1
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Vialetto E, Miele S, Goren MG, Yu J, Yu Y, Collias D, Beamud B, Osbelt L, Lourenço M, Strowig T, Brisse S, Barquist L, Qimron U, Bikard D, Beisel CL. Systematic interrogation of CRISPR antimicrobials in Klebsiella pneumoniae reveals nuclease-, guide- and strain-dependent features influencing antimicrobial activity. Nucleic Acids Res 2024:gkae281. [PMID: 38661215 DOI: 10.1093/nar/gkae281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 03/24/2024] [Accepted: 04/03/2024] [Indexed: 04/26/2024] Open
Abstract
CRISPR-Cas systems can be utilized as programmable-spectrum antimicrobials to combat bacterial infections. However, how CRISPR nucleases perform as antimicrobials across target sites and strains remains poorly explored. Here, we address this knowledge gap by systematically interrogating the use of CRISPR antimicrobials using multidrug-resistant and hypervirulent strains of Klebsiella pneumoniae as models. Comparing different Cas nucleases, DNA-targeting nucleases outperformed RNA-targeting nucleases based on the tested targets. Focusing on AsCas12a that exhibited robust targeting across different strains, we found that the elucidated modes of escape varied widely, restraining opportunities to enhance killing. We also encountered individual guide RNAs yielding different extents of clearance across strains, which were linked to an interplay between improper gRNA folding and strain-specific DNA repair and survival. To explore features that could improve targeting across strains, we performed a genome-wide screen in different K. pneumoniae strains that yielded guide design rules and trained an algorithm for predicting guide efficiency. Finally, we showed that Cas12a antimicrobials can be exploited to eliminate K. pneumoniae when encoded in phagemids delivered by T7-like phages. Altogether, our results highlight the importance of evaluating antimicrobial activity of CRISPR antimicrobials across relevant strains and define critical parameters for efficient CRISPR-based targeting.
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Affiliation(s)
- Elena Vialetto
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Solange Miele
- Institut Pasteur, Université Paris Cité, Synthetic Biology, Paris, France
| | - Moran G Goren
- Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Jiaqi Yu
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Yanying Yu
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Daphne Collias
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Beatriz Beamud
- Institut Pasteur, Université Paris Cité, Synthetic Biology, Paris, France
| | - Lisa Osbelt
- Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Marta Lourenço
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Till Strowig
- Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Sylvain Brisse
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada
- University of Würzburg, Medical Faculty, 97080 Würzburg, Germany
| | - Udi Qimron
- Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel
| | - David Bikard
- Institut Pasteur, Université Paris Cité, Synthetic Biology, Paris, France
| | - Chase L Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
- University of Würzburg, Medical Faculty, 97080 Würzburg, Germany
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2
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Holtzman T, Nechooshtan R, Yosef I, Qimron U. Contracting the Host Range of Bacteriophage T7 Using a Continuous Evolution System. Methods Mol Biol 2024; 2793:85-100. [PMID: 38526725 DOI: 10.1007/978-1-0716-3798-2_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Bacteriophage T7 is an intracellular virus that recognizes its host via tail and tail fiber proteins known as receptor-binding proteins (RBPs). The RBPs attach to a specific lipopolysaccharide (LPS) displayed on the host. While there are various reports of phage host range expansion resulting from mutations in the RBP encoding genes, there is little evidence for contraction of host range. Notably, most experimental systems have not monitored changes in host range in the presence of several hosts simultaneously. Here, we use a continuous evolution system to show that T7 phages grown in the presence of five restrictive strains and one permissive host, each with a different LPS, gradually cease to recognize the restrictive strains. Remarkably, this result was obtained in experiments with six different permissive hosts. The altered specificity is due to mutations in the RBPs as determined by gene sequencing. The results of using this system demonstrate a major role for RBPs in restricting the range of futile infections, and this process can be harnessed to reduce the host range in applications such as recognition and elimination of a specific bacterial serotype by bacteriophages.
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Affiliation(s)
- Tzvi Holtzman
- Department of Clinical Microbiology and Immunology, School of Medicine, Tel Aviv University, Tel Aviv, Israel.
- Department of Biotechnology, Israel Institute for Biological Research, Ness Ziona, Israel.
| | - Ram Nechooshtan
- Department of Biotechnology, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Ido Yosef
- 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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3
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Mahata T, Molshanski-Mor S, Goren MG, Kohen-Manor M, Yosef I, Avram O, Salomon D, Qimron U. Inhibition of host cell division by T5 protein 008 (Hdi). Microbiol Spectr 2023; 11:e0169723. [PMID: 37888989 PMCID: PMC10714956 DOI: 10.1128/spectrum.01697-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 08/30/2023] [Indexed: 10/28/2023] Open
Abstract
IMPORTANCE We have identified a novel phage-encoded inhibitor of the major cytoskeletal protein in bacterial division, FtsZ. The inhibition is shown to confer T5 bacteriophage with a growth advantage in dividing hosts. Our studies demonstrate a strategy in bacteriophages to maximize their progeny number by inhibiting escape of one of the daughter cells of an infected bacterium. They further emphasize that FtsZ is a natural target for bacterial growth inhibition.
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Affiliation(s)
- Tridib Mahata
- Department of Clinical Microbiology and Immunology, School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shahar Molshanski-Mor
- Department of Clinical Microbiology and Immunology, School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Moran G. Goren
- Department of Clinical Microbiology and Immunology, School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Miriam Kohen-Manor
- Department of Clinical Microbiology and Immunology, School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ido Yosef
- Department of Clinical Microbiology and Immunology, School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Oren Avram
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Dor Salomon
- 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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4
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Yosef I, Mahata T, Goren MG, Degany OJ, Ben-Shem A, Qimron U. Highly active CRISPR-adaptation proteins revealed by a robust enrichment technology. Nucleic Acids Res 2023; 51:7552-7562. [PMID: 37326009 PMCID: PMC10415146 DOI: 10.1093/nar/gkad510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/24/2023] [Accepted: 06/01/2023] [Indexed: 06/17/2023] Open
Abstract
Natural prokaryotic defense via the CRISPR-Cas system requires spacer integration into the CRISPR array in a process called adaptation. To search for adaptation proteins with enhanced capabilities, we established a robust perpetual DNA packaging and transfer (PeDPaT) system that uses a strain of T7 phage to package plasmids and transfer them without killing the host, and then uses a different strain of T7 phage to repeat the cycle. We used PeDPaT to identify better adaptation proteins-Cas1 and Cas2-by enriching mutants that provide higher adaptation efficiency. We identified two mutant Cas1 proteins that show up to 10-fold enhanced adaptation in vivo. In vitro, one mutant has higher integration and DNA binding activities, and another has a higher disintegration activity compared to the wild-type Cas1. Lastly, we showed that their specificity for selecting a protospacer adjacent motif is decreased. The PeDPaT technology may be used for many robust screens requiring efficient and effortless DNA transduction.
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Affiliation(s)
- Ido Yosef
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Tridib Mahata
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Moran G Goren
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Or J Degany
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Adam Ben-Shem
- Department of Integrated Structural Biology, Equipe labellisée Ligue Contre le Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67404, France
| | - Udi Qimron
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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5
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Apjok G, Számel M, Christodoulou C, Seregi V, Vásárhelyi BM, Stirling T, Eszenyi B, Sári T, Vidovics F, Nagrand E, Kovács D, Szili P, Lantos II, Méhi O, Jangir PK, Herczeg R, Gálik B, Urbán P, Gyenesei A, Draskovits G, Nyerges Á, Fekete G, Bodai L, Zsindely N, Dénes B, Yosef I, Qimron U, Papp B, Pál C, Kintses B. Characterization of antibiotic resistomes by reprogrammed bacteriophage-enabled functional metagenomics in clinical strains. Nat Microbiol 2023; 8:410-423. [PMID: 36759752 PMCID: PMC9981461 DOI: 10.1038/s41564-023-01320-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 01/04/2023] [Indexed: 02/11/2023]
Abstract
Functional metagenomics is a powerful experimental tool to identify antibiotic resistance genes (ARGs) in the environment, but the range of suitable host bacterial species is limited. This limitation affects both the scope of the identified ARGs and the interpretation of their clinical relevance. Here we present a functional metagenomics pipeline called Reprogrammed Bacteriophage Particle Assisted Multi-species Functional Metagenomics (DEEPMINE). This approach combines and improves the use of T7 bacteriophage with exchanged tail fibres and targeted mutagenesis to expand phage host-specificity and efficiency for functional metagenomics. These modified phage particles were used to introduce large metagenomic plasmid libraries into clinically relevant bacterial pathogens. By screening for ARGs in soil and gut microbiomes and clinical genomes against 13 antibiotics, we demonstrate that this approach substantially expands the list of identified ARGs. Many ARGs have species-specific effects on resistance; they provide a high level of resistance in one bacterial species but yield very limited resistance in a related species. Finally, we identified mobile ARGs against antibiotics that are currently under clinical development or have recently been approved. Overall, DEEPMINE expands the functional metagenomics toolbox for studying microbial communities.
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Affiliation(s)
- Gábor Apjok
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary ,grid.9008.10000 0001 1016 9625Doctoral School of Biology, University of Szeged, Szeged, Hungary
| | - Mónika Számel
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary ,grid.9008.10000 0001 1016 9625Doctoral School of Biology, University of Szeged, Szeged, Hungary
| | - Chryso Christodoulou
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Viktória Seregi
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary ,HCEMM-BRC Translational Microbiology Research Group, Szeged, Hungary
| | - Bálint Márk Vásárhelyi
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Tamás Stirling
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary ,grid.9008.10000 0001 1016 9625Doctoral School of Biology, University of Szeged, Szeged, Hungary ,grid.481814.00000 0004 0479 9817Institute of Biochemistry, Biological Research Centre, National Laboratory for Health Security, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Bálint Eszenyi
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Tóbiás Sári
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary ,grid.9008.10000 0001 1016 9625Doctoral School of Biology, University of Szeged, Szeged, Hungary
| | - Fanni Vidovics
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Erika Nagrand
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Dorina Kovács
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Petra Szili
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary ,grid.9008.10000 0001 1016 9625Doctoral School of Multidisciplinary Medical Sciences, University of Szeged, Szeged, Hungary
| | - Ildikó Ilona Lantos
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Orsolya Méhi
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Pramod K. Jangir
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary ,grid.9008.10000 0001 1016 9625Doctoral School of Biology, University of Szeged, Szeged, Hungary ,grid.4991.50000 0004 1936 8948Present Address: Department of Zoology, University of Oxford, Oxford, UK
| | - Róbert Herczeg
- grid.9679.10000 0001 0663 9479Bioinformatics Research Group, Genomics and Bioinformatics Core Facility, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Bence Gálik
- grid.9679.10000 0001 0663 9479Bioinformatics Research Group, Genomics and Bioinformatics Core Facility, Szentágothai Research Centre, University of Pécs, Pécs, Hungary ,grid.48324.390000000122482838Department of Clinical Molecular Biology, Medical University of Bialystok, Bialystok, Poland
| | - Péter Urbán
- grid.9679.10000 0001 0663 9479Bioinformatics Research Group, Genomics and Bioinformatics Core Facility, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Attila Gyenesei
- grid.9679.10000 0001 0663 9479Bioinformatics Research Group, Genomics and Bioinformatics Core Facility, Szentágothai Research Centre, University of Pécs, Pécs, Hungary ,grid.48324.390000000122482838Department of Clinical Molecular Biology, Medical University of Bialystok, Bialystok, Poland
| | - Gábor Draskovits
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Ákos Nyerges
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Gergely Fekete
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - László Bodai
- grid.9008.10000 0001 1016 9625Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Nóra Zsindely
- grid.9008.10000 0001 1016 9625Department of Genetics, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Béla Dénes
- grid.432859.10000 0004 4647 7293Veterinary Diagnostic Directorate, National Food Chain Safety Office, Budapest, Hungary
| | - Ido Yosef
- grid.12136.370000 0004 1937 0546Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Udi Qimron
- grid.12136.370000 0004 1937 0546Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Balázs Papp
- grid.481814.00000 0004 0479 9817Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary ,grid.481814.00000 0004 0479 9817Institute of Biochemistry, Biological Research Centre, National Laboratory for Health Security, Eötvös Loránd Research Network (ELKH), Szeged, Hungary ,HCEMM-BRC Metabolic Systems Biology Lab, Szeged, Hungary
| | - Csaba Pál
- Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary.
| | - Bálint Kintses
- Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Eötvös Loránd Research Network (ELKH), Szeged, Hungary. .,HCEMM-BRC Translational Microbiology Research Group, Szeged, Hungary. .,Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary.
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6
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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7
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Mahata T, Qimron U. Thou shalt not cleave DNA-only repress transcription: A compact Cas protein representing a new CRISPR-Cas subtype. Mol Cell 2022; 82:4403-4404. [PMID: 36459982 DOI: 10.1016/j.molcel.2022.10.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 10/14/2022] [Accepted: 10/19/2022] [Indexed: 12/04/2022]
Abstract
Wu et al.1 characterize Cas12m, a compact Cas protein that silences transcription without cleaving DNA and is a prototype protein of the novel CRISPR-Cas subtype V-M.
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Affiliation(s)
- Tridib Mahata
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Udi Qimron
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
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8
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Dhanoa GK, Kushnir I, Qimron U, Roper DI, Sagona AP. Investigating the effect of bacteriophages on bacterial FtsZ localisation. Front Cell Infect Microbiol 2022; 12:863712. [PMID: 35967845 PMCID: PMC9372555 DOI: 10.3389/fcimb.2022.863712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
Escherichia coli is one of the most common Gram-negative pathogens and is responsible for infection leading to neonatal meningitis and sepsis. The FtsZ protein is a bacterial tubulin homolog required for cell division in most species, including E. coli. Several agents that block cell division have been shown to mislocalise FtsZ, including the bacteriophage λ-encoded Kil peptide, resulting in defective cell division and a filamentous phenotype, making FtsZ an attractive target for antimicrobials. In this study, we have used an in vitro meningitis model system for studying the effect of bacteriophages on FtsZ using fluorescent E. coli EV36/FtsZ-mCherry and K12/FtsZ-mNeon strains. We show localisation of FtsZ to the bacterial cell midbody as a single ring during normal growth conditions, and mislocalisation of FtsZ producing filamentous multi-ringed bacterial cells upon addition of the known inhibitor Kil peptide. We also show that when bacteriophages K1F-GFP and T7-mCherry were applied to their respective host strains, these phages can inhibit FtsZ and block bacterial cell division leading to a filamentous multi-ringed phenotype, potentially delaying lysis and increasing progeny number. This occurs in the exponential growth phase, as actively dividing hosts are needed. We present that ZapA protein is needed for phage inhibition by showing a phenotype recovery with a ZapA mutant strain, and we show that FtsI protein is also mislocalised upon phage infection. Finally, we show that the T7 peptide gp0.4 is responsible for the inhibition of FtsZ in K12 strains by observing a phenotype recovery with a T7Δ0.4 mutant.
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Affiliation(s)
- Gurneet K. Dhanoa
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Inbar Kushnir
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Udi Qimron
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - David I. Roper
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Antonia P. Sagona
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- *Correspondence: Antonia P. Sagona,
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9
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Isaev A, Drobiazko A, Sierro N, Gordeeva J, Yosef I, Qimron U, Ivanov NV, Severinov K. Phage T7 DNA mimic protein Ocr is a potent inhibitor of BREX defence. Nucleic Acids Res 2020; 48:7601-7602. [PMID: 32515786 PMCID: PMC7367171 DOI: 10.1093/nar/gkaa510] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Artem Isaev
- Skolkovo Institute of Science and Technology, Moscow 143028, Russia
| | - Alena Drobiazko
- Skolkovo Institute of Science and Technology, Moscow 143028, Russia
| | - Nicolas Sierro
- Philip Morris International R&D, Philip Morris Products S.A., Neuchatel 2000, Switzerland
| | - Julia Gordeeva
- Skolkovo Institute of Science and Technology, Moscow 143028, Russia
| | - Ido Yosef
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Udi Qimron
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Nikolai V Ivanov
- Philip Morris International R&D, Philip Morris Products S.A., Neuchatel 2000, Switzerland
| | - Konstantin Severinov
- Skolkovo Institute of Science and Technology, Moscow 143028, Russia.,Waksman Institute of Microbiology, Piscataway, NJ 08854, USA.,Institute of Gene Biology, Russian Academy of Sciences, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov str., 119334 Moscow, Russia
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10
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Isaev A, Drobiazko A, Sierro N, Gordeeva J, Yosef I, Qimron U, Ivanov NV, Severinov K. Phage T7 DNA mimic protein Ocr is a potent inhibitor of BREX defence. Nucleic Acids Res 2020; 48:5397-5406. [PMID: 32338761 PMCID: PMC7261183 DOI: 10.1093/nar/gkaa290] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/08/2020] [Accepted: 04/16/2020] [Indexed: 11/12/2022] Open
Abstract
BREX (for BacteRiophage EXclusion) is a superfamily of common bacterial and archaeal defence systems active against diverse bacteriophages. While the mechanism of BREX defence is currently unknown, self versus non-self differentiation requires methylation of specific asymmetric sites in host DNA by BrxX (PglX) methyltransferase. Here, we report that T7 bacteriophage Ocr, a DNA mimic protein that protects the phage from the defensive action of type I restriction-modification systems, is also active against BREX. In contrast to the wild-type phage, which is resistant to BREX defence, T7 lacking Ocr is strongly inhibited by BREX, and its ability to overcome the defence could be complemented by Ocr provided in trans. We further show that Ocr physically associates with BrxX methyltransferase. Although BREX+ cells overproducing Ocr have partially methylated BREX sites, their viability is unaffected. The result suggests that, similar to its action against type I R-M systems, Ocr associates with as yet unidentified BREX system complexes containing BrxX and neutralizes their ability to both methylate and exclude incoming phage DNA.
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Affiliation(s)
- Artem Isaev
- Skolkovo Institute of Science and Technology, Moscow 143028, Russia
| | - Alena Drobiazko
- Skolkovo Institute of Science and Technology, Moscow 143028, Russia
| | - Nicolas Sierro
- Philip Morris International R&D, Philip Morris Products S.A., Neuchatel 2000, Switzerland
| | - Julia Gordeeva
- Skolkovo Institute of Science and Technology, Moscow 143028, Russia
| | - Ido Yosef
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Udi Qimron
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Nikolai V Ivanov
- Philip Morris International R&D, Philip Morris Products S.A., Neuchatel 2000, Switzerland
| | - Konstantin Severinov
- Skolkovo Institute of Science and Technology, Moscow 143028, Russia
- Waksman Institute of Microbiology, Piscataway, NJ 08854, USA
- Institute of Gene Biology, Russian Academy of Sciences, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov str., 119334 Moscow, Russia
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11
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Edwards RA, Vega AA, Norman HM, Ohaeri M, Levi K, Dinsdale EA, Cinek O, Aziz RK, McNair K, Barr JJ, Bibby K, Brouns SJJ, Cazares A, de Jonge PA, Desnues C, Díaz Muñoz SL, Fineran PC, Kurilshikov A, Lavigne R, Mazankova K, McCarthy DT, Nobrega FL, Reyes Muñoz A, Tapia G, Trefault N, Tyakht AV, Vinuesa P, Wagemans J, Zhernakova A, Aarestrup FM, Ahmadov G, Alassaf A, Anton J, Asangba A, Billings EK, Cantu VA, Carlton JM, Cazares D, Cho GS, Condeff T, Cortés P, Cranfield M, Cuevas DA, De la Iglesia R, Decewicz P, Doane MP, Dominy NJ, Dziewit L, Elwasila BM, Eren AM, Franz C, Fu J, Garcia-Aljaro C, Ghedin E, Gulino KM, Haggerty JM, Head SR, Hendriksen RS, Hill C, Hyöty H, Ilina EN, Irwin MT, Jeffries TC, Jofre J, Junge RE, Kelley ST, Khan Mirzaei M, Kowalewski M, Kumaresan D, Leigh SR, Lipson D, Lisitsyna ES, Llagostera M, Maritz JM, Marr LC, McCann A, Molshanski-Mor S, Monteiro S, Moreira-Grez B, Morris M, Mugisha L, Muniesa M, Neve H, Nguyen NP, Nigro OD, Nilsson AS, O'Connell T, Odeh R, Oliver A, Piuri M, Prussin Ii AJ, Qimron U, Quan ZX, Rainetova P, Ramírez-Rojas A, Raya R, Reasor K, Rice GAO, Rossi A, Santos R, Shimashita J, Stachler EN, Stene LC, Strain R, Stumpf R, Torres PJ, Twaddle A, Ugochi Ibekwe M, Villagra N, Wandro S, White B, Whiteley A, Whiteson KL, Wijmenga C, Zambrano MM, Zschach H, Dutilh BE. Global phylogeography and ancient evolution of the widespread human gut virus crAssphage. Nat Microbiol 2019. [PMID: 31285584 DOI: 10.1038/s41564-019-04904-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
Abstract
Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.
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Affiliation(s)
- Robert A Edwards
- Department of Biology, San Diego State University, San Diego, CA, USA.
- The Viral Information Institute, San Diego State University, San Diego, CA, USA.
| | - Alejandro A Vega
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Holly M Norman
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Maria Ohaeri
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Kyle Levi
- Department of Computer Science, San Diego State University, San Diego, CA, USA
| | | | - Ondrej Cinek
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Katelyn McNair
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Jeremy J Barr
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Kyle Bibby
- Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Stan J J Brouns
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Adrian Cazares
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Patrick A de Jonge
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Christelle Desnues
- MEPHI, Aix-Marseille Université, IRD, AP-HM, CNRS, IHU Méditerranée Infection, Marseille, France
- Mediterranean Institute of Oceanography, Aix-Marseille Université, Université de Toulon, CNRS, IRD, UM 110, Marseille, France
| | - Samuel L Díaz Muñoz
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Alexander Kurilshikov
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Rob Lavigne
- Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Karla Mazankova
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - David T McCarthy
- EPHM Lab, Civil Engineering Department, Monash University, Clayton, Victoria, Australia
| | - Franklin L Nobrega
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Alejandro Reyes Muñoz
- Max Planck Tandem Group in Computational Biology, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
| | - German Tapia
- Department of Child Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Nicole Trefault
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Huechuraba, Chile
| | - Alexander V Tyakht
- Laboratory of Bioinformatics, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
- Department of Informational Technologies, ITMO University, Saint Petersburg, Russia
| | - Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | | | - Alexandra Zhernakova
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Frank M Aarestrup
- National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Abeer Alassaf
- Department of Pediatrics, School of Medicine, University of Jordan, Amman, Jordan
| | - Josefa Anton
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Abigail Asangba
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Emma K Billings
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Vito Adrian Cantu
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Jane M Carlton
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Daniel Cazares
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Gyu-Sung Cho
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Tess Condeff
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Pilar Cortés
- Departament de Genètica i de Microbiologia, Universitat Autònoma De Barcelona, Barcelona, Spain
| | - Mike Cranfield
- Wildlife Health Center, University of California, Davis, Davis, CA, USA
| | - Daniel A Cuevas
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Rodrigo De la Iglesia
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Przemyslaw Decewicz
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Michael P Doane
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Bashir Mukhtar Elwasila
- Department of Pediatrics and Child Health, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Charles Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Jingyuan Fu
- Department of Pediatrics, University Medical Center Groningen, Groningen, The Netherlands
| | - Cristina Garcia-Aljaro
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Elodie Ghedin
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Kristen M Gulino
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - John M Haggerty
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Steven R Head
- Next Generation Sequencing and Microarray Core Facility, The Scripps Research Institute, La Jolla, CA, USA
| | - Rene S Hendriksen
- National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Colin Hill
- School of Microbiology, University College Cork, Cork, Ireland
| | - Heikki Hyöty
- Department of Virology, School of Medicine, University of Tampere, Tampere, Finland
| | - Elena N Ilina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Mitchell T Irwin
- Department of Anthropology, Northern Illinois University, DeKalb, IL, USA
| | - Thomas C Jeffries
- School of Science and Health, Western Sydney University, Penrith, New South Wales, Australia
| | - Juan Jofre
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Randall E Junge
- Department of Animal Health, Columbus Zoo and Aquarium, Powell, OH, USA
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Martin Kowalewski
- Department Estacion Biologica Corrientes, Institution Museo Arg. Cs. Naturales-CONICET, Corrientes, Argentina
| | - Deepak Kumaresan
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Steven R Leigh
- Department of Anthropology, University of Colorado, Boulder, CO, USA
| | - David Lipson
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Montserrat Llagostera
- Departament de Genètica i de Microbiologia, Universitat Autònoma De Barcelona, Barcelona, Spain
| | - Julia M Maritz
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Linsey C Marr
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Angela McCann
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Shahar Molshanski-Mor
- Clinical Microbiology & Immunology, Sackler school of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Silvia Monteiro
- Laboratorio de Analises, Instituto Superior Tecnico, Universidade Lisboa, Lisboa, Portugal
| | - Benjamin Moreira-Grez
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Megan Morris
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Lawrence Mugisha
- CEHA, Kampala, Uganda
- COVAB, Makerere University, Kampala, Uganda
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Nam-Phuong Nguyen
- Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Olivia D Nigro
- College of Natural and Computational Sciences, Hawai'i Pacific University, Kaneohe, HI, USA
| | - Anders S Nilsson
- Department of Molecular Biosciences, Stockholm University, Stockholm, Sweden
| | - Taylor O'Connell
- Biological and Medical Informatics Program, San Diego State University, San Diego, CA, USA
| | - Rasha Odeh
- Department of Pediatrics, School of Medicine, University of Jordan, Amman, Jordan
| | - Andrew Oliver
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Mariana Piuri
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Aaron J Prussin Ii
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Udi Qimron
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Zhe-Xue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Petra Rainetova
- Centre of Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | | | | | - Kim Reasor
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Alessandro Rossi
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands
- Department of Biology, University of Padova, Padova, Italy
| | - Ricardo Santos
- Laboratorio de Analises, Instituto Superior Tecnico, Universidade Lisboa, Lisboa, Portugal
| | - John Shimashita
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Elyse N Stachler
- Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lars C Stene
- Department of Child Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Ronan Strain
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Rebecca Stumpf
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Pedro J Torres
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Alan Twaddle
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - MaryAnn Ugochi Ibekwe
- Department of Pediatrics, Federal Teaching Hospital Abakaliki, Ebonyi State University, Abakaliki, Nigeria
| | - Nicolás Villagra
- Escuela de Tecnología Médica, Universidad Andres Bello, Santiago, Chile
| | - Stephen Wandro
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Bryan White
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Andy Whiteley
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Katrine L Whiteson
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Henrike Zschach
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands.
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands.
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12
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Edwards RA, Vega AA, Norman HM, Ohaeri M, Levi K, Dinsdale EA, Cinek O, Aziz RK, McNair K, Barr JJ, Bibby K, Brouns SJJ, Cazares A, de Jonge PA, Desnues C, Díaz Muñoz SL, Fineran PC, Kurilshikov A, Lavigne R, Mazankova K, McCarthy DT, Nobrega FL, Reyes Muñoz A, Tapia G, Trefault N, Tyakht AV, Vinuesa P, Wagemans J, Zhernakova A, Aarestrup FM, Ahmadov G, Alassaf A, Anton J, Asangba A, Billings EK, Cantu VA, Carlton JM, Cazares D, Cho GS, Condeff T, Cortés P, Cranfield M, Cuevas DA, De la Iglesia R, Decewicz P, Doane MP, Dominy NJ, Dziewit L, Elwasila BM, Eren AM, Franz C, Fu J, Garcia-Aljaro C, Ghedin E, Gulino KM, Haggerty JM, Head SR, Hendriksen RS, Hill C, Hyöty H, Ilina EN, Irwin MT, Jeffries TC, Jofre J, Junge RE, Kelley ST, Khan Mirzaei M, Kowalewski M, Kumaresan D, Leigh SR, Lipson D, Lisitsyna ES, Llagostera M, Maritz JM, Marr LC, McCann A, Molshanski-Mor S, Monteiro S, Moreira-Grez B, Morris M, Mugisha L, Muniesa M, Neve H, Nguyen NP, Nigro OD, Nilsson AS, O'Connell T, Odeh R, Oliver A, Piuri M, Prussin Ii AJ, Qimron U, Quan ZX, Rainetova P, Ramírez-Rojas A, Raya R, Reasor K, Rice GAO, Rossi A, Santos R, Shimashita J, Stachler EN, Stene LC, Strain R, Stumpf R, Torres PJ, Twaddle A, Ugochi Ibekwe M, Villagra N, Wandro S, White B, Whiteley A, Whiteson KL, Wijmenga C, Zambrano MM, Zschach H, Dutilh BE. Global phylogeography and ancient evolution of the widespread human gut virus crAssphage. Nat Microbiol 2019; 4:1727-1736. [PMID: 31285584 DOI: 10.1101/527796] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 05/22/2019] [Indexed: 05/26/2023]
Abstract
Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.
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Affiliation(s)
- Robert A Edwards
- Department of Biology, San Diego State University, San Diego, CA, USA.
- The Viral Information Institute, San Diego State University, San Diego, CA, USA.
| | - Alejandro A Vega
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Holly M Norman
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Maria Ohaeri
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Kyle Levi
- Department of Computer Science, San Diego State University, San Diego, CA, USA
| | | | - Ondrej Cinek
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Katelyn McNair
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Jeremy J Barr
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Kyle Bibby
- Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Stan J J Brouns
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Adrian Cazares
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Patrick A de Jonge
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Christelle Desnues
- MEPHI, Aix-Marseille Université, IRD, AP-HM, CNRS, IHU Méditerranée Infection, Marseille, France
- Mediterranean Institute of Oceanography, Aix-Marseille Université, Université de Toulon, CNRS, IRD, UM 110, Marseille, France
| | - Samuel L Díaz Muñoz
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Alexander Kurilshikov
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Rob Lavigne
- Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Karla Mazankova
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - David T McCarthy
- EPHM Lab, Civil Engineering Department, Monash University, Clayton, Victoria, Australia
| | - Franklin L Nobrega
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Alejandro Reyes Muñoz
- Max Planck Tandem Group in Computational Biology, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
| | - German Tapia
- Department of Child Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Nicole Trefault
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Huechuraba, Chile
| | - Alexander V Tyakht
- Laboratory of Bioinformatics, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
- Department of Informational Technologies, ITMO University, Saint Petersburg, Russia
| | - Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | | | - Alexandra Zhernakova
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Frank M Aarestrup
- National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Abeer Alassaf
- Department of Pediatrics, School of Medicine, University of Jordan, Amman, Jordan
| | - Josefa Anton
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Abigail Asangba
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Emma K Billings
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Vito Adrian Cantu
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Jane M Carlton
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Daniel Cazares
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Gyu-Sung Cho
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Tess Condeff
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Pilar Cortés
- Departament de Genètica i de Microbiologia, Universitat Autònoma De Barcelona, Barcelona, Spain
| | - Mike Cranfield
- Wildlife Health Center, University of California, Davis, Davis, CA, USA
| | - Daniel A Cuevas
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Rodrigo De la Iglesia
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Przemyslaw Decewicz
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Michael P Doane
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Bashir Mukhtar Elwasila
- Department of Pediatrics and Child Health, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Charles Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Jingyuan Fu
- Department of Pediatrics, University Medical Center Groningen, Groningen, The Netherlands
| | - Cristina Garcia-Aljaro
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Elodie Ghedin
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Kristen M Gulino
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - John M Haggerty
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Steven R Head
- Next Generation Sequencing and Microarray Core Facility, The Scripps Research Institute, La Jolla, CA, USA
| | - Rene S Hendriksen
- National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Colin Hill
- School of Microbiology, University College Cork, Cork, Ireland
| | - Heikki Hyöty
- Department of Virology, School of Medicine, University of Tampere, Tampere, Finland
| | - Elena N Ilina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Mitchell T Irwin
- Department of Anthropology, Northern Illinois University, DeKalb, IL, USA
| | - Thomas C Jeffries
- School of Science and Health, Western Sydney University, Penrith, New South Wales, Australia
| | - Juan Jofre
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Randall E Junge
- Department of Animal Health, Columbus Zoo and Aquarium, Powell, OH, USA
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Martin Kowalewski
- Department Estacion Biologica Corrientes, Institution Museo Arg. Cs. Naturales-CONICET, Corrientes, Argentina
| | - Deepak Kumaresan
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Steven R Leigh
- Department of Anthropology, University of Colorado, Boulder, CO, USA
| | - David Lipson
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Montserrat Llagostera
- Departament de Genètica i de Microbiologia, Universitat Autònoma De Barcelona, Barcelona, Spain
| | - Julia M Maritz
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Linsey C Marr
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Angela McCann
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Shahar Molshanski-Mor
- Clinical Microbiology & Immunology, Sackler school of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Silvia Monteiro
- Laboratorio de Analises, Instituto Superior Tecnico, Universidade Lisboa, Lisboa, Portugal
| | - Benjamin Moreira-Grez
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Megan Morris
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Lawrence Mugisha
- CEHA, Kampala, Uganda
- COVAB, Makerere University, Kampala, Uganda
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Nam-Phuong Nguyen
- Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Olivia D Nigro
- College of Natural and Computational Sciences, Hawai'i Pacific University, Kaneohe, HI, USA
| | - Anders S Nilsson
- Department of Molecular Biosciences, Stockholm University, Stockholm, Sweden
| | - Taylor O'Connell
- Biological and Medical Informatics Program, San Diego State University, San Diego, CA, USA
| | - Rasha Odeh
- Department of Pediatrics, School of Medicine, University of Jordan, Amman, Jordan
| | - Andrew Oliver
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Mariana Piuri
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Aaron J Prussin Ii
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Udi Qimron
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Zhe-Xue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Petra Rainetova
- Centre of Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | | | | | - Kim Reasor
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Alessandro Rossi
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands
- Department of Biology, University of Padova, Padova, Italy
| | - Ricardo Santos
- Laboratorio de Analises, Instituto Superior Tecnico, Universidade Lisboa, Lisboa, Portugal
| | - John Shimashita
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Elyse N Stachler
- Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lars C Stene
- Department of Child Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Ronan Strain
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Rebecca Stumpf
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Pedro J Torres
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Alan Twaddle
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - MaryAnn Ugochi Ibekwe
- Department of Pediatrics, Federal Teaching Hospital Abakaliki, Ebonyi State University, Abakaliki, Nigeria
| | - Nicolás Villagra
- Escuela de Tecnología Médica, Universidad Andres Bello, Santiago, Chile
| | - Stephen Wandro
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Bryan White
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Andy Whiteley
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Katrine L Whiteson
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Henrike Zschach
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands.
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands.
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13
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Yosef I, Edry‐Botzer L, Globus R, Shlomovitz I, Munitz A, Gerlic M, Qimron U. A genetic system for biasing the sex ratio in mice. EMBO Rep 2019; 20:e48269. [PMID: 31267640 PMCID: PMC6680165 DOI: 10.15252/embr.201948269] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/14/2019] [Accepted: 05/27/2019] [Indexed: 01/10/2023] Open
Abstract
Biasing the sex ratio of populations of different organisms, including plants, insects, crustacean, and fish, has been demonstrated by genetic and non-genetic approaches. However, biasing the sex ratio of mammalian populations has not been demonstrated genetically. Here, we provide a first proof of concept for such a genetic system in mammals by crossing two genetically engineered mouse lines. The maternal line encodes a functional Cas9 protein on an autosomal chromosome, whereas the paternal line encodes guide RNAs on the Y chromosome targeting vital mouse genes. After fertilization, the presence of both the Y-encoded guide RNAs from the paternal sperm and the Cas9 protein from the maternal egg targets the vital genes in males. We show that these genes are specifically targeted in males and that this breeding consequently self-destructs solely males. Our results pave the way for a genetic system that allows biased sex production of livestock.
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Affiliation(s)
- Ido Yosef
- Department of Clinical Microbiology and ImmunologySackler School of MedicineTel Aviv UniversityTel AvivIsrael
| | - Liat Edry‐Botzer
- Department of Clinical Microbiology and ImmunologySackler School of MedicineTel Aviv UniversityTel AvivIsrael
| | - Rea Globus
- Department of Clinical Microbiology and ImmunologySackler School of MedicineTel Aviv UniversityTel AvivIsrael
| | - Inbar Shlomovitz
- Department of Clinical Microbiology and ImmunologySackler School of MedicineTel Aviv UniversityTel AvivIsrael
| | - Ariel Munitz
- Department of Clinical Microbiology and ImmunologySackler School of MedicineTel Aviv UniversityTel AvivIsrael
| | - Motti Gerlic
- Department of Clinical Microbiology and ImmunologySackler School of MedicineTel Aviv UniversityTel AvivIsrael
| | - Udi Qimron
- Department of Clinical Microbiology and ImmunologySackler School of MedicineTel Aviv UniversityTel AvivIsrael
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14
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Reichman H, Itan M, Rozenberg P, Yarmolovski T, Brazowski E, Varol C, Gluck N, Shapira S, Arber N, Qimron U, Karo-Atar D, Lee JJ, Munitz A. Activated Eosinophils Exert Antitumorigenic Activities in Colorectal Cancer. Cancer Immunol Res 2019; 7:388-400. [PMID: 30665890 DOI: 10.1158/2326-6066.cir-18-0494] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 10/14/2018] [Accepted: 12/17/2018] [Indexed: 12/23/2022]
Abstract
Immunotherapies targeting T lymphocytes are revolutionizing cancer therapy but only benefit a subset of patients, especially in colorectal cancer. Thus, additional insight into the tumor microenvironment (TME) is required. Eosinophils are bone marrow-derived cells that have been largely studied in the context of allergic diseases and parasite infections. Although tumor-associated eosinophilia has been described in various solid tumors including colorectal cancer, knowledge is still missing regarding eosinophil activities and even the basic question of whether the TME promotes eosinophil recruitment without additional manipulation (e.g., immunotherapy) is unclear. Herein, we report that eosinophils are recruited into developing tumors during induction of inflammation-induced colorectal cancer and in mice with the Apcmin /+ genotype, which develop spontaneous intestinal adenomas. Using adoptive transfer and cytokine neutralization experiments, we demonstrate that the TME supported prolonged eosinophil survival independent of IL5, an eosinophil survival cytokine. Tumor-infiltrating eosinophils consisted of degranulating eosinophils and were essential for tumor rejection independently of CD8+ T cells. Transcriptome and proteomic analysis revealed an IFNγ-linked signature for intratumoral eosinophils that was different from that of macrophages. Our data establish antitumorigenic roles for eosinophils in colorectal cancer. These findings may facilitate the development of pharmacologic treatments that could unleash antitumor responses by eosinophils, especially in colorectal cancer patients displaying eosinophilia.
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Affiliation(s)
- Hadar Reichman
- Department of Clinical Microbiology and Immunology, the Sackler School of Medicine, Tel Aviv University, Ramat Aviv, Israel
| | - Michal Itan
- Department of Clinical Microbiology and Immunology, the Sackler School of Medicine, Tel Aviv University, Ramat Aviv, Israel
| | - Perri Rozenberg
- Department of Clinical Microbiology and Immunology, the Sackler School of Medicine, Tel Aviv University, Ramat Aviv, Israel
| | - Tal Yarmolovski
- Department of Clinical Microbiology and Immunology, the Sackler School of Medicine, Tel Aviv University, Ramat Aviv, Israel
| | - Eli Brazowski
- Research Center for Digestive Tract and Disorders and Liver Diseases, Tel Aviv Sourasky Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Chen Varol
- Research Center for Digestive Tract and Disorders and Liver Diseases, Tel Aviv Sourasky Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Nathan Gluck
- Research Center for Digestive Tract and Disorders and Liver Diseases, Tel Aviv Sourasky Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shiran Shapira
- Integrated Cancer Prevention Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Nadir Arber
- Integrated Cancer Prevention Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Udi Qimron
- Department of Clinical Microbiology and Immunology, the Sackler School of Medicine, Tel Aviv University, Ramat Aviv, Israel
| | - Danielle Karo-Atar
- Department of Clinical Microbiology and Immunology, the Sackler School of Medicine, Tel Aviv University, Ramat Aviv, Israel
| | - James J Lee
- Division of Pulmonary Medicine, Department of Biochemistry and Molecular Biology, Mayo Clinic Arizona, Scottsdale, Arizona
| | - Ariel Munitz
- Department of Clinical Microbiology and Immunology, the Sackler School of Medicine, Tel Aviv University, Ramat Aviv, Israel.
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15
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Abstract
We recently developed a platform where phage-transducing particles optimize DNA delivery to a wide range of hosts. Here, we use this platform to optimize DNA transduction into hosts that naturally restrict specific DNA sequences. We first show that a specific plasmid is restricted for transduction into a particular Salmonella strain. Using the platform, we select for a mutated plasmid that overcomes the restriction barrier. Insertion of the non-mutated sequence into a permissive plasmid restricts transduction. We further show that epigenetic modification enables the DNA to evade restriction by the putative defense system. Our results validate this straightforward genetic approach for optimization of DNA transduction into new hosts.
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Affiliation(s)
- Oren Auster
- a Department of Clinical Microbiology and Immunology , Sackler School of Medicine, Tel Aviv University , Tel Aviv , Israel
| | - Rea Globus
- a Department of Clinical Microbiology and Immunology , Sackler School of Medicine, Tel Aviv University , Tel Aviv , Israel
| | - Ido Yosef
- a Department of Clinical Microbiology and Immunology , Sackler School of Medicine, Tel Aviv University , Tel Aviv , Israel
| | - Udi Qimron
- a Department of Clinical Microbiology and Immunology , Sackler School of Medicine, Tel Aviv University , Tel Aviv , Israel
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16
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Goren MG, Doron S, Globus R, Amitai G, Sorek R, Qimron U. Repeat Size Determination by Two Molecular Rulers in the Type I-E CRISPR Array. Cell Rep 2017; 16:2811-2818. [PMID: 27626652 PMCID: PMC5039180 DOI: 10.1016/j.celrep.2016.08.043] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 08/01/2016] [Accepted: 08/12/2016] [Indexed: 12/24/2022] Open
Abstract
Prokaryotic adaptive immune systems are composed of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins. These systems adapt to new threats by integrating short nucleic acids, termed spacers, into the CRISPR array. The functional motifs in the repeat and the mechanism by which a constant repeat size is maintained are still elusive. Here, through a series of mutations within the repeat of the CRISPR-Cas type I-E, we identify motifs that are crucial for adaptation and show that they serve as anchor sites for two molecular rulers determining the size of the new repeat. Adaptation products from various repeat mutants support a model in which two motifs in the repeat bind to two different sites in the adaptation complex that are 8 and 16 bp away from the active site. This model significantly extends our understanding of the adaptation process and broadens the scope of its applications. Inverted repeats in the type I-E CRISPR-Cas system are essential for adaptation Each inverted repeat encodes a motif serving as an anchor site for a molecular ruler These molecular rulers determine the spacer insertion site regardless of the sequence The findings support a model considering all known steps in spacer adaptation
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Affiliation(s)
- Moran G Goren
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Shany Doron
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rea Globus
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Gil Amitai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rotem Sorek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Udi Qimron
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel.
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17
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Tabib-Salazar A, Liu B, Shadrin A, Burchell L, Wang Z, Wang Z, Goren MG, Yosef I, Qimron U, Severinov K, Matthews SJ, Wigneshweraraj S. Full shut-off of Escherichia coli RNA-polymerase by T7 phage requires a small phage-encoded DNA-binding protein. Nucleic Acids Res 2017; 45:7697-7707. [PMID: 28486695 PMCID: PMC5569994 DOI: 10.1093/nar/gkx370] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 04/24/2017] [Indexed: 11/13/2022] Open
Abstract
Infection of Escherichia coli by the T7 phage leads to rapid and selective inhibition of the bacterial RNA polymerase (RNAP) by the 7 kDa T7 protein Gp2. We describe the identification and functional and structural characterisation of a novel 7 kDa T7 protein, Gp5.7, which adopts a winged helix-turn-helix-like structure and specifically represses transcription initiation from host RNAP-dependent promoters on the phage genome via a mechanism that involves interaction with DNA and the bacterial RNAP. Whereas Gp2 is indispensable for T7 growth in E. coli, we show that Gp5.7 is required for optimal infection outcome. Our findings provide novel insights into how phages fine-tune the activity of the host transcription machinery to ensure both successful and efficient phage progeny development.
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Affiliation(s)
- Aline Tabib-Salazar
- MRC Centre for Molecular Microbiology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Bing Liu
- MRC Centre for Molecular Microbiology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Andrey Shadrin
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow 142290, Russia
| | - Lynn Burchell
- MRC Centre for Molecular Microbiology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Zhexin Wang
- MRC Centre for Molecular Microbiology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Zhihao Wang
- MRC Centre for Molecular Microbiology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Moran G Goren
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ido Yosef
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Udi Qimron
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Konstantin Severinov
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, 190 Frelinghuysen Road, Piscataway, NJ 08854-8020, USA
| | - Steve J Matthews
- MRC Centre for Molecular Microbiology and Infection, Imperial College London, London SW7 2AZ, UK
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18
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Globus R, Qimron U. Crystal-clear memories of a bacterium. Science 2017; 357:1096-1097. [PMID: 28912231 DOI: 10.1126/science.aao4929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Indexed: 11/02/2022]
Affiliation(s)
- Rea Globus
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Udi Qimron
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
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19
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Abstract
Generating plants with increased yields while maintaining low production and maintenance costs is highly important since plants are the major food source for humans and animals, as well as important producers of chemicals, pharmaceuticals, and fuels. Gene editing approaches, particularly the CRISPR-Cas system, are the preferred methods for improving crops, enabling quick, robust, and accurate gene manipulation. Nevertheless, new breeds of genetically modified crops have initiated substantial debates concerning their biosafety, commercial use, and regulation. Here, we discuss the challenges facing genetic engineering of crops by CRISPR-cas, and highlight the pros and cons of using this tool.
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Affiliation(s)
- Rea Globus
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Udi Qimron
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
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20
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Yosef I, Goren MG, Globus R, Molshanski-Mor S, Qimron U. Extending the Host Range of Bacteriophage Particles for DNA Transduction. Mol Cell 2017; 66:721-728.e3. [DOI: 10.1016/j.molcel.2017.04.025] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 04/10/2017] [Accepted: 04/27/2017] [Indexed: 01/21/2023]
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21
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Abstract
We present a CRISPR-Cas based technique for deleting genes from the T7 bacteriophage genome. A DNA fragment encoding homologous arms to the target gene to be deleted is first cloned into a plasmid. The T7 phage is then propagated in Escherichia coli harboring this plasmid. During this propagation, some phage genomes undergo homologous recombination with the plasmid, thus deleting the targeted gene. To select for these genomes, the CRISPR-Cas system is used to cleave non-edited genomes, enabling isolation of the desired recombinant phages. This protocol allows seamless deletion of desired genes in a T7 phage, and can be expanded to other phages and other types of genetic manipulations as well.
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Affiliation(s)
- Miriam Manor
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Udi Qimron
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
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22
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Goren M, Yosef I, Qimron U. Sensitizing pathogens to antibiotics using the CRISPR-Cas system. Drug Resist Updat 2016; 30:1-6. [PMID: 28363331 DOI: 10.1016/j.drup.2016.11.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 10/20/2016] [Accepted: 11/22/2016] [Indexed: 01/10/2023]
Abstract
The extensive use of antibiotics over the last century has resulted in a significant artificial selection pressure for antibiotic-resistant pathogens to evolve. Various strategies to fight these pathogens have been introduced including new antibiotics, naturally-derived enzymes/peptides that specifically target pathogens and bacteriophages that lyse these pathogens. A new tool has recently been introduced in the fight against drug-resistant pathogens-the prokaryotic defense mechanism-clustered regularly interspaced short palindromic repeats-CRISPR associated (CRISPR-Cas) system. The CRISPR-Cas system acts as a nuclease that can be guided to cleave any target DNA, allowing sophisticated, yet feasible, manipulations of pathogens. Here, we review pioneering studies that use the CRISPR-Cas system to specifically edit bacterial populations, eliminate their resistance genes and combine these two strategies in order to produce an artificial selection pressure for antibiotic-sensitive pathogens. We suggest that intelligent design of this system, along with efficient delivery tools into pathogens, may significantly reduce the threat of antibiotic-resistant pathogens.
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Affiliation(s)
- Moran Goren
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ido Yosef
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Udi Qimron
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
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23
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Yosef I, Edgar R, Levy A, Amitai G, Sorek R, Munitz A, Qimron U. Natural selection underlies apparent stress-induced mutagenesis in a bacteriophage infection model. Nat Microbiol 2016; 1:16047. [DOI: 10.1038/nmicrobiol.2016.47] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 03/11/2016] [Indexed: 11/09/2022]
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24
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Yosef I, Manor M, Qimron U. Counteracting selection for antibiotic-resistant bacteria. Bacteriophage 2016; 6:e1096996. [PMID: 27144084 DOI: 10.1080/21597081.2015.1096996] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 09/13/2015] [Accepted: 09/15/2015] [Indexed: 12/29/2022]
Abstract
The occurrence of antibiotic-resistant bacterial pathogens is on the rise because antibiotics exert selection pressure that kills only the antibiotic-sensitive pathogens. Sanitation and cleansing of hospital surfaces and the skin of medical personnel do not counteract this selective pressure, but rather indiscriminately reduce total pathogens on treated surfaces. Here, we discuss two recently introduced genetic strategies, based on temperate bacteriophages as DNA-delivery vehicles, that aim to sensitize bacteria to antibiotics and selectively kill the antibiotic-resistant ones. Outlooks for rendering one such approach more efficient and applicable are proposed. We believe that using an end product designed according to the provided principles on hospital surfaces and in hand-sanitizers will facilitate substitution of antibiotic-resistant pathogens with sensitive ones.
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Affiliation(s)
- Ido Yosef
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University , Tel Aviv , Israel
| | - Miriam Manor
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University , Tel Aviv , Israel
| | - Udi Qimron
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University , Tel Aviv , Israel
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25
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26
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Abstract
The increasing threat of pathogen resistance to antibiotics requires the development of novel antimicrobial strategies. Here we present a proof of concept for a genetic strategy that aims to sensitize bacteria to antibiotics and selectively kill antibiotic-resistant bacteria. We use temperate phages to deliver a functional clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated (Cas) system into the genome of antibiotic-resistant bacteria. The delivered CRISPR-Cas system destroys both antibiotic resistance-conferring plasmids and genetically modified lytic phages. This linkage between antibiotic sensitization and protection from lytic phages is a key feature of the strategy. It allows programming of lytic phages to kill only antibiotic-resistant bacteria while protecting antibiotic-sensitized bacteria. Phages designed according to this strategy may be used on hospital surfaces and hand sanitizers to facilitate replacement of antibiotic-resistant pathogens with sensitive ones.
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Affiliation(s)
- Ido Yosef
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Miriam Manor
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ruth Kiro
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Udi Qimron
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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Levy A, Goren MG, Yosef I, Auster O, Manor M, Amitai G, Edgar R, Qimron U, Sorek R. CRISPR adaptation biases explain preference for acquisition of foreign DNA. Nature 2015; 520:505-510. [PMID: 25874675 PMCID: PMC4561520 DOI: 10.1038/nature14302] [Citation(s) in RCA: 270] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 02/09/2015] [Indexed: 12/21/2022]
Abstract
CRISPR-Cas (clustered, regularly interspaced short palindromic repeats coupled with CRISPR-associated proteins) is a bacterial immunity system that protects against invading phages or plasmids. In the process of CRISPR adaptation, short pieces of DNA ('spacers') are acquired from foreign elements and integrated into the CRISPR array. So far, it has remained a mystery how spacers are preferentially acquired from the foreign DNA while the self chromosome is avoided. Here we show that spacer acquisition is replication-dependent, and that DNA breaks formed at stalled replication forks promote spacer acquisition. Chromosomal hotspots of spacer acquisition were confined by Chi sites, which are sequence octamers highly enriched on the bacterial chromosome, suggesting that these sites limit spacer acquisition from self DNA. We further show that the avoidance of self is mediated by the RecBCD double-stranded DNA break repair complex. Our results suggest that, in Escherichia coli, acquisition of new spacers largely depends on RecBCD-mediated processing of double-stranded DNA breaks occurring primarily at replication forks, and that the preference for foreign DNA is achieved through the higher density of Chi sites on the self chromosome, in combination with the higher number of forks on the foreign DNA. This model explains the strong preference to acquire spacers both from high copy plasmids and from phages.
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Affiliation(s)
- Asaf Levy
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Moran G Goren
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ido Yosef
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Oren Auster
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Miriam Manor
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Gil Amitai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rotem Edgar
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Udi Qimron
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Rotem Sorek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
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Yosef I, Kiro R, Molshanski-Mor S, Edgar R, Qimron U. Different approaches for using bacteriophages against antibiotic-resistant bacteria. Bacteriophage 2014; 4:e28491. [PMID: 24653944 DOI: 10.4161/bact.28491] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Revised: 02/03/2014] [Accepted: 03/10/2014] [Indexed: 01/21/2023]
Abstract
Bacterial resistance to antibiotics is an emerging threat requiring urgent solutions. Ever since their discovery, lytic bacteriophages have been suggested as therapeutic agents, but their application faces various obstacles: sequestration of the phage by the spleen and liver, antibodies against the phage, narrow host range, poor accessibility to the infected tissue, and bacterial resistance. Variations on bacteriophage use have been suggested, such as temperate phages as gene-delivery vehicles into pathogens. This approach, which is proposed to sensitize pathogens residing on hospital surfaces and medical personnel's skin, and its prospects are described in this addendum. Furthermore, phage-encoded products have been proposed as weapons against antibiotic resistance in bacteria. We describe a new phage protein which was identified during basic research into T7 bacteriophages. This protein may serendipitously prove useful for treating antibiotic-resistant pathogens. We believe that further basic research will lead to novel strategies in the fight against antibiotic-resistant bacteria.
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Affiliation(s)
- Ido Yosef
- Department of Clinical Microbiology and Immunology; Sackler School of Medicine; Tel Aviv University; Tel Aviv, Israel
| | - Ruth Kiro
- Department of Clinical Microbiology and Immunology; Sackler School of Medicine; Tel Aviv University; Tel Aviv, Israel
| | - Shahar Molshanski-Mor
- Department of Clinical Microbiology and Immunology; Sackler School of Medicine; Tel Aviv University; Tel Aviv, Israel
| | - Rotem Edgar
- Department of Clinical Microbiology and Immunology; Sackler School of Medicine; Tel Aviv University; Tel Aviv, Israel
| | - Udi Qimron
- Department of Clinical Microbiology and Immunology; Sackler School of Medicine; Tel Aviv University; Tel Aviv, Israel
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Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated (Cas) system has recently been used to engineer genomes of various organisms, but surprisingly, not those of bacteriophages (phages). Here we present a method to genetically engineer the Escherichia coli phage T7 using the type I-E CRISPR-Cas system. T7 phage genome is edited by homologous recombination with a DNA sequence flanked by sequences homologous to the desired location. Non-edited genomes are targeted by the CRISPR-Cas system, thus enabling isolation of the desired recombinant phages. This method broadens CRISPR Cas-based editing to phages and uses a CRISPR-Cas type other than type II. The method may be adjusted to genetically engineer any bacteriophage genome.
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Affiliation(s)
- Ruth Kiro
- Department of Clinical Microbiology and Immunology; Sackler School of Medicine; Tel Aviv University; Tel Aviv, Israel
| | - Dror Shitrit
- Department of Clinical Microbiology and Immunology; Sackler School of Medicine; Tel Aviv University; Tel Aviv, Israel
| | - Udi Qimron
- Department of Clinical Microbiology and Immunology; Sackler School of Medicine; Tel Aviv University; Tel Aviv, Israel
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31
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Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated (Cas) system has recently been used to engineer genomes of various organisms, but surprisingly, not those of bacteriophages (phages). Here we present a method to genetically engineer the Escherichia coli phage T7 using the type I-E CRISPR-Cas system. T7 phage genome is edited by homologous recombination with a DNA sequence flanked by sequences homologous to the desired location. Non-edited genomes are targeted by the CRISPR-Cas system, thus enabling isolation of the desired recombinant phages. This method broadens CRISPR Cas-based editing to phages and uses a CRISPR-Cas type other than type II. The method may be adjusted to genetically engineer any bacteriophage genome.
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Affiliation(s)
- Ruth Kiro
- Department of Clinical Microbiology and Immunology; Sackler School of Medicine; Tel Aviv University; Tel Aviv, Israel
| | - Dror Shitrit
- Department of Clinical Microbiology and Immunology; Sackler School of Medicine; Tel Aviv University; Tel Aviv, Israel
| | - Udi Qimron
- Department of Clinical Microbiology and Immunology; Sackler School of Medicine; Tel Aviv University; Tel Aviv, Israel
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32
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Sberro H, Leavitt A, Kiro R, Koh E, Peleg Y, Qimron U, Sorek R. Discovery of functional toxin/antitoxin systems in bacteria by shotgun cloning. Mol Cell 2013; 50:136-48. [PMID: 23478446 DOI: 10.1016/j.molcel.2013.02.002] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Revised: 11/21/2012] [Accepted: 01/31/2013] [Indexed: 01/21/2023]
Abstract
Toxin-antitoxin (TA) modules, composed of a toxic protein and a counteracting antitoxin, play important roles in bacterial physiology. We examined the experimental insertion of 1.5 million genes from 388 microbial genomes into an Escherichia coli host using more than 8.5 million random clones. This revealed hundreds of genes (toxins) that could only be cloned when the neighboring gene (antitoxin) was present on the same clone. Clustering of these genes revealed TA families widespread in bacterial genomes, some of which deviate from the classical characteristics previously described for such modules. Introduction of these genes into E. coli validated that the toxin toxicity is mitigated by the antitoxin. Infection experiments with T7 phage showed that two of the new modules can provide resistance against phage. Moreover, our experiments revealed an "antidefense" protein in phage T7 that neutralizes phage resistance. Our results expose active fronts in the arms race between bacteria and phage.
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Affiliation(s)
- Hila Sberro
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
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Goren MG, Yosef I, Auster O, Qimron U. Experimental definition of a clustered regularly interspaced short palindromic duplicon in Escherichia coli. J Mol Biol 2012; 423:14-6. [PMID: 22771574 DOI: 10.1016/j.jmb.2012.06.037] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 06/25/2012] [Accepted: 06/26/2012] [Indexed: 10/28/2022]
Abstract
We analyzed sequences of newly inserted repeats in an Escherichia coli CRISPR (clustered regularly interspaced short palindromic repeats) array in vivo and showed that a base previously thought to belong to the repeat is actually derived from a protospacer. Based on further experimental results, we propose to use the term "duplicon" for a repeated sequence in a CRISPR array that serves as a template for a new duplicon. Our findings suggest the possibility of redrawing the borders between repeats, spacers, and protospacer adjacent motifs.
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Affiliation(s)
- Moran G Goren
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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34
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Yosef I, Goren MG, Qimron U. Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli. Nucleic Acids Res 2012; 40:5569-76. [PMID: 22402487 PMCID: PMC3384332 DOI: 10.1093/nar/gks216] [Citation(s) in RCA: 475] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2011] [Revised: 02/17/2012] [Accepted: 02/18/2012] [Indexed: 02/03/2023] Open
Abstract
The clustered regularly interspaced short palindromic repeats and their associated proteins (CRISPR/Cas) constitute a recently identified prokaryotic defense mechanism against invading nucleic acids. Activity of the CRISPR/Cas system comprises of three steps: (i) insertion of alien DNA sequences into the CRISPR array to prevent future attacks, in a process called 'adaptation', (ii) expression of the relevant proteins, as well as expression and processing of the array, followed by (iii) RNA-mediated interference with the alien nucleic acid. Here we describe a robust assay in Escherichia coli to explore the hitherto least-studied process, adaptation. We identify essential genes and DNA elements in the leader sequence and in the array which are essential for the adaptation step. We also provide mechanistic insights on the insertion of the repeat-spacer unit by showing that the first repeat serves as the template for the newly inserted repeat. Taken together, our results elucidate fundamental steps in the adaptation process of the CRISPR/Cas system.
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Affiliation(s)
| | | | - Udi Qimron
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
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35
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Abstract
Bacteria, like mammals, have to constantly defend themselves from viral attack. Like mammals, they use both innate and adaptive defense mechanisms. In this point of view we highlight the commonalities between defense systems of bacteria and mammals. Our focus is on the recently discovered bacterial adaptive immune system, the clustered regularly interspaced short palindromic repeats (CRISPR) and their associated proteins (Cas). We suggest that fundamental aspects of CRISPR/Cas immunity may be viewed in light of the vast accumulated knowledge on the mammalian immune system, and propose that further insights will be revealed by thorough comparison between the systems.
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Affiliation(s)
- Moran Goren
- Tel Aviv University, Clinical Microbiology and Immunology, Sackler School of Medicine, Ramat Aviv, Tel Aviv 69978, Israel
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36
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Marintcheva B, Qimron U, Yu Y, Tabor S, Richardson CC. Mutations in the gene 5 DNA polymerase of bacteriophage T7 suppress the dominant lethal phenotype of gene 2.5 ssDNA binding protein lacking the C-terminal phenylalanine. Mol Microbiol 2009. [DOI: 10.1111/j.1365-2958.2009.06778.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Marintcheva B, Qimron U, Yu Y, Tabor S, Richardson CC, Richardson C. Mutations in the gene 5 DNA polymerase of bacteriophage T7 suppress the dominant lethal phenotype of gene 2.5 ssDNA binding protein lacking the C-terminal phenylalanine. Mol Microbiol 2009; 72:869-80. [PMID: 19400798 DOI: 10.1111/j.1365-2958.2009.06682.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Gene 2.5 of bacteriophage T7 encodes a ssDNA binding protein (gp2.5) essential for DNA replication. The C-terminal phenylalanine of gp2.5 is critical for function and mutations in that position are dominant lethal. In order to identify gp2.5 interactions we designed a screen for suppressors of gp2.5 lacking the C-terminal phenylalanine. Screening for suppressors of dominant lethal mutations of essential genes is challenging as the phenotype prevents propagation. We select for phage encoding a dominant lethal version of gene 2.5, whose viability is recovered via second-site suppressor mutation(s). Functional gp2.5 is expressed in trans for propagation of the unviable phage and allows suppression to occur via natural selection. The isolated intragenic suppressors support the critical role of the C-terminal phenylalanine. Extragenic suppressor mutations occur in several genes encoding enzymes of DNA metabolism. We have focused on the suppressor mutations in gene 5 encoding the T7 DNA polymerase (gp5) as the gp5/gp2.5 interaction is well documented. The suppressor mutations in gene 5 are necessary and sufficient to suppress the lethal phenotype of gp2.5 lacking the C-terminal phenylalanine. The affected residues map in proximity to aromatic residues and to residues in contact with DNA in the crystal structure of T7 DNA polymerase-thioredoxin.
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Affiliation(s)
- Boriana Marintcheva
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
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38
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Tran NQ, Tabor S, Rezende LF, Qimron U, Richardson CC. Gene 1.7 of Bacteriophage T7 Confers Sensitivity of Phage Growth to Dideoxythymidine. FASEB J 2008. [DOI: 10.1096/fasebj.22.1_supplement.651.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ngoc Quang Tran
- Department of Biological Chemistry and Molecular PharmacologyHarvard Medical SchoolBostonMA
| | - Stanley Tabor
- Department of Biological Chemistry and Molecular PharmacologyHarvard Medical SchoolBostonMA
| | - Lisa F. Rezende
- Department of Biological Chemistry and Molecular PharmacologyHarvard Medical SchoolBostonMA
| | - Udi Qimron
- Department of Biological Chemistry and Molecular PharmacologyHarvard Medical SchoolBostonMA
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39
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Qimron U, Kulczyk AW, Hamdan SM, Tabor S, Richardson CC. Inadequate inhibition of host RNA polymerase restricts T7 bacteriophage growth on hosts overexpressing udk. Mol Microbiol 2007; 67:448-57. [PMID: 18067538 DOI: 10.1111/j.1365-2958.2007.06058.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Overexpression of udk, an Escherichia coli gene encoding a uridine/cytidine kinase, interferes with T7 bacteriophage growth. We show here that inhibition of T7 phage growth by udk overexpression can be overcome by inhibition of host RNA polymerase. Overexpression of gene 2, whose product inhibits host RNA polymerase, restores T7 phage growth on hosts overexpressing udk. In addition, rifampicin, an inhibitor of host RNA polymerase, restores the burst size of T7 phage on udk-overexpressing hosts to normal. In agreement with these findings, suppressor mutants that overcome the inhibition arising from udk overexpression gain the ability to grow on hosts that are resistant to inhibition of RNA polymerase by gene 2 protein, and suppressor mutants that overcome a lack of gene 2 protein gain the ability to grow on hosts that overexpress udk. Mutations that eliminate or weaken strong promoters for host RNA polymerase in T7 DNA, and mutations in T7 gene 3.5 that affect its interaction with T7 RNA polymerase, also reduce the interference with T7 growth by host RNA polymerase. We propose a general model for the requirement of host RNA polymerase inhibition.
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Affiliation(s)
- Udi Qimron
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
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Hamdan SM, Johnson DE, Tanner NA, Lee JB, Qimron U, Tabor S, van Oijen AM, Richardson CC. Dynamic DNA helicase-DNA polymerase interactions assure processive replication fork movement. Mol Cell 2007; 27:539-49. [PMID: 17707227 DOI: 10.1016/j.molcel.2007.06.020] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2007] [Revised: 05/11/2007] [Accepted: 06/19/2007] [Indexed: 11/20/2022]
Abstract
A single copy of bacteriophage T7 DNA polymerase and DNA helicase advance the replication fork with a processivity greater than 17,000 nucleotides. Nonetheless, the polymerase transiently dissociates from the DNA without leaving the replisome. Ensemble and single-molecule techniques demonstrate that this dynamic processivity is made possible by two modes of DNA polymerase-helicase interaction. During DNA synthesis the polymerase and the helicase interact at a high-affinity site. In this polymerizing mode, the polymerase dissociates from the DNA approximately every 5000 bases. The polymerase, however, remains bound to the helicase via an electrostatic binding mode that involves the acidic C-terminal tail of the helicase and a basic region in the polymerase to which the processivity factor also binds. The polymerase transfers via the electrostatic interaction around the hexameric helicase in search of the primer-template.
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Affiliation(s)
- Samir M Hamdan
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
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41
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Qimron U, Marintcheva B, Tabor S, Richardson CC. Genomewide screens for Escherichia coli genes affecting growth of T7 bacteriophage. Proc Natl Acad Sci U S A 2006; 103:19039-44. [PMID: 17135349 PMCID: PMC1748173 DOI: 10.1073/pnas.0609428103] [Citation(s) in RCA: 146] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2006] [Indexed: 11/18/2022] Open
Abstract
Use of bacteriophages as a therapy for bacterial infection has been attempted over the last century. Such an endeavor requires the elucidation of basic aspects of the host-virus interactions and the resistance mechanisms of the host. Two recently developed bacterial collections now enable a genomewide search of the genetic interactions between Escherichia coli and bacteriophages. We have screened >85% of the E. coli genes for their ability to inhibit growth of T7 phage and >90% of the host genes for their ability to be used by the virus. In addition to identifying all of the known interactions, several other interactions have been identified. E. coli CMP kinase is essential for T7 growth, whereas overexpression of the E. coli uridine/cytidine kinase inhibits T7 growth. Mutations in any one of nine genes that encode enzymes for the synthesis of the E. coli lipopolysaccharide receptor for T7 adsorption leads to T7 resistance. Selection of T7 phage that can recognize these altered receptors has enabled the construction of phage to which the host is 100-fold less resistant.
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Affiliation(s)
- Udi Qimron
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Boriana Marintcheva
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Stanley Tabor
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Charles C. Richardson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
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Crampton DJ, Ohi M, Qimron U, Walz T, Richardson CC. Oligomeric states of bacteriophage T7 gene 4 primase/helicase. J Mol Biol 2006; 360:667-77. [PMID: 16777142 DOI: 10.1016/j.jmb.2006.05.037] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2006] [Revised: 05/08/2006] [Accepted: 05/15/2006] [Indexed: 11/27/2022]
Abstract
Electron microscopic and crystallographic data have shown that the gene 4 primase/helicase encoded by bacteriophage T7 can form both hexamers and heptamers. After cross-linking with glutaraldehyde to stabilize the oligomeric protein, hexamers and heptamers can be distinguished either by negative stain electron microscopy or electrophoretic analysis using polyacrylamide gels. We find that hexamers predominate in the presence of either dTTP or beta,gamma-methylene dTTP whereas the ratio between hexamers and heptamers is nearly the converse in the presence of dTDP. When formed, heptamers are unable to efficiently bind either single-stranded DNA or double-stranded DNA. We postulate that a switch between heptamer to hexamer may provide a ring-opening mechanism for the single-stranded DNA binding pathway. Accordingly, we observe that in the presence of both nucleoside di- and triphosphates the gene 4 protein exists as a hexamer when bound to single-stranded DNA and as a mixture of heptamer and hexamer when not bound to single-stranded DNA. Furthermore, altering regions of the gene 4 protein postulated to be conformational switches for dTTP-dependent helicase activity leads to modulation of the heptamer to hexamer ratio.
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Affiliation(s)
- Donald J Crampton
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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43
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Abstract
T7 DNA primase is composed of a catalytic RNA polymerase domain (RPD) and a zinc-binding domain (ZBD) connected by an unstructured linker. The two domains are required to initiate the synthesis of the diribonucleotide pppAC and its extension into a functional primer pppACCC (de novo synthesis), as well as for the extension of exogenous AC diribonucleotides into an ACCC primer (extension synthesis). To explore the mechanism underlying the RPD and ZBD interactions, we have changed the length of the linker between them. Wild-type T7 DNA primase is 10-fold superior in de novo synthesis compared to T7 DNA primase having a shorter linker. However, the primase having the shorter linker exhibits a two-fold enhancement in its extension synthesis. T7 DNA primase does not catalyze extension synthesis by a ZBD of one subunit acting on a RPD of an adjacent subunit (trans mode), whereas de novo synthesis is feasible in this mode. We propose a mechanism for primer initiation and extension based on these findings.
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Affiliation(s)
- Udi Qimron
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Seung-Joo Lee
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Samir M Hamdan
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Charles C Richardson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Ave. Building C2, Room 219, Boston, MA 02115, USA. Tel.: +1 617 432 1864; Fax: +1 617 432 3362; E-mail:
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Gazit R, Gruda R, Elboim M, Arnon TI, Katz G, Achdout H, Hanna J, Qimron U, Landau G, Greenbaum E, Zakay-Rones Z, Porgador A, Mandelboim O. Lethal influenza infection in the absence of the natural killer cell receptor gene Ncr1. Nat Immunol 2006; 7:517-23. [PMID: 16565719 DOI: 10.1038/ni1322] [Citation(s) in RCA: 453] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2006] [Accepted: 02/16/2006] [Indexed: 12/20/2022]
Abstract
The elimination of viruses and tumors by natural killer cells is mediated by specific natural killer cell receptors. To study the in vivo function of a principal activating natural killer cell receptor, NCR1 (NKp46 in humans), we replaced the gene encoding this receptor (Ncr1) with a green fluorescent protein reporter cassette. There was enhanced spread of certain tumors in 129/Sv but not C57BL/6 Ncr1(gfp/gfp) mice, and influenza virus infection was lethal in both 129/Sv and C57BL/6 Ncr1(gfp/gfp) mice. We noted accumulation of natural killer cells at the site of influenza infection by tracking the green fluorescent protein. Our results demonstrate a critical function for Ncr1 in the in vivo eradication of influenza virus.
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Affiliation(s)
- Roi Gazit
- The Lautenberg Center for General and Tumor Immunology, The Hebrew University Hadassah Medical School, Jerusalem 91120, Israel
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Qimron U, Lee S, Hamdan SM, Richardson CC. Role of the linker between the zinc binding domain and the polymerization domain of the bacteriophage T7 DNA primase. FASEB J 2006. [DOI: 10.1096/fasebj.20.5.a910-c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Udi Qimron
- Biological Chemistry and Molecular PharmacologyHarvard Medical School240 Longwood Ave.BostonMA02115
| | - Seung‐Joo Lee
- Biological Chemistry and Molecular PharmacologyHarvard Medical School240 Longwood Ave.BostonMA02115
| | - Samir M Hamdan
- Biological Chemistry and Molecular PharmacologyHarvard Medical School240 Longwood Ave.BostonMA02115
| | - Charles C Richardson
- Biological Chemistry and Molecular PharmacologyHarvard Medical School240 Longwood Ave.BostonMA02115
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Hummel S, Apte RN, Qimron U, Vitacolonna M, Porgador A, Zöller M. Tumor Vaccination by Salmonella typhimurium After Transformation with a Eukaryotic Expression Vector in Mice. J Immunother 2005; 28:467-79. [PMID: 16113603 DOI: 10.1097/01.cji.0000170359.92090.8b] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Transformed attenuated Salmonella typhimurium (ST) have been suggested as an efficient means of tumor vaccination. However, ST themselves might be immunosuppressive, and the question has arisen as to whether this impedes vaccination efficacy even if ST are transformed with a eukaryotic expression vector such that "tumor antigen" will be transcribed by the host. The question was evaluated using a mutant SL7207, where the yej operon, which interferes with MHC I-mediated presentation, had been inactivated (SL7207DeltayejE). Mice were vaccinated with SL7207 or SL7207DeltayejE transformed with a eukaryotic expression vector carrying the lacZ or the gp100 gene and later received lacZ-transfected RENCA or YC8 or gp100-expressing B16F1 tumor cells. In vaccinated mice, tumor growth started with a delay and some animals remained tumor-free; however, the tumor growth rate remained unaltered. No significant difference was seen between SL7207DeltayejE versus SL7207 vaccinated mice. The latter finding contrasted with ex vivo analyses where vaccination with SL7207DeltayejE, compared with SL7207, induced a significantly stronger response, including nonadaptive defense mechanisms. The failure to detect a superior vaccination efficacy of SL7207DeltayejE in vivo could be attributed to a stronger effect of the yej operon on MHC-mediated antigen presentation when driven by a prokaryotic promoter. Also, additional Salmonella genes apparently interfere with maintenance of a sustained immune response. Thus, the immunosuppressive yej operon affects innate and adaptive immunity. However, when ST are carriers for eukaryotic-expressed tumor antigens, yej does not severely hamper induction of an immune response.
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Affiliation(s)
- Susanne Hummel
- Department of Tumor Progression and Tumor Defense, German Cancer Research Center, Heidelberg, Germany.
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Yosef I, Bloushtain N, Shapira M, Qimron U. Restoration of gene function by homologous recombination: from PCR to gene expression in one step. Appl Environ Microbiol 2005; 70:7156-60. [PMID: 15574912 PMCID: PMC535207 DOI: 10.1128/aem.70.12.7156-7160.2004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have developed a simple method for single-step cloning of any PCR product into a plasmid. A novel selection principle has been applied, in which activation of a drug selection marker is achieved following homologous recombination. In this method a DNA fragment is amplified by PCR with standard oligonucleotides that contain flanking tails derived from the host plasmid and the complete lambdaPR or rrnA1 promoter regions. The resulting PCR product is then electroporated into an Escherichia coli strain harboring both the phage lambda Red functions and the host plasmid. Upon homologous recombination of the PCR fragment into the plasmid, expression of a drug selection marker is fully induced due to restoration of its truncated promoter, thus allowing appropriate selection. Recombinant plasmid vectors encoding beta-galactosidase and neomycin phosphotransferase were constructed by using this method in two well-known Red systems. This cloning strategy significantly reduces both the time and costs associated with cloning procedures.
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Affiliation(s)
- Ido Yosef
- Department of Microbiology and Immunology, Faculty of Health Sciences, Ben Gurion University of the Negev, Beer-Sheva, Israel
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Qimron U, Madar N, Mittrücker HW, Zilka A, Yosef I, Bloushtain N, Kaufmann SHE, Rosenshine I, Apte RN, Porgador A. Identification of Salmonella typhimurium genes responsible for interference with peptide presentation on MHC class I molecules: Deltayej Salmonella mutants induce superior CD8+ T-cell responses. Cell Microbiol 2004; 6:1057-70. [PMID: 15469434 DOI: 10.1111/j.1462-5822.2004.00418.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Salmonella-derived epitopes are presented on MHC molecules by antigen-presenting cells, and both CD4+ and CD8+ T cells participate in protective immunity to Salmonella. Therefore, mechanisms that allow Salmonella to escape specific immune recognition are likely to have evolved in this bacterial pathogen. To identify Salmonella genes, which potentially interfere with the MHC class I (MHC-I) presentation pathway, Tn10d transposon mutagenesis was performed. More than 3000 mutants, statistically covering half of the Salmonella genome, were individually screened for altered peptide presentation by infected macrophages. Two mutants undergoing enhanced antigen presentation by macrophages were identified, carrying a Tn10d insertion in the yej operon. This phenotype was validated by specific inactivation and complementation experiments. In accordance with their enhanced MHC-I presentation phenotype, we showed that (i) specific CD8+ T cells were elicited at a higher level in mice, in response to immunization with yej mutants compared to their parental strain in two different experimental settings; and (ii) yej mutants were superior vaccine carriers for heterologous antigens compared to the parental strain in a tumour model.
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Affiliation(s)
- Udi Qimron
- Department of Microbiology and Immunology, Faculty of Health Sciences and the Cancer Research Center, Ben Gurion University of the Negev, 84105 Beer Sheva, Israel
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Bloushtain N, Qimron U, Bar-Ilan A, Hershkovitz O, Gazit R, Fima E, Korc M, Vlodavsky I, Bovin NV, Porgador A. Membrane-associated heparan sulfate proteoglycans are involved in the recognition of cellular targets by NKp30 and NKp46. J Immunol 2004; 173:2392-401. [PMID: 15294952 DOI: 10.4049/jimmunol.173.4.2392] [Citation(s) in RCA: 113] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Lysis of virus-infected and tumor cells by NK cells is mediated via natural cytotoxicity receptors (NCRs). We have recently shown that the NKp44 and NKp46 NCRs, but not the NKp30, recognize viral hemagglutinins. In this study we explored the nature of the cellular ligands recognized by the NKp30 and NKp46 NCRs. We demonstrate that target cell surface heparan sulfate proteoglycans (HSPGs) are recognized by NKp30 and NKp46 and that 6-O-sulfation and N-acetylation state of the glucose building unit affect this recognition and lysis by NK cells. Tumor cells expressing cell surface heparanase, CHO cells lacking membranal heparan sulfate and glypican-1-suppressed pancreatic cancer cells manifest reduced recognition by NKp30 and NKp46 and are lysed to a lesser extent by NK cells. Our results are the first clue for the identity of the ligands for NKp30 and NKp46. Whether the ligands are particular HSPGs, unusual heparan sulfate epitopes, or a complex of HSPGs and either other protein or lipid moieties remains to be further explored.
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Affiliation(s)
- Noga Bloushtain
- Department of Microbiology and Immunology, Faculty of Health Sciences, and the Cancer Research Center, Ben Gurion University of the Negev, Beer Sheva, Israel
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Qimron U, Paul L, Bar-Haim E, Bloushtain N, Eisenbach L, Staats HF, Porgador A. Non-replicating mucosal and systemic vaccines: quantitative and qualitative differences in the Ag-specific CD8(+) T cell population in different tissues. Vaccine 2004; 22:1390-4. [PMID: 15063561 DOI: 10.1016/j.vaccine.2003.11.043] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2003] [Revised: 10/06/2003] [Accepted: 11/04/2003] [Indexed: 11/28/2022]
Abstract
Directed dissemination of Ag-specific CD8(+) T cells to infected organs or cancerous tissues is a prerequisite for optimal immunotherapy. Ag-specific CD8(+) T cells were quantitated in systemic and mucosal tissues after nasal, rectal, or cutaneous immunization with CTL epitope peptide and the adjuvant cholera toxin (CT). Mucosal and cutaneous immunization induced Ag-specific CD8(+) lymphocytes that were detectable in both mucosal and systemic compartments, suggesting a less strict distribution pattern than that known for B cells. However, optimal localization, activation and phenotype of these cells correlated with the route of immunization. In accordance with this observation, protection against a mucosal challenge with a virus expressing the CTL epitope was superior in mucosally-immunized animals.
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Affiliation(s)
- Udi Qimron
- Department of Microbiology and Immunology, Faculty of Health Sciences and the Cancer Research Center, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
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