vivo Synthesized Donor ssDNA in Escherichia coli. Cells 2020; 9:E467. [PMID: 32085579 PMCID: PMC7072734 DOI: 10.3390/cells9020467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/07/2020] [Accepted: 02/12/2020] [Indexed: 12/11/2022] Open
Abstract
As a key element of genome editing, donor DNA introduces the desired exogenous sequence while working with other crucial machinery such as CRISPR-Cas or recombinases. However, current methods for the delivery of donor DNA into cells are both inefficient and complicated. Here, we developed a new methodology that utilizes rolling circle replication and Cas9 mediated (RC-Cas-mediated) in vivo single strand DNA (ssDNA) synthesis. A single-gene rolling circle DNA replication system from Gram-negative bacteria was engineered to produce circular ssDNA from a Gram-positive parent plasmid at a designed sequence in Escherichia coli. Furthermore, it was demonstrated that the desired linear ssDNA fragment could be cut out using CRISPR-associated protein 9 (CRISPR-Cas9) nuclease and combined with lambda Red recombinase as donor for precise genome engineering. Various donor ssDNA fragments from hundreds to thousands of nucleotides in length were synthesized in E. coli cells, allowing successive genome editing in growing cells. We hope that this RC-Cas-mediated in vivo ssDNA on-site synthesis system will be widely adopted as a useful new tool for dynamic genome editing.
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Affiliation(s)
- Min Hao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (M.H.); (Z.W.); (H.Q.); (P.Y.); (J.Q.)
- Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Zhaoguan Wang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (M.H.); (Z.W.); (H.Q.); (P.Y.); (J.Q.)
- Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Hongyan Qiao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (M.H.); (Z.W.); (H.Q.); (P.Y.); (J.Q.)
- Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Peng Yin
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (M.H.); (Z.W.); (H.Q.); (P.Y.); (J.Q.)
- Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Jianjun Qiao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (M.H.); (Z.W.); (H.Q.); (P.Y.); (J.Q.)
- Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Hao Qi
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (M.H.); (Z.W.); (H.Q.); (P.Y.); (J.Q.)
- Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
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Rodrigues JL, Gomes D, Rodrigues LR. A Combinatorial Approach to Optimize the Production of Curcuminoids From Tyrosine in Escherichia coli. Front Bioeng Biotechnol 2020; 8:59. [PMID: 32117938 PMCID: PMC7019186 DOI: 10.3389/fbioe.2020.00059] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 01/23/2020] [Indexed: 12/14/2022] Open
Abstract
Curcuminoids are well-known for their therapeutic properties. However, their extraction from natural sources is environmentally unfriendly, expensive and limited by seasonal variability, highlighting the need for alternative production processes. We propose an optimized artificial biosynthetic pathway to produce curcuminoids, including curcumin, in Escherichia coli. This pathway involves six enzymes, tyrosine ammonia lyase (TAL), 4-coumarate 3-hydroxylase (C3H), caffeic acid O-methyltransferase (COMT), 4-coumarate-CoA ligase (4CL), diketide-CoA synthase (DCS), and curcumin synthase (CURS1). Curcuminoids pathway was divided in two modules, the first module included TAL, C3H and COMT and the second one 4CL, DCS and CURS1. Optimizing the first module of the pathway, from tyrosine to ferulic acid, enabled obtaining the highest ferulic acid titer reported so far (1325.1 μM). Afterward, ferulic acid was used as substrate to optimize the second module of the pathway. We achieved the highest concentration of curcumin ever reported (1529.5 μM), corresponding to a 59.4% increase. Subsequently, curcumin and other curcuminoids were produced from tyrosine (using the whole pathway) in mono-culture. The production increased comparing to a previously reported pathway that used a caffeoyl-CoA O-methyltransferase enzyme (to convert caffeoyl-CoA to feruloyl-CoA) instead of COMT (to convert caffeic to ferulic acid). Additionally, the potential of a co-culture approach was evaluated to further improve curcuminoids production by reducing cells metabolic burden. We used one E. coli strain able to convert tyrosine to ferulic acid and another able to convert the hydroxycinnamic acids produced by the first one to curcuminoids. The co-culture strategies tested led to 6.6 times increase of total curcuminoids (125.8 μM) when compared to the mono-culture system. The curcuminoids production achieved in this study corresponds to a 6817% improvement. In addition, by using an inoculation ratio of 2:1, although total curcuminoids production decreased, curcumin production was enhanced and reached 43.2 μM, corresponding to an improvement of 160% comparing to mono-culture system. To our knowledge, these values correspond to the highest titers of curcuminoids obtained to date. These results demonstrate the enormous potential of modular co-culture engineering to produce curcumin, and other curcuminoids, from tyrosine.
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Affiliation(s)
- Joana L Rodrigues
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Daniela Gomes
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Lígia R Rodrigues
- Centre of Biological Engineering, University of Minho, Braga, Portugal
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Li ZH, Meng H, Ma B, Tao X, Liu M, Wang FQ, Wei DZ. Immediate, multiplexed and sequential genome engineering facilitated by CRISPR/Cas9 in Saccharomyces cerevisiae. J Ind Microbiol Biotechnol 2020; 47:83-96. [PMID: 31768773 DOI: 10.1007/s10295-019-02251-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 11/11/2019] [Indexed: 01/22/2023]
Abstract
A method called Cas-3P allowing for immediate, multiplexed and sequential genome engineering was developed using one plasmid expressing Cas9 and three marked plasmid backbones (P1, P2 and P3) for guide RNA (gRNA) expression. The three marked gRNA plasmid backbones were recurred in a P1-P2-P3 order for sequential gene targeting, without construction of any additional plasmid and elimination of gRNA plasmid by induction in each round. The efficiency of direct gRNA plasmid curing mediated by Cas-3P was more than 40% in sequential gene targeting. Besides, Cas-3P allowed single-, double- and triple-loci gene targeting with an efficiency of 75%, 36.8% and 8.2% within 3-4 days, respectively. Through three sequential rounds of gene targeting within 10 days, S. cerevisiae was optimized for the production of patchoulol by replacing one promoter, overexpressing three genes and disrupting four genes. The work is important for practical application in the cell factory engineering of S. cerevisiae.
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Affiliation(s)
- Zhen-Hai Li
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Hao Meng
- Hunan Norchem Pharmaceutical Co Ltd, ChangSha, China
| | - Bin Ma
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Xinyi Tao
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Min Liu
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China.
| | - Feng-Qing Wang
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China.
| | - Dong-Zhi Wei
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
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Tripathi NK, Shrivastava A. Recent Developments in Bioprocessing of Recombinant Proteins: Expression Hosts and Process Development. Front Bioeng Biotechnol 2019; 7:420. [PMID: 31921823 PMCID: PMC6932962 DOI: 10.3389/fbioe.2019.00420] [Citation(s) in RCA: 249] [Impact Index Per Article: 49.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Accepted: 11/29/2019] [Indexed: 12/22/2022] Open
Abstract
Infectious diseases, along with cancers, are among the main causes of death among humans worldwide. The production of therapeutic proteins for treating diseases at large scale for millions of individuals is one of the essential needs of mankind. Recent progress in the area of recombinant DNA technologies has paved the way to producing recombinant proteins that can be used as therapeutics, vaccines, and diagnostic reagents. Recombinant proteins for these applications are mainly produced using prokaryotic and eukaryotic expression host systems such as mammalian cells, bacteria, yeast, insect cells, and transgenic plants at laboratory scale as well as in large-scale settings. The development of efficient bioprocessing strategies is crucial for industrial production of recombinant proteins of therapeutic and prophylactic importance. Recently, advances have been made in the various areas of bioprocessing and are being utilized to develop effective processes for producing recombinant proteins. These include the use of high-throughput devices for effective bioprocess optimization and of disposable systems, continuous upstream processing, continuous chromatography, integrated continuous bioprocessing, Quality by Design, and process analytical technologies to achieve quality product with higher yield. This review summarizes recent developments in the bioprocessing of recombinant proteins, including in various expression systems, bioprocess development, and the upstream and downstream processing of recombinant proteins.
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Affiliation(s)
- Nagesh K. Tripathi
- Bioprocess Scale Up Facility, Defence Research and Development Establishment, Gwalior, India
| | - Ambuj Shrivastava
- Division of Virology, Defence Research and Development Establishment, Gwalior, India
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Xin X, Li J, Zhao D, Li S, Xie Q, Li Z, Fan F, Bi C, Zhang X. Double-Check Base Editing for Efficient A to G Conversions. ACS Synth Biol 2019; 8:2629-2634. [PMID: 31765564 DOI: 10.1021/acssynbio.9b00284] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
With the development of CRISPR/Cas9 technology, a new generation of editing methods that convert specific bases has enabled precise single-base mutations. To date, conversion of cytosine to thymidine and adenine to guanine has been achieved using the cytidine deaminase APOBEC1 and adenosine deaminase (TadA), respectively. However, the base editing efficiency can be unacceptably low in some cell types or at certain target loci. One reason might be the lack of a selective pressure against the survival of nonedited cells. Few studies on ABE in prokaryotes have been reported, probably due to the relatively low editing efficiency of TadA. Improving the editing efficiency is the key for establishing base editing techniques and especially the ABE technologies. In this work, a selective pressure against nonedited cells was implemented to increase the base editing efficiency. First, we fused nCas9 or dCas9 with TadA to compare the editing efficiency of nCas9-TadA and dCas9-TadA fusion complexes in the model prokaryote Escherichia coli. While nCas9-TadA was able to achieve A to G base editing (ABE) with a moderate efficiency, dCas9-TadA had a very low efficiency. To enrich for edited cells and increase the base-editing efficiency, we utilized the induction of double-strand breaks by active Cas9, which leads to the death of prokaryotic cells. By introducing an inducible active Cas9 with the same editing gRNA as the nCas9-TadA in the base editing process, the cells with nonedited target bases remained vulnerable to Cas9 and were eliminated. Thus, a double-check base editing (DBE) method was established, which significantly improved the editing efficiency of ABE in E. coli, reaching 99.0% for some sites. By placing a selective pressure against nonedited cells, the DBE strategy might also be applied to various scenarios to increase the efficiency of many different base editing targets or even for epigenetic DNA modification techniques.
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Affiliation(s)
- Xiuqing Xin
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
| | - Ju Li
- College of Life Science, Tianjin Normal University, Tianjin 300387, PR China
| | - Dongdong Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
| | - Siwei Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
| | - Qianwen Xie
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, PR China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
| | - Zhongkang Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
| | - Feiyu Fan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
| | - Changhao Bi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China
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Koko I, Song AAL, Masarudin MJ, Abdul Rahim R. Engineering integrative vectors based on phage site-specific recombination mechanism for Lactococcus lactis. BMC Biotechnol 2019; 19:82. [PMID: 31775775 PMCID: PMC6882331 DOI: 10.1186/s12896-019-0575-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 11/07/2019] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Site-specific integration system allows foreign DNA to be integrated into the specific site of the host genome, enabling stable expression of heterologous protein. In this study, integrative vectors for secretion and surface display of proteins were constructed based on a lactococcal phage TP901-1 integrating system. RESULTS The constructed integration system comprises of a lactococcal promoter (PnisA or P170), phage attachment site (attP) from bacteriophage TP901-1, a signal peptide (USP45 or SPK1) for translocation of the target protein, and a PrtP344 anchor domain in the case of the integrative vectors for surface display. There were eight successfully constructed integrative vectors with each having a different combination of promoter and signal peptide; pS1, pS2, pS3 and pS4 for secretion, and pSD1, pSD2, pSD3 and pSD4 for surface display of desired protein. The integration of the vectors into the host genome was assisted by a helper vector harbouring the integrase gene. A nuclease gene was used as a reporter and was successfully integrated into the L. lactis genome and Nuc was secreted or displayed as expected. The signal peptide SPK1 was observed to be superior to USP45-LEISSTCDA fusion in the secretion of Nuc. As for the surface display integrative vector, all systems developed were comparable with the exception of the combination of P170 promoter with USP45 signal peptide which gave very low signals in whole cell ELISA. CONCLUSION The engineered synthetic integrative vectors have the potential to be used for secretion or surface display of heterologous protein production in lactococcal expression system for research or industrial purposes, especially in live vaccine delivery.
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Affiliation(s)
- Innanurdiani Koko
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM, Serdang, Selangor Malaysia
| | - Adelene Ai-Lian Song
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM, Serdang, Selangor Malaysia
- Institute of Bioscience, University Putra Malaysia, 43400 UPM Serdang, Selangor Malaysia
| | - Mas Jaffri Masarudin
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM, Serdang, Selangor Malaysia
- Institute of Bioscience, University Putra Malaysia, 43400 UPM Serdang, Selangor Malaysia
| | - Raha Abdul Rahim
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 UPM, Serdang, Selangor Malaysia
- Institute of Bioscience, University Putra Malaysia, 43400 UPM Serdang, Selangor Malaysia
- Chancellory, Universiti Teknikal Malaysia, 76100 Durian Tunggal, Melaka, Malaysia
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Kopp J, Slouka C, Spadiut O, Herwig C. The Rocky Road From Fed-Batch to Continuous Processing With E. coli. Front Bioeng Biotechnol 2019; 7:328. [PMID: 31824931 PMCID: PMC6880763 DOI: 10.3389/fbioe.2019.00328] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 10/28/2019] [Indexed: 12/21/2022] Open
Abstract
Escherichia coli still serves as a beloved workhorse for the production of many biopharmaceuticals as it fulfills essential criteria, such as having fast doubling times, exhibiting a low risk of contamination, and being easy to upscale. Most industrial processes in E. coli are carried out in fed-batch mode. However, recent trends show that the biotech industry is moving toward time-independent processing, trying to improve the space-time yield, and especially targeting constant quality attributes. In the 1950s, the term "chemostat" was introduced for the first time by Novick and Szilard, who followed up on the previous work performed by Monod. Chemostat processing resulted in a major hype 10 years after its official introduction. However, enthusiasm decreased as experiments suffered from genetic instabilities and physiology issues. Major improvements in strain engineering and the usage of tunable promotor systems facilitated chemostat processes. In addition, critical process parameters have been identified, and the effects they have on diverse quality attributes are understood in much more depth, thereby easing process control. By pooling the knowledge gained throughout the recent years, new applications, such as parallelization, cascade processing, and population controls, are applied nowadays. However, to control the highly heterogeneous cultivation broth to achieve stable productivity throughout long-term cultivations is still tricky. Within this review, we discuss the current state of E. coli fed-batch process understanding and its tech transfer potential within continuous processing. Furthermore, the achievements in the continuous upstream applications of E. coli and the continuous downstream processing of intracellular proteins will be discussed.
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Affiliation(s)
- Julian Kopp
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, Vienna, Austria
| | - Christoph Slouka
- Research Area Biochemical Engineering, Institute of Chemical Engineering, Vienna, Austria
| | - Oliver Spadiut
- Research Area Biochemical Engineering, Institute of Chemical Engineering, Vienna, Austria
| | - Christoph Herwig
- Christian Doppler Laboratory for Mechanistic and Physiological Methods for Improved Bioprocesses, Vienna, Austria
- Research Area Biochemical Engineering, Institute of Chemical Engineering, Vienna, Austria
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43
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Cui Y, Dong H, Ma Y, Zhang D. Strategies for Applying Nonhomologous End Joining-Mediated Genome Editing in Prokaryotes. ACS Synth Biol 2019; 8:2194-2202. [PMID: 31525995 DOI: 10.1021/acssynbio.9b00179] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The emergence of genome editing technology based on the CRISPR/Cas system enabled revolutionary progress in genetic engineering. Double-strand breaks (DSBs), which can be induced by the CRISPR/Cas9 system, cause serious DNA damage that can be repaired by a homologous recombination (HR) system or the nonhomologous end joining (NHEJ) pathway. However, many bacterial species have a very weak HR system. Thus, the NHEJ pathway can be used in prokaryotes. Starting with a brief introduction of the mechanism of the NHEJ pathway, this review focuses on current research and details of applications of NHEJ in eukaryotes, which forms the theoretical basis for the application of the NHEJ system in prokaryotes.
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44
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Ou X, Wu X, Peng F, Zeng Y, Li H, Xu P, Chen G, Guo Z, Yang J, Zong M, Lou W. Metabolic engineering of a robustEscherichia colistrain with a dual protection system. Biotechnol Bioeng 2019; 116:3333-3348. [DOI: 10.1002/bit.27165] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 08/28/2019] [Accepted: 09/01/2019] [Indexed: 12/26/2022]
Affiliation(s)
- Xiao‐Yang Ou
- Lab of Applied Biocatalysis, School of Food Science and EngineeringSouth China University of TechnologyGuangzhou China
| | - Xiao‐Ling Wu
- Lab of Applied Biocatalysis, School of Food Science and EngineeringSouth China University of TechnologyGuangzhou China
| | - Fei Peng
- Lab of Applied Biocatalysis, School of Food Science and EngineeringSouth China University of TechnologyGuangzhou China
| | - Ying‐Jie Zeng
- Lab of Applied Biocatalysis, School of Food Science and EngineeringSouth China University of TechnologyGuangzhou China
| | - Hui‐Xian Li
- Lab of Applied Biocatalysis, School of Food Science and EngineeringSouth China University of TechnologyGuangzhou China
| | - Pei Xu
- Lab of Applied Biocatalysis, School of Food Science and EngineeringSouth China University of TechnologyGuangzhou China
| | - Gu Chen
- Lab of Applied Biocatalysis, School of Food Science and EngineeringSouth China University of TechnologyGuangzhou China
| | - Ze‐Wang Guo
- Lab of Applied Biocatalysis, School of Food Science and EngineeringSouth China University of TechnologyGuangzhou China
| | - Ji‐Guo Yang
- Lab of Applied Biocatalysis, School of Food Science and EngineeringSouth China University of TechnologyGuangzhou China
- Innovation Center of Bioactive Molecule Development and ApplicationSouth China Institute of Collaborative InnovationDongguan China
| | - Min‐Hua Zong
- Lab of Applied Biocatalysis, School of Food Science and EngineeringSouth China University of TechnologyGuangzhou China
- Guangdong Province Key Laboratory for Green Processing of Natural Products and Product SafetySouth China University of TechnologyGuangzhou China
| | - Wen‐Yong Lou
- Lab of Applied Biocatalysis, School of Food Science and EngineeringSouth China University of TechnologyGuangzhou China
- Innovation Center of Bioactive Molecule Development and ApplicationSouth China Institute of Collaborative InnovationDongguan China
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45
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Huang C, Ding T, Wang J, Wang X, Guo L, Wang J, Zhu L, Bi C, Zhang X, Ma X, Huo YX. CRISPR-Cas9-assisted native end-joining editing offers a simple strategy for efficient genetic engineering in Escherichia coli. Appl Microbiol Biotechnol 2019; 103:8497-8509. [PMID: 31501938 DOI: 10.1007/s00253-019-10104-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 08/07/2019] [Accepted: 08/26/2019] [Indexed: 12/17/2022]
Abstract
Unlike eukaryotes, prokaryotes are less proficient in homologous recombination (HR) and non-homologous end-joining (NHEJ). All existing genomic editing methods for Escherichia coli (E. coli) rely on exogenous HR or NHEJ systems to repair DNA double-strand breaks (DSBs). Although an E. coli native end-joining (ENEJ) system has been reported, its potential in genetic engineering has not yet been explored. Here, we present a CRISPR-Cas9-assisted native end-joining editing and show that ENEJ-dependent DNA repair can be used to conduct rapid and efficient deletion of chromosome fragments up to 83 kb or gene inactivation. Moreover, the positive rate and editing efficiency are independent of high-efficiency competent cells. The method requires neither exogenous DNA repair systems nor introduced editing template. The Cas9-sgRNA complex is the only foreign element in this method. This study is the first successful engineering effort to utilize ENEJ mechanism in genomic editing and provides an effective strategy for genetic engineering in bacteria that are inefficient in HR and NHEJ.
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Affiliation(s)
- Chaoyong Huang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, People's Republic of China
| | - Tingting Ding
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, People's Republic of China.,UCLA (Suzhou) Institute for Technology Advancement, 10 Yueliangwan Road, Suzhou Industrial Park, Suzhou, 215123, People's Republic of China
| | - Jingge Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, People's Republic of China
| | - Xueqin Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, People's Republic of China
| | - Liwei Guo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, People's Republic of China
| | - Jialei Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, People's Republic of China
| | - Lin Zhu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, People's Republic of China
| | - Changhao Bi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
| | - Xiaoyan Ma
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, People's Republic of China
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, People's Republic of China. .,UCLA (Suzhou) Institute for Technology Advancement, 10 Yueliangwan Road, Suzhou Industrial Park, Suzhou, 215123, People's Republic of China.
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46
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CRISPR technologies for stem cell engineering and regenerative medicine. Biotechnol Adv 2019; 37:107447. [PMID: 31513841 DOI: 10.1016/j.biotechadv.2019.107447] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/03/2019] [Accepted: 09/06/2019] [Indexed: 12/13/2022]
Abstract
CRISPR/Cas9 system exploits the concerted action of Cas9 nuclease and programmable single guide RNA (sgRNA), and has been widely used for genome editing. The Cas9 nuclease activity can be abolished by mutation to yield the catalytically deactivated Cas9 (dCas9). Coupling with the customizable sgRNA for targeting, dCas9 can be fused with transcription repressors to inhibit specific gene expression (CRISPR interference, CRISPRi) or fused with transcription activators to activate the expression of gene of interest (CRISPR activation, CRISPRa). Here we introduce the principles and recent advances of these CRISPR technologies, their delivery vectors and review their applications in stem cell engineering and regenerative medicine. In particular, we focus on in vitro stem cell fate manipulation and in vivo applications such as prevention of retinal and muscular degeneration, neural regeneration, bone regeneration, cartilage tissue engineering, as well as treatment of diseases in blood, skin and liver. Finally, the challenges to translate CRISPR to regenerative medicine and future perspectives are discussed and proposed.
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47
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Shen CC, Hsu MN, Chang CW, Lin MW, Hwu JR, Tu Y, Hu YC. Synthetic switch to minimize CRISPR off-target effects by self-restricting Cas9 transcription and translation. Nucleic Acids Res 2019; 47:e13. [PMID: 30462300 PMCID: PMC6379646 DOI: 10.1093/nar/gky1165] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 10/17/2018] [Accepted: 11/02/2018] [Indexed: 12/27/2022] Open
Abstract
CRISPR/Cas9 is a powerful genome editing system but uncontrolled Cas9 nuclease expression triggers off-target effects and even in vivo immune responses. Inspired by synthetic biology, here we built a synthetic switch that self-regulates Cas9 expression not only in the transcription step by guide RNA-aided self-cleavage of cas9 gene, but also in the translation step by L7Ae:K-turn repression system. We showed that the synthetic switch enabled simultaneous transcriptional and translational repression, hence stringently attenuating the Cas9 expression. The restricted Cas9 expression induced high efficiency on-target indel mutation while minimizing the off-target effects. Furthermore, we unveiled the correlation between Cas9 expression kinetics and on-target/off-target mutagenesis. The synthetic switch conferred detectable Cas9 expression and concomitant high frequency on-target mutagenesis at as early as 6 h, and restricted the Cas9 expression and off-target effects to minimal levels through 72 h. The synthetic switch is compact enough to be incorporated into viral vectors for self-regulation of Cas9 expression, thereby providing a novel 'hit and run' strategy for in vivo genome editing.
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Affiliation(s)
- Chih-Che Shen
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Mu-Nung Hsu
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Chin-Wei Chang
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Mei-Wei Lin
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan.,Biomedical Technology and Device Research Laboratories, Industrial Technology Research Institute, Hsinchu, Taiwan
| | - Jih-Ru Hwu
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan.,Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu, Taiwan
| | - Yi Tu
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Yu-Chen Hu
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan.,Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu, Taiwan
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48
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Wang Y, Liu Y, Li J, Yang Y, Ni X, Cheng H, Huang T, Guo Y, Ma H, Zheng P, Wang M, Sun J, Ma Y. Expanding targeting scope, editing window, and base transition capability of base editing in
Corynebacterium glutamicum. Biotechnol Bioeng 2019; 116:3016-3029. [DOI: 10.1002/bit.27121] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 07/03/2019] [Accepted: 07/08/2019] [Indexed: 01/02/2023]
Affiliation(s)
- Yu Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin China
| | - Ye Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin China
| | - Junwei Li
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin China
- College of BiotechnologyTianjin University of Science and Technology Tianjin China
| | - Yi Yang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin China
| | - Xiaomeng Ni
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin China
| | - Haijiao Cheng
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin China
| | - Teng Huang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin China
| | - Yanmei Guo
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin China
| | - Hongwu Ma
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin China
| | - Ping Zheng
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin China
| | - Meng Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin China
| | - Jibin Sun
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin China
| | - Yanhe Ma
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin China
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Ding Y, Wang KF, Wang WJ, Ma YR, Shi TQ, Huang H, Ji XJ. Increasing the homologous recombination efficiency of eukaryotic microorganisms for enhanced genome engineering. Appl Microbiol Biotechnol 2019; 103:4313-4324. [DOI: 10.1007/s00253-019-09802-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/26/2019] [Accepted: 03/27/2019] [Indexed: 11/28/2022]
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Li L, Liu X, Wei K, Lu Y, Jiang W. Synthetic biology approaches for chromosomal integration of genes and pathways in industrial microbial systems. Biotechnol Adv 2019; 37:730-745. [PMID: 30951810 DOI: 10.1016/j.biotechadv.2019.04.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 04/01/2019] [Accepted: 04/01/2019] [Indexed: 12/14/2022]
Abstract
Industrial biotechnology is reliant on native pathway engineering or foreign pathway introduction for efficient biosynthesis of target products. Chromosomal integration, with intrinsic genetic stability, is an indispensable step for reliable expression of homologous or heterologous genes and pathways in large-scale and long-term fermentation. With advances in synthetic biology and CRISPR-based genome editing approaches, a wide variety of novel enabling technologies have been developed for single-step, markerless, multi-locus genomic integration of large biochemical pathways, which significantly facilitate microbial overproduction of chemicals, pharmaceuticals and other value-added biomolecules. Notably, the newly discovered homology-mediated end joining strategy could be widely applicable for high-efficiency genomic integration in a number of homologous recombination-deficient microbes. In this review, we explore the fundamental principles and characteristics of genomic integration, and highlight the development and applications of targeted integration approaches in the three representative industrial microbial systems, including Escherichia coli, actinomycetes and yeasts.
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Affiliation(s)
- Lei Li
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xiaocao Liu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Keke Wei
- Department of Biochemistry, Shanghai Institute of Pharmaceutical Industry, Shanghai 201210, China
| | - Yinhua Lu
- College of Life Sciences, Shanghai Normal University, 200232, China.
| | - Weihong Jiang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
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