Tuesday, November 1, 2022
HomeMicrobiologyBacteriophage genome engineering with CRISPR–Cas13a

Bacteriophage genome engineering with CRISPR–Cas13a


  • Kortright, Ok. E., Chan, B. Ok., Koff, J. L. & Turner, P. E. Phage remedy: a renewed method to fight antibiotic-resistant micro organism. Cell Host Microbe 25, 219–232 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Pires, D. P., Cleto, S., Sillankorva, S., Azeredo, J. & Lu, T. Ok. Genetically engineered phages: a evaluation of advances during the last decade. Microbiol. Mol. Biol. Rev. 80, 523–543 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Doss, J., Culbertson, Ok., Hahn, D., Camacho, J. & Barekzi, N. A evaluation of phage remedy towards bacterial pathogens of aquatic and terrestrial organisms.Viruses 9, 50 (2017).

    Article 
    PubMed Central 

    Google Scholar
     

  • Nobrega, F. L., Costa, A. R., Kluskens, L. D. & Azeredo, J. Revisiting phage remedy: new functions for previous assets. Traits Microbiol. 23, 185–191 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Łusiak-Szelachowska, M. et al. Phage neutralization by sera of sufferers receiving phage remedy. Viral Immunol. 27, 295–304 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Weber-Dąbrowska, B. et al. Bacteriophage procurement for therapeutic functions. Entrance. Microbiol. 7, 1177 (2016).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lu, T. Ok. & Koeris, M. S. The subsequent era of bacteriophage remedy. Curr. Opin. Microbiol. 14, 524–531 (2011).

    Article 
    PubMed 

    Google Scholar
     

  • Lenneman, B. R., Fernbach, J., Loessner, M. J., Lu, T. Ok. & Kilcher, S. Enhancing phage remedy by way of artificial biology and genome engineering. Curr. Opin. Biotechnol. 68, 151–159 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ando, H., Lemire, S., Pires, D. P. & Lu, T. Ok. Engineering modular viral scaffolds for focused bacterial inhabitants enhancing. Cell Syst. 1, 187–196 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Mahichi, F., Synnott, A. J., Yamamichi, Ok., Osada, T. & Tanji, Y. Web site-specific recombination of T2 phage utilizing IP008 lengthy tail fiber genes offers a focused methodology for increasing host vary whereas retaining lytic exercise. FEMS Microbiol. Lett. 295, 211–217 (2009).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Matsuda, T. et al. Lysis-deficient bacteriophage remedy decreases endotoxin and inflammatory mediator launch and improves survival in a murine peritonitis mannequin. Surgical procedure 137, 639–646 (2005).

    Article 
    PubMed 

    Google Scholar
     

  • Monteiro, R., Pires, D. P., Costa, A. R. & Azeredo, J. Phage remedy: going temperate? Traits Microbiol. 27, 368–378 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kilcher, S. & Loessner, M. J. Engineering bacteriophages as versatile biologics. Traits Microbiol. 27, 355–367 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Marinelli, L. J., Hatfull, G. F. & Piuri, M. Recombineering: a strong software for modification of bacteriophage genomes. Bacteriophage 2, 5–14 (2012).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Deveau, H., Garneau, J. E. & Moineau, S. CRISPR/Cas system and its function in phage-bacteria interactions. Annu. Rev. Microbiol. 64, 475–493 (2010).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Hille, F. et al. The Biology of CRISPR–Cas: back and forth. Cell 172, 1239–1259 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Mayo-Muñoz, D. et al. Anti-CRISPR-based and CRISPR-based genome enhancing of Sulfolobus islandicus rod-shaped virus 2.Viruses 10, 695 (2018).

    Article 
    PubMed Central 

    Google Scholar
     

  • Samson, J. E., Magadan, A. H., Sabri, M. & Moineau, S. Revenge of the phages: defeating bacterial defences. Nat. Rev. Microbiol. 11, 675–687 (2013).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Malone, L. M., Birkholz, N. & Fineran, P. C. Conquering CRISPR: how phages overcome bacterial adaptive immunity. Curr. Opin. Biotechnol. 68, 30–36 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Mendoza, S. D. et al. A bacteriophage nucleus-like compartment shields DNA from CRISPR nucleases. Nature 577, 244–248 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Malone, L. M. et al. A jumbo phage that varieties a nucleus-like construction evades CRISPR–Cas DNA focusing on however is weak to sort III RNA-based immunity. Nat. Microbiol. 5, 48–55 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Guan, J. & Bondy-Denomy, J.Intracellular group by jumbo bacteriophages.J. Bacteriol. 203, e00362-20 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Abudayyeh, O. O. et al. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science 353, aaf5573 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

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

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

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

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • East-Seletsky, A. et al. Two distinct RNase actions of CRISPR–C2c2 allow guide-RNA processing and RNA detection. Nature 538, 270–273 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Meeske, A. J. & Marraffini, L. A. RNA information complementarity prevents self-targeting in sort VI CRISPR programs. Mol. Cell 71, 791–801.e3 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • M Iyer, L., Anantharaman, V., Krishnan, A., Maxwell Burroughs, A. & Aravind, L. Jumbo phages: a comparative genomic overview of core features and adaptions for organic conflicts.Viruses 13, 63 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Al-Shayeb, B. et al. Clades of giant phages from throughout Earth’s ecosystems. Nature 578, 425–431 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Aylett, C. H. S., Izoré, T., Amos, L. A. & Löwe, J. Construction of the tubulin/FtsZ-like protein TubZ from Pseudomonas bacteriophage ΦKZ. J. Mol. Biol. 425, 2164–2173 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chaikeeratisak, V. et al. The phage nucleus and tubulin spindle are conserved amongst giant Pseudomonas phages. Cell Rep. 20, 1563–1571 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chaikeeratisak, V. et al. Viral capsid trafficking alongside treadmilling tubulin filaments in micro organism. Cell 177, 1771–1780.e12 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kraemer, J. A. et al. A phage tubulin assembles dynamic filaments by an atypical mechanism to middle viral DNA inside the host cell. Cell 149, 1488–1499 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chaikeeratisak, V. et al. Meeting of a nucleus-like construction throughout viral replication in micro organism. Science 355, 194–197 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wu, W., Thomas, J. A., Cheng, N., Black, L. W. & Steven, A. C. Bubblegrams reveal the inside physique of bacteriophage ΦKZ. Science 335, 182 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Thomas, J. A. et al. Intensive proteolysis of head and inside physique proteins by a morphogenetic protease within the large Pseudomonas aeruginosa phage ΦKZ. Mol. Microbiol. 84, 324–339 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chan, B. Ok. et al. Phage choice restores antibiotic sensitivity in MDR Pseudomonas aeruginosa. Sci. Rep. 6, 26717 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chan, B. Ok. et al. Phage remedy of an aortic graft contaminated with Pseudomonas aeruginosa. Evol. Med. Public Well being 2018, 60–66 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sepúlveda-Robles, O., Kameyama, L. & Guarneros, G. Excessive range and novel species of Pseudomonas aeruginosa bacteriophages. Appl. Environ. Microbiol. 78, 4510–4515 (2012).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cruz-Plancarte, I., Cazares, A. & Guarneros, G. Genomic and transcriptional mapping of PaMx41, archetype of a brand new lineage of bacteriophages infecting Pseudomonas aeruginosa. Appl. Environ. Microbiol. 82, 6541–6547 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Huiting, E. et al. Bacteriophages antagonize cGAS-like immunity in micro organism. Preprint at bioRxiv https://doi.org/10.1101/2022.03.30.486325 (2022).

  • Skennerton, C. T. et al. Phage encoded H-NS: a possible Achilles heel within the bacterial defence system. PLoS ONE 6, e20095 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Pul, U. et al. Identification and characterization of E. coli CRISPR–cas promoters and their silencing by H-NS. Mol. Microbiol. 75, 1495–1512 (2010).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Hampton, H. G., Watson, B. N. J. & Fineran, P. C. The arms race between micro organism and their phage foes. Nature 577, 327–336 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Vlot, M. et al. Bacteriophage DNA glucosylation impairs goal DNA binding by sort I and II however not by sort V CRISPR–Cas effector complexes. Nucleic Acids Res. 46, 873–885 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Bryson, A. L. et al. Covalent modification of bacteriophage T4 DNA inhibits CRISPR–Cas9. mBio 6, e00648 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Liu, Y. et al. Covalent modifications of the bacteriophage genome confer a level of resistance to bacterial CRISPR programs.J. Virol. 94, e01630-20 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Davidson, A. R. et al. Anti-CRISPRs: protein inhibitors of CRISPR–Cas programs. Annu. Rev. Biochem. 89, 309–332 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

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

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Adler, B. et al. RNA-targeting CRISPR–Cas13 offers broad-spectrum phage immunity. Preprint at bioRxiv https://doi.org/10.1101/2022.03.25.485874 (2022).

  • Krylov, V. N. et al. Pseudomonas bacteriophage ΦKZ incorporates an inside physique in its capsid. Can. J. Microbiol. 30, 758–762 (1984).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • van Beljouw, S. P. B. et al. The gRAMP CRISPR–Cas effector is an RNA endonuclease complexed with a caspase-like peptidase. Science 373, 1349–1353 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Özcan, A. et al. Programmable RNA focusing on with the single-protein CRISPR effector Cas7-11. Nature 597, 720–725 (2021).

    Article 
    PubMed 

    Google Scholar
     

  • RELATED ARTICLES

    LEAVE A REPLY

    Please enter your comment!
    Please enter your name here

    Most Popular

    Recent Comments