Escherichia coli phage SU10 belongs to the genus Kuravirus from the class Caudoviricetes of phages with short non-contractile tails. In contrast to other short-tailed phages, the tails of Kuraviruses elongate upon cell attachment. Here we show that the virion of SU10 has a prolate head, containing genome and ejection proteins, and a tail, which is formed of portal, adaptor, nozzle, and tail needle proteins and decorated with long and short fibers. The binding of the long tail fibers to the receptors in the outer bacterial membrane induces the straightening of nozzle proteins and rotation of short tail fibers. After the re-arrangement, the nozzle proteins and short tail fibers alternate to form a nozzle that extends the tail by 28 nm. Subsequently, the tail needle detaches from the nozzle proteins and five types of ejection proteins are released from the SU10 head. The nozzle with the putative extension formed by the ejection proteins enables the delivery of the SU10 genome into the bacterial cytoplasm. It is likely that this mechanism of genome delivery, involving the formation of the tail nozzle, is employed by all Kuraviruses.

Central European Institute of Technology Kamenice 753 5 625 00 Brno Czech Republic

Department of Molecular Biosciences The Wenner Gren Institute Stockholm University 106 91 Stockholm Sweden

Faculty of Science Masaryk University Kamenice 753 5 625 00 Brno Czech Republic

Zobrazit více v PubMed

Ackermann H-W, Nguyen Y-M, Delage R. Un nouveau bactériophage d’entérobactéries à tête allongée et queue courte. Annales de. l’Institut Pasteur / Virologie. 1981;132:229–234.

Mirzaei MK, Eriksson H, Kasuga K, Haggård-Ljungquist E, Nilsson AS. Genomic, Proteomic, Morphological, and Phylogenetic Analyses of vB_EcoP_SU10, a Podoviridae Phage with C3 Morphology. PLoS ONE. 2011;9:e116294. PubMed PMC

Savalia D, et al. Genomic and Proteomic Analysis of phiEco32, a Novel Escherichia coli Bacteriophage. J. Mol. Biol. 2008;377:774–789. PubMed PMC

Kropinski AM, Lingohr EJ, Ackermann H-W. The genome sequence of enterobacterial phage 7-11, which possesses an unusually elongated head. Arch. Virol. 2011;156:149–151. PubMed

Kaper JB, Nataro JP, Mobley HLT. Pathogenic Escherichia coli. Nat. Rev. Microbiol. 2004;2:123–140. PubMed

Górski A, et al. Phage Therapy: What Have We Learned? Viruses. 2018;10:288. PubMed PMC

Haines MEK, et al. Analysis of Selection Methods to Develop Novel Phage Therapy Cocktails Against Antimicrobial Resistant Clinical Isolates of Bacteria. Front. Microbiol. 2021;12:613529. PubMed PMC

Terwilliger A, et al. Phage Therapy Related Microbial Succession Associated with Successful Clinical Outcome for a Recurrent Urinary Tract Infection. Viruses. 2021;13:2049. PubMed PMC

Fokine A, Rossmann MG. Molecular architecture of tailed double-stranded DNA phages. Bacteriophage. 2014;4:e28281. PubMed PMC

Casjens, S. R. & Molineux, I. J. Short Noncontractile Tail Machines: Adsorption and DNA Delivery by Podoviruses. in 143–179 10.1007/978-1-4614-0980-9_7 (2012). PubMed

Leiman PG, et al. The Structures of Bacteriophages K1E and K1-5 Explain Processive Degradation of Polysaccharide Capsules and Evolution of New Host Specificities. J Molecular Biol. 2007;371:836–849. PubMed

Tang L, Marion WR, Cingolani G, Prevelige PE, Johnson JE. Three-dimensional structure of the bacteriophage P22 tail machine. EMBO J. 2005;24:2087–2095. PubMed PMC

Cuervo A, et al. Structural Characterization of the Bacteriophage T7 Tail Machinery. J. Biol. Chem. 2013;288:26290–26299. PubMed PMC

Olia AS, Casjens S, Cingolani G. Structure of phage P22 cell envelope–penetrating needle. Nat. Struct. Mol. Biol. 2007;14:1221–1226. PubMed

Cuervo A, et al. Structures of T7 bacteriophage portal and tail suggest a viral DNA retention and ejection mechanism. Nat. Commun. 2019;10:3746. PubMed PMC

Hrebík D, et al. Structure and genome ejection mechanism of Staphylococcus aureus phage P68. Sci. Adv. 2019;5:eaaw7414. PubMed PMC

Choi K, et al. Insight into DNA and Protein Transport in Double-stranded DNA Viruses: The Structure of Bacteriophage N4. Microsc. Microanalysis. 2008;14:1574–1575. PubMed PMC

Jiang W, et al. Structure of epsilon15 bacteriophage reveals genome organization and DNA packaging/injection apparatus. Nature. 2006;439:612–616. PubMed PMC

Jin Y, et al. Bacteriophage P22 ejects all of its internal proteins before its genome. Virology. 2015;485:128–134. PubMed PMC

Grayson P, Molineux IJ. Is phage DNA ‘injected’ into cells—biologists and physicists can agree. Curr. Opin. Microbiol. 2007;10:401–409. PubMed PMC

Van Valen D, et al. A Single-Molecule Hershey-Chase Experiment. Curr. Biol. 2012;22:1339–1343. PubMed PMC

Molineux IJ, Panja D. Popping the cork: mechanisms of phage genome ejection. Nat. Rev. Microbiol. 2013;11:194–204. PubMed

Evilevitch A. The mobility of packaged phage genome controls ejection dynamics. Elife. 2018;7:e37345. PubMed PMC

Chen Y-J, et al. Two-Stage Dynamics of In Vivo Bacteriophage Genome Ejection. Phys. Rev. X. 2018;8:021029.

Duda RL, Teschke CM. The amazing HK97 fold: versatile results of modest differences. Curr. Opin. Virol. 2019;36:9–16. PubMed PMC

Chang JT, et al. Visualizing the Structural Changes of Bacteriophage Epsilon15 and Its Salmonella Host during Infection. J. Mol. Biol. 2010;402:731–740. PubMed PMC

Chang J, Weigele P, King J, Chiu W, Jiang W. Asymmetric Reconstruction of Bacteriophage P22 Reveals Organization of its DNA Packaging and Infecting Machinery. Structure. 2006;14:1073–1082. PubMed

Chen W, et al. Structural changes of a bacteriophage upon DNA packaging and maturation. Protein Cell. 2020;11:374–379. PubMed PMC

Lokareddy RK, et al. Portal protein functions akin to a DNA-sensor that couples genome-packaging to icosahedral capsid maturation. Nat. Commun. 2017;8:14310. PubMed PMC

Bayfield OW, et al. Cryo-EM structure and in vitro DNA packaging of a thermophilic virus with supersized T=7 capsids. Proc. Natl Acad. Sci. 2019;116:3556–3561. PubMed PMC

Pyra A, et al. Tail tubular protein A: a dual-function tail protein of Klebsiella pneumoniae bacteriophage KP32. Sci. Rep. 2017;7:2223. PubMed PMC

Kęsik-Szeloch A, et al. Characterising the biology of novel lytic bacteriophages infecting multidrug resistant Klebsiella pneumoniae. Virol. J. 2013;10:100. PubMed PMC

Fülöp V, Jones DT. β Propellers: structural rigidity and functional diversity. Curr. Opin. Struct. Biol. 1999;9:715–721. PubMed

Jumper J, et al. Highly accurate protein structure prediction with AlphaFold. Nature. 2021;596:583–589. PubMed PMC

Kostyuchenko VA, et al. Three-dimensional structure of bacteriophage T4 baseplate. Nat. Struct. Mol. Biol. 2003;10:688–693. PubMed

Bartual SG, et al. Structure of the bacteriophage T4 long tail fiber receptor-binding tip. Proc. Natl Acad. Sci. 2010;107:20287–20292. PubMed PMC

Pellizza L, et al. Structure of the putative long tail fiber receptor-binding tip of a novel temperate bacteriophage from the Antarctic bacterium Bizionia argentinensis JUB59. J. Struct. Biol. 2020;212:107595. PubMed

Harada K, et al. Crystal structure of the C-terminal domain of Mu phage central spike and functions of bound calcium ion. Biochimica et. Biophysica Acta (BBA) - Proteins Proteom. 2013;1834:284–291. PubMed

Browning C, Shneider MM, Bowman VD, Schwarzer D, Leiman PG. Phage Pierces the Host Cell Membrane with the Iron-Loaded Spike. Structure. 2012;20:326–339. PubMed

Olia AS, Casjens S, Cingolani G. Structural plasticity of the phage P22 tail needle gp26 probed with xenon gas. Protein Sci. 2009;18:537–548. PubMed PMC

Taylor NMI, et al. Structure of the T4 baseplate and its function in triggering sheath contraction. Nature. 2016;533:346–352. PubMed

Yamashita E, et al. The host-binding domain of the P2 phage tail spike reveals a trimeric iron-binding structure. Acta Crystallogr. Sect. F. Struct. Biol. Crystallization Commun. 2011;67:837–841. PubMed PMC

Brinkers S, Dietrich HRC, de Groote FH, Young IT, Rieger B. The persistence length of double stranded DNA determined using dark field tethered particle motion. J. Chem. Phys. 2009;130:215105. PubMed

Parent KN, et al. OmpA and OmpC are critical host factors for bacteriophage Sf6 entry in S higella. Mol. Microbiol. 2014;92:47–60. PubMed PMC

Parent KN, Gilcrease EB, Casjens SR, Baker TS. Structural evolution of the P22-like phages: Comparison of Sf6 and P22 procapsid and virion architectures. Virology. 2012;427:177–188. PubMed PMC

Reyes-Robles T, et al. Vibrio cholerae Outer Membrane Vesicles Inhibit Bacteriophage Infection. J. Bacteriol. 2018;200:e00792-17. PubMed PMC

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

Zhang K. Gctf: Real-time CTF determination and correction. J. Struct. Biol. 2016;193:1–12. PubMed PMC

Kremer JR, Mastronarde DN, McIntosh JR. Computer Visualization of Three-Dimensional Image Data Using IMOD. J. Struct. Biol. 1996;116:71–76. PubMed

Heumann JM, Hoenger A, Mastronarde DN. Clustering and variance maps for cryo-electron tomography using wedge-masked differences. J. Struct. Biol. 2011;175:288–299. PubMed PMC

Nicastro D, et al. The Molecular Architecture of Axonemes Revealed by Cryoelectron Tomography. Science (1979) 2006;313:944–948. PubMed

Wagner T, et al. SPHIRE-crYOLO is a fast and accurate fully automated particle picker for cryo-EM. Commun. Biol. 2019;2:218. PubMed PMC

Zivanov J, et al. New tools for automated high-resolution cryo-EM structure determination in RELION-3. Elife. 2018;7:e42166. PubMed PMC

de la Rosa-Trevín JM, et al. Xmipp 3.0: An improved software suite for image processing in electron microscopy. J. Struct. Biol. 2013;184:321–328. PubMed

Shaikh TR, et al. SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs. Nat. Protoc. 2008;3:1941–1974. PubMed PMC

Tang G, et al. EMAN2: An extensible image processing suite for electron microscopy. J. Struct. Biol. 2007;157:38–46. PubMed

Pfab J, Phan NM, Si D. DeepTracer for fast de novo cryo-EM protein structure modeling and special studies on CoV-related complexes. Proc Natl Acad Sci USA. 2021;118:e2017525118. PubMed PMC

Afonine PV, et al. Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Crystallogr. Section D Struct. Biol. 2018;74:531–544. PubMed PMC

Croll TI. ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Acta Crystallogr. Section D Struct. Biol. 2018;74:519–530. PubMed PMC

Goddard TD, et al. UCSF ChimeraX: Meeting modern challenges in visualization and analysis. Protein Sci. 2018;27:14–25. PubMed PMC

Pettersen EF, et al. UCSF ChimeraX: Structure visualization for researchers, educators, and developers. Protein Sci. 2021;30:70–82. PubMed PMC

Pettersen EF, et al. UCSF Chimera—A visualization system for exploratory research and analysis. J Comput. Chem. 2004;25:1605–1612. PubMed

Schindelin J, et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods. 2012;9:676–682. PubMed PMC

Himes BA, Zhang P. emClarity: software for high-resolution cryo-electron tomography and subtomogram averaging. Nat. Methods. 2018;15:955–961. PubMed PMC

Burt A, et al. Complete structure of the chemosensory array core signalling unit in an E. coli minicell strain. Nat. Commun. 2020;11:743. PubMed PMC

Suhanovsky MM, Teschke CM. Nature׳s favorite building block: Deciphering folding and capsid assembly of proteins with the HK97-fold. Virology. 2015;479–480:487–497. PubMed PMC

Are kuravirus capsid diameters quantized? The first all-atom genome tracing method for double-stranded DNA viruses