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Structure and genome ejection mechanism of Staphylococcus aureus phage P68

. 2019 Oct ; 5 (10) : eaaw7414. [epub] 20191016

Language English Country United States Media electronic-ecollection

Document type Journal Article, Research Support, Non-U.S. Gov't

Phages infecting Staphylococcus aureus can be used as therapeutics against antibiotic-resistant bacterial infections. However, there is limited information about the mechanism of genome delivery of phages that infect Gram-positive bacteria. Here, we present the structures of native S. aureus phage P68, genome ejection intermediate, and empty particle. The P68 head contains 72 subunits of inner core protein, 15 of which bind to and alter the structure of adjacent major capsid proteins and thus specify attachment sites for head fibers. Unlike in the previously studied phages, the head fibers of P68 enable its virion to position itself at the cell surface for genome delivery. The unique interaction of one end of P68 DNA with one of the 12 portal protein subunits is disrupted before the genome ejection. The inner core proteins are released together with the DNA and enable the translocation of phage genome across the bacterial membrane into the cytoplasm.

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Chhibber S., Kaur T., Sandeep K., Co-therapy using lytic bacteriophage and linezolid: Effective treatment in eliminating methicillin resistant Staphylococcus aureus (MRSA) from diabetic foot infections. PLOS ONE 8, e56022 (2013). PubMed PMC

European Centre for Disease Prevention and Control/European Medicines Agency, “The bacterial challenge: Time to react” (ECDC/EMEA Joint Technical Report, European Centre for Disease Prevention and Control/European Medicines Agency, 2009).

Kurlenda J., Grinholc M., Alternative therapies in Staphylococcus aureus diseases. Acta Biochim. Pol. 59, 171–184 (2012). PubMed

World Health Organization, Global Priority List of Antibiotic-Resistant Bacteria to Guide Research, Discovery, and Development of New Antibiotics (World Health Organization, 2017).

Takemura-Uchiyama I., Uchiyama J., Osanai M., Morimoto N., Asagiri T., Ujihara T., Daibata M., Sugiura T., Matsuzaki S., Experimental phage therapy against lethal lung-derived septicemia caused by Staphylococcus aureus in mice. Microbes Infect. 16, 512–517 (2014). PubMed

Aleshkin A. V., Ershova O. N., Volozhantsev N. V., Svetoch E. A., Popova A. V., Rubalskii E. O., Borzilov A. I., Aleshkin V. A., Afanas’ev S. S., Karaulov A. V., Galimzyanov K. M., Rubalsky O. V., Bochkareva S. S., Phagebiotics in treatment and prophylaxis of healthcare-associated infections. Bacteriophage 6, e1251379 (2017). PubMed PMC

Leiman P. G., Battisti A. J., Bowman V. D., Stummeyer K., Mühlenhoff M., Gerardy-Schahn R., Scholl D., Molineux I. J., The structures of bacteriophages K1E and K1-5 explain processive degradation of polysaccharide capsules and evolution of new host specificities. J. Mol. Biol. 371, 836–849 (2007). PubMed

Hu B., Margolin W., Molineux I. J., Liu J., The bacteriophage T7 virion undergoes extensive structural remodeling during infection. Science 339, 576–579 (2013). PubMed PMC

Xiang Y., Morais M. C., Battisti A. J., Grimes S., Jardine P. J., Anderson D. L., Rossmann M. G., Structural changes of bacteriophage phi29 upon DNA packaging and release. EMBO J. 25, 5229–5239 (2006). PubMed PMC

Aksyuk A. A., Bowman V. D., Kaufmann B., Fields C., Klose T., Holdaway H. A., Fischetti V. A., Rossmann M. G., Structural investigations of a Podoviridae streptococcus phage C1, implications for the mechanism of viral entry. Proc. Natl. Acad. Sci. U.S.A. 109, 14001–14006 (2012). PubMed PMC

Jiang W., Baker M. L., Jakana J., Weigele P. R., King J., Chiu W., Backbone structure of the infectious epsilon15 virus capsid revealed by electron cryomicroscopy. Nature 451, 1130–1134 (2008). PubMed

Baker M. L., Hryc C. F., Zhang Q., Wu W., Jakana J., Haase-Pettingell C., Afonine P. V., Adams P. D., King J. A., Jiang W., Chiu W., Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modeling. Proc. Natl. Acad. Sci. U.S.A. 110, 12301–12306 (2013). PubMed PMC

Jiang W., Chang J., Jakana J., Weigele P., King J., Chiu W., Structure of epsilon15 bacteriophage reveals genome organization and DNA packaging/injection apparatus. Nature 439, 612–616 (2006). PubMed PMC

Chen D.-H., Baker M. L., Hryc C. F., DiMaio F., Jakana J., Wu W., Dougherty M., Haase-Pettingell C., Schmid M. F., Jiang W., Baker D., King J. A., Chiu W., Structural basis for scaffolding-mediated assembly and maturation of a dsDNA virus. Proc. Natl. Acad. Sci. U.S.A. 108, 1355–1360 (2011). PubMed PMC

Lander G. C., Khayat R., Li R., Prevelige P. E., Potter C. S., Carragher B., Johnson J. E., The P22 tail machine at subnanometer resolution reveals the architecture of an infection conduit. Structure 17, 789–799 (2009). PubMed PMC

Li X., Gerlach D., du X., Larsen J., Stegger M., Kühner P., Peschel A., Xia G., Winstel V., An accessory wall teichoic acid glycosyltransferase protects Staphylococcus aureus from the lytic activity of Podoviridae. Sci. Rep. 5, 17219 (2015). PubMed PMC

Steinbacher S., Baxa U., Miller S., Weintraub A., Seckler R., Huber R., Crystal structure of phage P22 tailspike protein complexed with Salmonella sp. O-antigen receptors. Proc. Natl. Acad. Sci. U.S.A. 93, 10584–10588 (1996). PubMed PMC

Steinbacher S., Seckler R., Miller S., Steipe B., Huber R., Reinemer P., Crystal structure of P22 tailspike protein: Interdigitated subunits in a thermostable trimer. Science 265, 383–386 (1994). PubMed

Xiang Y., Leiman P. G., Li L., Grimes S., Anderson D. L., Rossmann M. G., Crystallographic insights into the autocatalytic assembly mechanism of a bacteriophage tail spike. Mol. Cell 34, 375–386 (2009). PubMed PMC

Stummeyer K., Dickmanns A., Muhlenhoff M., Gerardy-Schahn R., Ficner R., Crystal structure of the polysialic acid–degrading endosialidase of bacteriophage K1F. Nat. Struct. Mol. Biol. 12, 90–96 (2005). PubMed

Olia A. S., Prevelige P. E. Jr., Johnson J. E., Cingolani G., Three-dimensional structure of a viral genome-delivery portal vertex. Nat. Struct. Mol. Biol. 18, 597–603 (2011). PubMed PMC

Bhardwaj A., Sankhala R. S., Olia A. S., Brooke D., Casjens S. R., Taylor D. J., Prevelige P. E. Jr., Cingolani G., Structural plasticity of the protein plug that traps newly packaged genomes in Podoviridae Virions. J. Biol. Chem. 291, 215–226 (2016). PubMed PMC

Vybiral D., Takáč M., Loessner M., Witte A., von Ahsen U., Bläsi U., Complete nucleotide sequence and molecular characterization of two lytic Staphylococcus aureus phages: 44AHJD and P68. FEMS Microbiol. Lett. 219, 275–283 (2003). PubMed

Morais M. C., Kanamaru S., Badasso M. O., Koti J. S., Owen B. A. L., McMurray C. T., Anderson D. L., Rossmann M. G., Bacteriophage φ29 scaffolding protein gp7 before and after prohead assembly. Nat. Struct. Biol. 10, 572–576 (2003). PubMed

Dearborn A. D., Wall E. A., Kizziah J. L., Klenow L., Parker L. K., Manning K. A., Spilman M. S., Spear J. M., Christie G. E., Dokland T., Competing scaffolding proteins determine capsid size during mobilization of Staphylococcus aureus pathogenicity islands. eLife 6, e30822 (2017). PubMed PMC

Wikoff W. R., Liljas L., Duda R. L., Tsuruta H., Hendrix R. W., Johnson J. E., Topologically linked protein rings in the bacteriophage HK97 capsid. Science 289, 2129–2133 (2000). PubMed

Sun L., Zhang X., Gao S., Rao P. A., Padilla-Sanchez V., Chen Z., Sun S., Xiang Y., Subramaniam S., Rao V. B., Rossmann M. G., Cryo-EM structure of the bacteriophage T4 portal protein assembly at near-atomic resolution. Nat. Commun. 6, 7548 (2015). PubMed PMC

Lebedev A. A., Krause M. H., Isidro A. L., Vagin A. A., Orlova E. V., Turner J., Dodson E. J., Tavares P., Antson A. A., Structural framework for DNA translocation via the viral portal protein. EMBO J. 26, 1984–1994 (2007). PubMed PMC

Simpson A. A., Tao Y., Leiman P. G., Badasso M. O., He Y., Jardine P. J., Olson N. H., Morais M. C., Grimes S., Anderson D. L., Baker T. S., Rossmann M. G., Structure of the bacteriophage φ29 DNA packaging motor. Nature 408, 745–750 (2000). PubMed PMC

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. 113, 9351–9356 (2016). PubMed PMC

Lokareddy R. K., Sankhala R. S., Roy A., Afonine P. V., Motwani T., Teschke C. M., Parent K. N., Cingolani G., Portal protein functions akin to a DNA-sensor that couples genome-packaging to icosahedral capsid maturation. Nat. Commun. 8, 14310 (2017). PubMed PMC

Tremblay D. M., Tegoni M., Spinelli S., Campanacci V., Blangy S., Huyghe C., Desmyter A., Labrie S., Moineau S., Cambillau C., Receptor-binding protein of Lactococcus lactis phages: Identification and characterization of the saccharide receptor-binding site. J. Bacteriol. 188, 2400–2410 (2006). PubMed PMC

Ricagno S., Campanacci V., Blangy S., Spinelli S., Tremblay D., Moineau S., Tegoni M., Cambillau C., Crystal structure of the receptor-binding protein head domain from Lactococcus lactis phage bIL170. J. Virol. 80, 9331–9335 (2006). PubMed PMC

Desmyter A., Farenc C., Mahony J., Spinelli S., Bebeacua C., Blangy S., Veesler D., van Sinderen D., Cambillau C., Viral infection modulation and neutralization by camelid nanobodies. Proc. Natl. Acad. Sci. U.S.A. 110, E1371–E1379 (2013). PubMed PMC

Takáč M., Bläsi U., Phage P68 virion-associated protein 17 displays activity against clinical isolates of Staphylococcus aureus. Antimicrob. Agents Chemother. 49, 2934–2940 (2005). PubMed PMC

Nelson D., Schuch R., Chahales P., Zhu S., Fischetti V. A., PlyC: A multimeric bacteriophage lysin. Proc. Natl. Acad. Sci. U.S.A. 103, 10765–10770 (2006). PubMed PMC

McGowan S., Buckle A. M., Mitchell M. S., Hoopes J. T., Gallagher D. T., Heselpoth R. D., Shen Y., Reboul C. F., Law R. H. P., Fischetti V. A., Whisstock J. C., Nelson D. C., X-ray crystal structure of the streptococcal specific phage lysin PlyC. Proc. Natl. Acad. Sci. U.S.A. 109, 12752–12757 (2012). PubMed PMC

Koç C., Xia G., Kühner P., Spinelli S., Roussel A., Cambillau C., Stehle T., Structure of the host-recognition device of Staphylococcus aureus phage ϕ11. Sci. Rep. 6, 27581 (2016). PubMed PMC

Xu L., Benson S. D., Butcher S. J., Bamford D. H., Burnett R. M., The receptor binding protein P2 of PRD1, a virus targeting antibiotic-resistant bacteria, has a novel fold suggesting multiple functions. Structure 11, 309–322 (2003). PubMed

Sycheva L. V., Shneider M. M., Sykilinda N. N., Ivanova M. A., Miroshnikov K. A., Leiman P. G., Crystal structure and location of gp131 in the bacteriophage phiKZ virion. Virology 434, 257–264 (2012). PubMed

Xu J., Gui M., Wang D., Xiang Y., The bacteriophage ϕ29 tail possesses a pore-forming loop for cell membrane penetration. Nature 534, 544–547 (2016). PubMed

Zheng S. Q., Palovcak E., Armache J.-P., Verba K. A., Cheng Y., Agard D. A., MotionCor2: Anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017). PubMed PMC

Rohou A., Grigorieff N., CTFFIND4: Fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 192, 216–221 (2015). PubMed PMC

Tang G., Peng L., Baldwin P. R., Mann D. S., Jiang W., Rees I., Ludtke S. J., EMAN2: An extensible image processing suite for electron microscopy. J. Struct. Biol. 157, 38–46 (2007). PubMed

Scheres S. H., RELION: Implementation of a Bayesian approach to cryo-EM structure determination. J. Struct. Biol. 180, 519–530 (2012). PubMed PMC

Guo F., Jiang W., Single particle cryo-electron microscopy and 3-D reconstruction of viruses. Methods Mol. Biol. 1117, 401–443 (2014). PubMed PMC

de la Rosa-Trevín J. M., Otón J., Marabini R., Zaldívar A., Vargas J., Carazo J. M., Sorzano C. O., Xmipp 3.0: An improved software suite for image processing in electron microscopy. J. Struct. Biol. 184, 321–328 (2013). PubMed

Chang J., Weigele P., King J., Chiu W., Jiang W., Cryo-EM asymmetric reconstruction of bacteriophage P22 reveals organization of its DNA packaging and infecting machinery. Structure 14, 1073–1082 (2006). PubMed

Pettersen E. F., Goddard T. D., Huang C. C., Couch G. S., Greenblatt D. M., Meng E. C., Ferrin T. E., UCSF Chimera—A visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004). PubMed

Pintilie G. D., Zhang J., Goddard T. D., Chiu W., Gossard D. C., Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions. J. Struct. Biol. 170, 427–438 (2010). PubMed PMC

Ilca S. L., Kotecha A., Sun X., Poranen M. M., Stuart D. I., Huiskonen J. T., Localized reconstruction of subunits from electron cryomicroscopy images of macromolecular complexes. Nat. Commun. 6, 8843 (2015). PubMed PMC

Emsley P., Cowtan K., Coot: Model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132 (2004). PubMed

Murshudov G. N., Skubák P., Lebedev A. A., Pannu N. S., Steiner R. A., Nicholls R. A., Winn M. D., Long F., Vagin A. A., REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr. D Biol. Crystallogr. 67, 355–367 (2011). PubMed PMC

Adams P. D., Afonine P. V., Bunkóczi G., Chen V. B., Davis I. W., Echols N., Headd J. J., Hung L. W., Kapral G. J., Grosse-Kunstleve R. W., McCoy A. J., Moriarty N. W., Oeffner R., Read R. J., Richardson D. C., Richardson J. S., Terwilliger T. C., Zwart P. H., PHENIX: A comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213–221 (2010). PubMed PMC

Kabsch W., Integration, scaling, space-group assignment and post-refinement. Acta Crystallogr. D Biol. Crystallogr. 66, 133–144 (2010). PubMed PMC

Kleywegt G. J., Read R. J., Not your average density. Structure 5, 1557–1569 (1997). PubMed

McCoy A. J., Grosse-Kunstleve R. W., Adams P. D., Winn M. D., Storoni L. C., Read R. J., Phaser crystallographic software. J. Appl. Cryst. 40, 658–674 (2007). PubMed PMC

Langer G., Cohen S. X., Lamzin V. S., Perrakis A., Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7. Nat. Protoc. 3, 1171–1179 (2008). PubMed PMC

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