An ssDNA virus infecting archaea: A new lineage of viruses with a membrane envelope

Molecular Microbiology

Volumn 72, Issue 2, 2009, Pages 307-319

  Pietilä, Maija K ^a   Roine, Elina ^a   Paulin, Lars ^a   Kalkkinen, Nisse ^a   Bamford, Dennis H ^a  

^a UNIVERSITY OF HELSINKI   (Finland)

Author keywords

[No Author keywords available]

Indexed keywords

LIPID; SINGLE STRANDED DNA; VIRUS PROTEIN;

ARCHAEBACTERIUM; ARTICLE; CYTOLYSIS; DNA VIRUS; DOUBLE STRANDED DNA BREAK; ELECTRON MICROSCOPY; GENE SEQUENCE; GENOME; HALORUBRUM PLEOMORPHIC VIRUS 1; ISOLATION PROCEDURE; LIPID ANALYSIS; NONHUMAN; OPEN READING FRAME; PLASMID; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN STRUCTURE; SPECIES DIVERSITY; VIRION; VIRUS ENVELOPE; VIRUS GENE; VIRUS MORPHOLOGY;

ARCHAEAL VIRUSES; DNA VIRUSES; DNA, SINGLE-STRANDED; DNA, VIRAL; GENOME, VIRAL; HALORUBRUM; MICROSCOPY, ELECTRON; SEQUENCE ANALYSIS, DNA; VIRAL ENVELOPE PROTEINS; VIRION;

ARCHAEA; HALORUBRUM; SSDNA VIRUSES;

EID: 64149084027     PISSN: 0950382X     EISSN: 13652958     Source Type: Journal    
DOI: 10.1111/j.1365-2958.2009.06642.x     Document Type: Article

References (52)

1. Ackermann, H.W. (2007) 5500 phages examined in the electron microscope. Arch Virol 152 : 227 243.
2. Ackermann, H.W. Kropinski, A.M. (2007) Curated list of prokaryote viruses with fully sequenced genomes. Res Microbiol 158 : 555 566.
3. Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W. Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25 : 3389 3402.
4. Arahal, D.R., Dewhirst, F.E., Paster, B.J., Volcani, B.E. Ventosa, A. (1996) Phylogenetic analyses of some extremely halophilic archaea isolated from Dead Sea water, determined on the basis of their 16S rRNA sequences. Appl Environ Microbiol 62 : 3779 3786.
5. Arnold, H.P., Ziese, U. Zillig, W. (2000) SNDV, a novel virus of the extremely thermophilic and acidophilic archaeon Sulfolobus. Virology 272 : 409 416.
6. Bamford, D.H. (2003) Do viruses form lineages across different domains of life? Res Microbiol 154 : 231 236.
7. Bamford, D.H., Ravantti, J.J., Rönnholm, G., Laurinavičius, S., Kukkaro, P., Dyall-Smith, M., et al. (2005a) Constituents of SH1, a novel lipid-containing virus infecting the halophilic euryarchaeon Haloarcula hispanica. J Virol 79 : 9097 9107.
8. Bamford, D.H., Grimes, J.M. Stuart, D.I. (2005b) What does structure tell us about virus evolution? Curr Opin Struct Biol 15 : 655 663.
9. Bath, C. Dyall-Smith, M.L. (1998) His1, an archaeal virus of the Fuselloviridae family that infects Haloarcula hispanica. J Virol 72 : 9392 9395.
10. Bath, C., Cukalac, T., Porter, K. Dyall-Smith, M.L. (2006) His1 and His2 are distantly related, spindle-shaped haloviruses belonging to the novel virus group, Salterprovirus. Virology 350 : 228 239.
11. Benson, S.D., Bamford, J.K., Bamford, D.H. Burnett, R.M. (2004) Does common architecture reveal a viral lineage spanning all three domains of life? Mol Cell 16 : 673 685.
12. Besemer, J. Borodovsky, M. (1999) Heuristic approach to deriving models for gene finding. Nucleic Acids Res 27 : 3911 3920.
13. Bradford, M.M. (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72 : 248 254.
14. Dyall-Smith, M., Tang, S.L. Bath, C. (2003) Haloarchaeal viruses: how diverse are they? Res Microbiol 154 : 309 313.
15. Dybvig, K., Nowak, J.A., Sladek, T.L. Maniloff, J. (1985) Identification of an enveloped phage, mycoplasma virus L172, that contains a 14-kilobase single-stranded DNA genome. J Virol 53 : 384 390.
16. Edwards, U., Rogall, T., Blöcker, H., Emde, M. Böttger, E.C. (1989) Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Res 17 : 7843 7853.
17. Fauquet, C.M., Mayo, M.A., Maniloff, J., Desselberger, U. Ball, L.A. (eds) (2005) Virus Taxonomy, Eighth Report of the International Committee on Taxonomy of Viruses. London : Elsevier. Academic Press.
18. Folch, J., Lees, M. Sloane Stanley, G.H. (1957) A simple method for the isolation and purification of total lipides from animal tissues. J Biol Chem 226 : 497 509.
19. Guixa-Boixareu, N., Calderón-Paz, J.I., Heldal, M., Bratbak, G. Pedrós-Alió, C. (1996) Viral lysis and bacterivory as prokaryotic loss factors along a salinity gradient. Aquat Microb Ecol 11 : 215 227.
20. Häring, M., Rachel, R., Peng, X., Garrett, R.A. Prangishvili, D. (2005a) Viral diversity in hot springs of Pozzuoli, Italy, and characterization of a unique archaeal virus, Acidianus bottle-shaped virus, from a new family, the Ampullaviridae. J Virol 79 : 9904 9911.
21. Häring, M., Vestergaard, G., Rachel, R., Chen, L., Garrett, R.A. Prangishvili, D. (2005b) Virology: independent virus development outside a host. Nature 436 : 1101 1102.
22. Hayashi, M., Hayashi, M.N. Spiegelman, S. (1963) Replicating form of a single-stranded DNA virus: isolation and properties. Science 140 : 1313 1316.
23. Holmes, M., Pfeifer, F. Dyall-Smith, M. (1994) Improved shuttle vectors for Haloferax volcanii including a dual-resistance plasmid. Gene 146 : 117 121.
24. Holmes, M.L., Pfeifer, F. Dyall-Smith, M.L. (1995) Analysis of the halobacterial plasmid pHK2 minimal replicon. Gene 153 : 117 121.
25. Ilyina, T.V. Koonin, E.V. (1992) Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria. Nucleic Acids Res 20 : 3279 3285.
26. Jäälinoja, H.T., Roine, E., Laurinmäki, P., Kivelä, H.M., Bamford, D.H. Butcher, S.J. (2008) Structure and host-cell interaction of SH1, a membrane-containing, halophilic euryarchaeal virus. Proc Natl Acad Sci USA 105 : 8008 8013.
27. Janekovic, D., Wunderl, S., Holz, I., Zillig, W., Gierl, A. Neumann, H. (1983) TTV1, TTV2 and TTV3, a family of viruses of the extremely thermophilic, anaerobic, sulphur reducing archaebacterium Thermoproteus tenax. Mol Gen Genet 102 : 39 45.
28. Kates, M. (1972) Techniques of Lipidology: Isolation, Analysis and Identification of Lipids. Amsterdam : North-Holland Publishing Co.
29. König, H., Rachel, R. Claus, H. (2007) Proteinaceous surface layers of Archaea: ultrastructure and biochemistry. In Archaea - Molecular and Cellular Biology. Cavicchioli, R. (ed.). Washington, DC : American Soc. Microbiol. Press, pp. 315 340.
30. Krupovič, M. Bamford, D.H. (2007) Putative prophages related to lytic tailless marine dsDNA phage PM2 are widespread in the genomes of aquatic bacteria. BMC Genomics 8 : 236.
31. Matsudaira, P. (1987) Sequence from picomole quantities of proteins electroblotted onto polyvinylidene difluoride membranes. J Biol Chem 262 : 10035 10038.
32. Mei, Y., Chen, J., Sun, D., Chen, D., Yang, Y., Shen, P. Chen, X. (2007) Induction and preliminary characterization of a novel halophage SNJ1 from lysogenic Natrinema sp. F5. Can J Microbiol 53 : 1106 1110.
33. Nuttall, S.D. Dyall-Smith, M.L. (1993) HF1 and HF2: novel bacteriophages of halophilic archaea. Virology 197 : 678 684.
34. Oren, A., Bratbak, G. Heldal, M. (1997) Occurrence of virus-like particles in the Dead Sea. Extremophiles 1 : 143 149.
35. Pagaling, E., Haigh, R.D., Grant, W.D., Cowan, D.A., Jones, B.E., Ma, Y., et al. (2007) Sequence analysis of an archaeal virus isolated from a hypersaline lake in Inner Mongolia, China. BMC Genomics 8 : 410.
36. Porter, K., Russ, B.E. Dyall-Smith, M.L. (2007) Virus-host interactions in salt lakes. Curr Opin Microbiol 10 : 418 424.
37. Poutanen, M., Salusjärvi, L., Ruohonen, L., Penttilä, M. Kalkkinen, N. (2001) Use of matrix-assisted laser desorption/ionization time-of-flight mass mapping and nanospray liquid chromatography/electrospray ionization tandem mass spectrometry sequence tag analysis for high sensitivity identification of yeast proteins separated by two-dimensional gel electrophoresis. Rapid Commun Mass Spectrom 15 : 1685 1692.
38. Prangishvili, D. Garrett, R.A. (2005) Viruses of hyperthermophilic Crenarchaea. Trends Microbiol 13 : 535 542.
39. Prangishvili, D., Forterre, P. Garrett, R.A. (2006a) Viruses of the Archaea: a unifying view. Nat Rev Microbiol 4 : 837 848.
40. Prangishvili, D., Garrett, R.A. Koonin, E.V. (2006b) Evolutionary genomics of archaeal viruses: unique viral genomes in the third domain of life. Virus Res 117 : 52 67.
41. Rice, P., Longden, I. Bleasby, A. (2000) EMBOSS: the European molecular biology open software suite. Trends Genet 16 : 276 277.
42. Schägger, H. von Jagow, G. (1987) Tricine-sodium dodecyl sulfate-polyacrylamide gel electrophoresis for the separation of proteins in the range from 1 to 100 kDa. Anal Biochem 166 : 368 379.
43. Schleper, C., Kubo, K. Zillig, W. (1992) The particle SSV1 from the extremely thermophilic archaeon Sulfolobus is a virus: demonstration of infectivity and of transfection with viral DNA. Proc Natl Acad Sci USA 89 : 7645 7649.
44. Schnabel, H., Zillig, W., Pfäffle, M., Schnabel, R., Michel, H. Delius, H. (1982) Halobacterium halobium phage H. EMBO J 1 : 87 92.
45. Shevchenko, A., Wilm, M., Vorm, O. Mann, M. (1996) Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. Anal Chem 68 : 850 858.
46. Staden, R., Beal, K.F. Bonfield, J.K. (2000) The Staden package, 1998. Methods Mol Biol 132 : 115 130.
47. Strömsten, N.J., Bamford, D.H. Bamford, J.K. (2005) In vitro DNA packaging of PRD1: a common mechanism for internal-membrane viruses. J Mol Biol 348 : 617 629.
48. Walker, J.E., Saraste, M., Runswick, M.J. Gay, N.J. (1982) Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J 1 : 945 951.
49. Witte, A., Baranyi, U., Klein, R., Sulzner, M., Luo, C., Wanner, G., et al. (1997) Characterization of Natronobacterium magadii phage Ch1, a unique archaeal phage containing DNA and RNA. Mol Microbiol 23 : 603 616.
50. Woese, C.R., Kandler, O. Wheelis, M.L. (1990) Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 87 : 4576 4579.
51. Xiang, X., Chen, L., Huang, X., Luo, Y., She, Q. Huang, L. (2005) Sulfolobus tengchongensis spindle-shaped virus STSV1: virus-host interactions and genomic features. J Virol 79 : 8677 8686.
52. Zhang, Z., Schwartz, S., Wagner, L. Miller, W. (2000) A greedy algorithm for aligning DNA sequences. J Comput Biol 7 : 203 214.