Friday, September 20, 2024
No menu items!
HomeNatureDiverse viral cas genes antagonize CRISPR immunity

Diverse viral cas genes antagonize CRISPR immunity

  • Bondy-Denomy, J., Pawluk, A., Maxwell, K. L. & Davidson, A. R. Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system. Nature 493, 429–432 (2013).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Bondy-Denomy, J. et al. Multiple mechanisms for CRISPR–Cas inhibition by anti-CRISPR proteins. Nature 526, 136–139 (2015).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Rauch, B. J. et al. Inhibition of CRISPR–Cas9 with bacteriophage proteins. Cell 168, 150–158 e110 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Knott, G. J. et al. Broad-spectrum enzymatic inhibition of CRISPR–Cas12a. Nat. Struct. Mol. Biol. 26, 315–321 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Dong, L. et al. An anti-CRISPR protein disables type V Cas12a by acetylation. Nat. Struct. Mol. Biol. 26, 308–314 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Niu, Y. et al. A type I-F anti-CRISPR protein inhibits the CRISPR–Cas surveillance complex by ADP-ribosylation. Mol. Cell 80, 512–524 e515 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Sahakyan, H., Makarova, K. S. & Koonin, E. V. Search foroOrigins of anti-CRISPR proteins by structure comparison. CRISPR J. 6, 222–231 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chowdhury, S. et al. Structure reveals mechanisms of viral suppressors that intercept a CRISPR RNA-guided surveillance complex. Cell 169, 47–57 e11 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Rollins, M. F. et al. Structure reveals a mechanism of CRISPR-RNA-guided nuclease recruitment and anti-CRISPR viral mimicry. Mol. Cell 74, 132–142 e135 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Krupovic, M., Cvirkaite-Krupovic, V., Prangishvili, D. & Koonin, E. V. Evolution of an archaeal virus nucleocapsid protein from the CRISPR-associated Cas4 nuclease. Biol. Direct 10, 65 (2015).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hudaiberdiev, S. et al. Phylogenomics of Cas4 family nucleases. BMC Evol. Biol. 17, 232 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Goodman, D. A. & Stedman, K. M. Comparative genetic and genomic analysis of the novel fusellovirus Sulfolobus spindle-shaped virus 10. Virus Evol. 4, vey022 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhang, Z., Pan, S., Liu, T., Li, Y. & Peng, N. Cas4 nucleases can effect specific integration of CRISPR spacers. J. Bacteriol. 201, e00747–18 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Al-Shayeb, B. et al. Diverse virus-encoded CRISPR–Cas systems include streamlined genome editors. Cell 185, 4574–4586 e4516 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Meeske, A. J. & Marraffini, L. A. RNA guide complementarity prevents self-targeting in type VI CRISPR systems. Mol. Cell 71, 791–801 e793 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Meeske, A. J., Nakandakari-Higa, S. & Marraffini, L. A. Cas13-induced cellular dormancy prevents the rise of CRISPR-resistant bacteriophage. Nature 570, 241–245 (2019).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Meeske, A. J. et al. A phage-encoded anti-CRISPR enables complete evasion of type VI-A CRISPR–Cas immunity. Science 369, 54–59 (2020).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Williams, M. C. et al. Restriction endonuclease cleavage of phage DNA enables resuscitation from Cas13-induced bacterial dormancy. Nat. Microbiol. 8, 400–409 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lauer, P., Chow, M. Y., Loessner, M. J., Portnoy, D. A. & Calendar, R. Construction, characterization, and use of two Listeria monocytogenes site-specific phage integration vectors. J. Bacteriol. 184, 4177–4186 (2002).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Mahendra, C. et al. Broad-spectrum anti-CRISPR proteins facilitate horizontal gene transfer. Nat. Microbiol. 5, 620–629 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Osuna, B. A. et al. Critical anti-CRISPR locus repression by a bi-functional Cas9 inhibitor. Cell Host Microbe 28, 23–30 e25 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Osuna, B. A. et al. Listeria phages induce Cas9 degradation to protect lysogenic genomes. Cell Host Microbe 28, 31–40 e39 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lu, M. et al. Structure and genome editing of type I-B CRISPR–Cas. Nat. Commun. 15, 4126 (2024).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Luo, M. L., Mullis, A. S., Leenay, R. T. & Beisel, C. L. Repurposing endogenous type I CRISPR–Cas systems for programmable gene repression. Nucleic Acids Res. 43, 674–681 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Rath, D., Amlinger, L., Hoekzema, M., Devulapally, P. R. & Lundgren, M. Efficient programmable gene silencing by Cascade. Nucleic Acids Res. 43, 237–246 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Hu, C. et al. Allosteric control of type I-A CRISPR-Cas3 complexes and establishment as effective nucleic acid detection and human genome editing tools. Mol. Cell 82, 2754–2768 e2755 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Camargo, A. P. et al. IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata. Nucleic Acids Res. 51, D733–D743 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Krupovic, M., Makarova, K. S., Forterre, P., Prangishvili, D. & Koonin, E. V. Casposons: a new superfamily of self-synthesizing DNA transposons at the origin of prokaryotic CRISPR–Cas immunity. BMC Biol. 12, 36 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kapitonov, V. V., Makarova, K. S. & Koonin, E. V. ISC, a novel group of bacterial and archaeal DNA transposons that encode Cas9 homologs. J. Bacteriol. 198, 797–807 (2015).

    Article 
    PubMed 

    Google Scholar
     

  • Varble, A. et al. Prophage integration into CRISPR loci enables evasion of antiviral immunity in Streptococcus pyogenes. Nat. Microbiol. 6, 1516–1525 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Camara-Wilpert, S. et al. Bacteriophages suppress CRISPR–Cas immunity using RNA-based anti-CRISPRs. Nature 623, 601–607 (2023).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Rollie, C. et al. Targeting of temperate phages drives loss of type I CRISPR–Cas systems. Nature 578, 149–153 (2020).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Notredame, C., Higgins, D. G. & Heringa, J. T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302, 205–217 (2000).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Tamura, K., Stecher, G. & Kumar, S. MEGA11: molecular evolutionary genetics analysis version 11. Mol. Biol. Evol. 38, 3022–3027 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Makarova, K. S. et al. Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants. Nat. Rev. Microbiol. 18, 67–83 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lee, W. & Chen, S. L. Genome-tools: a flexible package for genome sequence analysis. Biotechniques 33, 1334–1341 (2002).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Russel, J., Pinilla-Redondo, R., Mayo-Munoz, D., Shah, S. A. & Sorensen, S. J. CRISPRCasTyper: automated identification, annotation, and classification of CRISPR–Cas loci. CRISPR J. 3, 462–469 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Krüger, D. H., Schroeder, C., Hansen, S. & Rosenthal, H. A. Active protection by bacteriophages T3 and T7 against E. coli B- and K-specific restriction of their DNA. Mol. Gen. Genet. 153, 99–106 (1977).

    Article 
    PubMed 

    Google Scholar
     

  • Yirmiya, E. et al. Phages overcome bacterial immunity via diverse anti-defence proteins. Nature 625, 352–359 (2024).

  • Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068–2069 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Gilchrist, C. L. M. & Chooi, Y. H. clinker & clustermap.js: automatic generation of gene cluster comparison figures. Bioinformatics 37, 2473–2475 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • RELATED ARTICLES

    Most Popular

    Recent Comments