Cysteine usage in Sulfolobus spindle-shaped virus 1 and extension to hyperthermophilic viruses in general

Virology

Volumn 376, Issue 2, 2008, Pages 270-278

  Menon, Smita K ^a   Maaty, Walid S ^a   Corn, G Judson ^a   Kwok, Stanley C ^b   Eilers, Brian J ^a   Kraft, Paul ^a   Gillitzer, Eric ^a   Young, Mark J ^a   Bothner, Brian ^a   Lawrence, C Martin ^a  

^a MONTANA STATE UNIVERSITY   (United States)

^b UNIVERSITY OF COLORADO   (United States)

Author keywords

Archaea; B116; B129; Crenarchaea; Crenarchaeal virus; Disulfide; F112; F93; Intracellular disulfide; Intramolecular disulfide; SSV; SSV1; Sulfolobus; Sulfolobus spindle shaped virus; Thermostability; Thermostable

Indexed keywords

CYSTEINE; GENOMIC RNA;

ARTICLE; BACTERIOPHAGE; CONTROLLED STUDY; DISULFIDE BOND; DNA BINDING; HYPERTHERMOPHILE; NONHUMAN; PRIORITY JOURNAL; PROTEIN STRUCTURE; PROTEOMICS; STRUCTURE ANALYSIS; SULFOLOBUS; THERMOSTABILITY; TRANSMISSION ELECTRON MICROSCOPY;

CYSTEINE; DISULFIDES; FUSELLOVIRIDAE; GENOME, VIRAL; HELIX-TURN-HELIX MOTIFS; HOT SPRINGS; MODELS, MOLECULAR; OPEN READING FRAMES; PROTEOME; SULFOLOBUS; VIRAL PROTEINS; WATER MICROBIOLOGY;

CRENARCHAEOTA; FUSELLOVIRIDAE; SUGARCANE STREAK VIRUS; SULFOLOBALES; SULFOLOBUS; SULFOLOBUS SPINDLE-SHAPED VIRUS 1;

EID: 44649088816     PISSN: 00426822     EISSN: 10960341     Source Type: Journal    
DOI: 10.1016/j.virol.2008.03.026     Document Type: Article

References (63)

1. Ahn D.G., Kim S.I., Rhee J.K., Kim K.P., Pan J.G., and Oh J.W. TTSV1, a new virus-like particle isolated from the hyperthermophilic crenarchaeote Thermoproteus tenax. Virology 351 2 (2006) 280-290
2. Aravind L., Anantharaman V., Balaji S., Babu M.M., and Iyer L.M. The many faces of the helix-turn-helix domain: transcription regulation and beyond. FEMS Microbiol. Rev. 29 2 (2005) 231-262
3. Argos P., Landy A., Abremski K., Egan J.B., Haggard-Ljungquist E., Hoess R.H., Kahn M.L., Kalionis B., Narayana S.V., Pierson III L.S., et al. The integrase family of site-specific recombinases: regional similarities and global diversity. EMBO J. 5 2 (1986) 433-440
4. Arnold H.P., Zillig W., Ziese U., Holz I., Crosby M., Utterback T., Weidmann J.F., Kristjanson J.K., Klenk H.P., Nelson K.E., and Fraser C.M. A novel Lipothrixvirus, SIFV, of the extremely thermophilic Crenarchaeon Sulfolobus. Virology 267 2 (2000) 252-266
5. Bailey S. The CCP4 suite - programs for protein crystallography. Acta Crystallogr. D50 (1994) 760-763
6. Banner D.W., Kokkinidis M., and Tsernoglou D. Structure of the ColE1 rop protein at 1.7 A resolution. J. Mol. Biol. 196 3 (1987) 657-675
7. Beeby M., Connor B.D., Ryttersgaard C., Boutz D.R., Perry L.J., and Yeates T.O. The genomics of disulfide bonding and protein stabilization in thermophiles. PLoS Biology 3 9 (2005) 1549-1558
8. Bettstetter M., Peng X., Garrett R.A., and Prangishvili D. AFV1, a novel virus infecting hyperthermophilic Archaea of the genus Acidianus. Virology 315 1 (2003) 68-79
9. Bradford M.M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72 (1976) 248-254
10. Eberle W., Pastore A., Sander C., and Rosch P. The structure of ColE1 rop in solution. J. Biomol. NMR 1 1 (1991) 71-82
11. Evans P. Scaling and assessment of data quality. Acta Crystallogr., D Biol. Crystallogr. 62 Pt 1 (2006) 72-82
12. Frols S., Gordon P.M., Panlilio M.A., Schleper C., and Sensen C.W. Elucidating the transcription cycle of the UV-inducible hyperthermophilic archaeal virus SSV1 by DNA microarrays. Virology 365 1 (2007) 48-59
13. Gauss G.H., Benas P., Wiedenheft B., Young M., Douglas T., and Lawrence C.M. Structure of the DPS-like protein from Sulfolobus solfataricus reveals a bacterioferritin-like dimetal binding site within a DPS-like dodecameric assembly. Biochemistry 45 36 (2006) 10815-10827
14. Gibrat J.-F., Madej T., and Bryant S.H. Surprising similarities in structure comparison. Curr. Opin. Struck. Biol. 6 3 (1996) 377-385
15. Gilbert H.F. Thiol/disulfide exchange equilibria and disulfide bond stability. Methods Enzymol. 251 (1995) 8-28
16. Gross E., Kastner D.B., Kaiser C.A., and Fass D. Structure of Ero1p, source of disulfide bonds for oxidative protein folding in the cell. Cell 117 5 (2004) 601-610
17. Haring M., Peng X., Brugger K., Rachel R., Stetter K.O., Garrett R.A., and Prangishvili D. Morphology and genome organization of the virus PSV of the hyperthermophilic archaeal genera Pyrobaculum and Thermoproteus: a novel virus family, the Globuloviridae. Virology 323 2 (2004) 233-242
18. Haring M., Vestergaard G., Rachel R., Chen L., Garrett R.A., and Prangishvili D. Virology: independent virus development outside a host. Nature 436 7054 (2005) 1101-1102
19. Helmer-Citterich M., Anceschi M.M., Banner D.W., and Cesareni G. Control of ColE1 replication: low affinity specific binding of Rop (Rom) to RNAI and RNAII. EMBO J. 7 2 (1988) 557-566
20. Hendrickson W.A., Horton J.R., and LeMaster D.M. Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): a vehicle for direct determination of three-dimensional structure. EMBO J. 9 5 (1990) 1665-1672
21. Hendrickson W.A., and Ogata C.M. Phase determination from multiwavelength anomalous diffraction measurements. In: Carter C.W., and Sweet R.M. (Eds). Macromolecular Crystallography, Part A Vol. 276 (1997), Academic Press, San Diego 494-523
22. Holm L., and Sander C. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233 1 (1993) 123-138
23. Iyer L.M., Aravind L., and Koonin E.V. Common origin of four diverse families of large eukaryotic DNA viruses. J. Virol. 75 23 (2001) 11720-11734
24. Jones T.A., Zou J.Y., Cowan S.W., and Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A47 (1991) 110-119
25. Kabsch W. A solution for the best rotation to relate two sets of vectors. Acta. Cryst. A32 (1976) 922-923
26. Kadokura H., Katzen F., and Beckwith J. Protein disulfide bond formation in prokaryotes. Annu Rev Biochem 72 (2003) 111-135
27. Koonin E.V. Archaebacterial virus SSV1 encodes a putative DnaA-like protein. Nucleic Acids Res 20 5 (1992) 1143
28. Kraft P., Kummel D., Oeckinghaus A., Gauss G.H., Wiedenheft B., Young M., and Lawrence C.M. Structure of D-63 from Sulfolobus spindle-shaped virus 1: surface properties of the dimeric four-helix bundle suggest an adaptor protein function. J. Virol. 78 14 (2004) 7438-7442
29. Kraft P., Oeckinghaus A., Kummel D., Gauss G.H., Gilmore J., Wiedenheft B., Young M., and Lawrence C.M. Crystal structure of F-93 from Sulfolobus spindle-shaped virus 1, a winged-helix DNA binding protein. J. Virol. 78 21 (2004) 11544-11550
30. Krogh A., Larsson B., von Heijne G., and Sonnhammer E.L. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305 3 (2001) 567-580
31. Larson E.T., Eilers B., Menon S., Reiter D., Ortmann A., Young M.J., and Lawrence C.M. A winged-helix protein from sulfolobus turreted icosahedral virus points toward stabilizing disulfide bonds in the intracellular proteins of a hyperthermophilic virus. Virology 368 (2007) 249-261
32. Larson E.T., Eilers B.J., Reiter D., Ortmann A.C., Young M.J., and Lawrence C.M. A new DNA binding protein highly conserved in diverse crenarchaeal viruses. Virology 363 2 (2007) 387-396
33. Laskowski R.A., MacArthur M.W., Moss D.S., and Thornton J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst. 26 (1993) 283-291
34. Leslie A.G. The integration of macromolecular diffraction data. Acta Crystallogr., D Biol. Crystallogr. 62 Pt 1 (2006) 48-57
35. Liu Y., Manna A., Li R., Martin W.E., Murphy R.C., Cheung A.L., and Zhang G. Crystal structure of the SarR protein from Staphylococcus aureus. Proc. Natl. Acad. Sci. U. S. A. 98 12 (2001) 6877-6882
36. Mallick P., Boutz D.R., Eisenberg D., and Yeates T.O. Genomic evidence that the intracellular proteins of archaeal microbes contain disulfide bonds. PNAS 99 15 (2002) 9679-9684
37. Martin A., Yeats S., Janekovic D., Reiter W.D., Aicher W., and Zillig W. SAV 1, a temperate U.V.-inducible DNA virus-like particle from the archaebacterium Sulfolobus acidocaldarius isolate B12. EMBO J. 3 9 (1984) 2165-2168
38. Murshudov G.N., Vagin A.A., and Dodson E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D53 (1997) 240-255
39. Muskhelishvili G., Palm P., and Zillig W. SSV1-encoded site-specific recombination system in Sulfolobus shibatae. Mol. Gen. Genet. 237 3 (1993) 334-342
40. O'Connor B.D., and Yeates T.O. GDAP: a web tool for genome-wide protein disulfide bond prediction. Nucleic Acids Res. 32 suppl_2 (2004) W360-W364
41. Ortmann A.C., Wiedenheft B., Douglas T., and Young M. Hot crenarchaeal viruses reveal deep evolutionary connections. Nat. Rev., Microbiol. 4 7 (2006) 520-528
42. Painter J., and Merritt E.A. Optimal description of a protein structure in terms of multiple groups undergoing TLS motion. Acta Crystallogr., D Biol. Crystallogr. 62 Pt 4 (2006) 439-450
43. Painter J., and Merritt E.A. TLSMD web server for the generation of multi-group TLS models. Journal of Applied Crystallography 39 1 (2006) 109-111
44. Palm P., Schleper C., Grampp B., Yeats S., McWilliam P., Reiter W.D., and Zillig W. Complete nucleotide sequence of the virus SSV1 of the archaebacterium Sulfolobus shibatae. Virology 185 1 (1991) 242-250
45. Prangishvili D., Arnold H.P., Gotz D., Ziese U., Holz I., Kristjansson J.K., and Zillig W. A novel virus family, the Rudiviridae: Structure, virus-host interactions and genome variability of the sulfolobus viruses SIRV1 and SIRV2. Genetics 152 4 (1999) 1387-1396
46. Prangishvili D., Garrett R.A., and Koonin E.V. Evolutionary genomics of archaeal viruses: Unique viral genomes in the third domain of life. Virus Res. 117 1 (2006) 52-67
47. Ramakrishnan V., Finch J.T., Graziano V., Lee P.L., and Sweet R.M. Crystal structure of globular domain of histone H5 and its implications for nucleosome binding. Nature 362 6417 (1993) 219-223
48. Reiter W.D., Palm P., Henschen A., Lottspeich F., Zillig W., and Grampp B. Identification and characterization of the genes encoding three structural proteins of the Sulfolobus virus-like particle SSV1. Mol. Genet. Gen. 206 1 (1987) 144-153
49. Rice G., Tang L., Stedman K., Roberto F., Spuhler J., Gillitzer E., Johnson J.E., Douglas T., and Young M. The structure of a thermophilic archaeal virus shows a double-stranded DNA viral capsid type that spans all domains of life. PNAS 101 20 (2004) 7716-7720
50. Schleper C., Kubo K., and Zillig W. 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 16 (1992) 7645-7649
51. Senkevich T.G., Weisberg A.S., and Moss B. Vaccinia virus E10R protein is associated with the membranes of intracellular mature virions and has a role in morphogenesis. Virology 278 1 (2000) 244-252
52. Senkevich T.G., White C.L., Koonin E.V., and Moss B. A viral member of the ERV1/ALR protein family participates in a cytoplasmic pathway of disulfide bond formation. Proc. Natl. Acad. Sci. U. S. A. 97 22 (2000) 12068-12073
53. Senkevich T.G., White C.L., Koonin E.V., and Moss B. Complete pathway for protein disulfide bond formation encoded by poxviruses. Proc. Natl. Acad. Sci. U. S. A. 99 10 (2002) 6667-6672
54. Senkevich T.G., White C.L., Weisberg A., Granek J.A., Wolffe E.J., Koonin E.V., and Moss B. Expression of the vaccinia virus A2.5L redox protein is required for virion morphogenesis. Virology 300 2 (2002) 296-303
55. Sonnhammer E.L., von Heijne G., and Krogh A. A hidden Markov model for predicting transmembrane helices in protein sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol. 6 (1998) 175-182
56. Stedman K.M., She Q., Phan H., Arnold H.P., Holz I., Garrett R.A., and Zillig W. Relationships between fuselloviruses infecting the extremely thermophilic archaeon Sulfolobus: SSV1 and SSV2. Res. Microbiol. 154 4 (2003) 295-302
57. Su H.P., Lin D.Y., and Garboczi D.N. The structure of G4, the poxvirus disulfide oxidoreductase essential for virus maturation and infectivity. J. Virol. 80 15 (2006) 7706-7713
58. Terwilliger T.C. Maximum likelihood density modification. Acta Crystallogr. D56 (2000) 965-972
59. Terwilliger T.C., and Berendzen J. Automated MAD and MIR structure solution. Acta Crystallogr. D55 (1999) 849-861
60. White C.L., Senkevich T.G., and Moss B. Vaccinia virus G4L glutaredoxin is an essential intermediate of a cytoplasmic disulfide bond pathway required for virion assembly. J. Virol. 76 2 (2002) 467-472
61. Wiedenheft B., Stedman K., Roberto F., Willits D., Gleske A.K., Zoeller L., Snyder J., Douglas T., and Young M. Comparative genomic analysis of hyperthermophilic archaeal Fuselloviridae viruses. J. Virol. 78 4 (2004) 1954-1961
62. Xiang X., Chen L., Huang X., Luo Y., She Q., and Huang L. Sulfolobus tengchongensis spindle-shaped virus STSV1: virus-host interactions and genomic features. J. Virol. 79 14 (2005) 8677-8686
63. Zheng N., Fraenkel E., Pabo C.O., and Pavletich N.P. Structural basis of DNA recognition by the heterodimeric cell cycle transcription factor E2F-DP. Genes Dev. 13 6 (1999) 666-674