1
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Christi K, Hudson J, Egan S. Current approaches to genetic modification of marine bacteria and considerations for improved transformation efficiency. Microbiol Res 2024; 284:127729. [PMID: 38663232 DOI: 10.1016/j.micres.2024.127729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 02/25/2024] [Accepted: 04/15/2024] [Indexed: 05/26/2024]
Abstract
Marine bacteria play vital roles in symbiosis, biogeochemical cycles and produce novel bioactive compounds and enzymes of interest for the pharmaceutical, biofuel and biotechnology industries. At present, investigations into marine bacterial functions and their products are primarily based on phenotypic observations, -omic type approaches and heterologous gene expression. To advance our understanding of marine bacteria and harness their full potential for industry application, it is critical that we have the appropriate tools and resources to genetically manipulate them in situ. However, current genetic tools that are largely designed for model organisms such as E. coli, produce low transformation efficiencies or have no transfer ability in marine bacteria. To improve genetic manipulation applications for marine bacteria, we need to improve transformation methods such as conjugation and electroporation in addition to identifying more marine broad host range plasmids. In this review, we aim to outline the reported methods of transformation for marine bacteria and discuss the considerations for each approach in the context of improving efficiency. In addition, we further discuss marine plasmids and future research areas including CRISPR tools and their potential applications for marine bacteria.
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Affiliation(s)
- Katrina Christi
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, Faculty of Science, The University of New South Wales, Kensington, NSW, Australia
| | - Jennifer Hudson
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, Faculty of Science, The University of New South Wales, Kensington, NSW, Australia
| | - Suhelen Egan
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, Faculty of Science, The University of New South Wales, Kensington, NSW, Australia.
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2
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Bloch S, Wegrzyn A. Editorial: Bacteriophage and host interactions. Front Microbiol 2024; 15:1422076. [PMID: 38881653 PMCID: PMC11177086 DOI: 10.3389/fmicb.2024.1422076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 05/24/2024] [Indexed: 06/18/2024] Open
Affiliation(s)
- Sylwia Bloch
- Department of Molecular Biology, University of Gdansk, Gdansk, Poland
| | - Alicja Wegrzyn
- University Center for Applied and Interdisciplinary Research, University of Gdansk, Gdansk, Poland
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3
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Giermasińska-Buczek K, Gawor J, Stefańczyk E, Gągała U, Żuchniewicz K, Rekosz-Burlaga H, Gromadka R, Łobocka M. Interaction of bacteriophage P1 with an epiphytic Pantoea agglomerans strain-the role of the interplay between various mobilome elements. Front Microbiol 2024; 15:1356206. [PMID: 38591037 PMCID: PMC10999674 DOI: 10.3389/fmicb.2024.1356206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/21/2024] [Indexed: 04/10/2024] Open
Abstract
P1 is a model, temperate bacteriophage of the 94 kb genome. It can lysogenize representatives of the Enterobacterales order. In lysogens, it is maintained as a plasmid. We tested P1 interactions with the biocontrol P. agglomerans L15 strain to explore the utility of P1 in P. agglomerans genome engineering. A P1 derivative carrying the Tn9 (cmR) transposon could transfer a plasmid from Escherichia coli to the L15 cells. The L15 cells infected with this derivative formed chloramphenicol-resistant colonies. They could grow in a liquid medium with chloramphenicol after adaptation and did not contain prophage P1 but the chromosomally inserted cmR marker of P1 Tn9 (cat). The insertions were accompanied by various rearrangements upstream of the Tn9 cat gene promoter and the loss of IS1 (IS1L) from the corresponding region. Sequence analysis of the L15 strain genome revealed a chromosome and three plasmids of 0.58, 0.18, and 0.07 Mb. The largest and the smallest plasmid appeared to encode partition and replication incompatibility determinants similar to those of prophage P1, respectively. In the L15 derivatives cured of the largest plasmid, P1 with Tn9 could not replace the smallest plasmid even if selected. However, it could replace the smallest and the largest plasmid of L15 if its Tn9 IS1L sequence driving the Tn9 mobility was inactivated or if it was enriched with an immobile kanamycin resistance marker. Moreover, it could develop lytically in the L15 derivatives cured of both these plasmids. Clearly, under conditions of selection for P1, the mobility of the P1 selective marker determines whether or not the incoming P1 can outcompete the incompatible L15 resident plasmids. Our results demonstrate that P. agglomerans can serve as a host for bacteriophage P1 and can be engineered with the help of this phage. They also provide an example of how antibiotics can modify the outcome of horizontal gene transfer in natural environments. Numerous plasmids of Pantoea strains appear to contain determinants of replication or partition incompatibility with P1. Therefore, P1 with an immobile selective marker may be a tool of choice in curing these strains from the respective plasmids to facilitate their functional analysis.
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Affiliation(s)
- Katarzyna Giermasińska-Buczek
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences (SGGW-WULS), Warsaw, Poland
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, Warsaw, Poland
| | - Jan Gawor
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, Warsaw, Poland
| | - Emil Stefańczyk
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, Warsaw, Poland
| | - Urszula Gągała
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences (SGGW-WULS), Warsaw, Poland
| | - Karolina Żuchniewicz
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, Warsaw, Poland
| | - Hanna Rekosz-Burlaga
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences (SGGW-WULS), Warsaw, Poland
| | - Robert Gromadka
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, Warsaw, Poland
| | - Małgorzata Łobocka
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, Warsaw, Poland
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4
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Ipoutcha T, Racharaks R, Huttelmaier S, Wilson CJ, Ozer EA, Hartmann EM. A synthetic biology approach to assemble and reboot clinically relevant Pseudomonas aeruginosa tailed phages. Microbiol Spectr 2024; 12:e0289723. [PMID: 38294230 PMCID: PMC10913387 DOI: 10.1128/spectrum.02897-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 12/17/2023] [Indexed: 02/01/2024] Open
Abstract
The rise in the frequency of antibiotic resistance has made bacterial infections, specifically Pseudomonas aeruginosa, a cause for greater concern. Phage therapy is a promising solution that uses naturally isolated phages to treat bacterial infections. Ecological limitations, which stipulate a discrete host range and the inevitable evolution of resistance, may be overcome through a better understanding of phage biology and the utilization of engineered phages. In this study, we developed a synthetic biology approach to construct tailed phages that naturally target clinically relevant strains of Pseudomonas aeruginosa. As proof of concept, we successfully cloned and assembled the JG024 and DMS3 phage genomes in yeast using transformation-associated recombination cloning and rebooted these two phage genomes in two different strains of P. aeruginosa. We identified factors that affected phage reboot efficiency like the phage species or the presence of antiviral defense systems in the bacterial strain. We have successfully extended this method to two other phage species and observed that the method enables the reboot of phages that are naturally unable to infect the strain used for reboot. This research represents a critical step toward the construction of clinically relevant, engineered P. aeruginosa phages.IMPORTANCEPseudomonas aeruginosa is a bacterium responsible for severe infections and a common major complication in cystic fibrosis. The use of antibiotics to treat bacterial infections has become increasingly difficult as antibiotic resistance has become more prevalent. Phage therapy is an alternative solution that is already being used in some European countries, but its use is limited by the narrow host range due to the phage receptor specificity, the presence of antiviral defense systems in the bacterial strain, and the possible emergence of phage resistance. In this study, we demonstrate the use of a synthetic biology approach to construct and reboot clinically relevant P. aeruginosa tailed phages. This method enables a significant expansion of possibilities through the construction of engineered phages for therapy applications.
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Affiliation(s)
- Thomas Ipoutcha
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, USA
| | - Ratanachat Racharaks
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, USA
| | - Stefanie Huttelmaier
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, USA
| | - Cole J. Wilson
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, USA
| | - Egon A. Ozer
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Erica M. Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, USA
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois, USA
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5
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Huan YW, Torraca V, Brown R, Fa-arun J, Miles SL, Oyarzún DA, Mostowy S, Wang B. P1 Bacteriophage-Enabled Delivery of CRISPR-Cas9 Antimicrobial Activity Against Shigella flexneri. ACS Synth Biol 2023; 12:709-721. [PMID: 36802585 PMCID: PMC10028697 DOI: 10.1021/acssynbio.2c00465] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Indexed: 02/22/2023]
Abstract
The discovery of clustered, regularly interspaced, short palindromic repeats (CRISPR) and the Cas9 RNA-guided nuclease provides unprecedented opportunities to selectively kill specific populations or species of bacteria. However, the use of CRISPR-Cas9 to clear bacterial infections in vivo is hampered by the inefficient delivery of cas9 genetic constructs into bacterial cells. Here, we use a broad-host-range P1-derived phagemid to deliver the CRISPR-Cas9 chromosomal-targeting system into Escherichia coli and the dysentery-causing Shigella flexneri to achieve DNA sequence-specific killing of targeted bacterial cells. We show that genetic modification of the helper P1 phage DNA packaging site (pac) significantly enhances the purity of packaged phagemid and improves the Cas9-mediated killing of S. flexneri cells. We further demonstrate that P1 phage particles can deliver chromosomal-targeting cas9 phagemids into S. flexneri in vivo using a zebrafish larvae infection model, where they significantly reduce the bacterial load and promote host survival. Our study highlights the potential of combining P1 bacteriophage-based delivery with the CRISPR chromosomal-targeting system to achieve DNA sequence-specific cell lethality and efficient clearance of bacterial infection.
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Affiliation(s)
- Yang W. Huan
- School
of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, U.K.
| | - Vincenzo Torraca
- Department
of Infection Biology, London School of Hygiene & Tropical Medicine, London WC1E 7HT, U.K.
- School
of Life Sciences, University of Westminster, London W1B 2HW, U.K.
| | - Russell Brown
- School
of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, U.K.
| | - Jidapha Fa-arun
- School
of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, U.K.
| | - Sydney L. Miles
- Department
of Infection Biology, London School of Hygiene & Tropical Medicine, London WC1E 7HT, U.K.
| | - Diego A. Oyarzún
- School
of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, U.K.
- School
of Informatics, University of Edinburgh, Edinburgh EH8 9AB, U.K.
| | - Serge Mostowy
- Department
of Infection Biology, London School of Hygiene & Tropical Medicine, London WC1E 7HT, U.K.
| | - Baojun Wang
- College
of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific
and Technological Innovation Center, Zhejiang
University, Hangzhou 310058, China
- Research
Center for Biological Computation, Zhejiang
Laboratory, Hangzhou 311100, China
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6
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Fa-Arun J, Huan YW, Darmon E, Wang B. Tail-Engineered Phage P2 Enables Delivery of Antimicrobials into Multiple Gut Pathogens. ACS Synth Biol 2023; 12:596-607. [PMID: 36731126 PMCID: PMC9942202 DOI: 10.1021/acssynbio.2c00615] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Bacteriophages can be reprogrammed to deliver antimicrobials for therapeutic and biocontrol purposes and are a promising alternative treatment to antimicrobial-resistant bacteria. Here, we developed a bacteriophage P4 cosmid system for the delivery of a Cas9 antimicrobial into clinically relevant human gut pathogens Shigella flexneri and Escherichia coli O157:H7. Our P4 cosmid design produces a high titer of cosmid-transducing units without contamination by a helper phage. Further, we demonstrate that genetic engineering of the phage tail fiber improves the transduction efficiency of cosmid DNA in S. flexneri M90T as well as allows recognition of a nonnative host, E. coli O157:H7. We show that the transducing units with the chimeric tails enhanced the overall Cas9-mediated killing of both pathogens. This study demonstrates the potential of our P4 cas9 cosmid system as a DNA sequence-specific antimicrobial against clinically relevant gut pathogenic bacteria.
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Affiliation(s)
- Jidapha Fa-Arun
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, United Kingdom
| | - Yang Wei Huan
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, United Kingdom
| | - Elise Darmon
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, United Kingdom
| | - Baojun Wang
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310058, China.,School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, United Kingdom.,Research Center for Biological Computation, Zhejiang Laboratory, Hangzhou 311100, China
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7
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Bednarek A, Giermasińska-Buczek K, Łobocka M. Efficient traceless modification of the P1 bacteriophage genome through homologous recombination with enrichment in double recombinants: A new perspective on the functional annotation of uncharacterized phage genes. Front Microbiol 2023; 14:1135870. [PMID: 37020717 PMCID: PMC10067587 DOI: 10.3389/fmicb.2023.1135870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 02/14/2023] [Indexed: 04/07/2023] Open
Abstract
The advent of high-throughput omic technologies has caused unprecedented progress in research on bacteriophages, the most abundant and still the least explored entities on earth. Despite the growing number of phage genomes sequenced and the rejuvenation of interest in phage therapy, the progress in the functional analysis of phage genes is slow. Simple and efficient techniques of phage genome targeted mutagenesis that would allow one to knock out particular genes precisely without polar effects in order to study the effect of these knock-outs on phage functions are lacking. Even in the case of model phages, the functions of approximately half of their genes are unknown. P1 is an enterobacterial temperate myophage of clinical significance, which lysogenizes cells as a plasmid. It has a long history of studies, serves as a model in basic research, is a gene transfer vector, and is a source of genetic tools. Its gene products have structural homologs in several other phages. In this perspective article, we describe a simple and efficient procedure of traceless P1 genome modification that could also serve to acquire targeted mutations in the genomes of certain other temperate phages and speed up functional annotations of phage genes.
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8
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Huan YW, Fa-Arun J, Wang B. The Role of O-antigen in P1 Transduction of Shigella flexneri and Escherichia coli with its Alternative S' Tail Fibre. J Mol Biol 2022; 434:167829. [PMID: 36116540 DOI: 10.1016/j.jmb.2022.167829] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/03/2022] [Accepted: 09/12/2022] [Indexed: 11/30/2022]
Abstract
Enterobacteria phage P1 expresses two types of tail fibre, S and S'. Despite the wide usage of phage P1 for transduction, the host range and the receptor for its alternative S' tail fibre was never determined. Here, a ΔS-cin Δpac E. coli P1 lysogenic strain was generated to allow packaging of phagemid DNA into P1 phage having either S or S' tail fibre. P1(S') could transduce phagemid DNA into Shigella flexneri 2a 2457O, Shigella flexneri 5a M90T and Escherichia coli O3 efficiently. Mutational analysis of the O-antigen assembly genes and LPS inhibition assays indicated that P1(S') transduction requires at least one O-antigen unit. E. coli O111:B4 LPS produced a high neutralising effect against P1(S') transduction, indicating that this E. coli strain could be susceptible to P1(S')-mediated transduction. Mutations in the O-antigen modification genes of S. flexneri 2a 2457O and S. flexneri 5a M90T did not cause significant changes to P1(S') transduction efficiency. A higher transduction efficiency of P1(S') improved the delivery of a cas9 antimicrobial phagemid into both S. flexneri 2457O and M90T. These findings provide novel insights into P1 tropism-switching, by identifying the bacterial strains which are susceptible to P1(S')-mediated transduction, as well as demonstrating its potential for delivering a DNA sequence-specific Cas9 antimicrobial into clinically relevant S. flexneri.
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Affiliation(s)
- Yang W Huan
- Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, United Kingdom
| | - Jidapha Fa-Arun
- Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, United Kingdom
| | - Baojun Wang
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310058, China; Research Centre of Biological Computation, Zhejiang Laboratory, Hangzhou 311100, China.
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9
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Al'Abri IS, Haller DJ, Li Z, Crook N. Inducible directed evolution of complex phenotypes in bacteria. Nucleic Acids Res 2022; 50:e58. [PMID: 35150576 PMCID: PMC9177967 DOI: 10.1093/nar/gkac094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 12/22/2021] [Accepted: 02/01/2022] [Indexed: 11/15/2022] Open
Abstract
Directed evolution is a powerful method for engineering biology in the absence of detailed sequence-function relationships. To enable directed evolution of complex phenotypes encoded by multigene pathways, we require large library sizes for DNA sequences >5–10 kb in length, elimination of genomic hitchhiker mutations, and decoupling of diversification and screening steps. To meet these challenges, we developed Inducible Directed Evolution (IDE), which uses a temperate bacteriophage to package large plasmids and transfer them to naive cells after intracellular mutagenesis. To demonstrate IDE, we evolved a 5-gene pathway from Bacillus licheniformis that accelerates tagatose catabolism in Escherichia coli, resulting in clones with 65% shorter lag times during growth on tagatose after only two rounds of evolution. Next, we evolved a 15.4 kb, 10-gene pathway from Bifidobacterium breve UC2003 that aids E. coli’s utilization of melezitose. After three rounds of IDE, we isolated evolved pathways that both reduced lag time by more than 2-fold and enabled 150% higher final optical density. Taken together, this work enhances the capacity and utility of a whole pathway directed evolution approach in E. coli.
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Affiliation(s)
- Ibrahim S Al'Abri
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Daniel J Haller
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Zidan Li
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Nathan Crook
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
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10
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Lam CN, Mehta-Kolte MG, Martins-Sorenson N, Eckert B, Lin PH, Chu K, Moghaddasi A, Goldman D, Nguyen H, Chan R, Nukala L, Suko S, Hanson B, Yuan R, Cady KC. A Tail Fiber Engineering Platform for Improved Bacterial Transduction-Based Diagnostic Reagents. ACS Synth Biol 2021; 10:1292-1299. [PMID: 33983709 DOI: 10.1021/acssynbio.1c00036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Bacterial transduction particles were critical to early advances in molecular biology and are currently experiencing a resurgence in interest within the diagnostic and therapeutic fields. The difficulty of developing a robust and specific transduction reagent capable of delivering a genetic payload to the diversity of strains constituting a given bacterial species or genus is a major impediment to their expanded utility as commercial products. While recent advances in engineering the reactivity of these reagents have made them more attractive for product development, considerable improvements are still needed. Here, we demonstrate a synthetic biology platform derived from bacteriophage P1 as a chassis to target transduction reagents against four clinically prevalent species within the Enterobacterales order. Bacteriophage P1 requires only a single receptor binding protein to enable attachment and injection into a target bacterium. By engineering and screening particles displaying a diverse array of chimeric receptor binding proteins, we generated a potential transduction reagent for a future rapid phenotypic carbapenem-resistant Enterobacterales diagnostic assay.
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Affiliation(s)
- Colin N. Lam
- Roche Molecular Systems, Santa Clara, California 95050, United States
| | | | | | - Barbara Eckert
- Roche Molecular Systems, Pleasanton, California 94588, United States
| | - Patrick H. Lin
- Roche Molecular Systems, Santa Clara, California 95050, United States
| | - Kristina Chu
- Roche Molecular Systems, Pleasanton, California 94588, United States
| | - Arrash Moghaddasi
- Roche Molecular Systems, Santa Clara, California 95050, United States
| | - Dylan Goldman
- Roche Molecular Systems, Santa Clara, California 95050, United States
| | - Hai Nguyen
- Roche Molecular Systems, Santa Clara, California 95050, United States
| | - Ryan Chan
- Roche Molecular Systems, Santa Clara, California 95050, United States
| | - Laxmi Nukala
- Roche Molecular Systems, Santa Clara, California 95050, United States
| | - Shawn Suko
- Roche Molecular Systems, Pleasanton, California 94588, United States
| | - Brett Hanson
- Roche Molecular Systems, Santa Clara, California 95050, United States
| | - Richard Yuan
- Roche Molecular Systems, Santa Clara, California 95050, United States
| | - Kyle C. Cady
- Roche Molecular Systems, Santa Clara, California 95050, United States
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11
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Abstract
Bacteriophages (phages) are ubiquitous in nature. These viruses play a number of central roles in microbial ecology and evolution by, for instance, promoting horizontal gene transfer (HGT) among bacterial species. The ability of phages to mediate HGT through transduction has been widely exploited as an experimental tool for the genetic study of bacteria. As such, bacteriophage P1 represents a prototypical generalized transducing phage with a broad host range that has been extensively employed in the genetic manipulation of Escherichia coli and a number of other model bacterial species. Here we demonstrate that P1 is capable of infecting, lysogenizing, and promoting transduction in members of the bacterial genus Sodalis, including the maternally inherited insect endosymbiont Sodalis glossinidius. While establishing new tools for the genetic study of these bacterial species, our results suggest that P1 may be used to deliver DNA to many Gram-negative endosymbionts in their insect host, thereby circumventing a culturing requirement to genetically manipulate these organisms. IMPORTANCE A large number of economically important insects maintain intimate associations with maternally inherited endosymbiotic bacteria. Due to the inherent nature of these associations, insect endosymbionts cannot be usually isolated in pure culture or genetically manipulated. Here we use a broad-host-range bacteriophage to deliver exogenous DNA to an insect endosymbiont and a closely related free-living species. Our results suggest that broad-host-range bacteriophages can be used to genetically alter insect endosymbionts in their insect host and, as a result, bypass a culturing requirement to genetically alter these bacteria.
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12
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Diversity of P1 phage-like elements in multidrug resistant Escherichia coli. Sci Rep 2019; 9:18861. [PMID: 31827120 PMCID: PMC6906374 DOI: 10.1038/s41598-019-54895-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 11/19/2019] [Indexed: 11/16/2022] Open
Abstract
The spread of multidrug resistance via mobile genetic elements is a major clinical and veterinary concern. Pathogenic Escherichia coli harbour antibiotic resistance and virulence genes mainly on plasmids, but also bacteriophages and hybrid phage-like plasmids. In this study, the genomes of three E. coli phage-like plasmids, pJIE250-3 from a human E. coli clinical isolate, pSvP1 from a porcine ETEC O157 isolate, and pTZ20_1P from a porcine commensal E. coli, were sequenced (PacBio RSII), annotated and compared. All three elements are coliphage P1 variants, each with unique adaptations. pJIE250-3 is a P1-derivative that has lost lytic functions and contains no accessory genes. In pTZ20_1P and pSvP1, a core P1-like genome is associated with insertion sequence-mediated acquisition of plasmid modules encoding multidrug resistance and virulence, respectively. The transfer ability of pTZ20_1P, carrying antibiotic resistance markers, was also tested and, although this element was not able to transfer by conjugation, it was able to lysogenize a commensal E. coli strain with consequent transfer of resistance. The incidence of P1-like plasmids (~7%) in our E. coli collections correlated well with that in public databases. This study highlights the need to investigate the contribution of phage-like plasmids to the successful spread of antibiotic resistant pathotypes.
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13
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Luo ML, Leenay RT, Beisel CL. Current and future prospects for CRISPR-based tools in bacteria. Biotechnol Bioeng 2015; 113:930-43. [PMID: 26460902 DOI: 10.1002/bit.25851] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 09/04/2015] [Accepted: 10/05/2015] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas systems have rapidly transitioned from intriguing prokaryotic defense systems to powerful and versatile biomolecular tools. This article reviews how these systems have been translated into technologies to manipulate bacterial genetics, physiology, and communities. Recent applications in bacteria have centered on multiplexed genome editing, programmable gene regulation, and sequence-specific antimicrobials, while future applications can build on advances in eukaryotes, the rich natural diversity of CRISPR-Cas systems, and the untapped potential of CRISPR-based DNA acquisition. Overall, these systems have formed the basis of an ever-expanding genetic toolbox and hold tremendous potential for our future understanding and engineering of the bacterial world.
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Affiliation(s)
- Michelle L Luo
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, 27695-7905
| | - Ryan T Leenay
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, 27695-7905
| | - Chase L Beisel
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, 27695-7905.
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14
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Ji W, Lee D, Wong E, Dadlani P, Dinh D, Huang V, Kearns K, Teng S, Chen S, Haliburton J, Heimberg G, Heineike B, Ramasubramanian A, Stevens T, Helmke KJ, Zepeda V, Qi LS, Lim WA. Specific gene repression by CRISPRi system transferred through bacterial conjugation. ACS Synth Biol 2014; 3:929-31. [PMID: 25409531 PMCID: PMC4277763 DOI: 10.1021/sb500036q] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
![]()
In
microbial communities, bacterial populations are commonly controlled
using indiscriminate, broad range antibiotics. There are few ways
to target specific strains effectively without disrupting the entire
microbiome and local environment. Here, we use conjugation, a natural
DNA horizontal transfer process among bacterial species, to deliver
an engineered CRISPR interference (CRISPRi) system for targeting specific
genes in recipient Escherichia coli cells. We show
that delivery of the CRISPRi system is successful and can specifically
repress a reporter gene in recipient cells, thereby establishing a
new tool for gene regulation across bacterial cells and potentially
for bacterial population control.
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Affiliation(s)
- Weiyue Ji
- Center for Systems and Synthetic
Biology, ‡Department of Cellular and Molecular
Pharmacology, §Department of Biochemistry and Biophysics, ∥Department of Bioengineering and
Therapeutic Sciences, ⊥Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California 94158, United States
- Department
of Bioengineering, ∇UC Berkeley−UCSF Graduate Program in
Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Bioengineering, ◆Department of Chemical
and Systems Biology, ¶Chemistry, Engineering,
and Medicine for Human Health (ChEM-H), Stanford University, Stanford, California 94305, United States
| | - Derrick Lee
- Center for Systems and Synthetic
Biology, ‡Department of Cellular and Molecular
Pharmacology, §Department of Biochemistry and Biophysics, ∥Department of Bioengineering and
Therapeutic Sciences, ⊥Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California 94158, United States
- Department
of Bioengineering, ∇UC Berkeley−UCSF Graduate Program in
Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Bioengineering, ◆Department of Chemical
and Systems Biology, ¶Chemistry, Engineering,
and Medicine for Human Health (ChEM-H), Stanford University, Stanford, California 94305, United States
| | - Eric Wong
- Center for Systems and Synthetic
Biology, ‡Department of Cellular and Molecular
Pharmacology, §Department of Biochemistry and Biophysics, ∥Department of Bioengineering and
Therapeutic Sciences, ⊥Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California 94158, United States
- Department
of Bioengineering, ∇UC Berkeley−UCSF Graduate Program in
Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Bioengineering, ◆Department of Chemical
and Systems Biology, ¶Chemistry, Engineering,
and Medicine for Human Health (ChEM-H), Stanford University, Stanford, California 94305, United States
| | - Priyanka Dadlani
- Center for Systems and Synthetic
Biology, ‡Department of Cellular and Molecular
Pharmacology, §Department of Biochemistry and Biophysics, ∥Department of Bioengineering and
Therapeutic Sciences, ⊥Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California 94158, United States
- Department
of Bioengineering, ∇UC Berkeley−UCSF Graduate Program in
Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Bioengineering, ◆Department of Chemical
and Systems Biology, ¶Chemistry, Engineering,
and Medicine for Human Health (ChEM-H), Stanford University, Stanford, California 94305, United States
| | - David Dinh
- Center for Systems and Synthetic
Biology, ‡Department of Cellular and Molecular
Pharmacology, §Department of Biochemistry and Biophysics, ∥Department of Bioengineering and
Therapeutic Sciences, ⊥Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California 94158, United States
- Department
of Bioengineering, ∇UC Berkeley−UCSF Graduate Program in
Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Bioengineering, ◆Department of Chemical
and Systems Biology, ¶Chemistry, Engineering,
and Medicine for Human Health (ChEM-H), Stanford University, Stanford, California 94305, United States
| | - Verna Huang
- Center for Systems and Synthetic
Biology, ‡Department of Cellular and Molecular
Pharmacology, §Department of Biochemistry and Biophysics, ∥Department of Bioengineering and
Therapeutic Sciences, ⊥Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California 94158, United States
- Department
of Bioengineering, ∇UC Berkeley−UCSF Graduate Program in
Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Bioengineering, ◆Department of Chemical
and Systems Biology, ¶Chemistry, Engineering,
and Medicine for Human Health (ChEM-H), Stanford University, Stanford, California 94305, United States
| | - Kendall Kearns
- Center for Systems and Synthetic
Biology, ‡Department of Cellular and Molecular
Pharmacology, §Department of Biochemistry and Biophysics, ∥Department of Bioengineering and
Therapeutic Sciences, ⊥Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California 94158, United States
- Department
of Bioengineering, ∇UC Berkeley−UCSF Graduate Program in
Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Bioengineering, ◆Department of Chemical
and Systems Biology, ¶Chemistry, Engineering,
and Medicine for Human Health (ChEM-H), Stanford University, Stanford, California 94305, United States
| | - Sherry Teng
- Center for Systems and Synthetic
Biology, ‡Department of Cellular and Molecular
Pharmacology, §Department of Biochemistry and Biophysics, ∥Department of Bioengineering and
Therapeutic Sciences, ⊥Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California 94158, United States
- Department
of Bioengineering, ∇UC Berkeley−UCSF Graduate Program in
Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Bioengineering, ◆Department of Chemical
and Systems Biology, ¶Chemistry, Engineering,
and Medicine for Human Health (ChEM-H), Stanford University, Stanford, California 94305, United States
| | - Susan Chen
- Center for Systems and Synthetic
Biology, ‡Department of Cellular and Molecular
Pharmacology, §Department of Biochemistry and Biophysics, ∥Department of Bioengineering and
Therapeutic Sciences, ⊥Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California 94158, United States
- Department
of Bioengineering, ∇UC Berkeley−UCSF Graduate Program in
Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Bioengineering, ◆Department of Chemical
and Systems Biology, ¶Chemistry, Engineering,
and Medicine for Human Health (ChEM-H), Stanford University, Stanford, California 94305, United States
| | - John Haliburton
- Center for Systems and Synthetic
Biology, ‡Department of Cellular and Molecular
Pharmacology, §Department of Biochemistry and Biophysics, ∥Department of Bioengineering and
Therapeutic Sciences, ⊥Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California 94158, United States
- Department
of Bioengineering, ∇UC Berkeley−UCSF Graduate Program in
Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Bioengineering, ◆Department of Chemical
and Systems Biology, ¶Chemistry, Engineering,
and Medicine for Human Health (ChEM-H), Stanford University, Stanford, California 94305, United States
| | - Graham Heimberg
- Center for Systems and Synthetic
Biology, ‡Department of Cellular and Molecular
Pharmacology, §Department of Biochemistry and Biophysics, ∥Department of Bioengineering and
Therapeutic Sciences, ⊥Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California 94158, United States
- Department
of Bioengineering, ∇UC Berkeley−UCSF Graduate Program in
Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Bioengineering, ◆Department of Chemical
and Systems Biology, ¶Chemistry, Engineering,
and Medicine for Human Health (ChEM-H), Stanford University, Stanford, California 94305, United States
| | - Benjamin Heineike
- Center for Systems and Synthetic
Biology, ‡Department of Cellular and Molecular
Pharmacology, §Department of Biochemistry and Biophysics, ∥Department of Bioengineering and
Therapeutic Sciences, ⊥Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California 94158, United States
- Department
of Bioengineering, ∇UC Berkeley−UCSF Graduate Program in
Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Bioengineering, ◆Department of Chemical
and Systems Biology, ¶Chemistry, Engineering,
and Medicine for Human Health (ChEM-H), Stanford University, Stanford, California 94305, United States
| | - Anusuya Ramasubramanian
- Center for Systems and Synthetic
Biology, ‡Department of Cellular and Molecular
Pharmacology, §Department of Biochemistry and Biophysics, ∥Department of Bioengineering and
Therapeutic Sciences, ⊥Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California 94158, United States
- Department
of Bioengineering, ∇UC Berkeley−UCSF Graduate Program in
Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Bioengineering, ◆Department of Chemical
and Systems Biology, ¶Chemistry, Engineering,
and Medicine for Human Health (ChEM-H), Stanford University, Stanford, California 94305, United States
| | - Thomas Stevens
- Center for Systems and Synthetic
Biology, ‡Department of Cellular and Molecular
Pharmacology, §Department of Biochemistry and Biophysics, ∥Department of Bioengineering and
Therapeutic Sciences, ⊥Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California 94158, United States
- Department
of Bioengineering, ∇UC Berkeley−UCSF Graduate Program in
Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Bioengineering, ◆Department of Chemical
and Systems Biology, ¶Chemistry, Engineering,
and Medicine for Human Health (ChEM-H), Stanford University, Stanford, California 94305, United States
| | - Kara J. Helmke
- Center for Systems and Synthetic
Biology, ‡Department of Cellular and Molecular
Pharmacology, §Department of Biochemistry and Biophysics, ∥Department of Bioengineering and
Therapeutic Sciences, ⊥Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California 94158, United States
- Department
of Bioengineering, ∇UC Berkeley−UCSF Graduate Program in
Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Bioengineering, ◆Department of Chemical
and Systems Biology, ¶Chemistry, Engineering,
and Medicine for Human Health (ChEM-H), Stanford University, Stanford, California 94305, United States
| | - Veronica Zepeda
- Center for Systems and Synthetic
Biology, ‡Department of Cellular and Molecular
Pharmacology, §Department of Biochemistry and Biophysics, ∥Department of Bioengineering and
Therapeutic Sciences, ⊥Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California 94158, United States
- Department
of Bioengineering, ∇UC Berkeley−UCSF Graduate Program in
Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Bioengineering, ◆Department of Chemical
and Systems Biology, ¶Chemistry, Engineering,
and Medicine for Human Health (ChEM-H), Stanford University, Stanford, California 94305, United States
| | - Lei S. Qi
- Center for Systems and Synthetic
Biology, ‡Department of Cellular and Molecular
Pharmacology, §Department of Biochemistry and Biophysics, ∥Department of Bioengineering and
Therapeutic Sciences, ⊥Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California 94158, United States
- Department
of Bioengineering, ∇UC Berkeley−UCSF Graduate Program in
Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Bioengineering, ◆Department of Chemical
and Systems Biology, ¶Chemistry, Engineering,
and Medicine for Human Health (ChEM-H), Stanford University, Stanford, California 94305, United States
| | - Wendell A. Lim
- Center for Systems and Synthetic
Biology, ‡Department of Cellular and Molecular
Pharmacology, §Department of Biochemistry and Biophysics, ∥Department of Bioengineering and
Therapeutic Sciences, ⊥Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California 94158, United States
- Department
of Bioengineering, ∇UC Berkeley−UCSF Graduate Program in
Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Bioengineering, ◆Department of Chemical
and Systems Biology, ¶Chemistry, Engineering,
and Medicine for Human Health (ChEM-H), Stanford University, Stanford, California 94305, United States
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15
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Abstract
CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) systems in bacteria and archaea employ CRISPR RNAs to specifically recognize the complementary DNA of foreign invaders, leading to sequence-specific cleavage or degradation of the target DNA. Recent work has shown that the accidental or intentional targeting of the bacterial genome is cytotoxic and can lead to cell death. Here, we have demonstrated that genome targeting with CRISPR-Cas systems can be employed for the sequence-specific and titratable removal of individual bacterial strains and species. Using the type I-E CRISPR-Cas system in Escherichia coli as a model, we found that this effect could be elicited using native or imported systems and was similarly potent regardless of the genomic location, strand, or transcriptional activity of the target sequence. Furthermore, the specificity of targeting with CRISPR RNAs could readily distinguish between even highly similar strains in pure or mixed cultures. Finally, varying the collection of delivered CRISPR RNAs could quantitatively control the relative number of individual strains within a mixed culture. Critically, the observed selectivity and programmability of bacterial removal would be virtually impossible with traditional antibiotics, bacteriophages, selectable markers, or tailored growth conditions. Once delivery challenges are addressed, we envision that this approach could offer a novel means to quantitatively control the composition of environmental and industrial microbial consortia and may open new avenues for the development of “smart” antibiotics that circumvent multidrug resistance and differentiate between pathogenic and beneficial microorganisms. Controlling the composition of microbial populations is a critical aspect in medicine, biotechnology, and environmental cycles. While different antimicrobial strategies, such as antibiotics, antimicrobial peptides, and lytic bacteriophages, offer partial solutions, what remains elusive is a generalized and programmable strategy that can distinguish between even closely related microorganisms and that allows for fine control over the composition of a microbial population. This study demonstrates that RNA-directed immune systems in bacteria and archaea called CRISPR-Cas systems can provide such a strategy. These systems can be employed to selectively and quantitatively remove individual bacterial strains based purely on sequence information, creating opportunities in the treatment of multidrug-resistant infections, the control of industrial fermentations, and the study of microbial consortia.
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16
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Programmable removal of bacterial strains by use of genome-targeting CRISPR-Cas systems. mBio 2014. [PMID: 24473129 DOI: 10.1128/mbio.00928-13.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) systems in bacteria and archaea employ CRISPR RNAs to specifically recognize the complementary DNA of foreign invaders, leading to sequence-specific cleavage or degradation of the target DNA. Recent work has shown that the accidental or intentional targeting of the bacterial genome is cytotoxic and can lead to cell death. Here, we have demonstrated that genome targeting with CRISPR-Cas systems can be employed for the sequence-specific and titratable removal of individual bacterial strains and species. Using the type I-E CRISPR-Cas system in Escherichia coli as a model, we found that this effect could be elicited using native or imported systems and was similarly potent regardless of the genomic location, strand, or transcriptional activity of the target sequence. Furthermore, the specificity of targeting with CRISPR RNAs could readily distinguish between even highly similar strains in pure or mixed cultures. Finally, varying the collection of delivered CRISPR RNAs could quantitatively control the relative number of individual strains within a mixed culture. Critically, the observed selectivity and programmability of bacterial removal would be virtually impossible with traditional antibiotics, bacteriophages, selectable markers, or tailored growth conditions. Once delivery challenges are addressed, we envision that this approach could offer a novel means to quantitatively control the composition of environmental and industrial microbial consortia and may open new avenues for the development of "smart" antibiotics that circumvent multidrug resistance and differentiate between pathogenic and beneficial microorganisms. IMPORTANCE Controlling the composition of microbial populations is a critical aspect in medicine, biotechnology, and environmental cycles. While different antimicrobial strategies, such as antibiotics, antimicrobial peptides, and lytic bacteriophages, offer partial solutions, what remains elusive is a generalized and programmable strategy that can distinguish between even closely related microorganisms and that allows for fine control over the composition of a microbial population. This study demonstrates that RNA-directed immune systems in bacteria and archaea called CRISPR-Cas systems can provide such a strategy. These systems can be employed to selectively and quantitatively remove individual bacterial strains based purely on sequence information, creating opportunities in the treatment of multidrug-resistant infections, the control of industrial fermentations, and the study of microbial consortia.
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17
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Kittleson JT, DeLoache W, Cheng HY, Anderson JC. Scalable plasmid transfer using engineered P1-based phagemids. ACS Synth Biol 2012; 1:583-9. [PMID: 23656280 DOI: 10.1021/sb300054p] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Dramatic improvements to computational, robotic, and biological tools have enabled genetic engineers to conduct increasingly sophisticated experiments. Further development of biological tools offers a route to bypass complex or expensive mechanical operations, thereby reducing the time and cost of highly parallelized experiments. Here, we engineer a system based on bacteriophage P1 to transfer DNA from one E. coli cell to another, bypassing the need for intermediate DNA isolation (e.g., minipreps). To initiate plasmid transfer, we refactored a native phage element into a DNA module capable of heterologously inducing phage lysis. After incorporating known cis-acting elements, we identified a novel cis-acting element that further improves transduction efficiency, exemplifying the ability of synthetic systems to offer insight into native ones. The system transfers DNAs up to 25 kilobases, the maximum assayed size, and operates well at microliter volumes, enabling manipulation of most routinely used DNAs. The system's large DNA capacity and physical coupling of phage particles to phagemid DNA suggest applicability to biosynthetic pathway evolution, functional proteomics, and ultimately, diverse molecular biology operations including DNA fabrication.
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Affiliation(s)
- Joshua T. Kittleson
- Department of Bioengineering, University of California, Berkeley, California 94720,
United States
| | - Will DeLoache
- Department of Bioengineering, University of California, Berkeley, California 94720,
United States
| | - Hsiao-Ying Cheng
- Department of Bioengineering, University of California, Berkeley, California 94720,
United States
| | - J. Christopher Anderson
- Department of Bioengineering, University of California, Berkeley, California 94720,
United States
- Berkeley National Laboratory, Physical Biosciences Division, QB3: California
Institute for Quantitative Biological Research, 327 Stanley Hall,
Berkeley, California 94720, United States
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18
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Tan Y, Zhang K, Rao X, Jin X, Huang J, Zhu J, Chen Z, Hu X, Shen X, Wang L, Hu F. Whole genome sequencing of a novel temperate bacteriophage ofP. aeruginosa: evidence of tRNA gene mediating integration of the phage genome into the host bacterial chromosome. Cell Microbiol 2006; 9:479-91. [PMID: 16965514 DOI: 10.1111/j.1462-5822.2006.00804.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Whole genome sequencing of a novel Pseudomonas aeruginosa temperate bacteriophage PaP3 has been completed. The genome contains 45 503 bp with GC content of 52.1%, without more than 100 bp sequence hitting homologue in all sequenced phage genomes. A total of 256 open reading frames (ORFs) are found in the genome, and 71 ORFs are predicated as coding sequence (CDS). All 71 CDS are divided into the two opposite direction groups, and both groups meet at the bidirectional terminator site locating the near middle of the genome. The genome is dsDNA with 5'-protruded cohesive ends and cohesive sequence is 'GCCGGCCCCTTTCCGCGTTA' (20 mer). There are four tRNA genes (tRNA(Asn), tRNA(Asp), tRNA(Tyr) and tRNA(Pro)) clustering at the 5'-terminal of the genome. Analysis of integration site of PaP3 in the host bacterial genome confirmed that the core sequence of (GGTCGTAGGTTCGAATCCTAC-21mer) locates at tRNA(Pro) gene within the attP region and at tRNA(Lys) gene in the attB region. The results indicated that 3'-end of tRNA(Pro) gene of the PaP3 genome is involved in the integration reaction and 5'-end of tRNA(Lys) gene of host bacteria genome is hot spot of the integration.
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Affiliation(s)
- Yinling Tan
- Department of Microbiology, The Third Military Medical University, Chongqing 400038, China
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19
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Kropinski AM. Phage Therapy - Everything Old is New Again. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2006; 17:297-306. [PMID: 18382643 PMCID: PMC2095089 DOI: 10.1155/2006/329465] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The study of bacterial viruses (bacteriophages or phages) proved pivotal in the nascence of the disciplines of molecular biology and microbial genetics, providing important information on the central processes of the bacterial cell (DNA replication, transcription and translation) and on how DNA can be transferred from one cell to another. As a result of the pioneering genetics studies and modern genomics, it is now known that phages have contributed to the evolution of the microbial cell and to its pathogenic potential. Because of their ability to transmit genes, phages have been exploited to develop cloning vector systems. They also provide a plethora of enzymes for the modern molecular biologist. Until the introduction of antibiotics, phages were used to treat bacterial infections (with variable success). Western science is now having to re-evaluate the application of phage therapy - a therapeutic modality that never went out of vogue in Eastern Europe - because of the emergence of an alarming number of antibiotic-resistant bacteria. The present article introduces the reader to phage biology, and the benefits and pitfalls of phage therapy in humans and animals.
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Affiliation(s)
- Andrew M Kropinski
- Host and Pathogen Determinants, Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, Ontario; Department of Microbiology and Immunology, Queen’s University, Kingston, Ontario
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20
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Wilson JW, Figurski DH, Nickerson CA. VEX-capture: a new technique that allows in vivo excision, cloning, and broad-host-range transfer of large bacterial genomic DNA segments. J Microbiol Methods 2004; 57:297-308. [PMID: 15134879 DOI: 10.1016/j.mimet.2004.01.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2003] [Revised: 12/10/2003] [Accepted: 01/06/2004] [Indexed: 11/21/2022]
Abstract
We have developed a novel and easily performed procedure for the targeted excision, cloning, and broad-host-range transfer of large bacterial genomic DNA segments. This procedure, called Vector-mediated excision and Capture (VEX-Capture), represents a new molecular tool for the convenient manipulation and exchange of large (20-40+ kb) bacterial genomic fragments. VEX-Capture utilizes lox/Cre-mediated site-specific recombination for excision of the targeted genomic segment and homologous recombination for cloning of the excised DNA section onto a self-transmissible, broad-host-range IncP plasmid. The "captured" genomic DNA segment can then be transferred to a wide variety of Gram-negative hosts for basic research and bioengineering purposes. To demonstrate the utility and function of VEX-Capture, we have excised and cloned three separate genomic islands from the Salmonella typhimurium chromosome ranging in size from 26.7 to 40.0 kb. To test the ability of these islands to be established in different bacterial hosts, we transferred them to six other Gram-negative species and monitored their establishment via phenotypic and molecular analysis. RT-PCR was used to assay the expression of selected S. typhimurium island genes in the different species. This analysis led to the discovery that an island-encoded master regulator of S. typhimurium virulence functions is expressed in a species-specific manner. Our results demonstrate the potential for VEX-Capture to be used as a convenient genetic technique for fundamental biological applications in a wide variety of bacterial species.
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Affiliation(s)
- James W Wilson
- Program in Molecular Pathogenesis and Immunity, Department of Microbiology and Immunology, SL38 Tulane University Medical School, 1430 Tulane Avenue Rm. 5728, New Orleans, LA 70112, USA.
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