Stygiolobus rod-shaped virus and the interplay of crenarchaeal rudiviruses with the CRISPR antiviral system

Journal of Bacteriology

Volumn 190, Issue 20, 2008, Pages 6837-6845

  Vestergaard, Gisle ^a   Shah, Shiraz A ^a   Bize, Ariane ^b   Reitberger, Werner ^c   Reuter, Monika ^c   Phan, Hien ^a   Briegel, Ariane ^d   Rachel, Reinhard ^c   Garrett, Roger A ^a   Prangishvili, David ^b  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

^b INSTITUT PASTEUR   (France)

^c UNIVERSITY OF REGENSBURG   (Germany)

^d MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA; GLYCOSYLTRANSFERASE; METHYLTRANSFERASE; STRUCTURAL PROTEIN;

ACIDIANUS ROD SHAPED VIRUS 1; ARTICLE; CRENARCHAEOTA; DEFENSE MECHANISM; DNA REPLICATION; GENOME; LONG TERMINAL REPEAT; MICROORGANISM; NONHUMAN; NUCLEOTIDE SEQUENCE; PORTUGAL; PRIORITY JOURNAL; PROTEIN STRUCTURE; STYGIOLOBUS ROD SHAPED VIRUS; SULFOLOBUS ROD SHAPED VIRUS 1; SULFOLOBUS ROD SHAPED VIRUS 2; VIRION; VIRUS; VIRUS ISOLATION;

AZORES; CHROMOSOMES, ARCHAEAL; DNA, VIRAL; GENE ORDER; GENES, VIRAL; HOT SPRINGS; INDEL MUTATION; MACROMOLECULAR SUBSTANCES; MICROSCOPY, ELECTRON, TRANSMISSION; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; RUDIVIRIDAE; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, AMINO ACID; SULFOLOBACEAE; SYNTENY; VIRAL NONSTRUCTURAL PROTEINS; VIRAL STRUCTURAL PROTEINS; VIRION;

ACIDIANUS ROD-SHAPED VIRUS 1; ARCHAEA; CRENARCHAEOTA; RUDIVIRUS; STYGIOLOBUS; SULFOLOBUS;

EID: 53849141479     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.00795-08     Document Type: Article

References (36)

1. Altschul, S. F., T. L. Madden, A. A. Schaffer, 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.
2. Bettstetter, M., X. Peng, R. A. Garrett, and D. Prangishvili. 2003. AFV1, a novel virus infecting hyperthermophilic archaea of the genus Acidianus. Virology 315:68-79.
3. Bland, C., T. L. Ramsey, F. Sabree, M. Lowe, K. Brown, N. C. Kyrpides, and P. Hugenholtz. 2007. CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics 8:209.
4. Blum, H., W. Zillig, S. Mallok, H. Domdey, and D. Prangishvili. 2001. The genome of the archaeal virus SIRV1 has features in common with genomes of eukaryal viruses. Virology 281:6-9.
5. Brügger, K., P. Redder, and M. Skovgaard. 2003. MUTAGEN: multi-user tool for annotating genomes. Bioinformatics 19:2480-2481.
6. Eder, W., W. Ludwig, and R. Huber. 1999. Novel 16S rRNA gene sequences retrieved from highly saline brine sediments of Kebrit Deep, Red Sea. Arch. Microbiol. 172:213-218.
7. Edgar, R. C. 2004. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5:113.
8. Ginalski, K., A. Elofsson, D. Fischer, and L. Rychlewski. 2003. 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics 19:1015-1018.
9. Häring, M., X. Peng, K. Brügger, R. Rachel, K. O. Stetter, R. A. Garrett, and D. Prangishvili. 2004. Morphology and genome organization of the virus PSV of the hyperthermophilic archaeal genera Pyrobaculum and Thermoproteus: a novel virus family, the Globuloviridae. Virology 323:233-242.
10. Häring, M., G. Vestergaard, K. Brügger, R. Rachel, R. A. Garrett, and D. Prangishvili. 2005. Structure and genome organization of AFV2, a novel archaeal lipothrixvirus with unusual terminal and core structures. J. Bacteriol. 187:3855-3858.
11. Häring, M., G. Vestergaard, R. Rachel, L. Chen, R. A. Garrett, and D. Prangishvili. 2005. Virology: independent virus development outside a host. Nature 436:1101-1102.
12. Kessler, A., A. B. Brinkman, J. van der Oost, and D. Prangishvili. 2004. Transcription of the rod-shaped viruses SIRV1 and SIRV2 of the hyperthermophilic archaeon Sulfolobus. J. Bacteriol. 186:7745- 7753.
13. Kessler, A., G. Sezonov, J. I. Guijarro, N. Desnoues, T. Rose, M. Delepierre, S. D. Bell, and D. Prangishvili. 2006. A novel archaeal regulatory protein, Sta1, activates transcription from viral promoters. Nucleic Acids Res. 34:4837-4845.
14. Laemmli, U. K. 1970. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227:680-685.
15. Letunic, I., R. R. Copley, B. Pils, S. Pinkert, J. Schultz, and P. Börk. 2006. SMART 5: domains in the context of genomes and networks. Nucleic Acids Res. 34:D257-D260.
16. Lillestøl, R. K., P. Redder, R. A. Garrett, and K. Brügger. 2006. A putative viral defence mechanism in archaeal cells. Archaea 2:59-72.
17. Makarova, K. S., N. V. Grishin, S. A. Shabalina, Y. I. Wolf, and E. V. Koonin. 2006. A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biol. Direct 1:7.
18. Mojica, F. J., C. Diez-Villasenor, J. Garcia-Martinez, and E. Soria. 2005. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J. Mol. Evol. 60:174-182.
19. Ortmann, A. C., B. Wiedenheft, T. Douglas, and M. Young. 2006. Hot crenarchaeal viruses reveal deep evolutionary connections. Nat. Rev. Microbiol. 4:520-528.
20. Peng, X., H. Blum, Q. She, S. Mallok, K. Brügger, R. A. Garrett, W. Zillig, and D. Prangishvili. 2001. Sequences and replication of genomes of the archaeal rudiviruses SIRV1 and SIRV2: relationships to the archaeal lipothrixvirus SIFV and some eukaryal viruses. Virology 291:226-234.
21. Peng, X., A. Kessler, H. Phan, R. A. Garrett, and D. Prangishvili. 2004. Multiple variants of the archaeal DNA rudivirus SIRV1 in a single host and a novel mechanism of genomic variation. Mol. Microbiol. 54:366-375.
22. Prangishvili, D., H. P. Arnold, D. Gotz, U. Ziese, I. Holz, J. K. Kristjansson, and W. Zillig. 1999. A novel virus family, the Rudiviridae: structure, virus-host interactions and genome variability of the Sulfolobus viruses SIRV1 and SIRV2. Genetics 152:1387-1396.
23. Prangishvili, D., P. Forterre, and R. A. Garrett. 2006. Viruses of the Archaea: a unifying view. Nat. Rev. Microbiol. 4:837-848.
24. Prangishvili, D., and R. A. Garrett. 2005. Viruses of hyperthermophilic Crenarchaea. Trends Microbiol. 13:535-542.
25. Prangishvili, D., R. A. Garrett, and E. V. Koonin. 2006. Evolutionary genomics of archaeal viruses: unique viral genomes in the third domain of life. Virus Res. 117:52-67.
26. Prangishvili, D., G. Vestergaard, M. Häring, R. Aramayo, T. Basta, R. Rachel, and R. A. Garrett. 2006. Structural and genomic properties of the hyperthermophilic archaeal virus ATV with an extracellular stage of the reproductive cycle. J. Mol. Biol. 359:1203-1216.
27. Rachel, R., M. Bettstetter, B. P. Hedlund, M. Häring, A. Kessler, K. O. Stetter, and D. Prangishvili. 2002. Remarkable morphological diversity of viruses and virus-like particles in hot terrestrial environments. Arch. Virol. 147:2419-2429.
28. Reilin, A. 1998. Preparation of catalase crystals. University of Illinois at Urbana-Champaign, Urbana, IL. http://www.itg.uiuc.edu/publications/ techreports/98-009.
29. Rice, G., K. Stedman, J. Snyder, B. Wiedenheft, D. Willits, S. Brumfield, T. McDermott, and M. J. Young. 2001. Viruses from extreme thermal environments. Proc. Natl. Acad. Sci. USA 98:13341-13345.
30. 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.
31. Sæbø, P. E., S. M. Andersen, J. Myrseth, J. K. Lærdahl, and T. Rognes. 2005. PARALIGN: rapid and sensitive sequence similarity searches powered by parallel computing technology. Nucleic Acids Res. 33:W535-W539.
32. Snyder, J. C., B. Wiedenheft, M. Lavin, F. F. Roberto, J. Spuhler, A. C. Ortmann, T. Douglas, and M. Young. 2007. Virus movement maintains local virus population diversity. Proc. Natl. Acad. Sci. USA 104:19102-19107.
33. Steinmetz, N. F., A Bize, K. C. Findlay, G. P. Lomonossoff, M. Manchester, D. J. Evans, and D. Prangishvili. Site-specific and spatially controlled addressability of a new viral nanobuilding block: Sulfolobus islandicus rodshaped virus 2. Adv. Funct. Mat., in press.
34. Vestergaard, G., R. Aramayo, T. Basta, M. Häring, X. Peng, K. Brügger, L. Chen, R. Rachel, N. Boisset, R. A. Garrett, and D. Prangishvili. 2008. Structure of the Acidianus filamentous virus 3 and comparative genomics of related archaeal lipothrixviruses. J. Virol. 82:371-381.
35. 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.
36. Zillig, W., A. Kletzin, C. Schleper, I. Holz, D. Janekovic, H. Hain, M. Lanzendörfer, and J. K. Kristjansson. 1994. Screening for Sulfolobales, their plasmids and their viruses in Icelandic solfataras. System. Appl. Microbiol. 16:609-628.