CRISPR-Cas10-Assisted Structural Modification of Staphylococcal Kayvirus for Imaging and Biosensing Applications
Status In-Process Language English Country United States Media print-electronic
Document type Journal Article
PubMed
40720830
PubMed Central
PMC12362608
DOI
10.1021/acssynbio.5c00387
Knihovny.cz E-resources
- Keywords
- Bacteriophage, Biosensing Techniques, CRISPR-Cas10, Herelleviridae, Poly histidine Tag, Staphylococcus aureus,
- Publication type
- Journal Article MeSH
Recent advances in genome editing techniques based on CRISPR-Cas have opened up new possibilities in bacteriophage engineering and, thus, enabled key developments in medicine, nanotechnology, and synthetic biology. Although staphylococcal phage genomes have already been edited, the modification of their structural proteins has not yet been reported. Here, the structure of Staphylococcus phage 812h1 of the Kayvirus genus was modified by inserting a poly histidine tag into an exposed loop of the tail sheath protein. A two-strain editing strategy was applied, utilizing homologous recombination followed by CRISPR-Cas10-assisted counter-selection of the recombinant phages. The His-tagged phage particles can be recognized by specific antibodies, enabling the modified bacteriophages to be employed in numerous techniques. The attachment of the engineered phage to bacteria was visualized by fluorescence microscopy, and its functionality was confirmed using biolayer interferometry biosensing, enzyme-linked immunosorbent assay, and flow cytometry, demonstrating that the genetic modification did not impair its biological activity.
Central European Institute of Technology Masaryk University Brno 625 00 Czech Republic
Department of Biochemistry Faculty of Science Masaryk University Brno 625 00 Czech Republic
Department of Experimental Biology Faculty of Science Masaryk University Brno 611 37 Czech Republic
See more in PubMed
Clokie M. R. J., Millard A. D., Letarov A. V., Heaphy S.. Phages in Nature. Bacteriophage. 2011;1:31–45. doi: 10.4161/bact.1.1.14942. PubMed DOI PMC
Bárdy P., Pantůček R., Benešík M., Doškař J.. Genetically Modified Bacteriophages in Applied Microbiology. J. Appl. Microbiol. 2016;121:618–633. doi: 10.1111/jam.13207. PubMed DOI
Chen, Y. ; Batra, H. ; Dong, J. ; Chen, C. ; Rao, V. B. ; Tao, P. . Genetic Engineering of Bacteriophages against Infectious Diseases. Front. Microbiol. 2019, 10, (954). 10.3389/fmicb.2019.00954. PubMed DOI PMC
Pires D. P., Cleto S., Sillankorva S., Azeredo J., Lu T. K.. Genetically Engineered Phages: A Review of Advances over the Last Decade. Microbiol. Mol. Biol. Rev. 2016;80:523–543. doi: 10.1128/MMBR.00069-15. PubMed DOI PMC
Yosef I., Goren M. G., Globus R., Molshanski-Mor S., Qimron U.. Extending the Host Range of Bacteriophage Particles for DNA Transduction. Mol. Cell. 2017;66:721–728. doi: 10.1016/j.molcel.2017.04.025. PubMed DOI
Jia H.-J., Jia P.-P., Yin S., Bu L.-K., Yang G., Pei D.-S.. Engineering Bacteriophages for Enhanced Host Range and Efficacy: Insights from Bacteriophage-Bacteria Interactions. Front. Microbiol. 2023;14:1172635. doi: 10.3389/fmicb.2023.1172635. PubMed DOI PMC
Edgar R., Friedman N., Molshanski-Mor S., Qimron U.. Reversing Bacterial Resistance to Antibiotics by Phage-Mediated Delivery of Dominant Sensitive Genes. Appl. Environ. Microbiol. 2012;78:744–751. doi: 10.1128/AEM.05741-11. PubMed DOI PMC
Łobocka M., Dąbrowska K., Górski A.. Engineered Bacteriophage Therapeutics: Rationale, Challenges and Future. BioDrugs. 2021;35:255–280. doi: 10.1007/s40259-021-00480-z. PubMed DOI PMC
Meile, S. ; Du, J. ; Staubli, S. ; Grossmann, S. ; Koliwer-Brandl, H. ; Piffaretti, P. ; Leitner, L. ; Matter, C. I. ; Baggenstos, J. ; Hunold, L. ; et al. Engineered Reporter Phages for Detection of PubMed DOI PMC
Farooq U., Yang Q., Ullah M. W., Wang S.. Bacterial Biosensing: Recent Advances in Phage-Based Bioassays and Biosensors. Biosens. Bioelectron. 2018;118:204–216. doi: 10.1016/j.bios.2018.07.058. PubMed DOI
Bikard D., Euler C. W., Jiang W., Nussenzweig P. M., Goldberg G. W., Duportet X., Fischetti V. A., Marraffini L. A.. Exploiting CRISPR-Cas Nucleases to Produce Sequence-Specific Antimicrobials. Nat. Biotechnol. 2014;32:1146–1150. doi: 10.1038/nbt.3043. PubMed DOI PMC
Cobb L. H., Park J., Swanson E. A., Beard M. C., McCabe E. M., Rourke A. S., Seo K. S., Olivier A. K., Priddy L. B.. Crispr-Cas9Modified Bacteriophage for Treatment of Staphylococcus aureus Induced Osteomyelitis and Soft Tissue Infection. PloS One. 2019;14:e0220421. doi: 10.1371/journal.pone.0220421. PubMed DOI PMC
Gencay Y. E., Jasinskytė D., Robert C., Semsey S., Martínez V., Petersen A. Ø., Brunner K., de Santiago Torio A., Salazar A., Turcu I. C.. et al. Engineered Phage with Antibacterial CRISPR-Cas Selectively Reduce E. coli Burden in Mice. Nat. Biotechnol. 2024;42:265–274. doi: 10.1038/s41587-023-01759-y. PubMed DOI PMC
Ram G., Ross H. F., Novick R. P., Rodriguez-Pagan I., Jiang D.. Conversion of Staphylococcal Pathogenicity Islands to CRISPR-Carrying Antibacterial Agents That Cure Infections in Mice. Nat. Biotechnol. 2018;36:971–976. doi: 10.1038/nbt.4203. PubMed DOI PMC
Novick R. P.. Antibacterial Particles and Predatory Bacteria as Alternatives to Antibacterial Chemicals in the Era of Antibiotic Resistance. Curr. Opin. Microbiol. 2021;64:109–116. doi: 10.1016/j.mib.2021.09.016. PubMed DOI PMC
Shabbir, M. A. B. ; Hao, H. ; Shabbir, M. Z. ; Wu, Q. ; Sattar, A. ; Yuan, Z. . Bacteria vs. Bacteriophages: Parallel Evolution of Immune Arsenals. Front. Microbiol. 2016, 7, (1292). 10.3389/fmicb.2016.01292. PubMed DOI PMC
Rees P. J., Fry B. A.. The Morphology of Staphylococcal Bacteriophage K and DNA Metabolism in Infected Staphylococcus aureus . J. Gen. Virol. 1981;53:293–307. doi: 10.1099/0022-1317-53-2-293. PubMed DOI
Chaikeeratisak V., Nguyen K., Khanna K., Brilot A. F., Erb M. L., Coker J. K., Vavilina A., Newton G. L., Buschauer R., Pogliano K.. et al. Assembly of a Nucleus-Like Structure During Viral Replication in Bacteria. Science. 2017;355:194–197. doi: 10.1126/science.aal2130. PubMed DOI PMC
Kiro R., Shitrit D., Qimron U.. Efficient Engineering of a Bacteriophage Genome Using the Type I-E CRISPR-Cas System. RNA Biol. 2014;11:42–44. doi: 10.4161/rna.27766. PubMed DOI PMC
Tao P., Wu X., Tang W.-C., Zhu J., Rao V.. Engineering of Bacteriophage T4 Genome Using CRISPR-Cas9. ACS Synth. Biol. 2017;6:1952–1961. doi: 10.1021/acssynbio.7b00179. PubMed DOI PMC
Adler B. A., Hessler T., Cress B. F., Lahiri A., Mutalik V. K., Barrangou R., Banfield J., Doudna J. A.. Broad-Spectrum CRISPR-Cas13a Enables Efficient Phage Genome Editing. Nat. Microbiol. 2022;7:1967–1979. doi: 10.1038/s41564-022-01258-x. PubMed DOI PMC
Martel B., Moineau S.. CRISPR-Cas: An Efficient Tool for Genome Engineering of Virulent Bacteriophages. Nucleic Acids Res. 2014;42:9504–9513. doi: 10.1093/nar/gku628. PubMed DOI PMC
Box A. M., McGuffie M. J., O’Hara B. J., Seed K. D.. Functional Analysis of Bacteriophage Immunity through a Type I-E CRISPR-Cas System in Vibrio cholerae and Its Application in Bacteriophage Genome Engineering. J. Bacteriol. 2016;198:578–590. doi: 10.1128/JB.00747-15. PubMed DOI PMC
Lemay, M.-L. ; Renaud, A. C. ; Rousseau, G. M. ; Moineau, S. . Targeted Genome Editing of Virulent Phages Using CRISPR-Cas9. Bio-Protoc. 2018, 8, (e2674). 10.21769/BioProtoc.2674. PubMed DOI PMC
Shen J., Zhou J., Chen G.-Q., Xiu Z.-L.. Efficient Genome Engineering of a Virulent Klebsiella Bacteriophage Using CRISPR-Cas9. J. Virol. 2018;92:e00534-18. doi: 10.1128/JVI.00534-18. PubMed DOI PMC
Chen Y., Yan B., Chen W., Zhang X., Liu Z., Zhang Q., Li L., Hu M., Zhao X., Xu X.. Development of the CRISPR-Cas12a System for Editing of Pseudomonas aeruginosa Phages. iScience. 2024;27:110210. doi: 10.1016/j.isci.2024.110210. PubMed DOI PMC
Hupfeld M., Trasanidou D., Ramazzini L., Klumpp J., Loessner M. J., Kilcher S.. A Functional Type II-a CRISPR-Cas System from Listeria Enables Efficient Genome Editing of Large Non-Integrating Bacteriophage. Nucleic Acids Res. 2018;46:6920–6933. doi: 10.1093/nar/gky544. PubMed DOI PMC
Bari S. M. N., Walker F. C., Cater K., Aslan B., Hatoum-Aslan A.. Strategies for Editing Virulent Staphylococcal Phages Using CRISPR-Cas10. ACS Synth. Biol. 2017;6:2316–2325. doi: 10.1021/acssynbio.7b00240. PubMed DOI PMC
Nayeemul Bari S.M., Hatoum-Aslan A.. CRISPR-Cas10 Assisted Editing of Virulent Staphylococcal Phages. Methods Enzymol. 2019;616:385–409. doi: 10.1016/bs.mie.2018.10.023. PubMed DOI
Nováček J., Šiborová M., Benešík M., Pantůček R., Doškař J., Plevka P.. Structure and Genome Release of Twort-Like Myoviridae Phage with a Double-Layered Baseplate. Proc. Natl. Acad. Sci. U.S.A. 2016;113:9351–9356. doi: 10.1073/pnas.1605883113. PubMed DOI PMC
Eyer L., Pantůček R., Zdráhal Z., Konečná H., Kašpárek P., Růžičková V., Hernychová L., Preisler J., Doškař J.. Structural Protein Analysis of the Polyvalent Staphylococcal Bacteriophage 812. Proteomics. 2007;7:64–72. doi: 10.1002/pmic.200600280. PubMed DOI
Finstrlová A., Mašlaňová I., Blasdel Reuter B. G., Doškař J., Götz F., Pantůček R.. Global Transcriptomic Analysis of Bacteriophage-Host Interactions between a Kayvirus Therapeutic Phage and Staphylococcus aureus . Microbiol. Spectr. 2022;10:e00123-22. doi: 10.1128/spectrum.00123-22. PubMed DOI PMC
Botka, T. ; Pantůček, R. ; Mašlaňová, I. ; Benešík, M. ; Petráš, P. ; Růžičková, V. ; Havlíčková, P. ; Varga, M. ; Zemličková, H. ; Koláčková, I. ; et al. Lytic and Genomic Properties of Spontaneous Host-Range PubMed DOI PMC
Ajuebor J., Buttimer C., Arroyo-Moreno S., Chanishvili N., Gabriel E. M., O’Mahony J., McAuliffe O., Neve H., Franz C., Coffey A.. Comparison of Staphylococcus Phage K with Close Phage Relatives Commonly Employed in Phage Therapeutics. Antibiotics (Basel) 2018;7(37):37. doi: 10.3390/antibiotics7020037. PubMed DOI PMC
Petrovic Fabijan A., Lin R. C. Y., Ho J., Maddocks S., Ben Zakour N. L., Iredell J. R.. et al. Safety of Bacteriophage Therapy in Severe Staphylococcus aureus Infection. Nat. Microbiol. 2020;5:465–472. doi: 10.1038/s41564-019-0634-z. PubMed DOI
Bíňovský J., Šiborová M., Nováček J., Bárdy P., Baška R., Škubník K., Botka T., Benešík M., Pantůček R., Tripsianes K.. et al. Cell Attachment and Tail Contraction of Staphylococcus aureus Phage phi812. bioRxiv. 2024 doi: 10.1101/2024.09.19.613683. preprint. DOI
Penewit K., Holmes E. A., McLean K., Ren M., Waalkes A., Salipante S. J.. Efficient and Scalable Precision Genome Editing in Staphylococcus aureus through Conditional Recombineering and CRISPR/Cas9-Mediated Counterselection. mBio. 2018;9:e00067-18. doi: 10.1128/mBio.00067-18. PubMed DOI PMC
Needham, P. ; Page, R. C. ; Yehl, K. . Phage-Layer Interferometry: A Companion Diagnostic for Phage Therapy and a Bacterial Testing Platform. Sci. Rep. 2024, 14, (6026). 10.1038/s41598-024-55776-1. PubMed DOI PMC
Åman T., Auer S., Hytönen V. P., Määttä J. A.. Performance of Label-Free Biosensors as a Function of Layer Thickness. Biosens. Bioelectron. X. 2024;21:100556. doi: 10.1016/j.biosx.2024.100556. DOI
De Keyser P., Kalichuk V., Zögg T., Wohlkönig A., Schenck S., Brunner J., Pardon E., Steyaert J.. A Biosensor-Based Phage Display Selection Method for Automated, High-Throughput Nanobody Discovery. Biosens. Bioelectron. 2025;271:116951. doi: 10.1016/j.bios.2024.116951. PubMed DOI
Deisenhofer J.. Crystallographic Refinement and Atomic Models of a Human Fc Fragment and Its Complex with Fragment B of Protein a from Staphylococcus aureus at 2.9- and 2.8-.ANG. Resolution. Biochemistry. 1981;20:2361–2370. doi: 10.1021/bi00512a001. PubMed DOI
Kreiswirth B. N., Löfdahl S., Betley M. J., O’Reilly M., Schlievert P. M., Bergdoll M. S., Novick R. P.. The Toxic Shock Syndrome Exotoxin Structural Gene Is Not Detectably Transmitted by a Prophage. Nature. 1983;305:709–712. doi: 10.1038/305709a0. PubMed DOI
Nair D., Memmi G., Hernandez D., Bard J., Beaume M., Gill S., Francois P., Cheung A. L.. Whole-Genome Sequencing of Staphylococcus aureus Strain RN4220, a Key Laboratory Strain Used in Virulence Research, Identifies Mutations That Affect Not Only Virulence Factors but Also the Fitness of the Strain. J. Bacteriol. 2011;193:2332–2335. doi: 10.1128/JB.00027-11. PubMed DOI PMC
Wagner E., Doskar J., Götz F.. Physical and Genetic Map of the Genome of Staphylococcus carnosus TM300. Microbiology. 1998;144:509–517. doi: 10.1099/00221287-144-2-509. PubMed DOI
Charpentier E., Anton A. I., Barry P., Alfonso B., Fang Y., Novick R. P.. Novel Cassette-Based Shuttle Vector System for Gram-Positive Bacteria. Appl. Environ. Microbiol. 2004;70:6076–6085. doi: 10.1128/AEM.70.10.6076-6085.2004. PubMed DOI PMC
Jumper J., Evans R., Pritzel A., Green T., Figurnov M., Ronneberger O., Tunyasuvunakool K., Bates R., Zidek A., Potapenko A.. et al. Highly Accurate Protein Structure Prediction with AlphaFold. Nature. 2021;596:583–589. doi: 10.1038/s41586-021-03819-2. PubMed DOI PMC
Pettersen E. F., Goddard T. D., Huang C. C., Meng E. C., Couch G. S., Croll T. I., Morris J. H., Ferrin T. E.. UCSF ChimeraX: Structure Visualization for Researchers, Educators, and Developers. Protein Sci. 2021;30:70–82. doi: 10.1002/pro.3943. PubMed DOI PMC