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Bai S, Luo H, Tong H, Wu Y, Yuan Y. Advances on transfer and maintenance of large DNA in bacteria, fungi, and mammalian cells. Biotechnol Adv 2024; 76:108421. [PMID: 39127411 DOI: 10.1016/j.biotechadv.2024.108421] [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: 03/24/2023] [Revised: 05/07/2024] [Accepted: 08/04/2024] [Indexed: 08/12/2024]
Abstract
Advances in synthetic biology allow the design and manipulation of DNA from the scale of genes to genomes, enabling the engineering of complex genetic information for application in biomanufacturing, biomedicine and other areas. The transfer and subsequent maintenance of large DNA are two core steps in large scale genome rewriting. Compared to small DNA, the high molecular weight and fragility of large DNA make its transfer and maintenance a challenging process. This review outlines the methods currently available for transferring and maintaining large DNA in bacteria, fungi, and mammalian cells. It highlights their mechanisms, capabilities and applications. The transfer methods are categorized into general methods (e.g., electroporation, conjugative transfer, induced cell fusion-mediated transfer, and chemical transformation) and specialized methods (e.g., natural transformation, mating-based transfer, virus-mediated transfection) based on their applicability to recipient cells. The maintenance methods are classified into genomic integration (e.g., CRISPR/Cas-assisted insertion) and episomal maintenance (e.g., artificial chromosomes). Additionally, this review identifies the major technological advantages and disadvantages of each method and discusses the development for large DNA transfer and maintenance technologies.
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Affiliation(s)
- Song Bai
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, China; Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Han Luo
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, China; Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Hanze Tong
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, China; Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Yi Wu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, China; Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China. @tju.edu.cn
| | - Yingjin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072 Tianjin, China; Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
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2
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Kovacs CJ, Antonacci A, Graham A, Jessup F, Rankin W, Brasko B, Maguire F, Washington MA, Kua SC, Burpo FJ, Barnhill JC. Comparing Methods to Genetically Engineer Bacteriophage and Increase Host Range. Mil Med 2024; 189:e1488-e1496. [PMID: 38780999 DOI: 10.1093/milmed/usae226] [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] [Received: 06/15/2023] [Revised: 11/15/2023] [Accepted: 04/30/2024] [Indexed: 05/25/2024] Open
Abstract
INTRODUCTION Antibacterial resistance is an emerging problem in military medicine. Disruptions to the health care systems in war-torn countries that result from ongoing conflict can potentially exacerbate this problem and increase the risk to U.S. forces in the deployed environment. Therefore, novel therapies are needed to mitigate the impact of these potentially devastating infections on military operations. Bacteriophages are viruses that infect and kill bacteria. They can be delivered as therapeutic agents and offer a promising alternative to traditional antibiotic chemotherapy. There are several potential benefits to their use, including high specificity and comparative ease of use in the field setting. However, the process of engineering phages for military medical applications can be a laborious and time-consuming endeavor. This review examines available techniques and compares their efficacy. MATERIALS AND METHODS This review evaluates the scientific literature on the development and application of four methods of bacteriophage genome engineering and their consideration in the context of military applications. Preffered Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines were followed for a systematic review of available literature that met criteria for analysis and inclusion. The research completed for this review article originated from the United States Military Academy's library "Scout" search engine, which compiles results from 254 available databases (including PubMed, Google Scholar, and SciFinder). Particular attention was focused on identifying useful mechanistic insight into the nature of the engineering technique, the ease of use, and the applicability of the technique to countering the problem of antimicrobial resistance in the military setting. RESULTS A total of 52 studies were identified that met inclusion criteria following PRISMA guidelines. The bioengineering techniques analyzed included homologous recombination (12 articles), in vivo recombineering (9 articles), bacteriophage recombineering of electroporated DNA (7 articles), and the CRISPR-Cas system (10 articles). Rates of success and fidelity varied across each platform, and comparative benefits and drawbacks are considered. CONCLUSIONS Each of the phage engineering techniques addressed herein varies in amount of effort and overall success rate. CRISPR-Cas-facilitated modification of phage genomes presents a highly efficient method that does not require a lengthy purification and screening process. It therefore appears to be the method best suited for military medical applications.
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Affiliation(s)
- Christopher J Kovacs
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
- Defense Threat Reduction Agency, Fort Belvoir, VA 22060, USA
| | - Alessia Antonacci
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Abigail Graham
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Faye Jessup
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - William Rankin
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Brianna Brasko
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Fiona Maguire
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Michael A Washington
- Department of Clinical Investigation, Dwight D. Eisenhower Army Medical Center, Fort Gordon, GA 30905, USA
| | - Siang C Kua
- Department of Clinical Investigation, Dwight D. Eisenhower Army Medical Center, Fort Gordon, GA 30905, USA
| | - F John Burpo
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Jason C Barnhill
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
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3
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Loganathan K, Viswanathan B. Genome editing for phage design and uses for therapeutic applications. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 201:203-224. [PMID: 37770172 DOI: 10.1016/bs.pmbts.2023.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
The over usage of antibiotics leads to antibiotic abuse which in turn eventually raises resistance mechanisms among wide range of pathogens. Due to lack of experimental data of efficacy of phages as potential antimicrobial and therapeutic agent and also more specific and cumbersome isolation process against specific pathogens makes it not so feasible technology to be looked as an alternative therapy. But, recent developments in genome editing techniques enables programmed nuclease enzymes that has effectively improvised our methodology to make accurate changes in the genomes of prokaryote as well as eukaryote cells. It is already strengthening our ability to improvise genetic engineering to disease identification by facilitating the creation of more precise models to identify the root cause. The present chapter discusses on improvisation of phage therapy using recent genome editing tools and also shares data on the methods of usage of phages and their derivatives like proteins and enzymes such as lysins and depolymerases, as a potential therapeutic or prophylaxis agent. Methods involved in recombinant based techniques were also discussed in this chapter. Combination of traditional approach with modern tools has led to a potential development of phage-based therapeutics in near future.
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Jia HJ, Jia PP, Yin S, Bu LK, Yang G, Pei DS. Engineering bacteriophages for enhanced host range and efficacy: insights from bacteriophage-bacteria interactions. Front Microbiol 2023; 14:1172635. [PMID: 37323893 PMCID: PMC10264812 DOI: 10.3389/fmicb.2023.1172635] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/10/2023] [Indexed: 06/17/2023] Open
Abstract
Bacteriophages, the most abundant organisms on earth, have the potential to address the rise of multidrug-resistant bacteria resulting from the overuse of antibiotics. However, their high specificity and limited host range can hinder their effectiveness. Phage engineering, through the use of gene editing techniques, offers a means to enhance the host range of bacteria, improve phage efficacy, and facilitate efficient cell-free production of phage drugs. To engineer phages effectively, it is necessary to understand the interaction between phages and host bacteria. Understanding the interaction between the receptor recognition protein of bacteriophages and host receptors can serve as a valuable guide for modifying or replacing these proteins, thereby altering the receptor range of the bacteriophage. Research and development focused on the CRISPR-Cas bacterial immune system against bacteriophage nucleic acids can provide the necessary tools to promote recombination and counter-selection in engineered bacteriophage programs. Additionally, studying the transcription and assembly functions of bacteriophages in host bacteria can facilitate the engineered assembly of bacteriophage genomes in non-host environments. This review highlights a comprehensive summary of phage engineering methods, including in-host and out-of-host engineering, and the use of high-throughput methods to understand their role. The main aim of these techniques is to harness the intricate interactions between bacteriophages and hosts to inform and guide the engineering of bacteriophages, particularly in the context of studying and manipulating the host range of bacteriophages. By employing advanced high-throughput methods to identify specific bacteriophage receptor recognition genes, and subsequently introducing modifications or performing gene swapping through in-host recombination or out-of-host synthesis, it becomes possible to strategically alter the host range of bacteriophages. This capability holds immense significance for leveraging bacteriophages as a promising therapeutic approach against antibiotic-resistant bacteria.
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Affiliation(s)
- Huang-Jie Jia
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Pan-Pan Jia
- School of Public Health, Chongqing Medical University, Chongqing, China
| | - Supei Yin
- Urinary Nephropathy Center, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ling-Kang Bu
- College of Life Science, Henan Normal University, Xinxiang, China
| | - Guan Yang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - De-Sheng Pei
- School of Public Health, Chongqing Medical University, Chongqing, China
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5
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Khambhati K, Bhattacharjee G, Gohil N, Dhanoa GK, Sagona AP, Mani I, Bui NL, Chu DT, Karapurkar JK, Jang SH, Chung HY, Maurya R, Alzahrani KJ, Ramakrishna S, Singh V. Phage engineering and phage-assisted CRISPR-Cas delivery to combat multidrug-resistant pathogens. Bioeng Transl Med 2023; 8:e10381. [PMID: 36925687 PMCID: PMC10013820 DOI: 10.1002/btm2.10381] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/30/2022] [Accepted: 07/16/2022] [Indexed: 12/13/2022] Open
Abstract
Antibiotic resistance ranks among the top threats to humanity. Due to the frequent use of antibiotics, society is facing a high prevalence of multidrug resistant pathogens, which have managed to evolve mechanisms that help them evade the last line of therapeutics. An alternative to antibiotics could involve the use of bacteriophages (phages), which are the natural predators of bacterial cells. In earlier times, phages were implemented as therapeutic agents for a century but were mainly replaced with antibiotics, and considering the menace of antimicrobial resistance, it might again become of interest due to the increasing threat of antibiotic resistance among pathogens. The current understanding of phage biology and clustered regularly interspaced short palindromic repeats (CRISPR) assisted phage genome engineering techniques have facilitated to generate phage variants with unique therapeutic values. In this review, we briefly explain strategies to engineer bacteriophages. Next, we highlight the literature supporting CRISPR-Cas9-assisted phage engineering for effective and more specific targeting of bacterial pathogens. Lastly, we discuss techniques that either help to increase the fitness, specificity, or lytic ability of bacteriophages to control an infection.
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Affiliation(s)
- Khushal Khambhati
- Department of Biosciences, School of Science Indrashil University Rajpur Mehsana Gujarat India
| | - Gargi Bhattacharjee
- Department of Biosciences, School of Science Indrashil University Rajpur Mehsana Gujarat India
| | - Nisarg Gohil
- Department of Biosciences, School of Science Indrashil University Rajpur Mehsana Gujarat India
| | - Gurneet K Dhanoa
- School of Life Sciences University of Warwick, Gibbet Hill Campus Coventry United Kindgom
| | - Antonia P Sagona
- School of Life Sciences University of Warwick, Gibbet Hill Campus Coventry United Kindgom
| | - Indra Mani
- Department of Microbiology Gargi College, University of Delhi New Delhi India
| | - Nhat Le Bui
- Center for Biomedicine and Community Health International School, Vietnam National University Hanoi Vietnam
| | - Dinh-Toi Chu
- Center for Biomedicine and Community Health International School, Vietnam National University Hanoi Vietnam.,Faculty of Applied Sciences International School, Vietnam National University Hanoi Vietnam
| | | | - Su Hwa Jang
- Graduate School of Biomedical Science and Engineering Hanyang University Seoul South Korea.,Hanyang Biomedical Research Institute Hanyang University Seoul South Korea
| | - Hee Yong Chung
- Graduate School of Biomedical Science and Engineering Hanyang University Seoul South Korea.,Hanyang Biomedical Research Institute Hanyang University Seoul South Korea.,College of Medicine Hanyang University Seoul South Korea
| | - Rupesh Maurya
- Department of Biosciences, School of Science Indrashil University Rajpur Mehsana Gujarat India
| | - Khalid J Alzahrani
- Department of Clinical Laboratories Sciences College of Applied Medical Sciences, Taif University Taif Saudi Arabia
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering Hanyang University Seoul South Korea.,College of Medicine Hanyang University Seoul South Korea
| | - Vijai Singh
- Department of Biosciences, School of Science Indrashil University Rajpur Mehsana Gujarat India
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6
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Thomason LC, Costantino N, Li X, Court DL. Recombineering: Genetic Engineering in Escherichia coli Using Homologous Recombination. Curr Protoc 2023; 3:e656. [PMID: 36779782 PMCID: PMC10037674 DOI: 10.1002/cpz1.656] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
The bacterial chromosome and bacterial plasmids can be engineered in vivo by homologous recombination using either PCR products or synthetic double-stranded DNA (dsDNA) or single-stranded DNA as substrates. Multiple linear dsDNA molecules can be assembled into an intact plasmid. The technology of recombineering is possible because bacteriophage-encoded recombination proteins efficiently recombine sequences with homologies as short as 35 to 50 bases. Recombineering allows DNA sequences to be inserted or deleted without regard to the location of restriction sites and can also be used in combination with CRISPR/Cas targeting systems. © 2023 Wiley Periodicals LLC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA. Basic Protocol: Making electrocompetent cells and transforming with linear DNA Support Protocol 1: Selection/counter-selections for genome engineering Support Protocol 2: Creating and screening for oligo recombinants by PCR Support Protocol 3: Other methods of screening for unselected recombinants Support Protocol 4: Curing recombineering plasmids containing a temperature-sensitive replication function Support Protocol 5: Removal of the prophage by recombineering Alternate Protocol 1: Using CRISPR/Cas9 as a counter-selection following recombineering Alternate Protocol 2: Assembly of linear dsDNA fragments into functional plasmids Alternate Protocol 3: Retrieval of alleles onto a plasmid by gap repair Alternate Protocol 4: Modifying multicopy plasmids with recombineering Support Protocol 6: Screening for unselected plasmid recombinants Alternate Protocol 5: Recombineering with an intact λ prophage Alternate Protocol 6: Targeting an infecting λ phage with the defective prophage strains.
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Affiliation(s)
- Lynn C. Thomason
- Molecular Control and Genetics Section, RNA Biology Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland
| | - Nina Costantino
- formerly with Molecular Control and Genetics Section, RNA Biology Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland
| | - Xintian Li
- Armata Pharmaceuticals, 4503 Glencoe Avenue, Marina del Rey, CA 90292
| | - Donald L. Court
- Emeritus, Molecular Control and Genetics Section, RNA Biology Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland
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7
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Huss P, Chen J, Raman S. High-throughput approaches to understand and engineer bacteriophages. Trends Biochem Sci 2023; 48:187-197. [PMID: 36180320 PMCID: PMC9868059 DOI: 10.1016/j.tibs.2022.08.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 08/30/2022] [Accepted: 08/31/2022] [Indexed: 01/26/2023]
Abstract
Bacteriophage research has been vital to fundamental aspects of modern biology. Advances in metagenomics have revealed treasure troves of new and uncharacterized bacteriophages ('phages') that are not yet understood. However, our ability to find new phages has outpaced our understanding of how sequence encodes function in phages. Traditional approaches for characterizing phages are limited in scale and face hurdles in determining how changes in sequence drive function. We describe powerful emerging technologies that can be used to clarify sequence-function relationships in phages through high-throughput genome engineering. Using these approaches, up to 105 variants can be characterized through pooled selection experiments and deep sequencing. We describe caveats when using these tools and provide examples of basic science and engineering goals that are pursuable using these approaches.
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Affiliation(s)
- Phil Huss
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA; Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jackie Chen
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Srivatsan Raman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA.
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8
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Goren MG, Mahata T, Qimron U. An efficient, scarless, selection-free technology for phage engineering. RNA Biol 2023; 20:830-835. [PMID: 37846029 PMCID: PMC10583621 DOI: 10.1080/15476286.2023.2270344] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2023] [Indexed: 10/18/2023] Open
Abstract
Most recently developed phage engineering technologies are based on the CRISPR-Cas system. Here, we present a non-CRISPR-based method for genetically engineering the Escherichia coli phages T5, T7, P1, and λ by adapting the pORTMAGE technology, which was developed for engineering bacterial genomes. The technology comprises E. coli harbouring a plasmid encoding a potent recombinase and a gene transiently silencing a repair system. Oligonucleotides with the desired phage mutation are electroporated into E. coli followed by infection of the target bacteriophage. The high efficiency of this technology, which yields 1-14% of desired recombinants, allows low-throughput screening for the desired mutant. We have demonstrated the use of this technology for single-base substitutions, for deletions of 50-201 bases, for insertions of 20 bases, and for four different phages. The technology may also be readily modified for use across many additional bacterial and phage strains.[Figure: see text].
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Affiliation(s)
- Moran G. Goren
- Department of Clinical Microbiology and Immunology, School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Tridib Mahata
- Department of Clinical Microbiology and Immunology, School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Udi Qimron
- Department of Clinical Microbiology and Immunology, School of Medicine, Tel Aviv University, Tel Aviv, Israel
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9
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Abstract
The technology of recombineering, in vivo genetic engineering, was initially developed in Escherichia coli and uses bacteriophage-encoded homologous recombination proteins to efficiently recombine DNA at short homologies (35 to 50 nt). Because the technology is homology driven, genomic DNA can be modified precisely and independently of restriction site location. Recombineering uses linear DNA substrates that are introduced into the cell by electroporation; these can be PCR products, synthetic double-strand DNA (dsDNA), or single-strand DNA (ssDNA). Here we describe the applications, challenges, and factors affecting ssDNA and dsDNA recombineering in a variety of non-model bacteria, both Gram-negative and -positive, and recent breakthroughs in the field. We list different microbes in which the widely used phage λ Red and Rac RecET recombination systems have been used for in vivo genetic engineering. New homologous ssDNA and dsDNA recombineering systems isolated from non-model bacteria are also described. The Basic Protocol outlines a method for ssDNA recombineering in the non-model species of Shewanella. The Alternate Protocol describes the use of CRISPR/Cas as a counter-selection system in conjunction with recombineering to enhance recovery of recombinants. We provide additional background information, pertinent considerations for experimental design, and parameters critical for success. The design of ssDNA oligonucleotides (oligos) and various internet-based tools for oligo selection from genome sequences are also described, as is the use of oligo-mediated recombination. This simple form of genome editing uses only ssDNA oligo(s) and does not require an exogenous recombination system. The information presented here should help researchers identify a recombineering system suitable for their microbe(s) of interest. If no system has been characterized for a specific microbe, researchers can find guidance in developing a recombineering system from scratch. We provide a flowchart of decision-making paths for strategically applying annealase-dependent or oligo-mediated recombination in non-model and undomesticated bacteria. © 2022 Wiley Periodicals LLC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA. Basic Protocol: ssDNA recombineering in Shewanella species Alternate Protocol: ssDNA recombineering coupled to CRISPR/Cas9 in Shewanella species.
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Affiliation(s)
- Anna Corts
- Cultivarium, 490 Arsenal Way, Ste 110, Watertown, Massachusetts 02472
| | - Lynn C. Thomason
- Molecular Control and Genetics Section, RNA Biology Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland 21702
| | - Nina Costantino
- Molecular Control and Genetics Section, RNA Biology Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland 21702
| | - Donald L. Court
- Emeritus, Molecular Control and Genetics Section, RNA Biology Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland 21702
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10
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Cunliffe T, Parker AL, Jaramillo A. Pseudotyping Bacteriophage P2 Tail Fibers to Extend the Host Range for Biomedical Applications. ACS Synth Biol 2022; 11:3207-3215. [PMID: 36084285 PMCID: PMC9594776 DOI: 10.1021/acssynbio.1c00629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Bacteriophages (phages) represent powerful potential treatments against antibiotic-resistant bacterial infections. Antibiotic-resistant bacteria represent a significant threat to global health, with an estimated 70% of infection-causing bacteria being resistant to one or more antibiotics. Developing novel antibiotics against the limited number of cellular targets is expensive and time-consuming, and bacteria can rapidly develop resistance. While bacterial resistance to phage can evolve, bacterial resistance to phage does not appear to spread through lateral gene transfer, and phage may similarly adapt through mutation to recover infectivity. Phages have been identified for all known bacteria, allowing the strain-selective killing of pathogenic bacteria. Here, we re-engineered the Escherichia coli phage P2 to alter its tropism toward pathogenic bacteria. Chimeric tail fibers formed between P2 and S16 genes were designed and generated through two approaches: homology- and literature-based. By presenting chimeric P2:S16 fibers on the P2 particle, our data suggests that the resultant phages were effectively detargeted from the native P2 cellular target, lipopolysaccharide, and were instead able to infect via the proteinaceous receptor, OmpC, the natural S16 receptor. Our work provides evidence that pseudotyping P2 is feasible and can be used to extend the host range of P2 to alternative receptors. Extension of this work could produce alternative chimeric tail fibers to target pathogenic bacterial threats. Our engineering of P2 allows adsorption through a heterologous outer-membrane protein without culturing in its native host, thus providing a potential means of engineering designer phages against pathogenic bacteria from knowledge of their surface proteome.
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Affiliation(s)
- Tabitha
G. Cunliffe
- Division
of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14
4XN, U.K.,School
of Life Sciences, University of Warwick, Coventry CV4 7AL, U.K.
| | - Alan L. Parker
- Division
of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14
4XN, U.K.,Systems
Immunity University Research Institute, School of Medicine, Cardiff University, Heath Park, Cardiff CF14
4XN, U.K.,. Phone: +44 2922 510 231
| | - Alfonso Jaramillo
- School
of Life Sciences, University of Warwick, Coventry CV4 7AL, U.K.,De
Novo Synthetic Biology Laboratory, I2SysBio, CSIC-University of Valencia, Parc Científic Universitat de València, Calle Catedrático Agustín
Escardino, 9, 46980 Paterna, Spain,. Phone: +34 963 543 056
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11
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Isaev A, Andriianov A, Znobishcheva E, Zorin E, Morozova N, Severinov K. Editing of Phage Genomes—Recombineering-assisted SpCas9 Modification of Model Coliphages T7, T5, and T3. Mol Biol 2022. [DOI: 10.1134/s0026893322060073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract
Bacteriophages—viruses that infect bacterial cells—are the most abundant biological entities on Earth. The use of phages in fundamental research and industry requires tools for precise manipulation of their genomes. Yet, compared to bacterial genome engineering, modification of phage genomes is challenging because of the lack of selective markers and thus requires laborious screenings of recombinant/mutated phage variants. The development of the CRISPR-Cas technologies allowed to solve this issue by the implementation of negative selection that eliminates the parental phage genomes. In this manuscript, we summarize current methods of phage genome engineering and their coupling with CRISPR-Cas technologies. We also provide examples of our successful application of these methods for introduction of specific insertions, deletions, and point mutations in the genomes of model Escherichia coli lytic phages T7, T5, and T3.
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12
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Abstract
Bacteriophages are the most abundant entities in the biosphere, and many genomes of rare and novel bacteriophages have been sequenced to date. However, bacteriophage functional genomics has been limited by a lack of effective research methods. Clustered regularly interspaced short palindromic repeat/CRISPR-associated gene (CRISPR–Cas) systems provide bacteriophages with a new mechanism for attacking host bacteria as well as new tools for study bacteriophage functional genomics. It has been reported that bacteriophages are not only the driving elements of the evolution of prokaryote CRISPR arrays but also the targets of CRISPR–Cas systems. In this study, a phage genome editing platform based on the heterologous CRISPR–Cas9 system was theoretically designed, and a Vibrio natriegens phage TT4P2 genome editing experiment was carried out in vivo in the host bacterium Vibrio natriegens TT4 to achieve phage gene deletion and replacement. The construction of this phage genome editing platform is expected to solve the problem of insufficient research on phage gene diversity, promote the development of phage synthetic biology and nanotechnology, and even accelerate the discovery of new molecular biology tools. IMPORTANCE Bacteriophages are the most numerous organisms on earth and are known for their diverse lifestyles. Since the discovery of bacteriophages, our knowledge of the wider biological world has undergone immense and unforeseen changes. A variety of V. natriegens phages have been detected, but few have been well characterized. CRISPR was first documented in Escherichia coli in 1987. It has been reported that the CRISPR–Cas system can target and cleave invaders, including bacteriophages, in a sequence-specific manner. Here, we show that the construction of a phage genome editing platform based on the heterologous CRISPR–Cas9 system can achieve V. natriegens phage TT4P2 gene editing and can also improve the efficiency and accuracy of phage TT4P2 gene editing.
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13
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Łobocka M, Dąbrowska K, Górski A. Engineered Bacteriophage Therapeutics: Rationale, Challenges and Future. BioDrugs 2021; 35:255-280. [PMID: 33881767 PMCID: PMC8084836 DOI: 10.1007/s40259-021-00480-z] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2021] [Indexed: 12/20/2022]
Abstract
The current problems with increasing bacterial resistance to antibacterial therapies, resulting in a growing frequency of incurable bacterial infections, necessitates the acceleration of studies on antibacterials of a new generation that could offer an alternative to antibiotics or support their action. Bacteriophages (phages) can kill antibiotic-sensitive as well as antibiotic-resistant bacteria, and thus are a major subject of such studies. Their efficacy in curing bacterial infections has been demonstrated in in vivo experiments and in the clinic. Unlike antibiotics, phages have a narrow range of specificity, which makes them safe for commensal microbiota. However, targeting even only the most clinically relevant strains of pathogenic bacteria requires large collections of well characterized phages, whose specificity would cover all such strains. The environment is a rich source of diverse phages, but due to their complex relationships with bacteria and safety concerns, only some naturally occurring phages can be considered for therapeutic applications. Still, their number and diversity make a detailed characterization of all potentially promising phages virtually impossible. Moreover, no single phage combines all the features required of an ideal therapeutic agent. Additionally, the rapid acquisition of phage resistance by bacteria may make phages already approved for therapy ineffective and turn the search for environmental phages of better efficacy and new specificity into an endless race. An alternative strategy for acquiring phages with desired properties in a short time with minimal cost regarding their acquisition, characterization, and approval for therapy could be based on targeted genome modifications of phage isolates with known properties. The first example demonstrating the potential of this strategy in curing bacterial diseases resistant to traditional therapy is the recent successful treatment of a progressing disseminated Mycobacterium abscessus infection in a teenage patient with the use of an engineered phage. In this review, we briefly present current methods of phage genetic engineering, highlighting their advantages and disadvantages, and provide examples of genetically engineered phages with a modified host range, improved safety or antibacterial activity, and proven therapeutic efficacy. We also summarize novel uses of engineered phages not only for killing pathogenic bacteria, but also for in situ modification of human microbiota to attenuate symptoms of certain bacterial diseases and metabolic, immune, or mental disorders.
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Affiliation(s)
- Małgorzata Łobocka
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, Warsaw, Poland
| | - Krystyna Dąbrowska
- Institute of Immunology and Experimental Therapy of the Polish Academy of Sciences, Wrocław, Poland
| | - Andrzej Górski
- Institute of Immunology and Experimental Therapy of the Polish Academy of Sciences, Wrocław, Poland
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14
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Wetzel KS, Guerrero-Bustamante CA, Dedrick RM, Ko CC, Freeman KG, Aull HG, Divens AM, Rock JM, Zack KM, Hatfull GF. CRISPY-BRED and CRISPY-BRIP: efficient bacteriophage engineering. Sci Rep 2021; 11:6796. [PMID: 33762639 PMCID: PMC7990910 DOI: 10.1038/s41598-021-86112-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 03/10/2021] [Indexed: 02/07/2023] Open
Abstract
Genome engineering of bacteriophages provides opportunities for precise genetic dissection and for numerous phage applications including therapy. However, few methods are available for facile construction of unmarked precise deletions, insertions, gene replacements and point mutations in bacteriophages for most bacterial hosts. Here we describe CRISPY-BRED and CRISPY-BRIP, methods for efficient and precise engineering of phages in Mycobacterium species, with applicability to phages of a variety of other hosts. This recombineering approach uses phage-derived recombination proteins and Streptococcus thermophilus CRISPR-Cas9.
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Affiliation(s)
- Katherine S Wetzel
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | | | - Rebekah M Dedrick
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Ching-Chung Ko
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Krista G Freeman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Haley G Aull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Ashley M Divens
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
- Department of Biomedical Sciences, West Virginia University, Morgantown, WV, 26506, USA
| | - Jeremy M Rock
- Department of Host-Pathogen Biology, The Rockefeller University, New York, NY, 10065, USA
| | - Kira M Zack
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
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15
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Abstract
Bacteriophages are viruses whose ubiquity in nature and remarkable specificity to their host bacteria enable an impressive and growing field of tunable biotechnologies in agriculture and public health. Bacteriophage capsids, which house and protect their nucleic acids, have been modified with a range of functionalities (e.g., fluorophores, nanoparticles, antigens, drugs) to suit their final application. Functional groups naturally present on bacteriophage capsids can be used for electrostatic adsorption or bioconjugation, but their impermanence and poor specificity can lead to inconsistencies in coverage and function. To overcome these limitations, researchers have explored both genetic and chemical modifications to enable strong, specific bonds between phage capsids and their target conjugates. Genetic modification methods involve introducing genes for alternative amino acids, peptides, or protein sequences into either the bacteriophage genomes or capsid genes on host plasmids to facilitate recombinant phage generation. Chemical modification methods rely on reacting functional groups present on the capsid with activated conjugates under the appropriate solution pH and salt conditions. This review surveys the current state-of-the-art in both genetic and chemical bacteriophage capsid modification methodologies, identifies major strengths and weaknesses of methods, and discusses areas of research needed to propel bacteriophage technology in development of biosensors, vaccines, therapeutics, and nanocarriers.
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Affiliation(s)
| | - Julie M. Goddard
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Sam R. Nugen
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
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16
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Wannier TM, Ciaccia PN, Ellington AD, Filsinger GT, Isaacs FJ, Javanmardi K, Jones MA, Kunjapur AM, Nyerges A, Pal C, Schubert MG, Church GM. Recombineering and MAGE. NATURE REVIEWS. METHODS PRIMERS 2021; 1:7. [PMID: 35540496 PMCID: PMC9083505 DOI: 10.1038/s43586-020-00006-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/19/2020] [Indexed: 12/17/2022]
Abstract
Recombination-mediated genetic engineering, also known as recombineering, is the genomic incorporation of homologous single-stranded or double-stranded DNA into bacterial genomes. Recombineering and its derivative methods have radically improved genome engineering capabilities, perhaps none more so than multiplex automated genome engineering (MAGE). MAGE is representative of a set of highly multiplexed single-stranded DNA-mediated technologies. First described in Escherichia coli, both MAGE and recombineering are being rapidly translated into diverse prokaryotes and even into eukaryotic cells. Together, this modern set of tools offers the promise of radically improving the scope and throughput of experimental biology by providing powerful new methods to ease the genetic manipulation of model and non-model organisms. In this Primer, we describe recombineering and MAGE, their optimal use, their diverse applications and methods for pairing them with other genetic editing tools. We then look forward to the future of genetic engineering.
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Affiliation(s)
- Timothy M. Wannier
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Peter N. Ciaccia
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT, USA
- Systems Biology Institute, Yale University, West Haven, CT, USA
| | - Andrew D. Ellington
- Department of Molecular Biosciences, College of Natural Sciences, University of Texas at Austin, Austin, TX, USA
| | - Gabriel T. Filsinger
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Systems Biology, Harvard University, Cambridge, MA, USA
| | - Farren J. Isaacs
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT, USA
- Systems Biology Institute, Yale University, West Haven, CT, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Kamyab Javanmardi
- Department of Molecular Biosciences, College of Natural Sciences, University of Texas at Austin, Austin, TX, USA
| | - Michaela A. Jones
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA
| | - Aditya M. Kunjapur
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA
| | - Akos Nyerges
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Csaba Pal
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Max G. Schubert
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
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17
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λ Recombineering Used to Engineer the Genome of Phage T7. Antibiotics (Basel) 2020; 9:antibiotics9110805. [PMID: 33202746 PMCID: PMC7697293 DOI: 10.3390/antibiotics9110805] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/10/2020] [Accepted: 11/12/2020] [Indexed: 01/21/2023] Open
Abstract
Bacteriophage T7 and T7-like bacteriophages are valuable genetic models for lytic phage biology that have heretofore been intractable with in vivo genetic engineering methods. This manuscript describes that the presence of λ Red recombination proteins makes in vivo recombineering of T7 possible, so that single base changes and whole gene replacements on the T7 genome can be made. Red recombination functions also increase the efficiency of T7 genome DNA transfection of cells by ~100-fold. Likewise, Red function enables two other T7-like bacteriophages that do not normally propagate in E. coli to be recovered following genome transfection. These results constitute major technical advances in the speed and efficiency of bacteriophage T7 engineering and will aid in the rapid development of new phage variants for a variety of applications.
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18
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Duong MM, Carmody CM, Ma Q, Peters JE, Nugen SR. Optimization of T4 phage engineering via CRISPR/Cas9. Sci Rep 2020; 10:18229. [PMID: 33106580 PMCID: PMC7588440 DOI: 10.1038/s41598-020-75426-6] [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: 05/15/2020] [Accepted: 10/12/2020] [Indexed: 12/11/2022] Open
Abstract
A major limitation hindering the widespread use of synthetic phages in medical and industrial settings is the lack of an efficient phage-engineering platform. Classical T4 phage engineering and several newly proposed methods are often inefficient and time consuming and consequently, only able to produce an inconsistent range of genomic editing rates between 0.03-3%. Here, we review and present new understandings of the CRISPR/Cas9 assisted genome engineering technique that significantly improves the genomic editing rate of T4 phages. Our results indicate that crRNAs selection is a major rate limiting factor in T4 phage engineering via CRISPR/Cas9. We were able to achieve an editing rate of > 99% for multiple genes that functionalizes the phages for further applications. We envision that this improved phage-engineering platform will accelerate the fields of individualized phage therapy, biocontrol, and rapid diagnostics.
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Affiliation(s)
- Michelle M Duong
- Department of Food Science and Technology, Cornell University, Ithaca, NY, 14853, USA
| | - Caitlin M Carmody
- Department of Food Science and Technology, Cornell University, Ithaca, NY, 14853, USA
| | - Qinqin Ma
- Department of Food Science and Technology, Cornell University, Ithaca, NY, 14853, USA
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Joseph E Peters
- Department of Microbiology, Cornell University, Ithaca, NY, 14853, USA
| | - Sam R Nugen
- Department of Food Science and Technology, Cornell University, Ithaca, NY, 14853, USA.
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19
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Challenges & opportunities for phage-based in situ microbiome engineering in the gut. J Control Release 2020; 326:106-119. [DOI: 10.1016/j.jconrel.2020.06.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 06/14/2020] [Accepted: 06/15/2020] [Indexed: 12/16/2022]
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20
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Fehr AR. Bacterial Artificial Chromosome-Based Lambda Red Recombination with the I-SceI Homing Endonuclease for Genetic Alteration of MERS-CoV. Methods Mol Biol 2020; 2099:53-68. [PMID: 31883087 PMCID: PMC7121842 DOI: 10.1007/978-1-0716-0211-9_5] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Over the past two decades, several coronavirus (CoV) infectious clones have been engineered, allowing for the manipulation of their large viral genomes (~30 kb) using unique reverse genetic systems. These reverse genetic systems include targeted recombination, in vitro ligation, vaccinia virus vectors, and bacterial artificial chromosomes (BACs). Quickly after the identification of Middle East respiratory syndrome-CoV (MERS-CoV), both in vitro ligation and BAC-based reverse genetic technologies were engineered for MERS-CoV to study its basic biological properties, develop live-attenuated vaccines, and test antiviral drugs. Here, I will describe how lambda red recombination can be used with the MERS-CoV BAC to quickly and efficiently introduce virtually any type of genetic modification (point mutations, insertions, deletions) into the MERS-CoV genome and recover recombinant virus.
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Affiliation(s)
- Anthony R Fehr
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA.
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21
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Yeom H, Ryu T, Lee AC, Noh J, Lee H, Choi Y, Kim N, Kwon S. Cell-Free Bacteriophage Genome Synthesis Using Low-Cost Sequence-Verified Array-Synthesized Oligonucleotides. ACS Synth Biol 2020; 9:1376-1384. [PMID: 32383864 DOI: 10.1021/acssynbio.0c00051] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Synthesizing engineered bacteriophages (phages) for human use has potential in various applications ranging from drug screening using a phage display to clinical use using phage therapy. However, the engineering of phages conventionally involves the use of an in vivo system that has low production efficiency because of high virulence against the host and low transformation efficiency. To circumvent these issues, de novo phage genome synthesis using chemically synthesized oligonucleotides (oligos) has increased the potential for engineering phages in a cell-free system. Here, we present a cell-free, low-cost, de novo gene synthesis technology called Sniper assembly for phage genome construction. With massively parallel sequencing of microarray-synthesized oligos, we generated and identified approximately 100 000 clonal DNA clusters in vitro and 5000 error-free ones in a cell-free environment. To demonstrate its practical application, we synthesized the Acinetobacter phage AP205 genome (4268 bp) using 65 sequence-verified DNA clones. Compared to previous reports, Sniper assembly lowered the genome synthesis cost ($0.0137/bp) by producing low-cost sequence-verified DNA.
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Affiliation(s)
- Huiran Yeom
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, South Korea
| | - Taehoon Ryu
- Department of Molecular Genetic Engineering, Celemics, Inc., Seoul, 08506, Republic of Korea
| | - Amos Chungwon Lee
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jinsung Noh
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, South Korea
| | - Hansaem Lee
- Department of Molecular Genetic Engineering, Celemics, Inc., Seoul, 08506, Republic of Korea
| | - Yeongjae Choi
- Nano Systems Institute, Seoul National University, Seoul, 08826, Republic of Korea
| | - Namphil Kim
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, South Korea
| | - Sunghoon Kwon
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, South Korea
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, 08826, Republic of Korea
- Bio-MAX institute, Seoul National University, Seoul, 08826, Republic of Korea
- Inter-University Semiconductor Research Center, Seoul, 08826, Republic of Korea
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22
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Corts AD, Thomason LC, Gill RT, Gralnick JA. Efficient and Precise Genome Editing in Shewanella with Recombineering and CRISPR/Cas9-Mediated Counter-Selection. ACS Synth Biol 2019; 8:1877-1889. [PMID: 31277550 DOI: 10.1021/acssynbio.9b00188] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Dissimilatory metal-reducing bacteria, particularly those from the genus Shewanella, are of importance for bioremediation of metal contaminated sites and sustainable energy production. However, studies on this species have suffered from a lack of effective genetic tools for precise and high throughput genome manipulation. Here we report the development of a highly efficient system based on single-stranded DNA oligonucleotide recombineering coupled with CRISPR/Cas9-mediated counter-selection. Our system uses two plasmids: a sgRNA targeting vector and an editing vector, the latter harboring both Cas9 and the phage recombinase W3 Beta. Following the experimental analysis of Cas9 activity, we demonstrate the ability of this system to efficiently and precisely engineer different Shewanella strains with an average efficiency of >90% among total transformed cells, compared to ≃5% by recombineering alone, and regardless of the gene modified. We also show that different genetic changes can be introduced: mismatches, deletions, and small insertions. Surprisingly, we found that use of CRISPR/Cas9 alone allows selection of recombinase-independent S. oneidensis mutations, albeit at lower efficiency and frequency. With synthesized single-stranded DNA as substrates for homologous recombination and Cas9 as a counter-selectable marker, this new system provides a rapid, scalable, versatile, and scarless tool that will accelerate progress in Shewanella genomic engineering.
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Affiliation(s)
- Anna D. Corts
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota−Twin Cities, St. Paul, Minnesota 55108, United States
| | - Lynn C. Thomason
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Ryan T. Gill
- DTU BIOSUSTAIN, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Jeffrey A. Gralnick
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota−Twin Cities, St. Paul, Minnesota 55108, United States
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23
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Chen Y, Batra H, Dong J, Chen C, Rao VB, Tao P. Genetic Engineering of Bacteriophages Against Infectious Diseases. Front Microbiol 2019; 10:954. [PMID: 31130936 PMCID: PMC6509161 DOI: 10.3389/fmicb.2019.00954] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 04/15/2019] [Indexed: 12/19/2022] Open
Abstract
Bacteriophages (phages) are the most abundant and widely distributed organisms on Earth, constituting a virtually unlimited resource to explore the development of biomedical therapies. The therapeutic use of phages to treat bacterial infections (“phage therapy”) was conceived by Felix d’Herelle nearly a century ago. However, its power has been realized only recently, largely due to the emergence of multi-antibiotic resistant bacterial pathogens. Progress in technologies, such as high-throughput sequencing, genome editing, and synthetic biology, further opened doors to explore this vast treasure trove. Here, we review some of the emerging themes on the use of phages against infectious diseases. In addition to phage therapy, phages have also been developed as vaccine platforms to deliver antigens as part of virus-like nanoparticles that can stimulate immune responses and prevent pathogen infections. Phage engineering promises to generate phage variants with unique properties for prophylactic and therapeutic applications. These approaches have created momentum to accelerate basic as well as translational phage research and potential development of therapeutics in the near future.
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Affiliation(s)
- Yibao Chen
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Himanshu Batra
- Department of Biology, The Catholic University of America, Washington, DC, United States
| | - Junhua Dong
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Cen Chen
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Venigalla B Rao
- Department of Biology, The Catholic University of America, Washington, DC, United States
| | - Pan Tao
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China.,Department of Biology, The Catholic University of America, Washington, DC, United States
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24
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Engineering Bacteriophages as Versatile Biologics. Trends Microbiol 2019; 27:355-367. [DOI: 10.1016/j.tim.2018.09.006] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 09/04/2018] [Accepted: 09/24/2018] [Indexed: 01/21/2023]
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25
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Abdelkader K, Gerstmans H, Saafan A, Dishisha T, Briers Y. The Preclinical and Clinical Progress of Bacteriophages and Their Lytic Enzymes: The Parts are Easier than the Whole. Viruses 2019; 11:E96. [PMID: 30678377 PMCID: PMC6409994 DOI: 10.3390/v11020096] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 01/16/2019] [Accepted: 01/22/2019] [Indexed: 12/25/2022] Open
Abstract
The therapeutic potential of phages has been considered since their first identification more than a century ago. The evident concept of using a natural predator to treat bacterial infections has, however, since then been challenged considerably. Initially, the vast success of antibiotics almost eliminated the study of phages for therapy. Upon the renaissance of phage therapy research, the most provocative and unique properties of phages such as high specificity, self-replication and co-evolution prohibited a rapid preclinical and clinical development. On the one hand, the typical trajectory followed by small molecule antibiotics could not be simply translated into the preclinical analysis of phages, exemplified by the need for complex broad spectrum or personalized phage cocktails of high purity and the more complex pharmacokinetics. On the other hand, there was no fitting regulatory framework to deal with flexible and sustainable phage therapy approaches, including the setup and approval of adequate clinical trials. While significant advances are incrementally made to eliminate these hurdles, phage-inspired antibacterials have progressed in the slipstream of phage therapy, benefiting from the lack of hurdles that are typically associated with phage therapy. Most advanced are phage lytic enzymes that kill bacteria through peptidoglycan degradation and osmotic lysis. Both phages and their lytic enzymes are now widely considered as safe and have now progressed to clinical phase II to show clinical efficacy as pharmaceutical. Yet, more initiatives are needed to fill the clinical pipeline to beat the typical attrition rates of clinical evaluation and to come to a true evaluation of phages and phage lytic enzymes in the clinic.
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Affiliation(s)
- Karim Abdelkader
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Valentin Vaerwijckweg 1, B-9000 Ghent, Belgium.
- Department of Microbiology and Immunology, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62511, Egypt.
| | - Hans Gerstmans
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Valentin Vaerwijckweg 1, B-9000 Ghent, Belgium.
- MeBioS-Biosensors group, Department of Biosystems, KU Leuven, Willem de Croylaan 42, B-3001 Leuven, Belgium.
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21, B-3001 Leuven, Belgium.
| | - Amal Saafan
- Department of Microbiology and Immunology, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62511, Egypt.
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Menoufia University, Shebin ElKoum 51132, Egypt.
| | - Tarek Dishisha
- Department of Microbiology and Immunology, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62511, Egypt.
| | - Yves Briers
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Valentin Vaerwijckweg 1, B-9000 Ghent, Belgium.
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26
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Marinelli LJ, Piuri M, Hatfull GF. Genetic Manipulation of Lytic Bacteriophages with BRED: Bacteriophage Recombineering of Electroporated DNA. Methods Mol Biol 2019; 1898:69-80. [PMID: 30570724 DOI: 10.1007/978-1-4939-8940-9_6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We describe a recombineering-based method for the genetic manipulation of lytically replicating bacteriophages, focusing on mycobacteriophages. The approach utilizes recombineering-proficient strains of Mycobacterium smegmatis and employs a cotransformation strategy with purified phage genomic DNA and a mutagenic substrate, which selects for only those cells that are competent to take up DNA. The cotransformation method, combined with the high rates of recombination obtained in M. smegmatis recombineering strains, allows for the efficient and rapid generation of bacteriophage mutants.
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Affiliation(s)
- Laura J Marinelli
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Mariana Piuri
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, IQUIBICEN-CONICET, Buenos Aires, Argentina
- Laboratorio "Bacteriófagos y Aplicaciones Biotecnológicas", Departamento de Química Biológica, FCEyN, UBA, Ciudad Universitaria, Ciudad Autónoma de Buenos Aires, Argentina
| | - Graham F Hatfull
- Department of Biological Sciences and Pittsburgh Bacteriophage Institute, University of Pittsburgh, Pittsburgh, PA, USA
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27
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Abstract
Bacteriophage research has been instrumental to advancing many fields of biology, such as genetics, molecular biology, and synthetic biology. Many phage-derived technologies have been adapted for building gene circuits to program biological systems. Phages also exhibit significant medical potential as antibacterial agents and bacterial diagnostics due to their extreme specificity for their host, and our growing ability to engineer them further enhances this potential. Phages have also been used as scaffolds for genetically programmable biomaterials that have highly tunable properties. Furthermore, phages are central to powerful directed evolution platforms, which are being leveraged to enhance existing biological functions and even produce new ones. In this review, we discuss recent examples of how phage research is influencing these next-generation biotechnologies.
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Affiliation(s)
- Sebastien Lemire
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Kevin M Yehl
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Timothy K Lu
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; .,Synthetic Biology Group, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Pleška M, Guet CC. Effects of mutations in phage restriction sites during escape from restriction-modification. Biol Lett 2018; 13:rsbl.2017.0646. [PMID: 29237814 DOI: 10.1098/rsbl.2017.0646] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 11/15/2017] [Indexed: 01/21/2023] Open
Abstract
Restriction-modification systems are widespread genetic elements that protect bacteria from bacteriophage infections by recognizing and cleaving heterologous DNA at short, well-defined sequences called restriction sites. Bioinformatic evidence shows that restriction sites are significantly underrepresented in bacteriophage genomes, presumably because bacteriophages with fewer restriction sites are more likely to escape cleavage by restriction-modification systems. However, how mutations in restriction sites affect the likelihood of bacteriophage escape is unknown. Using the bacteriophage λ and the restriction-modification system EcoRI, we show that while mutation effects at different restriction sites are unequal, they are independent. As a result, the probability of bacteriophage escape increases with each mutated restriction site. Our results experimentally support the role of restriction site avoidance as a response to selection imposed by restriction-modification systems and offer an insight into the events underlying the process of bacteriophage escape.
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Affiliation(s)
- Maroš Pleška
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg 3400, Austria
| | - Călin C Guet
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg 3400, Austria
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The Bacteriophage Lambda CII Phenotypes for Complementation, Cellular Toxicity and Replication Inhibition Are Suppressed in cII-oop Constructs Expressing the Small RNA OOP. Viruses 2018. [PMID: 29518935 PMCID: PMC5869508 DOI: 10.3390/v10030115] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The temperate bacteriophage lambda (λ) CII protein is a positive regulator of transcription from promoter pE, a component of the lysogenic response. The expression of cII was examined in vectors devoid of phage transcription-modulating elements. Their removal enabled evaluating if the expression of the small RNA OOP, on its own, could suppress CII activities, including complementing for a lysogenic response, cell toxicity and causing rapid cellular loss of ColE1 plasmids. The results confirm that OOP RNA expression from the genetic element pO-oop-to can prevent the ability of plasmid-encoded CII to complement for a lysogenic response, suggesting that it serves as a powerful regulatory pivot in λ development. Plasmids with a pO promoter sequence of 45 nucleotides (pO45), containing the −10 and −35 regions for oop, were non-functional; whereas, plasmids with pO94 prevented CII complementation, CII-dependent plasmid loss and suppressed CII toxicity, suggesting the pO promoter has an extended DNA sequence. All three CII activities were eliminated by the deletion of the COOH-terminal 20 amino acids of CII. Host mutations in the hflA locus, in pcnB and in rpoB influenced CII activities. These studies suggest that the COOH-terminal end of CII likely interacts with the β-subunit of RNA polymerase.
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Kim Y, de la Torre A, Leal AA, Finkelstein IJ. Efficient modification of λ-DNA substrates for single-molecule studies. Sci Rep 2017; 7:2071. [PMID: 28522818 PMCID: PMC5437064 DOI: 10.1038/s41598-017-01984-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 04/05/2017] [Indexed: 01/15/2023] Open
Abstract
Single-molecule studies of protein-nucleic acid interactions frequently require site-specific modification of long DNA substrates. The bacteriophage λ is a convenient source of high quality long (48.5 kb) DNA. However, introducing specific sequences, tertiary structures, and chemical modifications into λ-DNA remains technically challenging. Most current approaches rely on multi-step ligations with low yields and incomplete products. Here, we describe a molecular toolkit for rapid preparation of modified λ-DNA. A set of PCR cassettes facilitates the introduction of recombinant DNA sequences into the λ-phage genome with 90-100% yield. Extrahelical structures and chemical modifications can be inserted at user-defined sites via an improved nicking enzyme-based strategy. As a proof-of-principle, we explore the interactions of S. cerevisiae Proliferating Cell Nuclear Antigen (yPCNA) with modified DNA sequences and structures incorporated within λ-DNA. Our results demonstrate that S. cerevisiae Replication Factor C (yRFC) can load yPCNA onto 5'-ssDNA flaps, (CAG)13 triplet repeats, and homoduplex DNA. However, yPCNA remains trapped on the (CAG)13 structure, confirming a proposed mechanism for triplet repeat expansion. We anticipate that this molecular toolbox will be broadly useful for other studies that require site-specific modification of long DNA substrates.
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Affiliation(s)
- Yoori Kim
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Armando de la Torre
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Andrew A Leal
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, 78712, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, 78712, USA.
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas, 78712, USA.
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Klebsiella Phage ΦK64-1 Encodes Multiple Depolymerases for Multiple Host Capsular Types. J Virol 2017; 91:JVI.02457-16. [PMID: 28077636 DOI: 10.1128/jvi.02457-16] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 12/22/2016] [Indexed: 11/20/2022] Open
Abstract
The genome of the multihost bacteriophage ΦK64-1, capable of infecting Klebsiella capsular types K1, K11, K21, K25, K30, K35, K64, and K69, as well as new capsular types KN4 and KN5, was analyzed and revealed that 11 genes (S1-1, S1-2, S1-3, S2-1, S2-2, S2-3, S2-4, S2-5, S2-6, S2-7, and S2-8) encode proteins with amino acid sequence similarity to tail fibers/spikes or lyases. S2-5 previously was shown to encode a K64 capsule depolymerase (K64dep). Specific capsule-degrading activities of an additional eight putative capsule depolymerases (S2-4 against K1, S1-1 against K11, S1-3 against K21, S2-2 against K25, S2-6 against K30/K69, S2-3 against K35, S1-2 against KN4, and S2-1 against KN5) was demonstrated by expression and purification of the recombinant proteins. Consistent with the capsular type-specific depolymerization activity of these gene products, phage mutants of S1-2, S2-2, S2-3, or S2-6 lost infectivity for KN4, K25, K35, or K30/K69, respectively, indicating that capsule depolymerase is crucial for infecting specific hosts. In conclusion, we identified nine functional capsule depolymerase-encoding genes in a bacteriophage and correlated activities of the gene products to all ten hosts of this phage, providing an example of type-specific host infection mechanisms in a multihost bacteriophage.IMPORTANCE We currently identified eight novel capsule depolymerases in a multihost Klebsiella bacteriophage and correlated the activities of the gene products to all hosts of this phage, providing an example of carriage of multiple depolymerases in a phage with a wide capsular type host spectrum. Moreover, we also established a recombineering system for modification of Klebsiella bacteriophage genomes and demonstrated the importance of capsule depolymerase for infecting specific hosts. Based on the powerful tool for modification of phage genome, further studies can be conducted to improve the understanding of mechanistic details of Klebsiella phage infection. Furthermore, the newly identified capsule depolymerases will be of great value for applications in capsular typing.
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Pires DP, Cleto S, Sillankorva S, Azeredo J, Lu TK. Genetically Engineered Phages: a Review of Advances over the Last Decade. Microbiol Mol Biol Rev 2016; 80:523-43. [PMID: 27250768 PMCID: PMC4981678 DOI: 10.1128/mmbr.00069-15] [Citation(s) in RCA: 238] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Soon after their discovery in the early 20th century, bacteriophages were recognized to have great potential as antimicrobial agents, a potential that has yet to be fully realized. The nascent field of phage therapy was adversely affected by inadequately controlled trials and the discovery of antibiotics. Although the study of phages as anti-infective agents slowed, phages played an important role in the development of molecular biology. In recent years, the increase in multidrug-resistant bacteria has renewed interest in the use of phages as antimicrobial agents. With the wide array of possibilities offered by genetic engineering, these bacterial viruses are being modified to precisely control and detect bacteria and to serve as new sources of antibacterials. In applications that go beyond their antimicrobial activity, phages are also being developed as vehicles for drug delivery and vaccines, as well as for the assembly of new materials. This review highlights advances in techniques used to engineer phages for all of these purposes and discusses existing challenges and opportunities for future work.
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Affiliation(s)
- Diana P Pires
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Sara Cleto
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Sanna Sillankorva
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Joana Azeredo
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Timothy K Lu
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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Abstract
The bacteriophage λ Red homologous recombination system has been studied over the past 50 years as a model system to define the mechanistic details of how organisms exchange DNA segments that share extended regions of homology. The λ Red system proved useful as a system to study because recombinants could be easily generated by co-infection of genetically marked phages. What emerged from these studies was the recognition that replication of phage DNA was required for substantial Red-promoted recombination in vivo, and the critical role that double-stranded DNA ends play in allowing the Red proteins access to the phage DNA chromosomes. In the past 16 years, however, the λ Red recombination system has gained a new notoriety. When expressed independently of other λ functions, the Red system is able to promote recombination of linear DNA containing limited regions of homology (∼50 bp) with the Escherichia coli chromosome, a process known as recombineering. This review explains how the Red system works during a phage infection, and how it is utilized to make chromosomal modifications of E. coli with such efficiency that it changed the nature and number of genetic manipulations possible, leading to advances in bacterial genomics, metabolic engineering, and eukaryotic genetics.
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Affiliation(s)
- Kenan C Murphy
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605
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Marinelli LJ, Hatfull GF, Piuri M. Recombineering: A powerful tool for modification of bacteriophage genomes. BACTERIOPHAGE 2014; 2:5-14. [PMID: 22666652 PMCID: PMC3357384 DOI: 10.4161/bact.18778] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Recombineering, a recently developed technique for efficient genetic manipulation of bacteria, is facilitated by phage-derived recombination proteins and has the advantage of using DNA substrates with short regions of homology. This system was first developed in E. coli but has since been adapted for use in other bacteria. It is now widely used in a number of different systems for a variety of purposes, and the construction of chromosomal gene knockouts, deletions, insertions, point mutations, as well as in vivo cloning, mutagenesis of bacterial artificial chromosomes and phasmids, and the construction of genomic libraries has been reported. However, these methods also can be effectively applied to the genetic modification of bacteriophage genomes, in both their prophage and lytically growing states. The ever-growing collection of fully sequenced bacteriophages raises more questions than they answer, including the unknown functions of vast numbers of genes with no known homologs and of unknown function. Recombineering of phage genomes is central to addressing these questions, enabling the simple construction of mutants, determination of gene essentiality, and elucidation of gene function. In turn, advances in our understanding of phage genomics should present similar recombineering tools for dissecting a multitude of other genetically naïve bacterial systems.
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36
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Martel B, Moineau S. CRISPR-Cas: an efficient tool for genome engineering of virulent bacteriophages. Nucleic Acids Res 2014; 42:9504-13. [PMID: 25063295 PMCID: PMC4132740 DOI: 10.1093/nar/gku628] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Bacteriophages are now widely recognized as major players in a wide variety of ecosystems. Novel genes are often identified in newly isolated phages as well as in environmental metavirome studies. Most of these novel viral genes have unknown functions but appear to be coding for small, non-structural proteins. To understand their biological role, very efficient genetic tools are required to modify them, especially in the genome of virulent phages. We first show that specific point mutations and large deletions can be engineered in the genome of the virulent phage 2972 using the Streptococcus thermophilus CRISPR-Cas Type II-A system as a selective pressure to increase recombination efficiencies. Of significance, all the plaques tested contained recombinant phages with the desired mutation. Furthermore, we show that the CRISPR-Cas engineering system can be used to efficiently introduce a functional methyltransferase gene into a virulent phage genome. Finally, synthetic CRISPR bacteriophage insensitive mutants were constructed by cloning a spacer-repeat unit in a low-copy vector illustrating the possibility to target multiple regions of the phage genome. Taken together, this data shows that the CRISPR-Cas system is an efficient and adaptable tool for editing the otherwise intractable genomes of virulent phages and to better understand phage-host interactions.
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Affiliation(s)
- Bruno Martel
- Département de biochimie, microbiologie et bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec city, Quebec, G1V 0A6, Canada Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Quebec City, Quebec, G1V 0A6, Canada
| | - Sylvain Moineau
- Département de biochimie, microbiologie et bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec city, Quebec, G1V 0A6, Canada Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Quebec City, Quebec, G1V 0A6, Canada
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37
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Hodyra K, Dąbrowska K. Molecular and chemical engineering of bacteriophages for potential medical applications. Arch Immunol Ther Exp (Warsz) 2014; 63:117-27. [PMID: 25048831 PMCID: PMC4359349 DOI: 10.1007/s00005-014-0305-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 05/20/2014] [Indexed: 12/19/2022]
Abstract
Recent progress in molecular engineering has contributed to the great progress of medicine. However, there are still difficult problems constituting a challenge for molecular biology and biotechnology, e.g. new generation of anticancer agents, alternative biosensors or vaccines. As a biotechnological tool, bacteriophages (phages) offer a promising alternative to traditional approaches. They can be applied as anticancer agents, novel platforms in vaccine design, or as target carriers in drug discovery. Phages also offer solutions for modern cell imaging, biosensor construction or food pathogen detection. Here we present a review of bacteriophage research as a dynamically developing field with promising prospects for further development of medicine and biotechnology.
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Affiliation(s)
- Katarzyna Hodyra
- Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, R. Weigla 12, 53-114, Wrocław, Poland
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38
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Thomason LC, Sawitzke JA, Li X, Costantino N, Court DL. Recombineering: genetic engineering in bacteria using homologous recombination. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 2014; 106:1.16.1-1.16.39. [PMID: 24733238 DOI: 10.1002/0471142727.mb0116s106] [Citation(s) in RCA: 147] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The bacterial chromosome and bacterial plasmids can be engineered in vivo by homologous recombination using PCR products and synthetic oligonucleotides as substrates. This is possible because bacteriophage-encoded recombination proteins efficiently recombine sequences with homologies as short as 35 to 50 bases. Recombineering allows DNA sequences to be inserted or deleted without regard to location of restriction sites. This unit first describes preparation of electrocompetent cells expressing the recombineering functions and their transformation with dsDNA or ssDNA. It then presents support protocols that describe several two-step selection/counter-selection methods of making genetic alterations without leaving any unwanted changes in the targeted DNA, and a method for retrieving onto a plasmid a genetic marker (cloning by retrieval) from the Escherichia coli chromosome or a co-electroporated DNA fragment. Additional protocols describe methods to screen for unselected mutations, removal of the defective prophage from recombineering strains, and other useful techniques.
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Affiliation(s)
- Lynn C Thomason
- Basic Science Program, GRCBL-Molecular Control & Genetics Section, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, Maryland
| | - James A Sawitzke
- Molecular Control and Genetics Section, Gene Regulation and Chromosome Biology, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland
| | - Xintian Li
- Molecular Control and Genetics Section, Gene Regulation and Chromosome Biology, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland
| | - Nina Costantino
- Molecular Control and Genetics Section, Gene Regulation and Chromosome Biology, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland
| | - Donald L Court
- Molecular Control and Genetics Section, Gene Regulation and Chromosome Biology, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland
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Poteete AR. Involvement of Escherichia coli DNA Replication Proteins in Phage Lambda Red-Mediated Homologous Recombination. PLoS One 2013; 8:e67440. [PMID: 23840702 PMCID: PMC3686724 DOI: 10.1371/journal.pone.0067440] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 05/20/2013] [Indexed: 11/19/2022] Open
Abstract
The Red recombination system of bacteriophage lambda is widely used for genetic engineering because of its ability to promote recombination between bacterial chromosomes or plasmids and linear DNA species introduced by electroporation. The process is known to be intimately tied to replication, but the cellular functions which participate with Red in this process are largely unknown. Here two such functions are identified: the GrpE-DnaK-DnaJ chaperone system, and DNA polymerase I. Mutations in either function are found to decrease the efficiency of Red recombination. grpE and dnaJ mutations which greatly decrease Red recombination with electroporated DNA species have only small effects on Red-mediated transduction. This recombination event specificity suggests that the involvement of GrpE-DnaJ-DnaK is not simply an effect on Red structure or stability.
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Affiliation(s)
- Anthony R. Poteete
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- * E-mail:
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40
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Sawitzke JA, Thomason LC, Bubunenko M, Li X, Costantino N, Court DL. Recombineering: highly efficient in vivo genetic engineering using single-strand oligos. Methods Enzymol 2013; 533:157-77. [PMID: 24182922 PMCID: PMC7518103 DOI: 10.1016/b978-0-12-420067-8.00010-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Recombineering provides the ability to make rapid, precise, and inexpensive genetic alterations to any DNA sequence, either in the chromosome or cloned onto a vector that replicates in E. coli (or other recombineering-proficient bacteria), and to do so in a highly efficient manner. Complicated genetic constructs that are impossible to make with in vitro genetic engineering can be created in days with recombineering. Recombineering with single-strand DNA (ssDNA) can be used to create single or multiple clustered point mutations, small or large (up to 10kb) deletions, and small (10-20 base) insertions such as sequence tags. Using optimized conditions, point mutations can be made with such high frequencies that they can be found without selection. This technology excels at creating both directed and random mutations.
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Affiliation(s)
- James A Sawitzke
- Molecular Control and Genetics Section, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, USA.
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Abstract
The homologous recombination systems of linear double-stranded (ds)DNA bacteriophages are required for the generation of genetic diversity, the repair of dsDNA breaks, and the formation of concatemeric chromosomes, the immediate precursor to packaging. These systems have been studied for decades as a means to understand the basic principles of homologous recombination. From the beginning, it was recognized that these recombinases are linked intimately to the mechanisms of phage DNA replication. In the last decade, however, investigators have exploited these recombination systems as tools for genetic engineering of bacterial chromosomes, bacterial artificial chromosomes, and plasmids. This recombinational engineering technology has been termed "recombineering" and offers a new paradigm for the genetic manipulation of bacterial chromosomes, which is far more efficient than the classical use of nonreplicating integration vectors for gene replacement. The phage λ Red recombination system, in particular, has been used to construct gene replacements, deletions, insertions, inversions, duplications, and single base pair changes in the Escherichia coli chromosome. This chapter discusses the components of the recombination systems of λ, rac prophage, and phage P22 and properties of single-stranded DNA annealing proteins from these and other phage that have been instrumental for the development of this technology. The types of genetic manipulations that can be made are described, along with proposed mechanisms for both double-stranded DNA- and oligonucleotide-mediated recombineering events. Finally, the impact of this technology to such diverse fields as bacterial pathogenesis, metabolic engineering, and mouse genomics is discussed.
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Affiliation(s)
- Kenan C Murphy
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA.
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42
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Roy P, Noad R. Use of bacterial artificial chromosomes in baculovirus research and recombinant protein expression: current trends and future perspectives. ISRN MICROBIOLOGY 2012; 2012:628797. [PMID: 23762754 PMCID: PMC3671692 DOI: 10.5402/2012/628797] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 08/16/2012] [Indexed: 11/23/2022]
Abstract
The baculovirus expression system is one of the most successful and widely used eukaryotic protein expression methods. This short review will summarise the role of bacterial artificial chromosomes (BACS) as an enabling technology for the modification of the virus genome. For many years baculovirus genomes have been maintained in E. coli as bacterial artificial chromosomes, and foreign genes have been inserted using a transposition-based system. However, with recent advances in molecular biology techniques, particularly targeting reverse engineering of the baculovirus genome by recombineering, new frontiers in protein expression are being addressed. In particular, BACs have facilitated the propagation of disabled virus genomes that allow high throughput protein expression. Furthermore, improvement in the selection of recombinant viral genomes inserted into BACS has enabled the expression of multiprotein complexes by iterative recombineering of the baculovirus genome.
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Affiliation(s)
- Polly Roy
- Department of Pathogen Molecular Biology, Faculty of Infectious Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
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Hayes S, Horbay MA, Hayes C. A CI-independent form of replicative inhibition: turn off of early replication of bacteriophage lambda. PLoS One 2012; 7:e36498. [PMID: 22590552 PMCID: PMC3349717 DOI: 10.1371/journal.pone.0036498] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2011] [Accepted: 04/02/2012] [Indexed: 11/18/2022] Open
Abstract
Several earlier studies have described an unusual exclusion phenotype exhibited by cells with plasmids carrying a portion of the replication region of phage lambda. Cells exhibiting this inhibition phenotype (IP) prevent the plating of homo-immune and hybrid hetero-immune lambdoid phages. We have attempted to define aspects of IP, and show that it is directed to repλ phages. IP was observed in cells with plasmids containing a λ DNA fragment including oop, encoding a short OOP micro RNA, and part of the lambda origin of replication, oriλ, defined by iteron sequences ITN1-4 and an adjacent high AT-rich sequence. Transcription of the intact oop sequence from its promoter, p(O) is required for IP, as are iterons ITN3-4, but not the high AT-rich portion of oriλ. The results suggest that IP silencing is directed to theta mode replication initiation from an infecting repλ genome, or an induced repλ prophage. Phage mutations suppressing IP, i.e., Sip, map within, or adjacent to cro or in O, or both. Our results for plasmid based IP suggest the hypothesis that there is a natural mechanism for silencing early theta-mode replication initiation, i.e. the buildup of λ genomes with oop(+)oriλ(+) sequence.
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Affiliation(s)
- Sidney Hayes
- Department of Microbiology and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, Canada.
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Abstract
An improved and rapid genomic engineering method has been developed for the construction of -custom-designed microorganisms by scarless chromosomal gene knockouts. This method, which can be performed in 2 days, permits restructuring of the Escherichia coli genome via scarless deletion of selected genomic regions. The deletion process is mediated by a special plasmid, pREDI, which carries two independent inducible promoters: (1) an arabinose-inducible promoter that drives expression of λ-RED recombination proteins, which carry out the replacement of a target genomic region with a marker-containing linear DNA cassette, and (2) a rhamnose-inducible promoter that drives expression of I-SceI endonuclease, which accomplishes deletion of the introduced marker by double-strand breakage - mediated intramolecular recombination. This genomic deletion is performed simply by changing the carbon source in the bacterial growth medium from arabinose to rhamnose. The efficiencies of targeted region replacement and deletion of the inserted linear DNA cassette are nearly 70 and 100%, respectively. This rapid and efficient procedure can be adapted for use in generating a variety of genome modifications.
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Affiliation(s)
- Bong Hyun Sung
- Industrial Biotechnology and Bioenergy Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon, South Korea
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45
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Thomas BS, Nishikawa S, Ito K, Chopra P, Sharma N, Evans DH, Tyrrell DLJ, Bathe OF, Rancourt DE. Peptide vaccination is superior to genetic vaccination using a recombineered bacteriophage λ subunit vaccine. Vaccine 2011; 30:998-1008. [PMID: 22210400 DOI: 10.1016/j.vaccine.2011.12.070] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Revised: 12/12/2011] [Accepted: 12/14/2011] [Indexed: 11/28/2022]
Abstract
Genetic immunization holds promise as a vaccination method, but has so far proven ineffective in large primate and human trials. Herein, we examined the relative merits of genetic immunization and peptide immunization using bacteriophage λ. Bacteriophage λ has proven effective in immune challenge models using both immunization methods, but there has never been a direct comparison of efficacy and of the quality of immune response. In the current study, this vector was produced using a combination of cis and trans phage display. When antibody titers were measured from immunized animals together with IL-2, IL-4 and IFNγ production from splenocytes in vitro, we found that proteins displayed on λ were superior at eliciting an immune response in comparison to genetic immunization with λ. We also found that the antibodies produced in response to immunization with λ displayed proteins bound more epitopes than those produced in response to genetic immunization. Finally, the general immune response to λ inoculation, whether peptide or genetic, was dominated by a Th1 response, as determined by IFNγ and IL-4 concentration, or by a higher concentration of IgG2a antibodies.
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Affiliation(s)
- Brad S Thomas
- Southern Alberta Cancer Research Institute, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Calgary, Calgary, AB, Canada.
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Isaacs FJ, Carr PA, Wang HH, Lajoie MJ, Sterling B, Kraal L, Tolonen AC, Gianoulis TA, Goodman DB, Reppas NB, Emig CJ, Bang D, Hwang SJ, Jewett MC, Jacobson JM, Church GM. Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science 2011; 333:348-53. [PMID: 21764749 PMCID: PMC5472332 DOI: 10.1126/science.1205822] [Citation(s) in RCA: 415] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We present genome engineering technologies that are capable of fundamentally reengineering genomes from the nucleotide to the megabase scale. We used multiplex automated genome engineering (MAGE) to site-specifically replace all 314 TAG stop codons with synonymous TAA codons in parallel across 32 Escherichia coli strains. This approach allowed us to measure individual recombination frequencies, confirm viability for each modification, and identify associated phenotypes. We developed hierarchical conjugative assembly genome engineering (CAGE) to merge these sets of codon modifications into genomes with 80 precise changes, which demonstrate that these synonymous codon substitutions can be combined into higher-order strains without synthetic lethal effects. Our methods treat the chromosome as both an editable and an evolvable template, permitting the exploration of vast genetic landscapes.
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Affiliation(s)
- Farren J. Isaacs
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Peter A. Carr
- Center for Bits and Atoms, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- MIT Media Lab, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Harris H. Wang
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Program in Biophysics, Harvard University, Cambridge, MA 02138, USA
- Program in Medical Engineering and Medical Physics, Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA
- Wyss Institute, Harvard University, Cambridge, MA 02115, USA
| | - Marc J. Lajoie
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Program in Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Bram Sterling
- Center for Bits and Atoms, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- MIT Media Lab, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Laurens Kraal
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Andrew C. Tolonen
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Tara A. Gianoulis
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute, Harvard University, Cambridge, MA 02115, USA
| | - Daniel B. Goodman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Program in Medical Engineering and Medical Physics, Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA
| | | | | | - Duhee Bang
- Department of Chemistry, Yonsei University, Shinchon 134, Seoul 120-749, Korea
| | - Samuel J. Hwang
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael C. Jewett
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Department of Chemical and Biological Engineering and Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Joseph M. Jacobson
- Center for Bits and Atoms, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- MIT Media Lab, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute, Harvard University, Cambridge, MA 02115, USA
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Madyagol M, Al-Alami H, Levarski Z, Drahovská H, Turňa J, Stuchlík S. Gene replacement techniques for Escherichia coli genome modification. Folia Microbiol (Praha) 2011; 56:253-63. [PMID: 21614539 DOI: 10.1007/s12223-011-0035-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 05/04/2011] [Indexed: 11/24/2022]
Abstract
The subject of this review covers modern experimental procedures for chromosomal gene replacement in Escherichia coli and related bacteria, which enable the specific substitution of targeted genome sequences with copies of those carrying defined mutations. Two principal methods for gene replacement were established. The first "in-out" method is based on integration of plasmid into bacterial chromosome and subsequent resolving of the cointegrate. The "linear fragment" method (recombineering) is based on homologous recombination mediated by short homology arms at the ends of linear DNA molecule. Many new protocols and improvements in targeted gene replacement were introduced during the last 10 years. These methods are well suited for high-throughput functional gene studies and for many biotechnological applications.
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Affiliation(s)
- Mahesh Madyagol
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Mlynská dolina, 842 15, Bratislava, Slovak Republic
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Poteete AR. Recombination phenotypes of Escherichia coli greA mutants. BMC Mol Biol 2011; 12:12. [PMID: 21453489 PMCID: PMC3078854 DOI: 10.1186/1471-2199-12-12] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2010] [Accepted: 03/31/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The elongation factor GreA binds to RNA polymerase and modulates transcriptional pausing. Some recent research suggests that the primary role of GreA may not be to regulate gene expression, but rather, to promote the progression of replication forks which collide with RNA polymerase, and which might otherwise collapse. Replication fork collapse is known to generate dsDNA breaks, which can be recombinogenic. It follows that GreA malfunction could have consequences affecting homologous recombination. RESULTS Escherichia coli mutants bearing substitutions of the active site acidic residues of the transcription elongation factor GreA, D41N and E44K, were isolated as suppressors of growth inhibition by a toxic variant of the bacteriophage lambda Red-beta recombination protein. These mutants, as well as a D41A greA mutant and a greA deletion, were tested for proficiency in recombination events. The mutations were found to increase the efficiency of RecA-RecBCD-mediated and RecA-Red-mediated recombination, which are replication-independent, and to decrease the efficiency of replication-dependent Red-mediated recombination. CONCLUSION These observations provide new evidence for a role of GreA in resolving conflicts between replication and transcription.
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Affiliation(s)
- Anthony R Poteete
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA.
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Sawitzke JA, Costantino N, Li XT, Thomason LC, Bubunenko M, Court C, Court DL. Probing cellular processes with oligo-mediated recombination and using the knowledge gained to optimize recombineering. J Mol Biol 2011; 407:45-59. [PMID: 21256136 PMCID: PMC3046259 DOI: 10.1016/j.jmb.2011.01.030] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Revised: 01/12/2011] [Accepted: 01/13/2011] [Indexed: 11/25/2022]
Abstract
Recombination with single-strand DNA oligonucleotides (oligos) in Escherichia coli is an efficient and rapid way to modify replicons in vivo. The generation of nucleotide alteration by oligo recombination provides novel assays for studying cellular processes. Single-strand exonucleases inhibit oligo recombination, and recombination is increased by mutating all four known exonucleases. Increasing oligo concentration or adding nonspecific carrier oligo titrates out the exonucleases. In a model for oligo recombination, λ Beta protein anneals the oligo to complementary single-strand DNA at the replication fork. Mismatches are created, and the methyl-directed mismatch repair (MMR) system acts to eliminate the mismatches inhibiting recombination. Three ways to evade MMR through oligo design include, in addition to the desired change (1) a C·C mismatch 6 bp from that change; (2) four or more adjacent mismatches; or (3) mismatches at four or more consecutive wobble positions. The latter proves useful for making high-frequency changes that alter only the target amino acid sequence and even allows modification of essential genes. Efficient uptake of DNA is important for oligo-mediated recombination. Uptake of oligos or plasmids is dependent on media and is 10,000-fold reduced for cells grown in minimal versus rich medium. Genomewide engineering technologies utilizing recombineering will benefit from both optimized recombination frequencies and a greater understanding of how biological processes such as DNA replication and cell division impact recombinants formed at multiple chromosomal loci. Recombination events at multiple loci in individual cells are described here.
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Affiliation(s)
- James A. Sawitzke
- Molecular Control and Genetics Section, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702
| | - Nina Costantino
- Molecular Control and Genetics Section, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702
| | - Xin-tian Li
- Molecular Control and Genetics Section, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702
| | - Lynn C. Thomason
- Gene Regulation and Chromosome Biology Laboratory, Basic Science Program, SAIC-Frederick, Inc., National Cancer Institute at Frederick, Frederick, MD 21702
| | - Mikhail Bubunenko
- Molecular Control and Genetics Section, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702
- Gene Regulation and Chromosome Biology Laboratory, Basic Science Program, SAIC-Frederick, Inc., National Cancer Institute at Frederick, Frederick, MD 21702
| | - Carolyn Court
- Transcription control section, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702
| | - Donald L. Court
- Molecular Control and Genetics Section, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702
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Bitrián M, Roodbarkelari F, Horváth M, Koncz C. BAC-recombineering for studying plant gene regulation: developmental control and cellular localization of SnRK1 kinase subunits. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 65:829-42. [PMID: 21235649 DOI: 10.1111/j.1365-313x.2010.04462.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Recombineering, permitting precise modification of genes within bacterial artificial chromosomes (BACs) through homologous recombination mediated by lambda phage-encoded Red proteins, is a widely used powerful tool in mouse, Caenorhabditis and Drosophila genetics. As Agrobacterium-mediated transfer of large DNA inserts from binary BACs and TACs into plants occurs at low frequency, recombineering is so far seldom exploited in the analysis of plant gene functions. We have constructed binary plant transformation vectors, which are suitable for gap-repair cloning of genes from BACs using recombineering methods previously developed for other organisms. Here we show that recombineering facilitates PCR-based generation of precise translational fusions between coding sequences of fluorescent reporter and plant proteins using galK-based exchange recombination. The modified target genes alone or as part of a larger gene cluster can be transferred by high-frequency gap-repair into plant transformation vectors, stably maintained in Agrobacterium and transformed without alteration into plants. Versatile application of plant BAC-recombineering is illustrated by the analysis of developmental regulation and cellular localization of interacting AKIN10 catalytic and SNF4 activating subunits of Arabidopsis Snf1-related (SnRK1) protein kinase using in vivo imaging. To validate full functionality and in vivo interaction of tagged SnRK1 subunits, it is demonstrated that immunoprecipitated SNF4-YFP is bound to a kinase that phosphorylates SnRK1 candidate substrates, and that the GFP- and YFP-tagged kinase subunits co-immunoprecipitate with endogenous wild type AKIN10 and SNF4.
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Affiliation(s)
- Marta Bitrián
- Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, D-50829 Cologne, Germany
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