1
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Asgharzadeh Kangachar S, Logel DY, Trofimova E, Zhu HX, Zaugg J, Schembri MA, Weynberg KD, Jaschke PR. Discovery and characterisation of new phage targeting uropathogenic Escherichia coli. Virology 2024; 597:110148. [PMID: 38941748 DOI: 10.1016/j.virol.2024.110148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 06/02/2024] [Accepted: 06/18/2024] [Indexed: 06/30/2024]
Abstract
Antimicrobial resistance is an escalating threat with few new therapeutic options in the pipeline. Urinary tract infections (UTIs) are one of the most prevalent bacterial infections globally and are prone to becoming recurrent and antibiotic resistant. We discovered and characterized six novel Autographiviridae and Guernseyvirinae bacterial viruses (phage) against uropathogenic Escherichia coli (UPEC), a leading cause of UTIs. The phage genomes were between 39,471 bp - 45,233 bp, with 45.0%-51.0% GC%, and 57-84 predicted coding sequences per genome. We show that tail fiber domain structure, predicted host capsule type, and host antiphage repertoire correlate with phage host range. In vitro characterisation of phage cocktails showed synergistic improvement against a mixed UPEC strain population and when sequentially dosed. Together, these phage are a new set extending available treatments for UTI from UPEC, and phage vM_EcoM_SHAK9454 represents a promising candidate for further improvement through engineering.
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Affiliation(s)
- Shahla Asgharzadeh Kangachar
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Dominic Y Logel
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia; ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Ellina Trofimova
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia; ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Hannah X Zhu
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia; ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Julian Zaugg
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Mark A Schembri
- Institute for Molecular Bioscience (IMB), University of Queensland, Brisbane, Queensland, Australia; School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Karen D Weynberg
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Paul R Jaschke
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia; ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia.
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2
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van den Berg DF, Costa AR, Esser JQ, Stanciu I, Geissler JQ, Zoumaro-Djayoon AD, Haas PJ, Brouns SJJ. Bacterial homologs of innate eukaryotic antiviral defenses with anti-phage activity highlight shared evolutionary roots of viral defenses. Cell Host Microbe 2024:S1931-3128(24)00266-X. [PMID: 39094584 DOI: 10.1016/j.chom.2024.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 05/21/2024] [Accepted: 07/09/2024] [Indexed: 08/04/2024]
Abstract
Prokaryotes have evolved a multitude of defense systems to protect against phage predation. Some of these resemble eukaryotic genes involved in antiviral responses. Here, we set out to systematically project the current knowledge of eukaryotic-like antiviral defense systems onto prokaryotic genomes, using Pseudomonas aeruginosa as a model organism. Searching for phage defense systems related to innate antiviral genes from vertebrates and plants, we uncovered over 450 candidates. We validated six of these phage defense systems, including factors preventing viral attachment, R-loop-acting enzymes, the inflammasome, ubiquitin pathway, and pathogen recognition signaling. Collectively, these defense systems support the concept of deep evolutionary links and shared antiviral mechanisms between prokaryotes and eukaryotes.
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Affiliation(s)
- Daan F van den Berg
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, the Netherlands; Kavli Institute of Nanoscience, Delft, the Netherlands
| | - Ana Rita Costa
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, the Netherlands; Kavli Institute of Nanoscience, Delft, the Netherlands
| | - Jelger Q Esser
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, the Netherlands; Kavli Institute of Nanoscience, Delft, the Netherlands
| | - Ilinka Stanciu
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, the Netherlands; Kavli Institute of Nanoscience, Delft, the Netherlands
| | - Jasper Q Geissler
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, the Netherlands; Kavli Institute of Nanoscience, Delft, the Netherlands
| | | | - Pieter-Jan Haas
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, the Netherlands
| | - Stan J J Brouns
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, the Netherlands; Kavli Institute of Nanoscience, Delft, the Netherlands.
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3
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Maestri A, Pons BJ, Pursey E, Chong CE, Gandon S, Custodio R, Olina A, Agapov A, Chisnall MAW, Grasso A, Paterson S, Szczelkun MD, Baker KS, van Houte S, Chevallereau A, Westra ER. The bacterial defense system MADS interacts with CRISPR-Cas to limit phage infection and escape. Cell Host Microbe 2024:S1931-3128(24)00264-6. [PMID: 39094583 DOI: 10.1016/j.chom.2024.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 04/23/2024] [Accepted: 07/08/2024] [Indexed: 08/04/2024]
Abstract
The constant arms race between bacteria and their parasites has resulted in a large diversity of bacterial defenses, with many bacteria carrying multiple systems. Here, we report the discovery of a phylogenetically widespread defense system, coined methylation-associated defense system (MADS), which is distributed across gram-positive and gram-negative bacteria. MADS interacts with a CRISPR-Cas system in its native host to provide robust and durable resistance against phages. While phages can acquire epigenetic-mediated resistance against MADS, co-existence of MADS and a CRISPR-Cas system limits escape emergence. MADS comprises eight genes with predicted nuclease, ATPase, kinase, and methyltransferase domains, most of which are essential for either self/non-self discrimination, DNA restriction, or both. The complex genetic architecture of MADS and MADS-like systems, relative to other prokaryotic defenses, points toward highly elaborate mechanisms of sensing infections, defense activation, and/or interference.
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Affiliation(s)
- Alice Maestri
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn TR10 9FE, UK
| | - Benoit J Pons
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn TR10 9FE, UK
| | - Elizabeth Pursey
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn TR10 9FE, UK
| | - Charlotte E Chong
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7ZB, UK; Department of Genetics, University of Cambridge, Downing Place, Cambridge CB2 3EH, UK
| | - Sylvain Gandon
- CEFE, CNRS, Université de Montpellier, EPHE, IRD, Montpellier 34293, France
| | - Rafael Custodio
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn TR10 9FE, UK
| | - Anna Olina
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn TR10 9FE, UK
| | - Aleksei Agapov
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn TR10 9FE, UK
| | - Matthew A W Chisnall
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn TR10 9FE, UK
| | - Anita Grasso
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn TR10 9FE, UK
| | - Steve Paterson
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Mark D Szczelkun
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Kate S Baker
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7ZB, UK; Department of Genetics, University of Cambridge, Downing Place, Cambridge CB2 3EH, UK
| | - Stineke van Houte
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn TR10 9FE, UK
| | - Anne Chevallereau
- Université Paris Cité, CNRS, INSERM, Institut Cochin, Paris 75014, France.
| | - Edze R Westra
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn TR10 9FE, UK.
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4
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Tian X, Li S, Wang C, Zhang Y, Feng X, Yan Q, Guo R, Wu F, Wu C, Wang Y, Huo X, Ma X. Gut virome-wide association analysis identifies cross-population viral signatures for inflammatory bowel disease. MICROBIOME 2024; 12:130. [PMID: 39026313 PMCID: PMC11256409 DOI: 10.1186/s40168-024-01832-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 05/08/2024] [Indexed: 07/20/2024]
Abstract
BACKGROUND The gut virome has been implicated in inflammatory bowel disease (IBD), yet a full understanding of the gut virome in IBD patients, especially across diverse geographic populations, is lacking. RESULTS In this study, we conducted a comprehensive gut virome-wide association study in a Chinese cohort of 71 IBD patients (15 with Crohn's disease and 56 with ulcerative colitis) and 77 healthy controls via viral-like particle (VLP) and bulk virome sequencing of their feces. By utilizing an integrated gut virus catalog tailored to the IBD virome, we revealed fundamental alterations in the gut virome in IBD patients. These characterized 139 differentially abundant viral signatures, including elevated phages predicted to infect Escherichia, Klebsiella, Enterococcus_B, Streptococcus, and Veillonella species, as well as IBD-depleted phages targeting Prevotella, Ruminococcus_E, Bifidobacterium, and Blautia species. Remarkably, these viral signatures demonstrated high consistency across diverse populations such as those in Europe and the USA, emphasizing their significance and broad relevance in the disease context. Furthermore, fecal virome transplantation experiments verified that the colonization of these IBD-characterized viruses can modulate experimental colitis in mouse models. CONCLUSIONS Building upon these insights into the IBD gut virome, we identified potential biomarkers for prognosis and therapy in IBD patients, laying the foundation for further exploration of viromes in related conditions. Video Abstract.
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Affiliation(s)
- Xiangge Tian
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Shenghui Li
- Puensum Genetech Institute, Wuhan, 430076, China
| | - Chao Wang
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Yanyan Zhang
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China
| | - Xiaoying Feng
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China
| | - Qiulong Yan
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China.
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China.
| | - Ruochun Guo
- Puensum Genetech Institute, Wuhan, 430076, China
| | - Fan Wu
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China
| | - Chunxue Wu
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China
| | - Yan Wang
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China
| | - Xiaokui Huo
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China.
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China.
| | - Xiaochi Ma
- Second Affiliated Hospital, Dalian Medical University, Dalian, 116023, China.
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, China.
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5
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Bullen NP, Johnson CN, Andersen SE, Arya G, Marotta SR, Lee YJ, Weigele PR, Whitney JC, Duerkop BA. An enterococcal phage protein broadly inhibits type IV restriction enzymes involved in antiphage defense. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.16.567456. [PMID: 38014348 PMCID: PMC10680825 DOI: 10.1101/2023.11.16.567456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
The prevalence of multidrug resistant (MDR) bacterial infections continues to rise as the development of antibiotics needed to combat these infections remains stagnant. MDR enterococci are a major contributor to this crisis. A potential therapeutic approach for combating MDR enterococci is bacteriophage (phage) therapy, which uses lytic viruses to infect and kill pathogenic bacteria. While phages that lyse some strains of MDR enterococci have been identified, other strains display high levels of resistance and the mechanisms underlying this resistance are poorly defined. Here, we use a CRISPR interference (CRISPRi) screen to identify a genetic locus found on a mobilizable plasmid from Enterococcus faecalis involved in phage resistance. This locus encodes a putative serine recombinase followed by a Type IV restriction enzyme (TIV-RE) that we show restricts the replication of phage phi47 in E. faecalis. We further find that phi47 evolves to overcome restriction by acquiring a missense mutation in a TIV-RE inhibitor protein. We show that this inhibitor, termed type IV restriction inhibiting factor A (tifA), binds and inactivates diverse TIV-REs. Overall, our findings advance our understanding of phage defense in drug-resistant E. faecalis and provide mechanistic insight into how phages evolve to overcome antiphage defense systems.
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Affiliation(s)
- Nathan P. Bullen
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada, L8S 4L8
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Cydney N. Johnson
- Department of Immunology and Microbiology, University of Colorado School – Anschutz Medical Campus, School of Medicine, Aurora, CO, USA, 80045
| | - Shelby E. Andersen
- Department of Immunology and Microbiology, University of Colorado School – Anschutz Medical Campus, School of Medicine, Aurora, CO, USA, 80045
| | - Garima Arya
- Department of Immunology and Microbiology, University of Colorado School – Anschutz Medical Campus, School of Medicine, Aurora, CO, USA, 80045
| | - Sonia R. Marotta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada, L8S 4L8
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Yan-Jiun Lee
- Research Department, New England Biolabs, Ipswich, MA, USA, 01938
| | - Peter R. Weigele
- Research Department, New England Biolabs, Ipswich, MA, USA, 01938
| | - John C. Whitney
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada, L8S 4L8
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Breck A. Duerkop
- Department of Immunology and Microbiology, University of Colorado School – Anschutz Medical Campus, School of Medicine, Aurora, CO, USA, 80045
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6
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Richmond-Buccola D, Hobbs SJ, Garcia JM, Toyoda H, Gao J, Shao S, Lee ASY, Kranzusch PJ. A large-scale type I CBASS antiphage screen identifies the phage prohead protease as a key determinant of immune activation and evasion. Cell Host Microbe 2024; 32:1074-1088.e5. [PMID: 38917809 PMCID: PMC11239291 DOI: 10.1016/j.chom.2024.05.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 02/27/2024] [Accepted: 05/30/2024] [Indexed: 06/27/2024]
Abstract
Cyclic oligonucleotide-based signaling system (CBASS) is an antiviral system that protects bacteria from phage infection and is evolutionarily related to human cGAS-STING immunity. cGAS-STING signaling is initiated by the recognition of viral DNA, but the molecular cues activating CBASS are incompletely understood. Using a screen of 975 type I CBASS operon-phage challenges, we show that operons with distinct cGAS/DncV-like nucleotidyltransferases (CD-NTases) and CD-NTase-associated protein (Cap) effectors exhibit marked patterns of phage restriction. We find that some type I CD-NTase enzymes require a C-terminal AGS-C immunoglobulin (Ig)-like fold domain for defense against select phages. Escaper phages evade CBASS via protein-coding mutations in virion assembly proteins, and acquired resistance is largely operon specific. We demonstrate that the phage Bas13 prohead protease interacts with the CD-NTase EcCdnD12 and can induce CBASS-dependent growth arrest in cells. Our results define phage virion assembly as a determinant of type I CBASS immune evasion and support viral protein recognition as a putative mechanism of cGAS-like enzyme activation.
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Affiliation(s)
- Desmond Richmond-Buccola
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Samuel J Hobbs
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Jasmine M Garcia
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Hunter Toyoda
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Jingjing Gao
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Sichen Shao
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Amy S Y Lee
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Philip J Kranzusch
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Parker Institute for Cancer Immunotherapy at Dana, Farber Cancer Institute, Boston, MA 02115, USA.
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7
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González-Delgado A, Lopez SC, Rojas-Montero M, Fishman CB, Shipman SL. Simultaneous multi-site editing of individual genomes using retron arrays. Nat Chem Biol 2024:10.1038/s41589-024-01665-7. [PMID: 38982310 DOI: 10.1038/s41589-024-01665-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 06/06/2024] [Indexed: 07/11/2024]
Abstract
During recent years, the use of libraries-scale genomic manipulations scaffolded on CRISPR guide RNAs have been transformative. However, these existing approaches are typically multiplexed across genomes. Unfortunately, building cells with multiple, nonadjacent precise mutations remains a laborious cycle of editing, isolating an edited cell and editing again. The use of bacterial retrons can overcome this limitation. Retrons are genetic systems composed of a reverse transcriptase and a noncoding RNA that contains an multicopy single-stranded DNA, which is reverse transcribed to produce multiple copies of single-stranded DNA. Here we describe a technology-termed a multitron-for precisely modifying multiple sites on a single genome simultaneously using retron arrays, in which multiple donor-encoding DNAs are produced from a single transcript. The multitron architecture is compatible with both recombineering in prokaryotic cells and CRISPR editing in eukaryotic cells. We demonstrate applications for this approach in molecular recording, genetic element minimization and metabolic engineering.
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Affiliation(s)
| | - Santiago C Lopez
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Graduate Program in Bioengineering, University of California, San Francisco and Berkeley, San Francisco, CA, USA
| | | | - Chloe B Fishman
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | - Seth L Shipman
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA.
- Chan Zuckerberg Biohub-San Francisco, San Francisco, CA, USA.
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8
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Liu T, Gao X, Chen R, Tang K, Liu Z, Wang P, Wang X. A nuclease domain fused to the Snf2 helicase confers antiphage defence in coral-associated Halomonas meridiana. Microb Biotechnol 2024; 17:e14524. [PMID: 38980956 PMCID: PMC11232893 DOI: 10.1111/1751-7915.14524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 06/26/2024] [Indexed: 07/11/2024] Open
Abstract
The coral reef microbiome plays a vital role in the health and resilience of reefs. Previous studies have examined phage therapy for coral pathogens and for modifying the coral reef microbiome, but defence systems against coral-associated bacteria have received limited attention. Phage defence systems play a crucial role in helping bacteria fight phage infections. In this study, we characterized a new defence system, Hma (HmaA-HmaB-HmaC), in the coral-associated Halomonas meridiana derived from the scleractinian coral Galaxea fascicularis. The Swi2/Snf2 helicase HmaA with a C-terminal nuclease domain exhibits antiviral activity against Escherichia phage T4. Mutation analysis revealed the nickase activity of the nuclease domain (belonging to PDD/EXK superfamily) of HmaA is essential in phage defence. Additionally, HmaA homologues are present in ~1000 bacterial and archaeal genomes. The high frequency of HmaA helicase in Halomonas strains indicates the widespread presence of these phage defence systems, while the insertion of defence genes in the hma region confirms the existence of a defence gene insertion hotspot. These findings offer insights into the diversity of phage defence systems in coral-associated bacteria and these diverse defence systems can be further applied into designing probiotics with high-phage resistance.
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Affiliation(s)
- Tianlang Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xinyu Gao
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ran Chen
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Kaihao Tang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Ziyao Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Pengxia Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Xiaoxue Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
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9
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Ledvina HE, Whiteley AT. Conservation and similarity of bacterial and eukaryotic innate immunity. Nat Rev Microbiol 2024; 22:420-434. [PMID: 38418927 DOI: 10.1038/s41579-024-01017-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2024] [Indexed: 03/02/2024]
Abstract
Pathogens are ubiquitous and a constant threat to their hosts, which has led to the evolution of sophisticated immune systems in bacteria, archaea and eukaryotes. Bacterial immune systems encode an astoundingly large array of antiviral (antiphage) systems, and recent investigations have identified unexpected similarities between the immune systems of bacteria and animals. In this Review, we discuss advances in our understanding of the bacterial innate immune system and highlight the components, strategies and pathogen restriction mechanisms conserved between bacteria and eukaryotes. We summarize evidence for the hypothesis that components of the human immune system originated in bacteria, where they first evolved to defend against phages. Further, we discuss shared mechanisms that pathogens use to overcome host immune pathways and unexpected similarities between bacterial immune systems and interbacterial antagonism. Understanding the shared evolutionary path of immune components across domains of life and the successful strategies that organisms have arrived at to restrict their pathogens will enable future development of therapeutics that activate the human immune system for the precise treatment of disease.
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Affiliation(s)
- Hannah E Ledvina
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Aaron T Whiteley
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA.
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10
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Shi Y, Masic V, Mosaiab T, Rajaratman P, Hartley-Tassell L, Sorbello M, Goulart CC, Vasquez E, Mishra BP, Holt S, Gu W, Kobe B, Ve T. Structural characterization of macro domain-containing Thoeris antiphage defense systems. SCIENCE ADVANCES 2024; 10:eadn3310. [PMID: 38924412 PMCID: PMC11204291 DOI: 10.1126/sciadv.adn3310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 05/20/2024] [Indexed: 06/28/2024]
Abstract
Thoeris defense systems protect bacteria from infection by phages via abortive infection. In these systems, ThsB proteins serve as sensors of infection and generate signaling nucleotides that activate ThsA effectors. Silent information regulator and SMF/DprA-LOG (SIR2-SLOG) containing ThsA effectors are activated by cyclic ADP-ribose (ADPR) isomers 2'cADPR and 3'cADPR, triggering abortive infection via nicotinamide adenine dinucleotide (NAD+) depletion. Here, we characterize Thoeris systems with transmembrane and macro domain (TM-macro)-containing ThsA effectors. We demonstrate that ThsA macro domains bind ADPR and imidazole adenine dinucleotide (IAD), but not 2'cADPR or 3'cADPR. Combining crystallography, in silico predictions, and site-directed mutagenesis, we show that ThsA macro domains form nucleotide-induced higher-order oligomers, enabling TM domain clustering. We demonstrate that ThsB can produce both ADPR and IAD, and we identify a ThsA TM-macro-specific ThsB subfamily with an active site resembling deoxy-nucleotide and deoxy-nucleoside processing enzymes. Collectively, our study demonstrates that Thoeris systems with SIR2-SLOG and TM-macro ThsA effectors trigger abortive infection via distinct mechanisms.
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Affiliation(s)
- Yun Shi
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Veronika Masic
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Tamim Mosaiab
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Premraj Rajaratman
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | | | - Mitchell Sorbello
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Cassia C. Goulart
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Eduardo Vasquez
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Biswa P. Mishra
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Stephanie Holt
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Weixi Gu
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD 4072, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Thomas Ve
- Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
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11
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Carabias A, Camara-Wilpert S, Mestre MR, Lopéz-Méndez B, Hendriks IA, Zhao R, Pape T, Fuglsang A, Luk SHC, Nielsen ML, Pinilla-Redondo R, Montoya G. Retron-Eco1 assembles NAD +-hydrolyzing filaments that provide immunity against bacteriophages. Mol Cell 2024; 84:2185-2202.e12. [PMID: 38788717 DOI: 10.1016/j.molcel.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 03/15/2024] [Accepted: 05/01/2024] [Indexed: 05/26/2024]
Abstract
Retrons are toxin-antitoxin systems protecting bacteria against bacteriophages via abortive infection. The Retron-Eco1 antitoxin is formed by a reverse transcriptase (RT) and a non-coding RNA (ncRNA)/multi-copy single-stranded DNA (msDNA) hybrid that neutralizes an uncharacterized toxic effector. Yet, the molecular mechanisms underlying phage defense remain unknown. Here, we show that the N-glycosidase effector, which belongs to the STIR superfamily, hydrolyzes NAD+ during infection. Cryoelectron microscopy (cryo-EM) analysis shows that the msDNA stabilizes a filament that cages the effector in a low-activity state in which ADPr, a NAD+ hydrolysis product, is covalently linked to the catalytic E106 residue. Mutations shortening the msDNA induce filament disassembly and the effector's toxicity, underscoring the msDNA role in immunity. Furthermore, we discovered a phage-encoded Retron-Eco1 inhibitor (U56) that binds ADPr, highlighting the intricate interplay between retron systems and phage evolution. Our work outlines the structural basis of Retron-Eco1 defense, uncovering ADPr's pivotal role in immunity.
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Affiliation(s)
- Arturo Carabias
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.
| | - Sarah Camara-Wilpert
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Mario Rodríguez Mestre
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Blanca Lopéz-Méndez
- Protein Purification and Characterization Facility, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Ivo A Hendriks
- Proteomics Department, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Ruiliang Zhao
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Tillmann Pape
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark; Core Facility for Integrated Microscopy (CFIM), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Anders Fuglsang
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Sean Hoi-Ching Luk
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Michael L Nielsen
- Proteomics Department, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Rafael Pinilla-Redondo
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark.
| | - Guillermo Montoya
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.
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12
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Saunier M, Fortier LC, Soutourina O. RNA-based regulation in bacteria-phage interactions. Anaerobe 2024; 87:102851. [PMID: 38583547 DOI: 10.1016/j.anaerobe.2024.102851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 03/24/2024] [Accepted: 04/02/2024] [Indexed: 04/09/2024]
Abstract
Interactions of bacteria with their viruses named bacteriophages or phages shape the bacterial genome evolution and contribute to the diversity of phages. RNAs have emerged as key components of several anti-phage defense systems in bacteria including CRISPR-Cas, toxin-antitoxin and abortive infection. Frequent association with mobile genetic elements and interplay between different anti-phage defense systems are largely discussed. Newly discovered defense systems such as retrons and CBASS include RNA components. RNAs also perform their well-recognized regulatory roles in crossroad of phage-bacteria regulatory networks. Both regulatory and defensive function can be sometimes attributed to the same RNA molecules including CRISPR RNAs. This review presents the recent advances on the role of RNAs in the bacteria-phage interactions with a particular focus on clostridial species including an important human pathogen, Clostridioides difficile.
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Affiliation(s)
- Marion Saunier
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France; Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Louis-Charles Fortier
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Olga Soutourina
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France; Institut Universitaire de France (IUF), Paris, France.
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13
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Shore SFH, Leinberger FH, Fozo EM, Berghoff BA. Type I toxin-antitoxin systems in bacteria: from regulation to biological functions. EcoSal Plus 2024:eesp00252022. [PMID: 38767346 DOI: 10.1128/ecosalplus.esp-0025-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 04/11/2024] [Indexed: 05/22/2024]
Abstract
Toxin-antitoxin systems are ubiquitous in the prokaryotic world and widely distributed among chromosomes and mobile genetic elements. Several different toxin-antitoxin system types exist, but what they all have in common is that toxin activity is prevented by the cognate antitoxin. In type I toxin-antitoxin systems, toxin production is controlled by an RNA antitoxin and by structural features inherent to the toxin messenger RNA. Most type I toxins are small membrane proteins that display a variety of cellular effects. While originally discovered as modules that stabilize plasmids, chromosomal type I toxin-antitoxin systems may also stabilize prophages, or serve important functions upon certain stress conditions and contribute to population-wide survival strategies. Here, we will describe the intricate RNA-based regulation of type I toxin-antitoxin systems and discuss their potential biological functions.
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Affiliation(s)
- Selene F H Shore
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Florian H Leinberger
- Institute for Microbiology and Molecular Biology, Justus-Liebig University, Giessen, Germany
| | - Elizabeth M Fozo
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Bork A Berghoff
- Institute for Microbiology and Molecular Biology, Justus-Liebig University, Giessen, Germany
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14
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Sandsdalen GD, Kumar A, Hjerde E. Exploring the Frozen Armory: Antiphage Defense Systems in Cold-Adapted Bacteria with a Focus on CRISPR-Cas Systems. Microorganisms 2024; 12:1028. [PMID: 38792857 PMCID: PMC11124354 DOI: 10.3390/microorganisms12051028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/15/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
Our understanding of the antiphage defense system arsenal in bacteria is rapidly expanding, but little is known about its occurrence in cold-adapted bacteria. In this study, we aim to shed light on the prevalence and distribution of antiphage defense systems in cold-adapted bacteria, with a focus on CRISPR-Cas systems. Using bioinformatics tools, Prokaryotic Antiviral Defense LOCator (PADLOC) and CRISPRCasTyper, we mapped the presence and diversity of antiphage defense systems in 938 available genomes of cold-adapted bacteria from diverse habitats. We confirmed that CRISPR-Cas systems are less frequent in cold-adapted bacteria, compared to mesophilic and thermophilic species. In contrast, several antiphage defense systems, such as dXTPases and DRTs, appear to be more frequently compared to temperate bacteria. Additionally, our study provides Cas endonuclease candidates with a potential for further development into cold-active CRISPR-Cas genome editing tools. These candidates could have broad applications in research on cold-adapted organisms. Our study provides a first-time map of antiphage defense systems in cold-adapted bacteria and a detailed overview of CRISPR-Cas diversity.
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Affiliation(s)
| | | | - Erik Hjerde
- Department of Chemistry, UiT the Arctic University of Norway, 9019 Tromsø, Norway; (G.D.S.); (A.K.)
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15
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Ren K, Zhou F, Zhang F, Yin M, Zhu Y, Wang S, Chen Y, Huang T, Wu Z, He J, Zhang A, Guo C, Huang Z. Discovery and structural mechanism of DNA endonucleases guided by RAGATH-18-derived RNAs. Cell Res 2024; 34:370-385. [PMID: 38575718 PMCID: PMC11061315 DOI: 10.1038/s41422-024-00952-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 03/09/2024] [Indexed: 04/06/2024] Open
Abstract
CRISPR-Cas systems and IS200/IS605 transposon-associated TnpBs have been utilized for the development of genome editing technologies. Using bioinformatics analysis and biochemical experiments, here we present a new family of RNA-guided DNA endonucleases. Our bioinformatics analysis initially identifies the stable co-occurrence of conserved RAGATH-18-derived RNAs (reRNAs) and their upstream IS607 TnpBs with an average length of 390 amino acids. IS607 TnpBs form programmable DNases through interaction with reRNAs. We discover the robust dsDNA interference activity of IS607 TnpB systems in bacteria and human cells. Further characterization of the Firmicutes bacteria IS607 TnpB system (ISFba1 TnpB) reveals that its dsDNA cleavage activity is remarkably sensitive to single mismatches between the guide and target sequences in human cells. Our findings demonstrate that a length of 20 nt in the guide sequence of reRNA achieves the highest DNA cleavage activity for ISFba1 TnpB. A cryo-EM structure of the ISFba1 TnpB effector protein bound by its cognate RAGATH-18 motif-containing reRNA and a dsDNA target reveals the mechanisms underlying reRNA recognition by ISFba1 TnpB, reRNA-guided dsDNA targeting, and the sensitivity of the ISFba1 TnpB system to base mismatches between the guide and target DNA. Collectively, this study identifies the IS607 TnpB family of compact and specific RNA-guided DNases with great potential for application in gene editing.
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Affiliation(s)
- Kuan Ren
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Fengxia Zhou
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China
- Westlake Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Fan Zhang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China.
| | - Mingyu Yin
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Yuwei Zhu
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Shouyu Wang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Yan Chen
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Tengjin Huang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Zixuan Wu
- Westlake Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Jiale He
- Westlake Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Anqi Zhang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Changyou Guo
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Zhiwei Huang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China.
- Westlake Center for Genome Editing, Westlake Laboratory of Life Sciences and Biomedicine, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
- New Cornerstone Science Laboratory, Shenzhen, Guangdong, China.
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16
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Olszak T, Augustyniak D, García-Romero I, Markwitz P, Gula G, Molinaro A, Valvano MA, Drulis-Kawa Z. Phage treatment of Pseudomonas aeruginosa yields a phage-resistant population with different susceptibility to innate immune responses and mild effects on metabolic profiles. Microbiol Res 2024; 282:127609. [PMID: 38428337 DOI: 10.1016/j.micres.2024.127609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/07/2024] [Accepted: 01/09/2024] [Indexed: 03/03/2024]
Abstract
In this study, we have investigated innate immune activation capacity and metabolic features of a population of P. aeruginosa PAO1 phage-resistant mutants with diverse genetic modification (large genomic deletions and point mutations) arising after exposure to phages targetting lipopolysaccharide (LPS) or Type-4 pili (T4P). Deletions led to the loss of genes involved in LPS synthesis, cell envelope permeability, efflux systems, biofilm production, oxidative stress tolerance, and DNA repair. Loss of LPS O antigen resulted in bacterial sensitivity to serum complement and stimulation of inflammatory cascades but did not cause increased phagocytosis, while T4P phage-resistant mutants were more effectively phagocytized than LPS-defective mutants. Changes in the utilization of different carbon, nitrogen, sulphur, and phosphorus sources were identified, especially in mutants where the two phage DNA persisted in the bacterial population (pseudolysogeny). However, the metabolic changes did not directly correlate with single-gene mutations or the large gene deletions, suggesting they reflect adaptive changes to the gene modifications that arise during the selection of resistant mutants. In contrast, phage-resistant mutants were susceptible to humoral innate immune responses, suggesting that phage resistance may be a beneficial outcome of phage therapy.
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Affiliation(s)
- Tomasz Olszak
- Department of Pathogen Biology and Immunology, Faculty of Biological Sciences, University of Wroclaw, Poland
| | - Daria Augustyniak
- Department of Pathogen Biology and Immunology, Faculty of Biological Sciences, University of Wroclaw, Poland
| | - Inmaculada García-Romero
- Wellcome Wolfson Institute for Experimental Medicine, Queen's University Belfast, United Kingdom
| | - Pawel Markwitz
- Department of Pathogen Biology and Immunology, Faculty of Biological Sciences, University of Wroclaw, Poland
| | - Grzegorz Gula
- Department of Pathogen Biology and Immunology, Faculty of Biological Sciences, University of Wroclaw, Poland
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario Monte Sant'Angelo, Naples, Italy
| | - Miguel A Valvano
- Wellcome Wolfson Institute for Experimental Medicine, Queen's University Belfast, United Kingdom
| | - Zuzanna Drulis-Kawa
- Department of Pathogen Biology and Immunology, Faculty of Biological Sciences, University of Wroclaw, Poland.
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17
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Martínez M, Rizzuto I, Molina R. Knowing Our Enemy in the Antimicrobial Resistance Era: Dissecting the Molecular Basis of Bacterial Defense Systems. Int J Mol Sci 2024; 25:4929. [PMID: 38732145 PMCID: PMC11084316 DOI: 10.3390/ijms25094929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024] Open
Abstract
Bacteria and their phage adversaries are engaged in an ongoing arms race, resulting in the development of a broad antiphage arsenal and corresponding viral countermeasures. In recent years, the identification and utilization of CRISPR-Cas systems have driven a renewed interest in discovering and characterizing antiphage mechanisms, revealing a richer diversity than initially anticipated. Currently, these defense systems can be categorized based on the bacteria's strategy associated with the infection cycle stage. Thus, bacterial defense systems can degrade the invading genetic material, trigger an abortive infection, or inhibit genome replication. Understanding the molecular mechanisms of processes related to bacterial immunity has significant implications for phage-based therapies and the development of new biotechnological tools. This review aims to comprehensively cover these processes, with a focus on the most recent discoveries.
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Affiliation(s)
| | | | - Rafael Molina
- Department of Crystallography and Structural Biology, Instituto de Química-Física Blas Cabrera, Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain
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18
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Kaur N, Pati PK. Retron Library Recombineering: Next Powerful Tool for Genome Editing after CRISPR/Cas. ACS Synth Biol 2024; 13:1019-1025. [PMID: 38480006 DOI: 10.1021/acssynbio.3c00667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
Retron library recombineering (RLR) is a powerful tool in the field of genome editing that exceeds the scope and specificity of the CRISPR/Cas technique. In RLR, single-stranded DNA produced in vivo by harnessing the in-built potential of bacterial retrons is used for replication-dependent genome editing. RLR introduces several genomic variations at once, resulting in pooled and barcoded variant libraries, thus permitting multiplexed applications. Retron-generated RT-DNA has already shown promise for use in genome editing. Thus, this new tool will result in fresh, intriguing, and surprising developments in molecular biology and its juncture with other disciplines of research, including medicine, agriculture, and microbiology. In this review, we discuss the current state of this brand-new tool that could eventually boost genome editing research.
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Affiliation(s)
- Navdeep Kaur
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
| | - Pratap Kumar Pati
- Department of Biotechnology, Guru Nanak Dev University, Amritsar 143005, Punjab, India
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19
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Wu Y, Garushyants SK, van den Hurk A, Aparicio-Maldonado C, Kushwaha SK, King CM, Ou Y, Todeschini TC, Clokie MRJ, Millard AD, Gençay YE, Koonin EV, Nobrega FL. Bacterial defense systems exhibit synergistic anti-phage activity. Cell Host Microbe 2024; 32:557-572.e6. [PMID: 38402614 PMCID: PMC11009048 DOI: 10.1016/j.chom.2024.01.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 01/23/2024] [Accepted: 01/30/2024] [Indexed: 02/27/2024]
Abstract
Bacterial defense against phage predation involves diverse defense systems acting individually and concurrently, yet their interactions remain poorly understood. We investigated >100 defense systems in 42,925 bacterial genomes and identified numerous instances of their non-random co-occurrence and negative association. For several pairs of defense systems significantly co-occurring in Escherichia coli strains, we demonstrate synergistic anti-phage activity. Notably, Zorya II synergizes with Druantia III and ietAS defense systems, while tmn exhibits synergy with co-occurring systems Gabija, Septu I, and PrrC. For Gabija, tmn co-opts the sensory switch ATPase domain, enhancing anti-phage activity. Some defense system pairs that are negatively associated in E. coli show synergy and significantly co-occur in other taxa, demonstrating that bacterial immune repertoires are largely shaped by selection for resistance against host-specific phages rather than negative epistasis. Collectively, these findings demonstrate compatibility and synergy between defense systems, allowing bacteria to adopt flexible strategies for phage defense.
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Affiliation(s)
- Yi Wu
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Sofya K Garushyants
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Anne van den Hurk
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | | | - Simran Krishnakant Kushwaha
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK; Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India
| | - Claire M King
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Yaqing Ou
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Thomas C Todeschini
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Martha R J Clokie
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Andrew D Millard
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | | | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Franklin L Nobrega
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK.
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20
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Cossart P, Hacker J, Holden DH, Normark S, Vogel J. Meeting report 'Microbiology 2023: from single cell to microbiome and host', an international interacademy conference in Würzburg. MICROLIFE 2024; 5:uqae008. [PMID: 38665235 PMCID: PMC11044969 DOI: 10.1093/femsml/uqae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024]
Abstract
On September 20-22 September 2023, the international conference 'Microbiology 2023: from single cell to microbiome and host' convened microbiologists from across the globe for a very successful symposium, showcasing cutting-edge research in the field. Invited lecturers delivered exceptional presentations covering a wide range of topics, with a major emphasis on phages and microbiomes, on the relevant bacteria within these ecosystems, and their multifaceted roles in diverse environments. Discussions also spanned the intricate analysis of fundamental bacterial processes, such as cell division, stress resistance, and interactions with phages. Organized by four renowned Academies, the German Leopoldina, the French Académie des sciences, the Royal Society UK, and the Royal Swedish Academy of Sciences, the symposium provided a dynamic platform for experts to share insights and discoveries, leaving participants inspired and eager to integrate new knowledge into their respective projects. The success of Microbiology 2023 prompted the decision to host the next quadrennial academic meeting in Sweden. This choice underscores the commitment to fostering international collaboration and advancing the frontiers of microbiological knowledge. The transition to Sweden promises to be an exciting step in the ongoing global dialogue and specific collaborations on microbiology, a field where researchers will continue to push the boundaries of knowledge, understanding, and innovation not only in health and disease but also in ecology.
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Affiliation(s)
| | - Jörg Hacker
- German National Academy of Science Leopoldina, Jägerberg 1, D-06108 Halle, Germany
| | - David H Holden
- Department of Infectious Disease, Centre for Bacterial Resistance Biology, Flowers Building, South Kensington Campus, Exhibition Road, Imperial College London, London SW7 2AZ, United Kingdom
| | - Staffan Normark
- Karolinska Institute, Tumor-och-cellbiologi, C1 Microbial Pathogenesis, 17177 Stockholm, Sweden
| | - Jörg Vogel
- Faculty of Medicine, Institute for Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Josef-Schneider-Str2/Gebaude D15; É. D-97080 Würzburg, Germany
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21
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Mayo-Muñoz D, Pinilla-Redondo R, Camara-Wilpert S, Birkholz N, Fineran PC. Inhibitors of bacterial immune systems: discovery, mechanisms and applications. Nat Rev Genet 2024; 25:237-254. [PMID: 38291236 DOI: 10.1038/s41576-023-00676-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2023] [Indexed: 02/01/2024]
Abstract
To contend with the diversity and ubiquity of bacteriophages and other mobile genetic elements, bacteria have developed an arsenal of immune defence mechanisms. Bacterial defences include CRISPR-Cas, restriction-modification and a growing list of mechanistically diverse systems, which constitute the bacterial 'immune system'. As a response, bacteriophages and mobile genetic elements have evolved direct and indirect mechanisms to circumvent or block bacterial defence pathways and ensure successful infection. Recent advances in methodological and computational approaches, as well as the increasing availability of genome sequences, have boosted the discovery of direct inhibitors of bacterial defence systems. In this Review, we discuss methods for the discovery of direct inhibitors, their diverse mechanisms of action and perspectives on their emerging applications in biotechnology and beyond.
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Affiliation(s)
- David Mayo-Muñoz
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin, New Zealand
| | - Rafael Pinilla-Redondo
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.
- Section of Microbiology, University of Copenhagen, Copenhagen, Denmark.
| | | | - Nils Birkholz
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Genetics Otago, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin, New Zealand
- Bioprotection Aotearoa, University of Otago, Dunedin, New Zealand
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.
- Genetics Otago, University of Otago, Dunedin, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin, New Zealand.
- Bioprotection Aotearoa, University of Otago, Dunedin, New Zealand.
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22
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Agapov A, Baker KS, Bedekar P, Bhatia RP, Blower TR, Brockhurst MA, Brown C, Chong CE, Fothergill JL, Graham S, Hall JP, Maestri A, McQuarrie S, Olina A, Pagliara S, Recker M, Richmond A, Shaw SJ, Szczelkun MD, Taylor TB, van Houte S, Went SC, Westra ER, White MF, Wright R. Multi-layered genome defences in bacteria. Curr Opin Microbiol 2024; 78:102436. [PMID: 38368839 DOI: 10.1016/j.mib.2024.102436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/20/2024]
Abstract
Bacteria have evolved a variety of defence mechanisms to protect against mobile genetic elements, including restriction-modification systems and CRISPR-Cas. In recent years, dozens of previously unknown defence systems (DSs) have been discovered. Notably, diverse DSs often coexist within the same genome, and some co-occur at frequencies significantly higher than would be expected by chance, implying potential synergistic interactions. Recent studies have provided evidence of defence mechanisms that enhance or complement one another. Here, we review the interactions between DSs at the mechanistic, regulatory, ecological and evolutionary levels.
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Affiliation(s)
- Aleksei Agapov
- ESI, Centre for Ecology and Conservation, University of Exeter, UK
| | - Kate S Baker
- Department of Genetics, University of Cambridge, CB2 3EH, UK
| | - Paritosh Bedekar
- ESI, Centre for Ecology and Conservation, University of Exeter, UK
| | - Rama P Bhatia
- ESI, Centre for Ecology and Conservation, University of Exeter, UK
| | - Tim R Blower
- Department of Biosciences, Durham University, Stockton Road, Durham DH1 3LE, UK
| | - Michael A Brockhurst
- Division of Evolution, Infection and Genomics, School of Biological Sciences, University of Manchester, Dover Street, Manchester M13 9PT, UK
| | - Cooper Brown
- School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | | | - Joanne L Fothergill
- Dept of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, UK
| | - Shirley Graham
- School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - James Pj Hall
- Dept of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, L69 7ZB, UK
| | - Alice Maestri
- ESI, Centre for Ecology and Conservation, University of Exeter, UK
| | - Stuart McQuarrie
- School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - Anna Olina
- ESI, Centre for Ecology and Conservation, University of Exeter, UK
| | | | - Mario Recker
- ESI, Centre for Ecology and Conservation, University of Exeter, UK
| | - Anna Richmond
- ESI, Centre for Ecology and Conservation, University of Exeter, UK
| | - Steven J Shaw
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS6 7YB, UK
| | - Mark D Szczelkun
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS6 7YB, UK
| | - Tiffany B Taylor
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | | | - Sam C Went
- Department of Biosciences, Durham University, Stockton Road, Durham DH1 3LE, UK
| | - Edze R Westra
- ESI, Centre for Ecology and Conservation, University of Exeter, UK.
| | - Malcolm F White
- School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - Rosanna Wright
- Division of Evolution, Infection and Genomics, School of Biological Sciences, University of Manchester, Dover Street, Manchester M13 9PT, UK
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23
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Martinez-Soto CE, McClelland M, Kropinski AM, Lin JT, Khursigara CM, Anany H. Multireceptor phage cocktail against Salmonella enterica to circumvent phage resistance. MICROLIFE 2024; 5:uqae003. [PMID: 38545601 PMCID: PMC10972627 DOI: 10.1093/femsml/uqae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/18/2024] [Accepted: 03/11/2024] [Indexed: 04/14/2024]
Abstract
Non-Typhoidal Salmonella (NTS) is one of the most common food-borne pathogens worldwide, with poultry products being the major vehicle for pathogenesis in humans. The use of bacteriophage (phage) cocktails has recently emerged as a novel approach to enhancing food safety. Here, a multireceptor Salmonella phage cocktail of five phages was developed and characterized. The cocktail targets four receptors: O-antigen, BtuB, OmpC, and rough Salmonella strains. Structural analysis indicated that all five phages belong to unique families or subfamilies. Genome analysis of four of the phages showed they were devoid of known virulence or antimicrobial resistance factors, indicating enhanced safety. The phage cocktail broad antimicrobial spectrum against Salmonella, significantly inhibiting the growth of all 66 strains from 20 serovars tested in vitro. The average bacteriophage insensitive mutant (BIM) frequency against the cocktail was 6.22 × 10-6 in S. Enteritidis, significantly lower than that of each of the individual phages. The phage cocktail reduced the load of Salmonella in inoculated chicken skin by 3.5 log10 CFU/cm2 after 48 h at 25°C and 15°C, and 2.5 log10 CFU/cm2 at 4°C. A genome-wide transduction assay was used to investigate the transduction efficiency of the selected phage in the cocktail. Only one of the four phages tested could transduce the kanamycin resistance cassette at a low frequency comparable to that of phage P22. Overall, the results support the potential of cocktails of phage that each target different host receptors to achieve complementary infection and reduce the emergence of phage resistance during biocontrol applications.
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Affiliation(s)
- Carlos E Martinez-Soto
- Guelph Research and Development Centre, Agriculture and Agri-Food
Canada, 93 Stone Rd W, N1G 5C9, Guelph, Ontario,
Canada
- Department of Molecular and Cellular Biology, College of Biological
Science, University of Guelph, 50 Stone Rd E, N1G 2W1,
Guelph, Ontario, Canada
| | - Michael McClelland
- Department of Microbiology and Molecular Genetics, School of Medicine,
University of California, Irvine, 811 Health Sciences Road,
CA 92614, United States
| | - Andrew M Kropinski
- Department of Pathobiology, Ontario Veterinary College, University of
Guelph, Guelph, 419 Gordon St, Guelph, ON N1G
2W1, Canada
| | - Janet T Lin
- Guelph Research and Development Centre, Agriculture and Agri-Food
Canada, 93 Stone Rd W, N1G 5C9, Guelph, Ontario,
Canada
| | - Cezar M Khursigara
- Department of Molecular and Cellular Biology, College of Biological
Science, University of Guelph, 50 Stone Rd E, N1G 2W1,
Guelph, Ontario, Canada
| | - Hany Anany
- Guelph Research and Development Centre, Agriculture and Agri-Food
Canada, 93 Stone Rd W, N1G 5C9, Guelph, Ontario,
Canada
- Department of Molecular and Cellular Biology, College of Biological
Science, University of Guelph, 50 Stone Rd E, N1G 2W1,
Guelph, Ontario, Canada
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24
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Ednacot EMQ, Morehouse BR. An OLD protein teaches us new tricks: prokaryotic antiviral defense. Nat Commun 2024; 15:2527. [PMID: 38514789 PMCID: PMC10957863 DOI: 10.1038/s41467-024-46925-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 03/14/2024] [Indexed: 03/23/2024] Open
Affiliation(s)
- Eirene Marie Q Ednacot
- Department of Molecular Biology and Biochemistry, School of Biological Sciences, University of California Irvine, Irvine, CA, 92697-3900, USA
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University of California Irvine, Irvine, CA, USA
| | - Benjamin R Morehouse
- Department of Molecular Biology and Biochemistry, School of Biological Sciences, University of California Irvine, Irvine, CA, 92697-3900, USA.
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University of California Irvine, Irvine, CA, USA.
- Center for Virus Research, University of California Irvine, Irvine, CA, USA.
- Institute for Immunology, University of California Irvine, Irvine, CA, USA.
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25
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Costa AR, van den Berg DF, Esser JQ, Muralidharan A, van den Bossche H, Bonilla BE, van der Steen BA, Haagsma AC, Fluit AC, Nobrega FL, Haas PJ, Brouns SJJ. Accumulation of defense systems in phage-resistant strains of Pseudomonas aeruginosa. SCIENCE ADVANCES 2024; 10:eadj0341. [PMID: 38394193 PMCID: PMC10889362 DOI: 10.1126/sciadv.adj0341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 01/22/2024] [Indexed: 02/25/2024]
Abstract
Prokaryotes encode multiple distinct anti-phage defense systems in their genomes. However, the impact of carrying a multitude of defense systems on phage resistance remains unclear, especially in a clinical context. Using a collection of antibiotic-resistant clinical strains of Pseudomonas aeruginosa and a broad panel of phages, we demonstrate that defense systems contribute substantially to defining phage host range and that overall phage resistance scales with the number of defense systems in the bacterial genome. We show that many individual defense systems target specific phage genera and that defense systems with complementary phage specificities co-occur in P. aeruginosa genomes likely to provide benefits in phage-diverse environments. Overall, we show that phage-resistant phenotypes of P. aeruginosa with at least 19 phage defense systems exist in the populations of clinical, antibiotic-resistant P. aeruginosa strains.
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Affiliation(s)
- Ana Rita Costa
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Daan F. van den Berg
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Jelger Q. Esser
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Aswin Muralidharan
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Halewijn van den Bossche
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Boris Estrada Bonilla
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Baltus A. van der Steen
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Anna C. Haagsma
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
| | - Ad C. Fluit
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, Netherlands
| | - Franklin L. Nobrega
- School of Biological Sciences, University of Southampton, SO17 1BJ Southampton, UK
| | - Pieter-Jan Haas
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, Netherlands
| | - Stan J. J. Brouns
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
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26
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Patel PH, Taylor VL, Zhang C, Getz LJ, Fitzpatrick AD, Davidson AR, Maxwell KL. Anti-phage defence through inhibition of virion assembly. Nat Commun 2024; 15:1644. [PMID: 38388474 PMCID: PMC10884400 DOI: 10.1038/s41467-024-45892-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/06/2024] [Indexed: 02/24/2024] Open
Abstract
Bacteria have evolved diverse antiviral defence mechanisms to protect themselves against phage infection. Phages integrated into bacterial chromosomes, known as prophages, also encode defences that protect the bacterial hosts in which they reside. Here, we identify a type of anti-phage defence that interferes with the virion assembly pathway of invading phages. The protein that mediates this defence, which we call Tab (for 'Tail assembly blocker'), is constitutively expressed from a Pseudomonas aeruginosa prophage. Tab allows the invading phage replication cycle to proceed, but blocks assembly of the phage tail, thus preventing formation of infectious virions. While the infected cell dies through the activity of the replicating phage lysis proteins, there is no release of infectious phage progeny, and the bacterial community is thereby protected from a phage epidemic. Prophages expressing Tab are not inhibited during their own lytic cycle because they express a counter-defence protein that interferes with Tab function. Thus, our work reveals an anti-phage defence that operates by blocking virion assembly, thereby both preventing formation of phage progeny and allowing destruction of the infected cell due to expression of phage lysis genes.
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Affiliation(s)
| | | | - Chi Zhang
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Landon J Getz
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | | | - Alan R Davidson
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Karen L Maxwell
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada.
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27
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Gerdes K. Diverse genetic contexts of HicA toxin domains propose a role in anti-phage defense. mBio 2024; 15:e0329323. [PMID: 38236063 PMCID: PMC10865869 DOI: 10.1128/mbio.03293-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024] Open
Abstract
Toxin-antitoxin (TA) modules are prevalent in prokaryotic genomes, often in substantial numbers. For instance, the Mycobacterium tuberculosis genome alone harbors close to 100 TA modules, half of which belong to a singular type. Traditionally ascribed multiple biological roles, recent insights challenge these notions and instead indicate a predominant function in phage defense. TAs are often located within Defense Islands, genomic regions that encode various defense systems. The analysis of genes within Defense Islands has unveiled a wide array of systems, including TAs that serve in anti-phage defense. Prokaryotic cells are equipped with anti-phage Viperins that, analogous to their mammalian counterparts, inhibit viral RNA transcription. Additionally, bacterial Structural Maintenance of Chromosome (SMC) proteins combat plasmid intrusion by recognizing foreign DNA signatures. This study undertakes a comprehensive bioinformatics analysis of genetic elements encoding the HicA double-stranded RNA-binding domain, complemented by protein structure modeling. The HicA toxin domains are found in at least 14 distinct contexts and thus exhibit a remarkable genetic diversity. Traditional bicistronic TA operons represent eight of these contexts, while four are characterized by monocistronic operons encoding fused HicA domains. Two contexts involve hicA adjacent to genes that encode bacterial Viperins. Notably, genes encoding RelE toxins are also adjacent to Viperin genes in some instances. This configuration hints at a synergistic enhancement of Viperin-mediated anti-phage action by HicA and RelE toxins. The discovery of a HicA domain merged with an SMC domain is compelling, prompting further investigation into its potential roles.IMPORTANCEProkaryotic organisms harbor a multitude of toxin-antitoxin (TA) systems, which have long puzzled scientists as "genes in search for a function." Recent scientific advancements have shed light on the primary role of TAs as anti-phage defense mechanisms. To gain an overview of TAs it is important to analyze their genetic contexts that can give hints on function and guide future experimental inquiries. This article describes a thorough bioinformatics examination of genes encoding the HicA toxin domain, revealing its presence in no fewer than 14 unique genetic arrangements. Some configurations notably align with anti-phage activities, underscoring potential roles in microbial immunity. These insights robustly reinforce the hypothesis that HicA toxins are integral components of the prokaryotic anti-phage defense repertoire. The elucidation of these genetic contexts not only advances our understanding of TAs but also contributes to a paradigm shift in how we perceive their functionality within the microbial world.
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Affiliation(s)
- Kenn Gerdes
- Kenn Gerdes is an independent researcher with the residence, Voldmestergade, Copenhagen, Denmark
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28
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Liu S, Liu H, Wang X, Shi L. The immune system of prokaryotes: potential applications and implications for gene editing. Biotechnol J 2024; 19:e2300352. [PMID: 38403433 DOI: 10.1002/biot.202300352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 11/30/2023] [Accepted: 12/28/2023] [Indexed: 02/27/2024]
Abstract
Gene therapy has revolutionized the treatment of genetic diseases. Spearheading this revolution are sophisticated genome editing methods such as TALENs, ZFNs, and CRISPR-Cas, which trace their origins back to prokaryotic immune systems. Prokaryotes have developed various antiviral defense systems to combat viral attacks and the invasion of genetic elements. The comprehension of these defense mechanisms has paved the way for the development of indispensable tools in molecular biology. Among them, restriction endonuclease originates from the innate immune system of bacteria. The CRISPR-Cas system, a widely applied genome editing technology, is derived from the prokaryotic adaptive immune system. Single-base editing is a precise editing tool based on CRISPR-Cas system that involves deamination of target base. It is worth noting that prokaryotes possess deamination enzymes as part of their defense arsenal over foreign genetic material. Furthermore, prokaryotic Argonauts (pAgo) proteins, also function in anti-phage defense, play an important role in complementing the CRISPR-Cas system by addressing certain limitations it may have. Recent studies have also shed light on the significance of Retron, a reverse transcription transposon previously showed potential in genome editing, has also come to light in the realm of prokaryotic immunity. These noteworthy findings highlight the importance of studying prokaryotic immune system for advancing genome editing techniques. Here, both the origin of prokaryotic immunity underlying aforementioned genome editing tools, and potential applications of deaminase, pAgo protein and reverse transcriptase in genome editing among prokaryotes were introduced, thus emphasizing the fundamental mechanism and significance of prokaryotic immunity.
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Affiliation(s)
- Siyang Liu
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Hongling Liu
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Xue Wang
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Lei Shi
- School of Life Sciences, Chongqing University, Chongqing, China
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29
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Khan AG, Rojas-Montero M, González-Delgado A, Lopez SC, Fang RF, Shipman SL. An experimental census of retrons for DNA production and genome editing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.25.577267. [PMID: 38328236 PMCID: PMC10849725 DOI: 10.1101/2024.01.25.577267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Retrons are bacterial immune systems that use reverse transcribed DNA as a detector of phage infection. They are also increasingly deployed as a component of biotechnology. For genome editing, for instance, retrons are modified so that the reverse transcribed DNA (RT-DNA) encodes an editing donor. Retrons are commonly found in bacterial genomes; thousands of unique retrons have now been predicted bioinformatically. However, only a small number have been characterized experimentally. Here, we add substantially to the corpus of experimentally studied retrons. We synthesized >100 previously untested retrons to identify the natural sequence of RT-DNA they produce, quantify their RT-DNA production, and test the relative efficacy of editing using retron-derived donors to edit bacterial genomes, phage genomes, and human genomes. We add 62 new empirically determined, natural RT-DNAs, which are not predictable from the retron sequence alone. We report a large diversity in RT-DNA production and editing rates across retrons, finding that top performing editors outperform those used in previous studies, and are drawn from a subset of the retron phylogeny.
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Affiliation(s)
- Asim G. Khan
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | | | | | - Santiago C. Lopez
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Graduate Program in Bioengineering, University of California, San Francisco and Berkeley, CA, USA
| | - Rebecca F. Fang
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Graduate Program in Neuroscience, University of California, San Francisco, CA, USA
| | - Seth L. Shipman
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub – San Francisco, San Francisco, CA
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30
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Burke KA, Urick CD, Mzhavia N, Nikolich MP, Filippov AA. Correlation of Pseudomonas aeruginosa Phage Resistance with the Numbers and Types of Antiphage Systems. Int J Mol Sci 2024; 25:1424. [PMID: 38338703 PMCID: PMC10855318 DOI: 10.3390/ijms25031424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Phage therapeutics offer a potentially powerful approach for combating multidrug-resistant bacterial infections. However, to be effective, phage therapy must overcome existing and developing phage resistance. While phage cocktails can reduce this risk by targeting multiple receptors in a single therapeutic, bacteria have mechanisms of resistance beyond receptor modification. A rapidly growing body of knowledge describes a broad and varied arsenal of antiphage systems encoded by bacteria to counter phage infection. We sought to understand the types and frequencies of antiphage systems present in a highly diverse panel of Pseudomonas aeruginosa clinical isolates utilized to characterize novel antibacterials. Using the web-server tool PADLOC (prokaryotic antiviral defense locator), putative antiphage systems were identified in these P. aeruginosa clinical isolates based on sequence homology to a validated and curated catalog of known defense systems. Coupling this host bacterium sequence analysis with host range data for 70 phages, we observed a correlation between existing phage resistance and the presence of higher numbers of antiphage systems in bacterial genomes. We were also able to identify antiphage systems that were more prevalent in highly phage-resistant P. aeruginosa strains, suggesting their importance in conferring resistance.
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Affiliation(s)
| | | | | | | | - Andrey A. Filippov
- Wound Infections Department, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; (K.A.B.); (C.D.U.); (N.M.); (M.P.N.)
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31
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Duan N, Hand E, Pheko M, Sharma S, Emiola A. Structure-guided discovery of anti-CRISPR and anti-phage defense proteins. Nat Commun 2024; 15:649. [PMID: 38245560 PMCID: PMC10799925 DOI: 10.1038/s41467-024-45068-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 01/12/2024] [Indexed: 01/22/2024] Open
Abstract
Bacteria use a variety of defense systems to protect themselves from phage infection. In turn, phages have evolved diverse counter-defense measures to overcome host defenses. Here, we use protein structural similarity and gene co-occurrence analyses to screen >66 million viral protein sequences and >330,000 metagenome-assembled genomes for the identification of anti-phage and counter-defense systems. We predict structures for ~300,000 proteins and perform large-scale, pairwise comparison to known anti-CRISPR (Acr) and anti-phage proteins to identify structural homologs that otherwise may not be uncovered using primary sequence search. This way, we identify a Bacteroidota phage Acr protein that inhibits Cas12a, and an Akkermansia muciniphila anti-phage defense protein, termed BxaP. Gene bxaP is found in loci encoding Bacteriophage Exclusion (BREX) and restriction-modification defense systems, but confers immunity independently. Our work highlights the advantage of combining protein structural features and gene co-localization information in studying host-phage interactions.
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Affiliation(s)
- Ning Duan
- Microbial Therapeutics Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Emily Hand
- Microbial Therapeutics Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Mannuku Pheko
- Microbial Therapeutics Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Shikha Sharma
- Microbial Therapeutics Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Akintunde Emiola
- Microbial Therapeutics Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA.
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32
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Liu J, Cui L, Shi X, Yan J, Wang Y, Ni Y, He J, Wang X. Generation of DNAzyme in Bacterial Cells by a Bacterial Retron System. ACS Synth Biol 2024; 13:300-309. [PMID: 38171507 DOI: 10.1021/acssynbio.3c00509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
DNAzymes are catalytically active single-stranded DNAs in which DNAzyme 10-23 (Dz 10-23) consists of a catalytic core and a substrate-binding arm that reduces gene expression through sequence-specific mRNA cleavage. However, the in vivo application of Dz 10-23 depends on exogenous delivery, which leads to its inability to be synthesized and stabilized in vivo, thus limiting its application. As a unique reverse transcription system, the bacterial retron system can synthesize single-stranded DNA in vivo using ncRNA msr/msd as a template. The objective of this work is to reduce target gene expression using Dz 10-23 generated in vivo by the retron system. In this regard, we successfully generated Dz 10-23 by cloning the Dz 10-23 coding sequence into the retron msd gene and tested its ability to reduce specific gene expression by examining the mRNA levels of cfp encoding cyan fluorescence protein and other functional genes such as mreB and ftsZ. We found that Dz had different repressive effects when targeting different mRNA regions, and in general, the repressive effect was stronger when targeting downstream of mRNAs. Our results also suggested that the reduction effect was due to cleavage of the substrate mRNA by Dz 10-23 rather than the antisense effect of the substrate-binding arm. Therefore, this study not only provided a retron-based method for the intracellular generation of Dz 10-23 but also demonstrated that Dz 10-23 could reduce gene expression by cleaving target mRNAs in cells. We believe that this new strategy would have great potential in the regulation of gene expression.
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Affiliation(s)
- Jie Liu
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Lina Cui
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Xinyu Shi
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Jiahao Yan
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yifei Wang
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yuyang Ni
- College of Life Sciences, Shangrao Normal University, Shangrao 334001, PR China
| | - Jin He
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Xun Wang
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
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33
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Tokuda M, Shintani M. Microbial evolution through horizontal gene transfer by mobile genetic elements. Microb Biotechnol 2024; 17:e14408. [PMID: 38226780 PMCID: PMC10832538 DOI: 10.1111/1751-7915.14408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 12/20/2023] [Accepted: 01/02/2024] [Indexed: 01/17/2024] Open
Abstract
Mobile genetic elements (MGEs) are crucial for horizontal gene transfer (HGT) in bacteria and facilitate their rapid evolution and adaptation. MGEs include plasmids, integrative and conjugative elements, transposons, insertion sequences and bacteriophages. Notably, the spread of antimicrobial resistance genes (ARGs), which poses a serious threat to public health, is primarily attributable to HGT through MGEs. This mini-review aims to provide an overview of the mechanisms by which MGEs mediate HGT in microbes. Specifically, the behaviour of conjugative plasmids in different environments and conditions was discussed, and recent methodologies for tracing the dynamics of MGEs were summarised. A comprehensive understanding of the mechanisms underlying HGT and the role of MGEs in bacterial evolution and adaptation is important to develop strategies to combat the spread of ARGs.
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Affiliation(s)
- Maho Tokuda
- Department of Environment and Energy Systems, Graduate School of Science and TechnologyShizuoka UniversityHamamatsuJapan
| | - Masaki Shintani
- Department of Environment and Energy Systems, Graduate School of Science and TechnologyShizuoka UniversityHamamatsuJapan
- Research Institute of Green Science and TechnologyShizuoka UniversityHamamatsuJapan
- Japan Collection of MicroorganismsRIKEN BioResource Research CenterIbarakiJapan
- Graduate School of Integrated Science and TechnologyShizuoka UniversityHamamatsuJapan
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34
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Yirmiya E, Leavitt A, Lu A, Ragucci AE, Avraham C, Osterman I, Garb J, Antine SP, Mooney SE, Hobbs SJ, Kranzusch PJ, Amitai G, Sorek R. Phages overcome bacterial immunity via diverse anti-defence proteins. Nature 2024; 625:352-359. [PMID: 37992756 DOI: 10.1038/s41586-023-06869-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 11/14/2023] [Indexed: 11/24/2023]
Abstract
It was recently shown that bacteria use, apart from CRISPR-Cas and restriction systems, a considerable diversity of phage resistance systems1-4, but it is largely unknown how phages cope with this multilayered bacterial immunity. Here we analysed groups of closely related Bacillus phages that showed differential sensitivity to bacterial defence systems, and discovered four distinct families of anti-defence proteins that inhibit the Gabija, Thoeris and Hachiman systems. We show that these proteins Gad1, Gad2, Tad2 and Had1 efficiently cancel the defensive activity when co-expressed with the respective defence system or introduced into phage genomes. Homologues of these anti-defence proteins are found in hundreds of phages that infect taxonomically diverse bacterial species. We show that the anti-Gabija protein Gad1 blocks the ability of the Gabija defence complex to cleave phage-derived DNA. Our data further reveal that the anti-Thoeris protein Tad2 is a 'sponge' that sequesters the immune signalling molecules produced by Thoeris TIR-domain proteins in response to phage infection. Our results demonstrate that phages encode an arsenal of anti-defence proteins that can disable a variety of bacterial defence mechanisms.
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Affiliation(s)
- Erez Yirmiya
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Azita Leavitt
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Allen Lu
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Adelyn E Ragucci
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Carmel Avraham
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ilya Osterman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Jeremy Garb
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Sadie P Antine
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sarah E Mooney
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Samuel J Hobbs
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Philip J Kranzusch
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
- Parker Institute for Cancer Immunotherapy at Dana-Farber Cancer Institute, Boston, MA, USA
| | - Gil Amitai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
| | - Rotem Sorek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
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35
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Oscorbin IP, Filipenko ML. A Novel Thermostable and Processive Reverse Transcriptase from a Group II Intron of Anoxybacillus flavithermus. Biomolecules 2023; 14:49. [PMID: 38254649 PMCID: PMC10813441 DOI: 10.3390/biom14010049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/22/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
Reverse transcriptases (RTs) are a family of enzymes that synthesize DNA using an RNA template and are involved in retrovirus propagation and telomere lengthening. In vitro, RTs are widely applied in various methods, including RNA-seq, RT-PCR, and RT-LAMP. Thermostable RTs from bacterial group II introns are promising tools for biotechnology due to their higher thermostability, fidelity, and processivity compared to commonly used M-MuLV RT and its mutants. However, the diversity of group II intron-encoded RTs is still understudied. In this work, we biochemically characterized a novel RT from a thermophilic bacterium, Anoxybacillus flavithermus, which was isolated from a hot spring in New Zealand and has an optimal growth temperature of around 60 °C. The cloned RT, named Afl RT, retained approximately 40% of the specific activity after a 45 min incubation at 50 °C. The optimal pH was 8.5, the optimal temperature was between 45 and 50 °C, and Mn2+ ions were found to be an optimal cofactor. The processivity analysis with MS2 phage gRNA (3569 b) demonstrated that Afl RT elongated fully up to 36% of the template molecules. In reverse transcription and RT-qLAMP, the enzyme allowed up to 10 copies of MS2 phage genomic RNA to be detected per reaction. Thus, Afl RT holds great potential for a variety of practical applications that require the use of thermostable and processive RTs.
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Affiliation(s)
- Igor P. Oscorbin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (ICBFM SB RAS), 8 Lavrentiev Avenue, 630090 Novosibirsk, Russia;
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Sasaki T, Takita S, Fujishiro T, Shintani Y, Nojiri S, Yasui R, Yonesaki T, Otsuka Y. Phage single-stranded DNA-binding protein or host DNA damage triggers the activation of the AbpAB phage defense system. mSphere 2023; 8:e0037223. [PMID: 37882551 PMCID: PMC10732053 DOI: 10.1128/msphere.00372-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 09/06/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE Although numerous phage defense systems have recently been discovered in bacteria, how these systems defend against phage propagation or sense phage infections remains unclear. The Escherichia coli AbpAB defense system targets several lytic and lysogenic phages harboring DNA genomes. A phage-encoded single-stranded DNA-binding protein, Gp32, activates this system similar to other phage defense systems such as Retron-Eco8, Hachiman, ShosTA, Nhi, and Hna. DNA replication inhibitors or defects in DNA repair factors activate the AbpAB system, even without phage infection. This is one of the few examples of activating phage defense systems without phage infection or proteins. The AbpAB defense system may be activated by sensing specific DNA-protein complexes.
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Affiliation(s)
- Takaomi Sasaki
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Saya Takita
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Takashi Fujishiro
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Yunosuke Shintani
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Satoki Nojiri
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Ryota Yasui
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan
| | - Tetsuro Yonesaki
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan
| | - Yuichi Otsuka
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
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37
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Amundsen SK, Smith GR. RecBCD enzyme: mechanistic insights from mutants of a complex helicase-nuclease. Microbiol Mol Biol Rev 2023; 87:e0004123. [PMID: 38047637 PMCID: PMC10732027 DOI: 10.1128/mmbr.00041-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023] Open
Abstract
SUMMARYRecBCD enzyme is a multi-functional protein that initiates the major pathway of homologous genetic recombination and DNA double-strand break repair in Escherichia coli. It is also required for high cell viability and aids proper DNA replication. This 330-kDa, three-subunit enzyme is one of the fastest, most processive helicases known and contains a potent nuclease controlled by Chi sites, hotspots of recombination, in DNA. RecBCD undergoes major changes in activity and conformation when, during DNA unwinding, it encounters Chi (5'-GCTGGTGG-3') and nicks DNA nearby. Here, we discuss the multitude of mutations in each subunit that affect one or another activity of RecBCD and its control by Chi. These mutants have given deep insights into how the multiple activities of this complex enzyme are coordinated and how it acts in living cells. Similar studies could help reveal how other complex enzymes are controlled by inter-subunit interactions and conformational changes.
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Affiliation(s)
| | - Gerald R. Smith
- Fred Hutchinson Cancer Center Seattle, Seattle, Washington, USA
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38
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Nicastro GG, Burroughs AM, Iyer L, Aravind L. Functionally comparable but evolutionarily distinct nucleotide-targeting effectors help identify conserved paradigms across diverse immune systems. Nucleic Acids Res 2023; 51:11479-11503. [PMID: 37889040 PMCID: PMC10681802 DOI: 10.1093/nar/gkad879] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/21/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023] Open
Abstract
While nucleic acid-targeting effectors are known to be central to biological conflicts and anti-selfish element immunity, recent findings have revealed immune effectors that target their building blocks and the cellular energy currency-free nucleotides. Through comparative genomics and sequence-structure analysis, we identified several distinct effector domains, which we named Calcineurin-CE, HD-CE, and PRTase-CE. These domains, along with specific versions of the ParB and MazG domains, are widely present in diverse prokaryotic immune systems and are predicted to degrade nucleotides by targeting phosphate or glycosidic linkages. Our findings unveil multiple potential immune systems associated with at least 17 different functional themes featuring these effectors. Some of these systems sense modified DNA/nucleotides from phages or operate downstream of novel enzymes generating signaling nucleotides. We also uncovered a class of systems utilizing HSP90- and HSP70-related modules as analogs of STAND and GTPase domains that are coupled to these nucleotide-targeting- or proteolysis-induced complex-forming effectors. While widespread in bacteria, only a limited subset of nucleotide-targeting effectors was integrated into eukaryotic immune systems, suggesting barriers to interoperability across subcellular contexts. This work establishes nucleotide-degrading effectors as an emerging immune paradigm and traces their origins back to homologous domains in housekeeping systems.
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Affiliation(s)
- Gianlucca G Nicastro
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, USA
| | - A Maxwell Burroughs
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, USA
| | - Lakshminarayan M Iyer
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, USA
| | - L Aravind
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, USA
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39
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Arkhipova IR, Yushenova IA. To Be Mobile or Not: The Variety of Reverse Transcriptases and Their Recruitment by Host Genomes. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1754-1762. [PMID: 38105196 DOI: 10.1134/s000629792311007x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 09/18/2023] [Accepted: 09/20/2023] [Indexed: 12/19/2023]
Abstract
Reverse transcriptases (RT), or RNA-dependent DNA polymerases, are unorthodox enzymes that originally added a new angle to the conventional view of the unidirectional flow of genetic information in the cell from DNA to RNA to protein. First discovered in vertebrate retroviruses, RTs were since re-discovered in most eukaryotes, bacteria, and archaea, spanning essentially all domains of life. For retroviruses, RTs provide the ability to copy the RNA genome into DNA for subsequent incorporation into the host genome, which is essential for their replication and survival. In cellular organisms, most RT sequences originate from retrotransposons, the type of self-replicating genetic elements that rely on reverse transcription to copy and paste their sequences into new genomic locations. Some retroelements, however, can undergo domestication, eventually becoming a valuable addition to the overall repertoire of cellular enzymes. They can be beneficial yet accessory, like the diversity-generating elements, or even essential, like the telomerase reverse transcriptases. Nowadays, ever-increasing numbers of domesticated RT-carrying genetic elements are being discovered. It may be argued that domesticated RTs and reverse transcription in general is more widespread in cellular organisms than previously thought, and that many important cellular functions, such as chromosome end maintenance, may evolve from an originally selfish process of converting RNA into DNA.
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Affiliation(s)
- Irina R Arkhipova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA.
| | - Irina A Yushenova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA 02543, USA.
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40
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Hardy A, Shomar H, Bernheim A. [Bacterial immunity: Uncovering a new world]. Med Sci (Paris) 2023; 39:862-868. [PMID: 38018930 DOI: 10.1051/medsci/2023163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023] Open
Abstract
Viruses are parasites that infect all living organisms, and bacteria are no exception. To defend themselves against their viruses (phages), bacteria have developed numerous and sophisticated defense mechanisms, our understanding of which is rapidly growing. In the 2000s, only a handful of mechanisms were known and only two of them seemed to be found in most bacteria. In 2018, a new key method based on genome analysis revealed that there were likely many others. Indeed, over the past five years, more than 150 new mechanisms have been discovered. It is now estimated that there are probably thousands. This remarkable diversity, paralleled with the tremendous viral diversity, is evident both in terms of possible combinations of systems in bacterial genomes and in molecular mechanisms. One of the most surprising observations emerging from the exploration of this diversity is the discovery of striking similarities between certain bacterial defense systems and antiviral systems in humans, as well as plant (and eukaryotes in general) immune systems. Contrary to the previously accepted paradigm, organisms as diverse as fungi, plants, bacteria and humans share certain molecular strategies to fight viral infections, suggesting that an underestimated part of eukaryotic antiviral immunity could have evolved from bacterial antiviral defense systems.
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Affiliation(s)
- Aël Hardy
- Institut Pasteur, université Paris Cité, Inserm U1284, Diversité moléculaire des microbes (Molecular Diversity of Microbes lab), 75015 Paris, France
| | - Helena Shomar
- Institut Pasteur, université Paris Cité, Inserm U1284, Diversité moléculaire des microbes (Molecular Diversity of Microbes lab), 75015 Paris, France
| | - Aude Bernheim
- Institut Pasteur, université Paris Cité, Inserm U1284, Diversité moléculaire des microbes (Molecular Diversity of Microbes lab), 75015 Paris, France
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41
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Song X, Lei S, Liu S, Liu Y, Fu P, Zeng Z, Yang K, Chen Y, Li M, She Q, Han W. Catalytically inactive long prokaryotic Argonaute systems employ distinct effectors to confer immunity via abortive infection. Nat Commun 2023; 14:6970. [PMID: 37914725 PMCID: PMC10620215 DOI: 10.1038/s41467-023-42793-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 10/20/2023] [Indexed: 11/03/2023] Open
Abstract
Argonaute proteins (Agos) bind short nucleic acids as guides and are directed by them to recognize target complementary nucleic acids. Diverse prokaryotic Agos (pAgos) play potential functions in microbial defense. The functions and mechanisms of a group of full-length yet catalytically inactive pAgos, long-B pAgos, remain unclear. Here, we show that most long-B pAgos are functionally connected with distinct associated proteins, including nucleases, Sir2-domain-containing proteins and trans-membrane proteins, respectively. The long-B pAgo-nuclease system (BPAN) is activated by guide RNA-directed target DNA recognition and performs collateral DNA degradation in vitro. In vivo, the system mediates genomic DNA degradation after sensing invading plasmid, which kills the infected cells and results in the depletion of the invader from the cell population. Together, the BPAN system provides immunoprotection via abortive infection. Our data also suggest that the defense strategy is employed by other long-B pAgos equipped with distinct associated proteins.
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Affiliation(s)
- Xinmi Song
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Sheng Lei
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Shunhang Liu
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Yanqiu Liu
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Pan Fu
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Zhifeng Zeng
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Ke Yang
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Yu Chen
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Ming Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Qunxin She
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, 266237, Jimo, Qingdao, China
| | - Wenyuan Han
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China.
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42
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Van Cauwenberghe J, Simms EL. How might bacteriophages shape biological invasions? mBio 2023; 14:e0188623. [PMID: 37812005 PMCID: PMC10653932 DOI: 10.1128/mbio.01886-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023] Open
Abstract
Invasions by eukaryotes dependent on environmentally acquired bacterial mutualists are often limited by the ability of bacterial partners to survive and establish free-living populations. Focusing on the model legume-rhizobium mutualism, we apply invasion biology hypotheses to explain how bacteriophages can impact the competitiveness of introduced bacterial mutualists. Predicting how phage-bacteria interactions affect invading eukaryotic hosts requires knowing the eco-evolutionary constraints of introduced and native microbial communities, as well as their differences in abundance and diversity. By synthesizing research from invasion biology, as well as bacterial, viral, and community ecology, we create a conceptual framework for understanding and predicting how phages can affect biological invasions through their effects on bacterial mutualists.
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Affiliation(s)
- Jannick Van Cauwenberghe
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
- Department of Integrative Biology, University of California, Berkeley, California, USA
| | - Ellen L. Simms
- Department of Integrative Biology, University of California, Berkeley, California, USA
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43
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Georjon H, Bernheim A. The highly diverse antiphage defence systems of bacteria. Nat Rev Microbiol 2023; 21:686-700. [PMID: 37460672 DOI: 10.1038/s41579-023-00934-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2023] [Indexed: 09/14/2023]
Abstract
Bacteria and their viruses have coevolved for billions of years. This ancient and still ongoing arms race has led bacteria to develop a vast antiphage arsenal. The development of high-throughput screening methods expanded our knowledge of defence systems from a handful to more than a hundred systems, unveiling many different molecular mechanisms. These findings reveal that bacterial immunity is much more complex than previously thought. In this Review, we explore recently discovered bacterial antiphage defence systems, with a particular focus on their molecular diversity, and discuss the ecological and evolutionary drivers and implications of the existing diversity of antiphage defence mechanisms.
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Affiliation(s)
- Héloïse Georjon
- Molecular Diversity of Microbes Lab, Institut Pasteur, Université Paris Cité, INSERM, Paris, France
| | - Aude Bernheim
- Molecular Diversity of Microbes Lab, Institut Pasteur, Université Paris Cité, INSERM, Paris, France.
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44
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López-Pérez J, Otero J, Sánchez-Osuna M, Erill I, Cortés P, Llagostera M. Impact of mutagenesis and lateral gene transfer processes in bacterial susceptibility to phage in food biocontrol and phage therapy. Front Cell Infect Microbiol 2023; 13:1266685. [PMID: 37842006 PMCID: PMC10569123 DOI: 10.3389/fcimb.2023.1266685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 09/12/2023] [Indexed: 10/17/2023] Open
Abstract
Introduction The emergence of resistance and interference mechanisms to phage infection can hinder the success of bacteriophage-based applications, but the significance of these mechanisms in phage therapy has not been determined. This work studies the emergence of Salmonella isolates with reduced susceptibility to a cocktail of three phages under three scenarios: i) Salmonella cultures (LAB), ii) biocontrol of cooked ham slices as a model of food safety (FOOD), and iii) oral phage therapy in broilers (PT). Methods S. Typhimurium ATCC 14028 RifR variants with reduced phage susceptibility were isolated from the three scenarios and conventional and molecular microbiology techniques were applied to study them. Results and discussion In LAB, 92% of Salmonella isolates lost susceptibility to all three phages 24 h after phage infection. This percentage was lower in FOOD, with 4.3% of isolates not susceptible to at least two of the three phages after seven days at 4°C following phage treatment. In PT, 9.7% and 3.3 % of isolates from untreated and treated broilers, respectively, displayed some mechanism of interference with the life cycle of some of the phages. In LAB and FOOD scenarios, resistant variants carrying mutations in rfc and rfaJ genes involved in lipopolysaccharide synthesis (phage receptor) were identified. However, in PT, the significant decrease of EOP, ECOI, and burst size observed in isolates was prompted by lateral gene transfer of large IncI1 plasmids, which may encode phage defense mechanisms. These data indicate that the acquisition of specific conjugative plasmids has a stronger impact than mutagenesis on the emergence of reduced phage-susceptibility bacteria in certain environments. In spite of this, neither mechanism seems to significantly impair the success of Salmonella biocontrol and oral phage therapy.
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Affiliation(s)
- Júlia López-Pérez
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Jennifer Otero
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- SK8 Biotech, Parc Científic de Barcelona, Barcelona, Spain
| | - Miquel Sánchez-Osuna
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Ivan Erill
- Department of Biological Sciences, University of Maryland, Baltimore, MD, United States
- Departament Enginyeria de la Informació i de les Comunicacions, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Pilar Cortés
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Montserrat Llagostera
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
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45
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Akritidou K, Thurtle-Schmidt BH. OLD family nuclease function across diverse anti-phage defense systems. Front Microbiol 2023; 14:1268820. [PMID: 37840731 PMCID: PMC10568477 DOI: 10.3389/fmicb.2023.1268820] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/14/2023] [Indexed: 10/17/2023] Open
Abstract
Bacteriophages constitute a ubiquitous threat to bacteria, and bacteria have evolved numerous anti-phage defense systems to protect themselves. These systems include well-studied phenomena such as restriction endonucleases and CRISPR, while emerging studies have identified many new anti-phage defense systems whose mechanisms are unknown or poorly understood. Some of these systems involve overcoming lysogenization defect (OLD) nucleases, a family of proteins comprising an ABC ATPase domain linked to a Toprim nuclease domain. Despite being discovered over 50 years ago, OLD nuclease function remained mysterious until recent biochemical, structural, and bioinformatic studies revealed that OLD nucleases protect bacteria by functioning in diverse anti-phage defense systems including the Gabija system and retrons. In this review we will highlight recent discoveries in OLD protein function and their involvement in multiple discrete anti-phage defense systems.
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46
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Kelly A, Went SC, Mariano G, Shaw LP, Picton DM, Duffner SJ, Coates I, Herdman-Grant R, Gordeeva J, Drobiazko A, Isaev A, Lee YJ, Luyten Y, Morgan RD, Weigele P, Severinov K, Wenner N, Hinton JCD, Blower TR. Diverse Durham collection phages demonstrate complex BREX defense responses. Appl Environ Microbiol 2023; 89:e0062323. [PMID: 37668405 PMCID: PMC10537673 DOI: 10.1128/aem.00623-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 07/10/2023] [Indexed: 09/06/2023] Open
Abstract
Bacteriophages (phages) outnumber bacteria ten-to-one and cause infections at a rate of 1025 per second. The ability of phages to reduce bacterial populations makes them attractive alternative antibacterials for use in combating the rise in antimicrobial resistance. This effort may be hindered due to bacterial defenses such as Bacteriophage Exclusion (BREX) that have arisen from the constant evolutionary battle between bacteria and phages. For phages to be widely accepted as therapeutics in Western medicine, more must be understood about bacteria-phage interactions and the outcomes of bacterial phage defense. Here, we present the annotated genomes of 12 novel bacteriophage species isolated from water sources in Durham, UK, during undergraduate practical classes. The collection includes diverse species from across known phylogenetic groups. Comparative analyses of two novel phages from the collection suggest they may be founding members of a new genus. Using this Durham phage collection, we determined that particular BREX defense systems were likely to confer a varied degree of resistance against an invading phage. We concluded that the number of BREX target motifs encoded in the phage genome was not proportional to the degree of susceptibility. IMPORTANCE Bacteriophages have long been the source of tools for biotechnology that are in everyday use in molecular biology research laboratories worldwide. Phages make attractive new targets for the development of novel antimicrobials. While the number of phage genome depositions has increased in recent years, the expected bacteriophage diversity remains underrepresented. Here we demonstrate how undergraduates can contribute to the identification of novel phages and that a single City in England can provide ample phage diversity and the opportunity to find novel technologies. Moreover, we demonstrate that the interactions and intricacies of the interplay between bacterial phage defense systems such as Bacteriophage Exclusion (BREX) and phages are more complex than originally thought. Further work will be required in the field before the dynamic interactions between phages and bacterial defense systems are fully understood and integrated with novel phage therapies.
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Affiliation(s)
- Abigail Kelly
- Department of Biosciences, Durham University, Durham, UK
| | - Sam C. Went
- Department of Biosciences, Durham University, Durham, UK
| | - Giuseppina Mariano
- Microbes in Health and Disease Theme, Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Liam P. Shaw
- Department of Biosciences, Durham University, Durham, UK
- Department of Biology, University of Oxford, Oxford, UK
| | | | | | - Isabel Coates
- Department of Biosciences, Durham University, Durham, UK
| | | | - Julia Gordeeva
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Alena Drobiazko
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Artem Isaev
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Yan-Jiun Lee
- New England Biolabs, Ipswich, Massachusetts, USA
| | | | | | | | | | - Nicolas Wenner
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Jay C. D. Hinton
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Tim R. Blower
- Department of Biosciences, Durham University, Durham, UK
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47
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Hsueh BY, Ferrell MJ, Sanath-Kumar R, Bedore AM, Waters CM. Replication cycle timing determines phage sensitivity to a cytidine deaminase toxin/antitoxin bacterial defense system. PLoS Pathog 2023; 19:e1011195. [PMID: 37683045 PMCID: PMC10511110 DOI: 10.1371/journal.ppat.1011195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 09/20/2023] [Accepted: 07/21/2023] [Indexed: 09/10/2023] Open
Abstract
Toxin-antitoxin (TA) systems are ubiquitous two-gene loci that bacteria use to regulate cellular processes such as phage defense. Here, we demonstrate the mechanism by which a novel type III TA system, avcID, is activated and confers resistance to phage infection. The toxin of the system (AvcD) is a deoxycytidylate deaminase that converts deoxycytidines (dC) to dexoyuridines (dU), while the RNA antitoxin (AvcI) inhibits AvcD activity. We have shown that AvcD deaminated dC nucleotides upon phage infection, but the molecular mechanism that activated AvcD was unknown. Here we show that the activation of AvcD arises from phage-induced inhibition of host transcription, leading to degradation of the labile AvcI. AvcD activation and nucleotide depletion not only decreases phage replication but also increases the formation of defective phage virions. Surprisingly, infection of phages such as T7 that are not inhibited by AvcID also lead to AvcI RNA antitoxin degradation and AvcD activation, suggesting that depletion of AvcI is not sufficient to confer protection against some phage. Rather, our results support that phage with a longer replication cycle like T5 are sensitive to AvcID-mediated protection while those with a shorter replication cycle like T7 are resistant.
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Affiliation(s)
- Brian Y. Hsueh
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
| | - Micah J. Ferrell
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
| | - Ram Sanath-Kumar
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
| | - Amber M. Bedore
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
| | - Christopher M. Waters
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
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48
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Doman JL, Pandey S, Neugebauer ME, An M, Davis JR, Randolph PB, McElroy A, Gao XD, Raguram A, Richter MF, Everette KA, Banskota S, Tian K, Tao YA, Tolar J, Osborn MJ, Liu DR. Phage-assisted evolution and protein engineering yield compact, efficient prime editors. Cell 2023; 186:3983-4002.e26. [PMID: 37657419 PMCID: PMC10482982 DOI: 10.1016/j.cell.2023.07.039] [Citation(s) in RCA: 45] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 05/07/2023] [Accepted: 07/28/2023] [Indexed: 09/03/2023]
Abstract
Prime editing enables a wide variety of precise genome edits in living cells. Here we use protein evolution and engineering to generate prime editors with reduced size and improved efficiency. Using phage-assisted evolution, we improved editing efficiencies of compact reverse transcriptases by up to 22-fold and generated prime editors that are 516-810 base pairs smaller than the current-generation editor PEmax. We discovered that different reverse transcriptases specialize in different types of edits and used this insight to generate reverse transcriptases that outperform PEmax and PEmaxΔRNaseH, the truncated editor used in dual-AAV delivery systems. Finally, we generated Cas9 domains that improve prime editing. These resulting editors (PE6a-g) enhance therapeutically relevant editing in patient-derived fibroblasts and primary human T-cells. PE6 variants also enable longer insertions to be installed in vivo following dual-AAV delivery, achieving 40% loxP insertion in the cortex of the murine brain, a 24-fold improvement compared to previous state-of-the-art prime editors.
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Affiliation(s)
- Jordan L Doman
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Smriti Pandey
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Monica E Neugebauer
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Meirui An
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Jessie R Davis
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Peyton B Randolph
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Amber McElroy
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Xin D Gao
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Aditya Raguram
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Michelle F Richter
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Kelcee A Everette
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Samagya Banskota
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Kathryn Tian
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Y Allen Tao
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Jakub Tolar
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Mark J Osborn
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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49
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Liu W, Zuo S, Shao Y, Bi K, Zhao J, Huang L, Xu Z, Lian J. Retron-mediated multiplex genome editing and continuous evolution in Escherichia coli. Nucleic Acids Res 2023; 51:8293-8307. [PMID: 37471041 PMCID: PMC10450171 DOI: 10.1093/nar/gkad607] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 07/02/2023] [Accepted: 07/07/2023] [Indexed: 07/21/2023] Open
Abstract
While there are several genome editing techniques available, few are suitable for dynamic and simultaneous mutagenesis of arbitrary targeted sequences in prokaryotes. Here, to address these limitations, we present a versatile and multiplex retron-mediated genome editing system (REGES). First, through systematic optimization of REGES, we achieve efficiency of ∼100%, 85 ± 3%, 69 ± 14% and 25 ± 14% for single-, double-, triple- and quadruple-locus genome editing, respectively. In addition, we employ REGES to generate pooled and barcoded variant libraries with degenerate RBS sequences to fine-tune the expression level of endogenous and exogenous genes, such as transcriptional factors to improve ethanol tolerance and biotin biosynthesis. Finally, we demonstrate REGES-mediated continuous in vivo protein evolution, by combining retron, polymerase-mediated base editing and error-prone transcription. By these case studies, we demonstrate REGES as a powerful multiplex genome editing and continuous evolution tool with broad applications in synthetic biology and metabolic engineering.
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Affiliation(s)
- Wenqian Liu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Siqi Zuo
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Youran Shao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Ke Bi
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Jiarun Zhao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Lei Huang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Zhinan Xu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
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50
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Cheng R, Huang F, Lu X, Yan Y, Yu B, Wang X, Zhu B. Prokaryotic Gabija complex senses and executes nucleotide depletion and DNA cleavage for antiviral defense. Cell Host Microbe 2023; 31:1331-1344.e5. [PMID: 37480847 DOI: 10.1016/j.chom.2023.06.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 05/03/2023] [Accepted: 06/27/2023] [Indexed: 07/24/2023]
Abstract
The Gabija complex is a prokaryotic antiviral system consisting of the GajA and GajB proteins. GajA was identified as a DNA nicking endonuclease but the functions of GajB and the complex remain unknown. Here, we show that synergy between GajA-mediated DNA cleavage and nucleotide hydrolysis by GajB initiates efficient abortive infection defense against virulent bacteriophages. The antiviral activity of GajA requires GajB, which senses DNA termini produced by GajA to hydrolyze (d)A/(d)GTP, depleting essential nucleotides. This ATPase activity of Gabija complex is only activated upon DNA binding. GajA binds to GajB to form stable complexes in vivo and in vitro. However, a functional Gabija complex requires a molecular ratio between GajB and GajA below 1:1, indicating stoichiometric regulation of the DNA/nucleotide processing complex. Thus, the Gabija system exhibits distinct and efficient antiviral defense through sequential sensing and activation of nucleotide depletion and DNA cleavage, causing a cascade suicide effect.
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Affiliation(s)
- Rui Cheng
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.
| | - Fengtao Huang
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen 518063, China
| | - Xueling Lu
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yan Yan
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Bingbing Yu
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Xionglue Wang
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Bin Zhu
- Key Laboratory of Molecular Biophysics, the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen 518063, China.
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