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The genome editing revolution. Trends Biotechnol 2023; 41:396-409. [PMID: 36709094 DOI: 10.1016/j.tibtech.2022.12.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/30/2022] [Accepted: 12/30/2022] [Indexed: 01/28/2023]
Abstract
A series of spectacular scientific discoveries and technological advances in the second half of the 20th century have provided the basis for the ongoing genome editing revolution. The elucidation of structural and functional features of DNA and RNA was followed by pioneering studies on genome editing: Molecular biotechnology was born. Since then, four decades followed during which progress of scientific insights and technological methods continued at an overwhelming pace. Fundamental insights into microbial host-virus interactions led to the development of tools for genome editing using restriction enzymes or the revolutionary CRISPR-Cas technology. In this review, we provide a historical overview of milestones that led to the genome editing revolution and speculate about future trends in biotechnology.
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Thomson NM, Zhang C, Trampari E, Pallen MJ. Creation of Golden Gate constructs for gene doctoring. BMC Biotechnol 2020; 20:54. [PMID: 33028286 PMCID: PMC7542709 DOI: 10.1186/s12896-020-00648-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 09/21/2020] [Indexed: 11/21/2022] Open
Abstract
Background Gene doctoring is an efficient recombination-based genetic engineering approach to mutagenesis of the bacterial chromosome that combines the λ-Red recombination system with a suicide donor plasmid that is cleaved in vivo to generate linear DNA fragments suitable for recombination. The use of a suicide donor plasmid makes Gene Doctoring more efficient than other recombineering technologies. However, generation of donor plasmids typically requires multiple cloning and screening steps. Results We constructed a simplified acceptor plasmid, called pDOC-GG, for the assembly of multiple DNA fragments precisely and simultaneously to form a donor plasmid using Golden Gate assembly. Successful constructs can easily be identified through blue-white screening. We demonstrated proof of principle by inserting a gene for green fluorescent protein into the chromosome of Escherichia coli. We also provided related genetic parts to assist in the construction of mutagenesis cassettes with a tetracycline-selectable marker. Conclusions Our plasmid greatly simplifies the construction of Gene Doctoring donor plasmids and allows for the assembly of complex, multi-part insertion or deletion cassettes with a free choice of target sites and selection markers. The tools we developed are applicable to gene editing for a wide variety of purposes in Enterobacteriaceae and potentially in other diverse bacterial families.
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Affiliation(s)
- Nicholas M Thomson
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Chuanzhen Zhang
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK.,National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China.,Guangdong Key Laboratory for Veterinary Drug Development and Safety evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Eleftheria Trampari
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Mark J Pallen
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK. .,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TU, UK. .,School of Veterinary Medicine, University of Surrey, Daphne Jackson Road, Guildford, Surrey, GU2 7AL, UK.
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Expression and purification of codon-optimized cre recombinase in E. coli. Protein Expr Purif 2020; 167:105546. [DOI: 10.1016/j.pep.2019.105546] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/15/2019] [Accepted: 11/24/2019] [Indexed: 12/31/2022]
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Li D, Zhang B, Li S, Zhou J, Cao H, Huang Y, Cui Z. A Novel Vector for Construction of Markerless Multicopy Overexpression Transformants in Pichia pastoris. Front Microbiol 2017; 8:1698. [PMID: 28955309 PMCID: PMC5601908 DOI: 10.3389/fmicb.2017.01698] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 08/23/2017] [Indexed: 01/08/2023] Open
Abstract
Pichia pastoris is widely used as a platform for heterologous protein expression because of its high volumetric productivity. Multicopy integration of the target gene is commonly used to improve the production of the target protein. Cre/lox recombination system is a powerful tool for the marker rescue during multiple integrations with one selection marker. Here we reported a novel expression vector based on the Cre/lox recombination system for multiple integrations of target gene to construct multicopy expression strain of P. pastoris. PAOX1 promoter was fused to cre to construct a methanol inducible Cre recombinase. The leakage expression of Cre recombinase in Escherichia coli was blocked by introducing the operator gene lacO. The expression vector designed pMCO-AOXα was stable in E. coli and could effectively rescue the Zeocin resistance gene for next round of integration in P. pastoris. Phytase AppA from E. coli was chosen as a reporter gene. Transformants with 2-16 copies of appA were constructed by using a single antibiotic. Expression of appA was gene dosage dependent when <12 copies were integrated. The protein yield increased 4.45-folds when 12 copies of appA were integrated comparing with the single copy integration. Our results showed that pMCO-AOXα was highly effective for rational construction of multicopy transformat in P. pastoris.
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Affiliation(s)
- Ding Li
- Key Laboratory of Agricultural Environmental Microbiology, College of Life Sciences, Nanjing Agricultural UniversityNanjing, China
| | - Bo Zhang
- Key Laboratory of Agricultural Environmental Microbiology, College of Life Sciences, Nanjing Agricultural UniversityNanjing, China
| | - Shuting Li
- College of Life Sciences, Nanjing Agricultural UniversityNanjing, China
| | - Jie Zhou
- Key Laboratory of Agricultural Environmental Microbiology, College of Life Sciences, Nanjing Agricultural UniversityNanjing, China
| | - Hui Cao
- Key Laboratory of Agricultural Environmental Microbiology, College of Life Sciences, Nanjing Agricultural UniversityNanjing, China
| | - Yan Huang
- Key Laboratory of Agricultural Environmental Microbiology, College of Life Sciences, Nanjing Agricultural UniversityNanjing, China
| | - Zhongli Cui
- Key Laboratory of Agricultural Environmental Microbiology, College of Life Sciences, Nanjing Agricultural UniversityNanjing, China
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Han T, Li Y, Shan Q, Liang W, Hao W, Li Y, Tan X, Gu J. Characterization of S -adenosylhomocysteine/Methylthioadenosine nucleosidase on secretion of AI-2 and biofilm formation of Escherichia coli. Microb Pathog 2017; 108:78-84. [DOI: 10.1016/j.micpath.2017.05.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 05/04/2017] [Accepted: 05/05/2017] [Indexed: 11/27/2022]
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A CRISPR-Cas9 Assisted Non-Homologous End-Joining Strategy for One-step Engineering of Bacterial Genome. Sci Rep 2016; 6:37895. [PMID: 27883076 PMCID: PMC5121644 DOI: 10.1038/srep37895] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 11/01/2016] [Indexed: 11/08/2022] Open
Abstract
Homologous recombination-mediated genome engineering has been broadly applied in prokaryotes with high efficiency and accuracy. However, this method is limited in realizing larger-scale genome editing with numerous genes or large DNA fragments because of the relatively complicated procedure for DNA editing template construction. Here, we describe a CRISPR-Cas9 assisted non-homologous end-joining (CA-NHEJ) strategy for the rapid and efficient inactivation of bacterial gene (s) in a homologous recombination-independent manner and without the use of selective marker. Our study show that CA-NHEJ can be used to delete large chromosomal DNA fragments in a single step that does not require homologous DNA template. It is thus a novel and powerful tool for bacterial genomes reducing and possesses the potential for accelerating the genome evolution.
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Liu X, Wei Y, Li Y, Li H, Yang X, Yi Y, Zhang Z. A Highly Efficient and Simple Construction Strategy for Producing Recombinant Baculovirus Bombyx mori Nucleopolyhedrovirus. PLoS One 2016; 11:e0152140. [PMID: 27008267 PMCID: PMC4805210 DOI: 10.1371/journal.pone.0152140] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 03/09/2016] [Indexed: 12/23/2022] Open
Abstract
The silkworm baculovirus expression system is widely used to produce recombinant proteins. Several strategies for constructing recombinant viruses that contain foreign genes have been reported. Here, we developed a novel defective-rescue BmNPV Bacmid (reBmBac) expression system. A CopyControl origin of replication was introduced into the viral genome to facilitate its genetic manipulation in Escherichia coli and to ensure the preparation of large amounts of high quality reBmBac DNA as well as high quality recombinant baculoviruses. The ORF1629, cathepsin and chitinase genes were partially deleted or rendered defective to improve the efficiency of recombinant baculovirus generation and the expression of foreign genes. The system was validated by the successful expression of luciferase reporter gene and porcine interferon γ. This system can be used to produce batches of recombinant baculoviruses and target proteins rapidly and efficiently in silkworms.
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Affiliation(s)
- Xingjian Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yonglong Wei
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yinü Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Haoyang Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xin Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongzhu Yi
- The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu Province, China
| | - Zhifang Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- * E-mail:
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Markerless Deletion System for Escherichia coli Using Short Homologous Sequences and Positive-Negative Selectable Cassette. Appl Biochem Biotechnol 2015; 176:1472-81. [PMID: 25957274 DOI: 10.1007/s12010-015-1658-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Accepted: 04/29/2015] [Indexed: 10/23/2022]
Abstract
Red homologous recombination has been extensively used in recombineering. Because foreign sequences, such as antibiotic resistance genes, FRT-sites, or loxP-sites, are often unwanted in mutant Escherichia coli, we established a markerless deletion system containing short homologous sequences, a positive-selectable marker (kan), and a negative-selectable marker (sacB) for E. coli. For markerless deletion of a specific region of the E. coli genome, a two-step recombination procedure using two different PCR fragments, which were amplified from pUC57-kan-sacB and pUC57-298, was performed. The generation of a pheA-tyrA deficient mutant demonstrated that this markerless deletion system was a simple and efficient method to generate markerless chromosomal deletions in E. coli.
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Mignon C, Sodoyer R, Werle B. Antibiotic-free selection in biotherapeutics: now and forever. Pathogens 2015; 4:157-81. [PMID: 25854922 PMCID: PMC4493468 DOI: 10.3390/pathogens4020157] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 03/09/2015] [Accepted: 03/23/2015] [Indexed: 11/16/2022] Open
Abstract
The continuously improving sophistication of molecular engineering techniques gives access to novel classes of bio-therapeutics and new challenges for their production in full respect of the strengthening regulations. Among these biologic agents are DNA based vaccines or gene therapy products and to a lesser extent genetically engineered live vaccines or delivery vehicles. The use of antibiotic-based selection, frequently associated with genetic manipulation of microorganism is currently undergoing a profound metamorphosis with the implementation and diversification of alternative selection means. This short review will present examples of alternatives to antibiotic selection and their context of application to highlight their ineluctable invasion of the bio-therapeutic world.
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Affiliation(s)
- Charlotte Mignon
- Technology Research Institute Bioaster, 317 avenue Jean-Jaurés, 69007 Lyon, France.
| | - Régis Sodoyer
- Technology Research Institute Bioaster, 317 avenue Jean-Jaurés, 69007 Lyon, France.
| | - Bettina Werle
- Technology Research Institute Bioaster, 317 avenue Jean-Jaurés, 69007 Lyon, France.
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Khetrapal V, Mehershahi K, Rafee S, Chen S, Lim CL, Chen SL. A set of powerful negative selection systems for unmodified Enterobacteriaceae. Nucleic Acids Res 2015; 43:e83. [PMID: 25800749 PMCID: PMC4513841 DOI: 10.1093/nar/gkv248] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 03/10/2015] [Indexed: 12/21/2022] Open
Abstract
Creation of defined genetic mutations is a powerful method for dissecting mechanisms of bacterial disease; however, many genetic tools are only developed for laboratory strains. We have designed a modular and general negative selection strategy based on inducible toxins that provides high selection stringency in clinical Escherichia coli and Salmonella isolates. No strain- or species-specific optimization is needed, yet this system achieves better selection stringency than all previously reported negative selection systems usable in unmodified E. coli strains. The high stringency enables use of negative instead of positive selection in phage-mediated generalized transduction and also allows transfer of alleles between arbitrary strains of E. coli without requiring phage. The modular design should also allow further extension to other bacteria. This negative selection system thus overcomes disadvantages of existing systems, enabling definitive genetic experiments in both lab and clinical isolates of E. coli and other Enterobacteriaceae.
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Affiliation(s)
- Varnica Khetrapal
- National University of Singapore, Department of Medicine, Yong Loo Lin School of Medicine, 1E Kent Ridge Road, NUHS Tower Block, Level 10, Singapore 119074
| | - Kurosh Mehershahi
- National University of Singapore, Department of Medicine, Yong Loo Lin School of Medicine, 1E Kent Ridge Road, NUHS Tower Block, Level 10, Singapore 119074
| | - Shazmina Rafee
- National University of Singapore, Department of Medicine, Yong Loo Lin School of Medicine, 1E Kent Ridge Road, NUHS Tower Block, Level 10, Singapore 119074
| | - Siyi Chen
- National University of Singapore, Department of Medicine, Yong Loo Lin School of Medicine, 1E Kent Ridge Road, NUHS Tower Block, Level 10, Singapore 119074
| | - Chiew Ling Lim
- National University of Singapore, Department of Medicine, Yong Loo Lin School of Medicine, 1E Kent Ridge Road, NUHS Tower Block, Level 10, Singapore 119074
| | - Swaine L Chen
- National University of Singapore, Department of Medicine, Yong Loo Lin School of Medicine, 1E Kent Ridge Road, NUHS Tower Block, Level 10, Singapore 119074 Genome Institute of Singapore, Infectious Diseases Group, 60 Biopolis Street, Genome, #02-01, Singapore 138672
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Role of capsule and O antigen in the virulence of uropathogenic Escherichia coli. PLoS One 2014; 9:e94786. [PMID: 24722484 PMCID: PMC3983267 DOI: 10.1371/journal.pone.0094786] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 03/19/2014] [Indexed: 01/08/2023] Open
Abstract
Urinary tract infection (UTI) is one of the most common bacterial infections in humans, with uropathogenic Escherichia coli (UPEC) the leading causative organism. UPEC has a number of virulence factors that enable it to overcome host defenses within the urinary tract and establish infection. The O antigen and the capsular polysaccharide are two such factors that provide a survival advantage to UPEC. Here we describe the application of the rpsL counter selection system to construct capsule (kpsD) and O antigen (waaL) mutants and complemented derivatives of three reference UPEC strains: CFT073 (O6:K2:H1), RS218 (O18:K1:H7) and 1177 (O1:K1:H7). We observed that while the O1, O6 and O18 antigens were required for survival in human serum, the role of the capsule was less clear and linked to O antigen type. In contrast, both the K1 and K2 capsular antigens provided a survival advantage to UPEC in whole blood. In the mouse urinary tract, mutation of the O6 antigen significantly attenuated CFT073 bladder colonization. Overall, this study contrasts the role of capsule and O antigen in three common UPEC serotypes using defined mutant and complemented strains. The combined mutagenesis-complementation strategy can be applied to study other virulence factors with complex functions both in vitro and in vivo.
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Tuntufye HN, Gwakisa PS, Goddeeris BM. In silico analysis of tkt1 from avian pathogenic Escherichia coli and its virulence evaluation in chickens. Res Microbiol 2013; 164:310-8. [PMID: 23376541 DOI: 10.1016/j.resmic.2013.01.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 11/19/2012] [Indexed: 12/13/2022]
Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) contain tktA and tktB which code for transketolases involved in the pentose phosphate pathway. Recent studies demonstrated that a third gene coding for transketolase 1 (tkt1) was located in a pathogenicity island of avian and human ExPEC belonging to phylogenetic group B2. In the present study, in silico analysis of tkt1 revealed 68% and 69% identity with tktA and tktB, respectively, of ExPEC and 68% identity with tktA and tktB of E. coli MG1655. The translated tkt1 shared 69% and 68% identity with TktA and TktB proteins, respectively, of ExPEC and E. coli MG1655. Phylogenetically, it is shown that the three genes (tktA, tktB and tkt1) cluster in three different clades. Further analysis suggests that tkt1 has been acquired though horizontal gene transfer from plant-associated bacteria within the family Enterobacteriaceae. Virulence studies were performed in order to evaluate whether tkt1 played a role in avian pathogenic E. coli CH2 virulence in chickens. The evaluation revealed that mutant virulence was slightly lower based on LD50 when compared to the wild type during infection of chickens, but there were no significant differences when the two strains were compared based on the number of deaths and lesion scores.
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Affiliation(s)
- Huruma Nelwike Tuntufye
- Department of Biosystems, Faculty of Bioscience Engineering, University of Leuven (KU Leuven), Kasteelpark Arenberg 30, B-3001 Heverlee, Belgium.
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Identification of Avian pathogenic Escherichia coli genes that are induced in vivo during infection in chickens. Appl Environ Microbiol 2012; 78:3343-51. [PMID: 22344666 DOI: 10.1128/aem.07677-11] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Avian pathogenic Escherichia coli (APEC) is associated with extraintestinal infections in poultry causing a variety of diseases collectively known as colibacillosis. The host and bacterial factors influencing and/or responsible for carriage and systemic translocation of APEC inside the host are poorly understood. Identification of such factors could help in the understanding of its pathogenesis and in the subsequent development of control strategies. Recombination-based in vivo expression technology (RIVET) was used to identify APEC genes specifically expressed during infection in chickens. A total of 21 clones with in vivo-induced promoters were isolated from chicken livers and spleens, indicative of systemic infection. DNA sequencing of the cloned fragments revealed that 12 of the genes were conserved E. coli genes (metH, lysA, pntA, purL, serS, ybjE, ycdK [rutC], wcaJ, gspL, sdsR, ylbE, and yjiY), 6 of the genes were phage related/associated, and 3 genes were pathogen specific (tkt1, irp2, and eitD). These genes are involved in various cellular functions, such as metabolism, cell envelope and integrity, transport systems, and virulence. Others were phage related or have yet-unknown functions.
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