Abstract
For many years, X-ray crystallography has been exclusively used by structural biologists for resolving virus structures and viral proteins at atomic resolution level. However, the discovery of electron microscopy, especially Cryo-electron microscopy (cryoEM), has enabled us to visualise the detailed structural features of biological macromolecules in a more accurate way. In recent years, cryoEM has made sudden progress in its use due to high-end microscopes, improved detectors and modernised software. It is now possible to get near-atomic resolution three-dimensional viral maps using cryoEM. Among viruses, the bacterial viruses or bacteriophages are the most fascinating objects for the structural biologists as they are highly symmetrical particles. The development of cryoEM has also made it easy to determine the structures of these highly symmetrical macromolecules at near-atomic resolution.
Similar content being viewed by others
References
Adams MH (1959) Bacteriophages. Wiley (Interscience), New York
William CS (2012) The strange history of phage therapy. Bacteriophage 2(2):130–133. https://doi.org/10.4161/bact.20757
Daniel BG, Jonathan ES, Chad WE, Vincent AF (2013) Novel bacteriophage lysin with broad lytic activity protects against mixed infection by Streptococcus pyogenes and methicillin-resistant Staphylococcus aureus. Antimicrob Agents Chemother 57(6):2743–2750. https://doi.org/10.1128/aac.02526-12
Yen M, Carrins LS, Camilli A (2017) A cocktail of three virulent bacteriophages prevents Vibrio cholerae infection in animal models. Nat Commun 1(8):14187. https://doi.org/10.1038/ncomms14187
Chattopadhyay DJ, Sarkar BL, Ansari MQ, Chakrabarti BK, Roy MK, Ghosh AN, Pal SC (1993) New phage ty** scheme for Vibrio cholerae O1 biotype El Tor strains. J Clin Microbiol 31:1579–1585
Taylor KA, Glaeser RM (1976) Electron microscopy of frozen, hydrated protein crystals. J Ultrastruct Res 55:448–456
Heide HG (1982) Design and operation of cold stages. Ultramicroscopy 10:125–154
McDowall AW, Chang JJ, Freeman R, Lepault J, Walter CA, Dubochet J (1983) Electron microscopy of frozen hydrated sections of vitreous ice and vitrified biological samples. J Microsc 131:1–9
DeRosier DJ, Klug A (1968) Reconstruction of three dimensional structures from electron micrographs. Nature 217:130–134. https://doi.org/10.1038/217130a
Roman IK, Josue GB, Inara A, Javier V, Andris K, Kaspars T, Jose C, Abraham JK (2016) Asymmetric cryo-EM reconstruction of phage MS2 reveals genome structure in situ. Nat Commun 7:12524
Chen Z, Sun L, Zhang Z, Fokine A, Sanchez VP, Hanein D, Jiang W, Rossmann MG, Rao VB (2017) Cryo-EM structure of the bacteriophage T4 isometric head at 3.3-Å resolution and its relevance to the assembly of icosahedral viruses. Proc Natl Acad Sci USA. 114(39):E8184–E8193. https://doi.org/10.1073/pnas
Rossmann MG (2013) Structure of viruses: a short history. Q Rev Biophys 46:133–180. https://doi.org/10.1017/s0033583513000012
Caspar DL (1956) Structure of bushy stunt virus. Nature 177:475–476
Klug A, Finch JT, Franklin RE (1957) Structure of turnip yellow mosaic virus. Nature 179:683–684. https://doi.org/10.1038/179683b0
Ruska H (1940) Visualization of bacteriophage lysis in the hypermicroscope. Naturwissenschaften 28:45–46
Hall CE (1966) Introduction to electron microscopy, 2nd edn. McGraw-Hill, New York
Brenner S, Horne RW (1959) A negative staining method for high resolution electron microscopy of viruses. Biochim Biophys Acta 34:103–110. https://doi.org/10.1016/0006-3002(59)90237-9
Crowther RA (1971) Procedures for three-dimensional reconstruction of spherical viruses by Fourier synthesis from electron micrographs. Philos Trans R Soc Lond B Biol 261:221–230. https://doi.org/10.1098/rstb.1971.0054
Rosenthal PB (2015) High symmetry to high resolution in biological electron microscopy: a commentary on Crowther (1971) ‘Procedures for three-dimensional reconstruction of spherical viruses by Fourier synthesis from electron micrographs’. Philos Trans R Soc Lond B Biol Sci 370:1666. https://doi.org/10.1098/rstb.2014.0345
Battisti AJ, Meng G, Winkler DC, Mcginnes LW, Plevka P, Steven AC, Morrison TG, Rossmann MG (2012) Structure and assembly of a paramyxovirus matrix protein. Proc Natl Acad Sci USA 109:13996–14000
Rossmann MG, Battisti AJ, Plevka P (2011) Future prospects, recent advances in electron cryomicroscopy. In: Ludtke SJ, Prasad BVV (eds) Advances in protein chemistry and structural biology, vol 82. Part B. Academic Press, San Diego, pp 101–121
Harrison SC (2010) Virology. Looking inside adenovirus. Science 329:1026–1027
Liu H, ** L, Koh SB, Atanasov I, Schein S, Wu L, Zhou ZH (2010) Atomic structure of human adenovirus by cryoEM reveals interactions among protein networks. Science 329:1038–1043
Reddy VS, Natchiar SK, Stewart PL, Nemerow GR (2010) Crystal structure of human adenovirus at 3.5 Å resolution. Science 329:1071–1075
Abad-Zapatero C, Abdel-Meguid SS, Johnson JE, Leslie AG, Rayment I, Rossmann MG, Suck D, Tsukihara T (1980) Structure of southern bean mosaic virus at 2.8 Å resolution. Nature 286:33–39
Harrison SC, Olson AJ, Schutt CE, Winkler FK, Bricogne G (1978) Tomato bushy stunt virus at 2.9 Å resolution. Nature 276:368–373
Jiang W, Tang L (2017) Atomic cryoEM structures of viruses. Curr Opin Struct Biol 46:122–129. https://doi.org/10.1016/j.sbi.2017.07.002
Chiu W, Baker ML, Jiang W, Dougherty M, Schmid MF (2005) Electron cryomicroscopy of biological machines at subnanometer resolution. Structure 13:363–372
Baker ML, Zhang J, Ludtke SJ, Chiu W (2010) CryoEM of macromolecular assemblies at near-atomic resolution. Nat Protoc 5:1697–1708
Hryc CF, Chen DH, Chiu W (2012) Near-atomic-resolution CryoEM for molecular virology. Curr Opin Virol 1(2):110–117. https://doi.org/10.1016/j.coviro.2011.05.019
Suloway C, Pulokas J, Fellmann D, Cheng A, Guerra F, Quispe J, Stagg S, Potter CS, Carragher B (2005) Automated molecular microscopy: the new Leginon system. J Struct Biol 151:41–60
Henderson R, Glaeser RM (1985) Quantitative analysis of image contrast in electron micrographs of beam sensitive crystals. Ultramicroscopy 16:139–150
Kuhlbrandt W (2014) The resolution revolution. Science 343:1443–1444
Nogales E (2015) Scheres SH (2015) Cryo-EM: a unique tool for the visualization of macromolecular complexity. Mol Cell 58(4):677–689. https://doi.org/10.1016/j.molcel.2015.02.019
Brilot AF, Chen JZ, Cheng A, Pan J, Harrison SC, Potter CS, Carragher B, Henderson R, Grigorieff N (2012) Beam-induced motion of vitrified specimen on holey carbon film. J Struct Biol 177:630–637
Campbell MG, Cheng A, Brilot AF, Moeller A, Lyumkis D, Veesler D, Pan J, Harrison SC, Potter CS, Carragher B, Grigorieff N (2012) Movies of ice-embedded particles enhance resolution in electron cryomicroscopy. Structure 20:1823–1828
Xueming L, Paul M, Shawn Z, Christopher RB, Michael BB, Sander G, David AA, Yifan C (2013) Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM. Nat Methods 10:584–590. https://doi.org/10.1038/nmeth.2472
Hayat MA, Miller SE (1990) Negative staining. In: Hayat MA, Miller SE (eds) Negative staining. McGraw-Hill Publishing Company, New York, pp 36–48
Carlo SD, Harris JR (2011) Negative staining and Cryo-negative staining of Macromolecules and Viruses for TEM. Micron 42(2):117–131. https://doi.org/10.1016/j.micron.2010.06.003
Dubochet J, McOowall AW (1981) Vitrification of pure water for electron microscopy. J Microsc 124:KP3–RP4
Thompson RF, Walker MC, Siebert A, Stephen PM, Neil AR (2016) An introduction to sample preparation and imaging by cryo-electron microscopy for structural biology. Methods 100:3–15. https://doi.org/10.1016/j.ymeth.2016.02.017
Baker LA, Rubinstein JL (2010) Radiation damage in electron cryomicroscopy. Methods Enzymol 481:371–388
Dubochet J, Adrian M, Chang JJ, Homo JC, Lepault J, McDowall AW (1988) Cryo-electron microscopy of vitrified specimens. Q Rev Biophys 21:129–228. https://doi.org/10.1017/s0033583500004297
Henderson R (2004) Realizing the potential of electron cryo-microscopy. Q Rev Biophys 37(1):3–13. https://doi.org/10.1017/s0033583504003920
Ackermann HW, Furniss AL, Kasatiya SS, Lee JV, Mbiquino A, Newman FS, Takeya K, Viev JF (1983) Morphology of Vibrio cholerae ty** phages. Ann Virol 134E:387–404
Leiman PG, Shneider MM (2012) Contractile tail machines of bacteriophages. Adv Exp Med Biol 726:93–114. https://doi.org/10.1007/978-1-4614-0980-9_5
Leiman PG, Arisaka F, Raaij MJ, Kostyuchenko VA, Aksyuk AA, Kanamaru S, Rossmann MG (2010) Morphogenesis of T4 tail and tail fibers. Virol J 3(7):355. https://doi.org/10.1186/1743-422x-7-355
Plisson C, White HE, Auzat I, Zafarani A, Sao-Jose C, Lhuillier S, Tavares P, Orlova EV (2007) Structure of bacteriophage SPP1 tail reveals trigger for DNA ejection. EMBO J 26(15):3720–3728
Pell LG, Kanelis V, Donaldson LW, Howell PL, Davidson AR (2009) The phage lambda major tail protein structure reveals a common evolution for long-tailed phages and the type VI bacterial secretion system. Proc Natl Acad Sci USA 106(11):4160–4165
Veesler D, Spinelli S, Mahony J, Lichiere J, Blangy S, Bricogne G, Legrand P, Ortiz-Lombardia M, Campanacci V, Sinderen D, Cambillau C (2012) Structure of the phage TP901-1 1.8 MDa baseplate suggests an alternative host adhesion mechanism. Proc Natl Acad Sci USA 109(23):8954–8958. https://doi.org/10.1073/pnas.1200966109
Sciara G, Bebeacua C, Bron P, Tremblay D, Ortiz-Lombardia M, Lichiere J, Heel MV, Campanacci V, Moineau S, Cambillau C (2010) Structure of lactococcal phage p2 baseplate and its mechanism of activation. Proc Natl Acad Sci USA 107(15):6852–6857
Leodevico LI, Terje HOD, Cynthia LM, Holland CR, Zorina B, Robert M, Rossmann MG, Baker TS, Nino LI (1995) DNA packaging intermediates of bacteriophage φX174. Structure 4:353–363. https://doi.org/10.1016/s0969-2126(01)00167-8
Fokine A, Chipman PR, Leiman PG, Mesyanzhinov VV, Rao VB, Rossmann MG (2004) Molecular architecture of the prolate head of bacteriophage T4. Proc Natl Acad Sci USA 101:6003–6008
Aksyuk AA, Leiman PG, Kurochkina LP, Schneider MM, Kostyuchenko V, Mesyanzhinov VV, Rossmann MG (2009) The tail sheath structure of bacteriophage T4: a molecular machine for infecting bacteria. EMBO J 28:821–829
Aksyuk AA, Kurochkina LP, Fokine A, Forouhar F, Mesyanzhinov VV, Tong L, Rossmann MG (2011) Structural conservation of the Myoviridae phage tail sheath protein fold. Structure 19:1885–1894
Kostyuchenko VA, Chipman PR, Leiman PG, Arisaka F, Mesyanzhinov VV, Rossmann MG (2005) The tail structure of bacteriophage T4 and its mechanism of contraction. Nat Struct Mol Biol 12:810–813
Kostyuchenko VA, Leiman PG, Chipman PR, Kanamaru S, Van MJ, Arisaka F, Mesyanzhinov VV, Rossmann MG (2003) Three-dimensional structure of bacteriophage T4 baseplate. Nat Struct Biol 10:688–693
Aksyuk AA, Leiman PG, Shneider MM, Mesyanzhinov VV, Rossmann MG (2009) The structure of gene product 6 of bacteriophage T4, the hinge-pin of the baseplate. Structure 17:800–808
Berget PB, King J (1978) Isolation and characterization of precursors in T4 baseplate assembly. The complex of gene 10 and gene 11 products. J Mol Biol 124:469–486
Coombs DF, Arisaka F (1994) T4 tail structure and function. In: Karam JD (ed) Molecular Biology of Bacteriophage T4. American Society for Microbiology, Washington, D.C., pp 259–281
Lander GC, Evilevitch A, Jeembaeva M, Potter CS, Carragher B, Johnson JE (2008) Bacteriophage lambda stabilization by auxiliary protein gpD: timing, location, mechanism of attachment determined by cryoEM. Structure 9:1399–1406. https://doi.org/10.1016/j.str.2008.05.016
Guoa F, Liua Z, Fanga P, Zhang Q, Wright ET, Wu W, Zhang C, Vago F, Rena Y, Jakana J, Chiu W, Serwer P, Jiang W (2014) Capsid expansion mechanism of bacteriophage T7 revealed by multistate atomic models derived from cryo-EM reconstructions. PNAS 111:E4606–E4614. https://doi.org/10.1073/pnas.1407020111
Hu B, Margolin W, Molineux IJ, Liu J (2013) The bacteriophage T7 virion undergoes extensive structural remodeling during infection. Science. https://doi.org/10.1126/science.1231887
Parent KN, Tang J, Cardone G, Gilcrease EB, Janssen ME, Olson NH, Casjens SR, Baker TS (2014) Three-dimensional reconstructions of the bacteriophage CUS-3 virion reveal a conserved coat protein I-domain but a distinct tailspike receptor-binding domain. Virology 464–465:55–66. https://doi.org/10.1016/j.virol.2014.06.017
Baker TS, Olson NH, Fuller SD (1999) Adding the third dimension to virus life cycles: three-dimensional reconstruction of Icosahedral viruses from cryo-electron micrographs. Microbiol Mol Biol Rev 63(4):862–922
Dokland T, Lindqvist BH, Fuller SD (1992) Image reconstruction from cryo-electron micrographs reveals the morphopoietic mechanism in the P2–P4 bacteriophage system. EMBO J 11(3):839–846
Butcher SJ, Manole V, Karhu NJ (2012) Lipid-containing viruses: bacteriophage PRD1 assembly. Adv Exp Med Biol 726:365–377. https://doi.org/10.1007/978-1-4614-0980-9_16
Butcher SJ, Bamford DH, Fuller SD (1995) DNA packaging orders the membrane of bacteriophage PRD1. EMBO J 14(24):6078–6086
Butcher SJ, Dokland T, Ojala PM, Bamford DH, Fuller SD (1997) Intermediates in the assembly pathway of the double-stranded RNA virus φ6. EMBO J 16(14):4477–4487
Clark CA, Beltrame J, Manning PA (1991) The oac gene encoding a lipopolysaccharide O-antigen acetylase maps adjacent to the integrase-encoding gene on the genome of Shigella flexneri bacteriophage Sf6. Gene 107(1):43
Verma NK, Brandt JM, Verma DJ, Lindberg AA (1991) Molecular characterization of the O-acetyl transferase gene of converting bacteriophage SF6 that adds group antigen 6 to Shigella flexneri. Mol Microbiol 1:71–75
Parent KN, Gilcrease EB, Casjens SR, Baker TS (2012) Structural evolution of the P22-like phages: comparison of Sf6 and P22 procapsid and virion architectures. Virology 427(2):177–188. https://doi.org/10.1016/j.virol.2012.01.040
Tang J, Lander GC, Olia AS, Li R, Casjens S, Prevelige PJ, Cingolani G, Baker TS, Johnson JE (2011) Peering down the barrel of a bacteriophage portal: the genome packaging and release valve in p22. Structure 19(4):496–502. https://doi.org/10.1016/j.str.2011.02.010
Mitra K, Ghosh AN (2007) Characterization of Vibrio cholerae O1 ElTor ty** phage S5. Arch Virol. https://doi.org/10.1007/s00705-007-1021-2
Dutta M, Ghosh AN (2007) Physicochemical Characterization of El Tor Vibriophage S20. Intervirology 50:264–272. https://doi.org/10.1159/000102469
Sen A, Ghosh AN (2017) Visualizing a Vibrio cholerae O1 El Tor ty** bacteriophage belonging to the Myoviridae group and the packaging of its genomic ends inside the phage capsid. J Biomol Struct Dyn 1:1–14. https://doi.org/10.1080/07391102.2017.1368416
Dai W, Hodes A, Hui WH, Gingery M, Miller JF, Zhou ZH (2010) Three-dimensional structure of tropism-switching Bordetella bacteriophage. PNAS 107(9):4347–4352. https://doi.org/10.1073/pnas.0915008107
Rajagopal BS, Reilly BE, Anderson DL (1993) Bacillus subtilis mutants defective in bacteriophage phi 29 head assembly. J Bacteriol 175(8):2357–2362
**ang Y, Morais MC, Battisti AJ, Grimes S, Jardine PJ, Anderson DL, Rossmann MG (2006) Structural changes of bacteriophage 29 upon DNA packaging and release. EMBO J 25:5229–5239
White HE, Sherman MB, Brasilès S, Jacquet E, Seavers P, Tavares P, Orlova EV (2012) Capsid structure and its stability at the late stages of bacteriophage SPP1 assembly. J Virol 86(12):6768–6777. https://doi.org/10.1128/JVI.00412-12
Sassi M, Bebeacua C, Drancourt M, Cambillaua C (2013) The first structure of a mycobacteriophage, the Mycobacterium abscessus subsp. bolletii Phage Araucaria. J Virol 87(14):8099–8109
Novácek J, Siborová M, Benešík M, Pant R, Doškar J, Plevka P (2016) Structure and genome release of Twort-like Myoviridae phage with a double-layered baseplate. PNAS 113(33):9351–9356. https://doi.org/10.1073/pnas.1605883113
Bebeacua C, Lai L, Vegge CS, Brøndsted L, Heel MV, Veesler D, Cambillauc C (2013) Visualizing a complete Siphoviridae member by single-particle electron microscopy: the structure of Lactococcal Phage TP901-1. J Virol 87:1061–1068
Bebeacua C, Tremblay D, Farenc C, Chartier MC, Sadovskaya I, Heel MV, Veesler D, Moineau S, Cambillaua C (2013) Structure, adsorption to host, and infection mechanism of virulent Lactococcal Phage p2. J Virol 87(22):12302–12312
Dai W, Fu C, Raytcheva D, Flanagan J, Khant HA, Liu X, Rochat RH, Pettinge CH, Piret J, Ludtke SJ, Nagayama K, Schmid MF, King JA, Chiu W (2013) Visualizing virus assembly intermediates inside marine cyanobacteria. Nature. https://doi.org/10.1038/nature12604
Davis JE, Strauss JH, Sinsheimer R (1961) Bacteriophage MS2: another RNA Phage. Science 134:1427
Koning RI, Blanco JG, Akopjana I, Vargas J, Kazaks A, Tars K, Carazo JS, Koster AJ (2016) Asymmetric cryo-EM reconstruction of phage MS2 reveals genome structure in situ. Nat Commun 26(7):12524. https://doi.org/10.1038/ncomms12524
Raoult D (2015) How the virophage compels the need to readdress the classification of microbes. Virology 477:119–124
Zhang X, Sun S, **ang Y, Wong J, Klose T, Raoult D, Rossmann MG (2012) Structure of Sputnik, a virophage, at 3.5-Å resolution. PNAS 109(45):18431–18436. https://doi.org/10.1073/pnas.1211702109
Bakhshinejad B, Karimi M, Sadeghizadeh M (2014) Bacteriophages and medical oncology: targeted gene therapy of cancer. Med Oncol 31(8):110. https://doi.org/10.1007/s12032-014-0110-9
Sun Z, Omari K, Kotecha A, Stuart DI, Poranen M, Huiskonen J (2017) Double-stranded RNA virus outer shell assembly by bona fide domain-swap**. Nat Commun 8:14814. https://doi.org/10.1038/ncomms14814
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Das, S., Ghosh, A.N. Recent Advancements in 3-D Structure Determination of Bacteriophages: from Negative Stain to CryoEM. J Indian Inst Sci 98, 247–260 (2018). https://doi.org/10.1007/s41745-018-0082-4
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s41745-018-0082-4