Identification of an anti-CRISPR protein that inhibits the CRISPR-Cas type I-B system in Clostridioides difficile
ABSTRACTCRISPR-Cas systems provide prokaryotic hosts with adaptive immunity against mobile genetic elements. Many bacteriophages encode anti-CRISPR (Acr) proteins that inhibit host defense. The identification of Acr proteins is challenging due to their small size and high sequence diversity, and onl...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
American Society for Microbiology
2023-12-01
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| Series: | mSphere |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/msphere.00401-23 |
| _version_ | 1797384677088034816 |
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| author | Polina Muzyukina Anton Shkaruta Noemi M. Guzman Jessica Andreani Adair L. Borges Joseph Bondy-Denomy Anna Maikova Ekaterina Semenova Konstantin Severinov Olga Soutourina |
| author_facet | Polina Muzyukina Anton Shkaruta Noemi M. Guzman Jessica Andreani Adair L. Borges Joseph Bondy-Denomy Anna Maikova Ekaterina Semenova Konstantin Severinov Olga Soutourina |
| author_sort | Polina Muzyukina |
| collection | DOAJ |
| description | ABSTRACTCRISPR-Cas systems provide prokaryotic hosts with adaptive immunity against mobile genetic elements. Many bacteriophages encode anti-CRISPR (Acr) proteins that inhibit host defense. The identification of Acr proteins is challenging due to their small size and high sequence diversity, and only a limited number has been characterized to date. In this study, we report the discovery of a novel Acr protein, AcrIB2, encoded by the φCD38-2 Clostridioides difficile phage that efficiently inhibits interference by the type I-B CRISPR-Cas system of the host and likely acts as a DNA mimic. Most C. difficile strains contain two cas operons, one encoding a full set of interference and adaptation proteins and another encoding interference proteins only. Unexpectedly, we demonstrate that only the partial operon is required for interference and is subject to inhibition by AcrIB2.IMPORTANCEClostridioides difficile is the widespread anaerobic spore-forming bacterium that is a major cause of potentially lethal nosocomial infections associated with antibiotic therapy worldwide. Due to the increase in severe forms associated with a strong inflammatory response and higher recurrence rates, a current imperative is to develop synergistic and alternative treatments for C. difficile infections. In particular, phage therapy is regarded as a potential substitute for existing antimicrobial treatments. However, it faces challenges because C. difficile has highly active CRISPR-Cas immunity, which may be a specific adaptation to phage-rich and highly crowded gut environment. To overcome this defense, C. difficile phages must employ anti-CRISPR mechanisms. Here, we present the first anti-CRISPR protein that inhibits the CRISPR-Cas defense system in this pathogen. Our work offers insights into the interactions between C. difficile and its phages, paving the way for future CRISPR-based applications and development of effective phage therapy strategies combined with the engineering of virulent C. difficile infecting phages. |
| first_indexed | 2024-03-08T21:40:07Z |
| format | Article |
| id | doaj.art-71128c6ead1449c1a691bf90e99cb7e8 |
| institution | Directory Open Access Journal |
| issn | 2379-5042 |
| language | English |
| last_indexed | 2024-03-08T21:40:07Z |
| publishDate | 2023-12-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mSphere |
| spelling | doaj.art-71128c6ead1449c1a691bf90e99cb7e82023-12-20T14:01:03ZengAmerican Society for MicrobiologymSphere2379-50422023-12-018610.1128/msphere.00401-23Identification of an anti-CRISPR protein that inhibits the CRISPR-Cas type I-B system in Clostridioides difficilePolina Muzyukina0Anton Shkaruta1Noemi M. Guzman2Jessica Andreani3Adair L. Borges4Joseph Bondy-Denomy5Anna Maikova6Ekaterina Semenova7Konstantin Severinov8Olga Soutourina9Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, FranceUniversité Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, FranceCenter for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, RussiaUniversité Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, FranceDepartment of Microbiology and Immunology, University of California, San Francisco, California, USADepartment of Microbiology and Immunology, University of California, San Francisco, California, USAUniversité Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, FranceWaksman Institute, Rutgers, State University of New Jersey, Piscataway, New Jersey, USAWaksman Institute, Rutgers, State University of New Jersey, Piscataway, New Jersey, USAUniversité Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, FranceABSTRACTCRISPR-Cas systems provide prokaryotic hosts with adaptive immunity against mobile genetic elements. Many bacteriophages encode anti-CRISPR (Acr) proteins that inhibit host defense. The identification of Acr proteins is challenging due to their small size and high sequence diversity, and only a limited number has been characterized to date. In this study, we report the discovery of a novel Acr protein, AcrIB2, encoded by the φCD38-2 Clostridioides difficile phage that efficiently inhibits interference by the type I-B CRISPR-Cas system of the host and likely acts as a DNA mimic. Most C. difficile strains contain two cas operons, one encoding a full set of interference and adaptation proteins and another encoding interference proteins only. Unexpectedly, we demonstrate that only the partial operon is required for interference and is subject to inhibition by AcrIB2.IMPORTANCEClostridioides difficile is the widespread anaerobic spore-forming bacterium that is a major cause of potentially lethal nosocomial infections associated with antibiotic therapy worldwide. Due to the increase in severe forms associated with a strong inflammatory response and higher recurrence rates, a current imperative is to develop synergistic and alternative treatments for C. difficile infections. In particular, phage therapy is regarded as a potential substitute for existing antimicrobial treatments. However, it faces challenges because C. difficile has highly active CRISPR-Cas immunity, which may be a specific adaptation to phage-rich and highly crowded gut environment. To overcome this defense, C. difficile phages must employ anti-CRISPR mechanisms. Here, we present the first anti-CRISPR protein that inhibits the CRISPR-Cas defense system in this pathogen. Our work offers insights into the interactions between C. difficile and its phages, paving the way for future CRISPR-based applications and development of effective phage therapy strategies combined with the engineering of virulent C. difficile infecting phages.https://journals.asm.org/doi/10.1128/msphere.00401-23Clostridioides difficiletype I-B CRISPR-Cas interferencecas operonsenteropathogenanti-CRISPRDNA mimicry |
| spellingShingle | Polina Muzyukina Anton Shkaruta Noemi M. Guzman Jessica Andreani Adair L. Borges Joseph Bondy-Denomy Anna Maikova Ekaterina Semenova Konstantin Severinov Olga Soutourina Identification of an anti-CRISPR protein that inhibits the CRISPR-Cas type I-B system in Clostridioides difficile mSphere Clostridioides difficile type I-B CRISPR-Cas interference cas operons enteropathogen anti-CRISPR DNA mimicry |
| title | Identification of an anti-CRISPR protein that inhibits the CRISPR-Cas type I-B system in Clostridioides difficile |
| title_full | Identification of an anti-CRISPR protein that inhibits the CRISPR-Cas type I-B system in Clostridioides difficile |
| title_fullStr | Identification of an anti-CRISPR protein that inhibits the CRISPR-Cas type I-B system in Clostridioides difficile |
| title_full_unstemmed | Identification of an anti-CRISPR protein that inhibits the CRISPR-Cas type I-B system in Clostridioides difficile |
| title_short | Identification of an anti-CRISPR protein that inhibits the CRISPR-Cas type I-B system in Clostridioides difficile |
| title_sort | identification of an anti crispr protein that inhibits the crispr cas type i b system in clostridioides difficile |
| topic | Clostridioides difficile type I-B CRISPR-Cas interference cas operons enteropathogen anti-CRISPR DNA mimicry |
| url | https://journals.asm.org/doi/10.1128/msphere.00401-23 |
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