Comparative Genomic Analysis of Hyperthermophilic Archaeal Fuselloviridae Viruses

Journal of Virology

Volumn 78, Issue 4, 2004, Pages 1954-1961

  Wiedenheft, Blake ^a   Stedman, Kenneth ^a,c   Roberto, Francisco ^b   Willits, Deborah ^a   Gleske, Anne Kathrin ^a   Zoeller, Luisa ^c   Snyder, Jamie ^a   Douglas, Trevor ^a   Young, Mark ^a  

^a MONTANA STATE UNIVERSITY   (United States)

^b IDAHO NATIONAL LABORATORY   (United States)

^c PORTLAND STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CIRCULAR DNA; DOUBLE STRANDED DNA; RECOMBINASE; TRANSFER RNA;

ARTICLE; BACTERIOPHAGE; DNA STRUCTURE; GENE LOCUS; GENE SEQUENCE; GENETIC CONSERVATION; GENOME ANALYSIS; GEOGRAPHIC DISTRIBUTION; HYPERTHERMIA; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PHYLOGENY; PRIORITY JOURNAL; RUSSIAN FEDERATION; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SULFOLOBUS; UNITED STATES; VIRUS DNA CELL DNA INTERACTION; VIRUS GENOME; VIRUS ISOLATION; VIRUS MORPHOLOGY;

ARCHAEAL VIRUSES; ATTACHMENT SITES, MICROBIOLOGICAL; BASE SEQUENCE; FRESH WATER; FUSELLOVIRIDAE; GENOME, VIRAL; GENOMICS; HEAT; MOLECULAR SEQUENCE DATA; RNA, TRANSFER; SULFOLOBUS; VIRUS INTEGRATION;

EID: 0842304503     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/JVI.78.4.1954-1961.2004     Document Type: Article

References (44)

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. Argos, P., A. Landy, K. Abremski, J. B. Egan, E. Haggard-Ljungquist, R. H. Hoess, M. L. Kahn, B. Kalionis, S. V. Narayana, L. S. Pierson III, N. Sternberg, and J. M. Leong. 1986. The integrase family of site-specific recombinases: regional similarities and global diversity. EMBO J. 5:433-440.
3. Arnold, H. P., Q. She, H. Phan, K. Stedman, D. Prangishvili, I. Holz, J. K. Kristjansson, R. Garrett, and W. Zillig. 1999. The genetic element pSSVx of the extremely thermophilic crenarchaeon Sulfolobus is a hybrid between a plasmid and a virus. Mol. Microbiol. 34:217-226.
4. Arnold, H. P., U. Ziese, and W. Zillig. 2000. SNDV, a novel virus of the extremely thermophilic and acidophilic archaeon Sulfolobus. Virology 272:409-416.
5. 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.
6. Benson, G. 1999. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27:573-580.
7. Campbell, A. M. 1992. Chromosomal insertion sites for phages and plasmids. J. Bacteriol. 174:7495-7499.
8. Cannio, R., P. Contursi, M. Rossi, and S. Bartolucci. 1998. An autonomously replicating transforming vector for Sulfolobus solfataricus. J. Bacteriol. 180:3237-3240.
9. Delcher, A. L., D. Harmon, S. Kasif, O. White, and S. L. Salzberg. 1999. Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 27:4636-4641.
10. Grogan, D., P. Palm, and W. Zillig. 1990. Isolate B12, which harbours a virus-like element, represents a new species of the archaebacterial genus Sulfolobus, Sulfolobus shibatae, sp. nov. Arch. Microbiol. 154:594-599.
11. Huelsenbeck, J. P., and F. Ronquist. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754-755.
12. Huelsenbeck, J. P., F. Ronquist, R. Nielsen, and J. P. Bollback. 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294:2310-2314.
13. Jeanmougin, F., J. D. Thompson, M. Gouy, D. G. Higgins, and T. J. Gibson. 1998. Multiple sequence alignment with Clustal X. Trends Biochem. Sci. 23:403-405.
14. Jonuscheit, M., E. Martusewitsch, K. M. Stedman, and C. Schleper. 2003. A reporter gene system for the hyperthermophilic archaeon Sulfolobus solfataricus based on a selectable and integrative shuttle vector. Mol. Microbiol. 48:1241-1252.
15. Keeling, P. J., H. P. Klenk, R. K. Singh, O. Feeley, C. Schleper, W. Zillig, W. F. Doolittle, and C. W. Sensen. 1996. Complete nucleotide sequence of the Sulfolobus islandicus multicopy plasmid pRN1. Plasmid 35:141-144.
16. Kletzin, A., A. Lieke, T. Urich, R. L. Charlebois, and C. W. Sensen. 1999. Molecular analysis of pDL10 from Acidianus ambivalens reveals a family of related plasmids from extremely thermophilic and acidophilic archaea. Genetics 152:1307-1314.
17. Martin, A., S. Yeats, D. Janekovic, W.-D. Reiter, W. Aicher, and W. Zillig. 1984. SAV1, a temperate U. V. inducible DNA virus like particle from the archaebacterium Sulfolobus acidocaldarius isolate B12. EMBO J. 3:2165-2168.
18. Muskhelishvili, G. 1994. The archaeal SSV integrase promotes intermolecular excisive recombination in-vitro. Syst. Appl. Microbiol. 16:605-608.
19. Muskhelishvili, G., P. Palm, and W. Zillig. 1993. SSV1-encoded site-specific recombination system in Sulfolobus shibatae. Mol. Gen. Genet. 237:334-342.
20. Nadal, M., G. Mirambeau, P. Forterre, W.-D. Reiter, and M. Duguet. 1986. Positively supercoiled DNA in a virus-like particle of an archaebacterium. Nature 321:256-258.
21. Nunes-Duby, 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.
22. Palm, P., C. Schleper, B. Grampp, S. Yeats, P. McWilliam, W.-D. Reiter, and W. Zillig. 1991. Complete nucleotide sequence of the virus SSV1 of the archaebacterium Sulfolobus shibatae. Virology 185:242-250.
23. Pedulla, M. L., M. E. Ford, J. M. Houtz, T. Karthikeyan, C. Wadsworth, J. A. Lewis, D. Jacobs-Sera, J. Falbo, J. Gross, N. R. Pannunzio, W. Brucker, V. Kumar, J. Kandasamy, L. Keenan, S. Bardarov, J. Kriakov, J. G. Lawrence, W. R. Jacobs, Jr., R. W. Hendrix, and G. F. Hatfull. 2003. Origins of highly mosaic mycobacteriophage genomes. Cell 113:171-182.
24. Peng, X., I. Holz, W. Zillig, R. A. Garrett, and Q. She. 2000. Evolution of the family of pRN plasmids and their integrase-mediated insertion into the chromosome of the crenarchaeon Sulfolobus solfataricus. J. Mol. Biol. 303:449-454.
25. Reiter, W.-D., and P. Palm. 1990. Identification and characterization of a defective SSV1 genome integrated into a tRNA gene in the archaebacterium Sulfolobus sp. B12. Mol. Gen. Genet. 221:65-71.
26. Reiter, W.-D., P. Palm, A. Henschen, F. Lottspeich, W. Zillig, and B. Grampp. 1987. Identification and characterization of the genes encoding three structural proteins of the Sulfolobus virus-like particle SSV1. Mol. Gen. Genet. 206:144-153.
27. Reiter, W.-D., P. Palm, and S. Yeats. 1989. Transfer RNA genes frequently serve as integration sites for prokaryotic genetic elements. Nucleic Acids Res. 17:1907-1914.
28. Reiter, W.-D., P. Palm, S. Yeats, and W. Zillig. 1987. Gene expression in archaebacteria: physical mapping of constitutive and UV-inducible transcripts from the Sulfolobus virus-like particle SSV1. Mol. Gen. Genet. 209:270-275.
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. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
31. 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. USA 89:7645-7649.
32. Serre, M. C., C. Letzelter, J. R. Garel, and M. Duguet. 2002. Cleavage properties of an archaeal site-specific recombinase, the SSV1 integrase. J. Biol. Chem. 277:16758-16767.
33. She, Q., R. K. Singh, F. Confalonieri, Y. Zivanovic, G. Allard, M. J. Awayez, C. C.-Y. Chan-Weiher, I. G. Clausen, B. A. Curtis, A. D. Moors, G. Erauso, C. Fletcher, P. M. K. Gordon, I. H.-D. Jong, A. C. Jeffries, C. J. Kozera, N. Medina, X. Peng, H. P. Thi-Ngoc, P. Redder, M. E. Schenk, C. Theriault, N. Tolstrup, R. L. Charlebois, W. F. Doolittle, M. Duguet, T. Gaasterland, R. A. Garrett, M. A. Ragan, C. W. Sensen, and J. V. D. Oost. 2001. The complete genome of the crenarchaeon Sulfolobus solfataricus P2. Proc. Natl. Acad. Sci. USA 98:7835-7840.
34. Stedman, K. M., C. Schleper, E. Rumpf, and W. Zillig. 1999. Genetic requirements for the function of the archaeal virus SSV1 in Sulfolobus solfataricus: construction and testing of viral shuttle vectors. Genetics 152:1397-1405.
35. Stedman, K. M., Q. She, H. Phan, H. P. Arnold, I. Holz, R. A. Garrett, and W. Zillig. 2003. Relationships between fuselloviruses infecting the extremely thermophilic archaeon Sulfolobus: SSV1 and SSV2. Res. Microbiol. 154:295-302.
36. Suzek, B. E., M. D. Ermolaeva, M. Schreiber, and S. L. Salzberg. 2001. A probabilistic method for identifying start codons in bacterial genomes. Bioinformatics 17:1123-1130.
37. Swofford, D. 2002. PAUP*4.0 phylogenetic analysis using parsimony (*and other methods), version 4 beta, 10th ed. Sinauer Associates, Sunderlund, Mass.
38. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
39. Whitaker, R. J., G. W. Grogan, and J. W. Taylor. 24 July 2003. Geographic barriers isolate endemic populations of hyperthermophilic archaea. Science 10.1126/science.1086909.
40. Wood, A. G., W. B. Whitman, and J. Konisky. 1989. Isolation and characterization of an archaebacterial viruslike particle from Methanococcus voltae A3. J. Bacteriol. 171:93-98.
41. Yeats, S., P. McWilliam, and W. Zillig. 1982. A plasmid in the archaebacterium Sulfolobus acidocaldarius. EMBO J. 1:1035-1038.
42. Zillig, W., H. P. Arnold, I. Holz, D. Prangishvili, A. Schweier, K. Stedman, Q. She, H. Phan, R. Garrett, and J. K. Kristjansson. 1998. Genetic elements in the extremely thermophilic archaeon Sulfolobus. Extremophiles 2:131-140.
43. Zillig, W., A. Kletzin, C. Schleper, I. Holz, D. Janekovic, J. Hain, M. Lanzendorfer, and J. K. Kristjansson. 1994. Screening for Sulfolobales, their plasmids, and their viruses in Icelandic solfataras. Syst. Appl. Microbiol. 16:609-628.
44. Zillig, W., K. O. Stetter, S. Wunderl, W. Schulz, H. Preiss, and H. Scholz. 1980. The Sulfolobus-"Caldariella" group: taxonomy on the basis of the structure of DNA-dependent RNA polymerases. Arch. Microbiol. 125:259-269.