New, closely related haloarchaeal viral elements with different nucleic acid types

Journal of Virology

Volumn 84, Issue 7, 2010, Pages 3682-3689

  Roine, Elina ^a   Kukkaro, Petra ^a,c   Paulin, Lars ^a   Laurinavičius, Simonas ^b   Domanska, Aušra ^a,d   Somerharju, Pentti ^b   Bamford, Dennis H ^a  

^a UNIVERSITY OF HELSINKI   (Finland)

^b UNIVERSITY OF HELSINKI   (Finland)

^c DUKE NUS MEDICAL SCHOOL   (Singapore)

^d Deutsches Krebsforshungszentrum ^*  (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA; NUCLEIC ACID; PHOSPHOLIPID; SINGLE STRANDED DNA;

ARTICLE; CHROMOSOME; GENE REPLICATION; GENETIC ANALYSIS; HALOARCULA; HALOARCULA HISPANICA; HALOARCULA HISPANICA PLEOMORPHIC VIRUS 1; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMID; PREDICTION; PRIORITY JOURNAL; VIRUS; VIRUS GENOME;

ARCHAEAL VIRUSES; DNA, VIRAL; GENOME, VIRAL; HALOARCULA; OPEN READING FRAMES; PHOSPHOLIPIDS; PLASMIDS; VIRAL PROTEINS;

ARCHAEA; DNA VIRUSES; HALOARCULA HISPANICA; HALOFERAX VOLCANII; HALORUBRUM;

EID: 77949366453     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/JVI.01879-09     Document Type: Article

References (64)

1. Abrescia, N. G. A., J. M. Grimes, E. E. Fry, J. J. Ravantti, D. H. Bamford, and D. I. Stuart. 2009. What does it take to make a virus: the concept of the viral "self." In P. G. Stockley and R. Twarock (ed.), Emerging topics in physical virology, in press. Imperial College Press, London, England.
2. Ackermann, H. W. 2007. 5500 Phages examined in the electron microscope. Arch. Virol. 152:227-243.
3. Altschul, S. F., T. L. Madden, A. A. Schäffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
4. Bamford, D. H. 2003. Do viruses form lineages across different domains of life? Res. Microbiol. 154:231-236.
5. Bamford, D. H., R. M. Burnett, and D. I. Stuart. 2002. Evolution of viral structure. Theor. Popul. Biol. 61:461-470.
6. Bamford, D. H., J. M. Grimes, and D. I. Stuart. 2005. What does structure tell us about virus evolution? Curr. Opin. Struct. Biol. 15:655-663.
7. Bamford, D. H., and L. Mindich. 1980. Electron microscopy of cells infected with nonsense mutants of bacteriophage Φ6. Virology 107:222-228.
8. Bamford, D. H., J. J. Ravantti, G. Rönnholm, S. Laurinavičius, P. Kukkaro, M. Dyall-Smith, P. Somerharju, N. Kalkkinen, and J. K. Bamford. 2005. Constituents of SH1, a novel lipid-containing virus infecting the halophilic euryarchaeon Haloarcula hispanica. J. Virol. 79:9097-9107.
9. Bartlett, E. M., and D. H. Lewis. 1970. Spectrophotometric determination of phosphate esters in the presence or absence of orthophosphate. Anal. Biochem. 36:159-167.
10. Bath, C., T. Cukalac, K. Porter, and M. L. Dyall-Smith. 2006. His1 and His2 are distantly related, spindle-shaped haloviruses belonging to the novel virus group, salterprovirus. Virology 350:228-239.
11. Bath, C., and M. L. Dyall-Smith. 1998. His1, an archaeal virus of the Fuselloviridae family that infects Haloarcula hispanica. J. Virol. 72:9392-9395.
12. Benson, S. D., J. K. Bamford, D. H. Bamford, and R. M. Burnett. 1999. Viral evolution revealed by bacteriophage PRD1 and human adenovirus coat protein structures. Cell 98:825-833.
13. Benson, S. D., J. K. Bamford, D. H. Bamford, and R. M. Burnett. 2004. Does common architecture reveal a viral lineage spanning all three domains of life? Mol. Cell 16:673-685.
14. Besemer, J., and M. Borodovsky. 1999. Heuristic approach to deriving models for gene finding. Nucleic Acids Res. 27:3911-3920.
15. 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.
16. Breitbart, M., P. Salamon, B. Andresen, J. M. Mahaffy, A. M. Segall, D. Mead, F. Azam, and F. Rohwer. 2002. Genomic analysis of uncultured marine viral communities. Proc. Natl. Acad. Sci. U. S. A. 99:14250-14255.
17. Brüssow, H. 2001. Phages of dairy bacteria. Annu. Rev. Microbiol. 55:283-303.
18. Brüssow, H., and R. W. Hendrix. 2002. Phage genomics: small is beautiful. Cell 108:13-16.
19. Campbell, A. 1994. Comparative molecular biology of lambdoid phages. Annu. Rev. Microbiol. 48:193-222.
20. Casjens, S. 2003. Prophages and bacterial genomics: what have we learned thus far? Mol. Microbiol. 49:277-300.
21. Casjens, S. R. 2008. Diversity among the tailed-bacteriophages that infect the Enterobacteriaceae. Res. Microbiol. 159:340-348.
22. Clore, A. J., and K. M. Stedman. 2007. The SSV1 viral integrase is not essential. Virology 361:103-111.
23. Corcelli, A., M. Colella, G. Mascolo, F. P. Fanizzi, and M. Kates. 2000. A novel glycolipid and phospholipid in the purple membrane. Biochemistry 39:3318-3326.
24. Desnues, C., B. Rodriguez-Brito, S. Rayhawk, S. Kelley, T. Tran, M. Haynes, H. Liu, M. Furlan, L. Wegley, B. Chau, Y. Ruan, D. Hall, F. E. Angly, R. A. Edwards, L. Li, R. V. Thurber, R. P. Reid, J. Siefert, V. Souza, D. L. Valentine, B. K. Swan, M. Breitbart, and F. Rohwer. 2008. Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature 452:340-343.
25. Diez, B., J. Anton, N. Guixa-Boixereu, C. Pedros-Alio, and F. Rodriguez-Valera. 2000. Pulsed-field gel electrophoresis analysis of virus assemblages present in a hypersaline environment. Int. Microbiol. 3:159-164.
26. Dinsdale, E. A., R. A. Edwards, D. Hall, F. Angly, M. Breitbart, J. M. Brulc, M. Furlan, C. Desnues, M. Haynes, L. Li, L. McDaniel, M. A. Moran, K. E. Nelson, C. Nilsson, R. Olson, J. Paul, B. R. Brito, Y. Ruan, B. K. Swan, R. Stevens, D. L. Valentine, R. V. Thurber, L. Wegley, B. A. White, and F. Rohwer. 2008. Functional metagenomic profiling of nine biomes. Nature 452:629-632.
27. Dittmer, J. C., and R. L. Lester. 1964. A simple, specific spray for the detection of phospholipids on thin-layer chromatograms. J. Lipid Res. 15: 126-127.
28. Fokine, A., P. G. Leiman, M. M. Shneider, B. Ahvazi, K. M. Boeshans, A. C. Steven, L. W. Black, V. V. Mesyanzhinov, and M. G. Rossmann. 2005. Structural and functional similarities between the capsid proteins of bacteriophages T4 and HK97 point to a common ancestry. Proc. Natl. Acad. Sci. U. S. A. 102:7163-7168.
29. Folch, J., M. Lees, and G. H. Sloane-Stanley. 1957. A simple method for the isolation and purification of total lipids from animal tissues. J. Biol. Chem. 226:497-509.
30. Gasteiger, E., A. Gattiker, C. Hoogland, I. Ivanyi, R. D. Appel, and A. Bairoch. 2003. ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res. 31:3784-3788.
31. Guixa-Boixereu, N., K. Lysnes, and C. Pedros-Alio. 1999. Viral lysis and bacterivory during a phytoplankton bloom in a coastal water microcosm. Appl. Environ. Microbiol. 65:1949-1958.
32. Holmes, M. L., and M. L. Dyall-Smith. 1990. A plasmid vector with a selectable marker for halophilic archaebacteria. J. Bacteriol. 172:756-761.
33. Holmes, M. L., S. D. Nuttall, and M. L. Dyall-Smith. 1991. Construction and use of halobacterial shuttle vectors and further studies on Haloferax DNA gyrase. J. Bacteriol. 173:3807-3813.
34. Holmes, M. L., F. Pfeifer, and M. L. Dyall-Smith. 1995. Analysis of the halobacterial plasmid pHK2 minimal replicon. Gene 153:117-121.
35. Huang, X., and W. Miller. 1991. A time-efficient, linear-space local similarity algorithm. Adv. Appl. Math. 12:337-357.
36. Ilyina, T. V., and E. V. Koonin. 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.
37. Jäälinoja, H. T., E. Roine, P. Laurinmäki, H. M. Kivelä, D. H. Bamford, and S. J. Butcher. 2008. Structure and host-cell interaction of SH1, a membrane-containing, halophilic euryarchaeal virus. Proc. Natl. Acad. Sci. U. S. A. 105:8008-8013.
38. Jalasvuori, M., S. T. Jaatinen, S. Laurinavičius, E. Ahola-Iivarinen, N. Kalkkinen, D. H. Bamford, and J. K. Bamford. 2009. The closest relatives of icosahedral viruses of thermophilic bacteria are among viruses and plasmids of the halophilic archaea. J. Virol. 83:9388-9397.
39. Koonin, E. V., Y. I. Wolf, K. Nagasaki, and V. V. Dolja. 2009. The complexity of the virus world. Nat. Rev. Microbiol. 7:250.
40. Koths, K., and D. Dressler. 1980. The rolling circle-capsid complex as an intermediate in ΦX DNA replication and viral assembly. J. Biol. Chem. 255:4328-4338.
41. Krogh, A., B. Larsson, G. von Heijne, and E. L. Sonnhammer. 2001. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305:567-580.
42. Krupovič, M., and D. H. Bamford. 2008. Virus evolution: how far does the double beta-barrel viral lineage extend? Nat. Rev. Microbiol. 6:941-948.
43. Kukkaro, P., and D. H. Bamford. 2009. Virus-host interactions in environments with a wide range of ionic strengths. Environ. Microbiol. Rep. 1:71-77.
44. Lubbers, M. W., N. R. Waterfield, T. P. Beresford, R. W. Le Page, and A. W. Jarvis. 1995. Sequencing and analysis of the prolate-headed lactococcal bacteriophage c2 genome and identification of the structural genes. Appl. Environ. Microbiol. 61:4348-4356.
45. Lupas, A., M. Van Dyke, and J. Stock. 1991. Predicting coiled coils from protein sequences. Science 252:1162-1164.
46. Nunes-Düby, S. E., H. J. Kwon, R. S. Tirumalai, T. Ellenberger, and A. Landy. 1998. Similarities and differences among 105 members of the Int. family of site-specific recombinases. Nucleic Acids Res. 26:391-406.
47. Oren, A., G. Bratbak, and M. Heldal. 1997. Occurrence of virus-like particles in the Dead Sea. Extremophiles 1:143-149.
48. Pfeiffer, F., A. Broicher, T. Gillich, K. Klee, J. Mejia, M. Rampp, and D. Oesterhelt. 2008. Genome information management and integrated data analysis with HaloLex. Arch. Microbiol. 190:281-299.
49. Pietilä, M. K., S. Laurinavičius, J. Sund, E. Roine, and D. H. Bamford. 2010. The ssDNA genome of novel archaeal virus HRPV-1 is enclosed in the envelope decorated with glycoprotein spikes. J. Virol. 84:788-798.
50. Pietilä, M. K., E. Roine, L. Paulin, N. Kalkkinen, and D. H. Bamford. 2009. An ssDNA virus infecting Archaea: a new lineage of viruses with a membrane envelope. Mol. Microbiol. 72:307-319.
51. Porter, K., P. Kukkaro, J. K. Bamford, C. Bath, H. M. Kivelä, M. L. Dyall-Smith, and D. H. Bamford. 2005. SH1: a novel, spherical halovirus isolated from an Australian hypersaline lake. Virology 335:22-33.
52. Porter, K., B. E. Russ, J. Yang, and M. L. Dyall-Smith. 2008. The transcription programme of the protein-primed halovirus SH1. Microbiology 154: 3599-3608.
53. Prangishvili, D., P. Forterre, and R. A. Garrett. 2006. Viruses of the Archaea: a unifying view. Nat. Rev. Microbiol. 4:837-848.
54. Rice, P., I. Longden, and A. Bleasby. 2000. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 16:276-277.
55. Rohwer, F., and R. V. Thurber. 2009. Viruses manipulate the marine environment. Nature 459:207-212.
56. Rutherford, K., J. Parkhill, J. Crook, T. Horsnell, P. Rice, M. A. Rajandream, and B. Barrell. 2000. Artemis: sequence visualization and annotation. Bioinformatics 16:944-945.
57. Saren, A. M., J. J. Ravantti, S. D. Benson, R. M. Burnett, L. Paulin, D. H. Bamford, and J. K. Bamford. 2005. A snapshot of viral evolution from genome analysis of the Tectiviridae family. J. Mol. Biol. 350:427-440.
58. Schleper, C., K. Kubo, and W. Zillig. 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. U. S. A. 89:7645-7649.
59. Schägger, H., and G. von Jagow. 1987. Tricine-sodium dodecyl sulfatepolyacrylamide gel electrophoresis for the separation of proteins in the range from 1 to 100 kDa. Anal. Biochem. 166:368-379.
60. Skipski, V. P., and M. Barclay. 1969. Thin-layer chromatography of lipids, p. 530-598. In J. M. Lowenstein (ed.), Lipids, vol. 14. Academic Press, Inc., New York, NY.
61. Staden, R., K. F. Beal, and J. K. Bonfield. 2000. The Staden package, 1998. Methods Mol. Biol. 132:115-130.
62. Stewart, C. R., S. R. Casjens, S. G. Cresawn, J. M. Houtz, A. L. Smith, M. E. Ford, C. L. Peebles, G. F. Hatfull, R. W. Hendrix, W. M. Huang, and M. L. Pedulla. 2009. The genome of Bacillus subtilis bacteriophage SPO1. J. Mol. Biol. 388:48-70.
63. Weigel, C., and H. Seitz. 2006. Bacteriophage replication modules. FEMS Microbiol. Rev. 30:321-381.
64. Vestergaard, G., M. Häring, X. Peng, R. Rachel, R. A. Garrett, and D. Prangishvili. 2005. A novel rudivirus, ARV1, of the hyperthermophilic archaeal genus Acidianus. Virology 336:83-92.