Fossil record of an archaeal HK97-like provirus

Virology

Volumn 417, Issue 2, 2011, Pages 362-368

  Heinemann, Joshua ^a   Maaty, Walid S ^a   Gauss, George H ^a   Akkaladevi, Narahari ^a   Brumfield, Susan K ^a   Rayaprolu, Vamseedhar ^a   Young, Mark J ^a   Lawrence, C Martin ^a   Bothner, Brian ^a  

^a MONTANA STATE UNIVERSITY   (United States)

Author keywords

Archaea; Bacteriophage; Encapsulin; Herpesvirus; HK97; Linocin; Particle; Provirus; Virus

Indexed keywords

CAPSID PROTEIN; LINCOMYCIN; SSO2749 PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; BACTERIOPHAGE; BACTERIOPHAGE HK97; CONTROLLED STUDY; DNA VIRUS; FOSSIL; GENE POOL; HERPES VIRUS; MOSAICISM; NONHUMAN; PRIORITY JOURNAL; PYROCOCCUS FURIOSUS; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS; SULFOLOBUS SOLFATARICUS; VIRUS LIKE AGENT;

ARCHAEAL PROTEINS; ARCHAEAL VIRUSES; MICROSCOPY, ELECTRON; MODELS, MOLECULAR; PROVIRUSES; PYROCOCCUS FURIOSUS; RECOMBINANT PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; SULFOLOBUS SOLFATARICUS; VIROSOMES;

ARCHAEA; CRENARCHAEOTA; EUKARYOTA; HERPESVIRIDAE; MIRIDAE; PYROCOCCUS FURIOSUS; SULFOLOBUS SOLFATARICUS;

EID: 80051922235     PISSN: 00426822     EISSN: 10960341     Source Type: Journal    
DOI: 10.1016/j.virol.2011.06.019     Document Type: Article

References (63)

1. Akita F., Chong K.T., Tanaka H., Yamashita E., Miyazaki N., Nakaishi Y., Suzuki M., Namba K., Ono Y., Tsukihara T., Nakagawa A. The crystal structure of a virus-like particle from the hyperthermophilic archaeon Pyrococcus furiosus provides insight into the evolution of viruses. J. Mol. Biol. 2007, 368(5):1469-1483.
2. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J.H., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25(17):3389-3402.
3. Arnold K., Bordoli L., Kopp J., Schwede T. The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 2006, 22(2):195-201.
4. Bamford D.H. Do viruses form lineages across different domains of life?. Res. Microbiol. 2003, 154(4):231-236.
5. Bamford D.H., Burnett R.M., Stuart D.I. Evolution of viral structure. Theor. Popul. Biol. 2002, 61(4):461-470.
6. Bamford D.H., Grimes J.M., Stuart D.I. What does structure tell us about virus evolution?. Curr. Opin. Struct. Biol. 2005, 15(6):655-663.
7. Brussow H., Canchaya C., Hardt W.D. Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion. Microbiol. Mol. Biol. Rev. 2004, 68(3):560-602.
8. Brussow H., Desiere F. Comparative phage genomics and the evolution of Siphoviridae: insights from dairy phages. Mol. Microbiol. 2001, 39(2):213-222.
9. Campbell A. Prophage insertion sites. Res. Microbiol. 2003, 154(4):277-282.
10. Chibani-Chennoufi S., Bruttin A., Dillmann M.L., Brussow H. Phage-host interaction: an ecological perspective. J. Bacteriol. 2004, 186(12):3677-3686.
11. Conway J.F., Duda R.L., Cheng N., Hendrix R.W., Steven A.C. Proteolytic and conformational control of virus capsid maturation-the bacteriophage-Hk97 system. J. Mol. Biol. 1995, 253(1):86-99.
12. Dlakic M. HHsvm: fast and accurate classification of profile-profile matches identified by HHsearch. Bioinformatics 2009, 25(23):3071-3076.
13. Drummond A.J., Ashton B., Buxton S., Cheung M., Cooper A., Heled J., Kearse M., Moir R., Stones-Havas S., Sturrock S., Thierer T., Wilson A. Geneious v5.3 Available from. http://www.geneious.com.
14. Dunigan D.D., Fitzgerald L.A., Van Etten J.L. Phycodnaviruses: a peek at genetic diversity. Virus Res. 2006, 117(1):119-132.
15. Forde S.E., Thompson J.N., Holt R.D., Bohannan B.J.M. Coevolution drives temporal changes in fitness and diversity across environments in a bacteria-bacteriophage interaction. Evolution 2008, 62(8):1830-1839.
16. Frols S., Gordon P.M.K., Panlilio M.A., Duggin I.G., Bell S.D., Sensen C.W., Schleper C. Response of the hyperthermophilic archaeon Sulfolobus solfataricus to UV damage. J. Bacteriol. 2007, 189(23):8708-8718.
17. Frols S., Gordon P.M.K., Panlilio M.A., Schleper C., Sensen C.W. Elucidating the transcription cycle of the UV-inducible hyperthermophilic archaeal virus SSV1 by DNA microarrays. Virology 2007, 365(1):48-59.
18. Fulton J., Bothner B., Lawrence M., Johnson J.E., Douglas T., Young M. Genetics, biochemistry and structure of the archaeal virus STIV. Biochem. Soc. Trans. 2009, 37:114-117.
19. Guex N., Peitsch M.C. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 1997, 18(15):2714-2723.
20. Hatfull G.F. Bacteriophage genomics. Curr. Opin. Microbiol. 2008, 11(5):447-453.
21. Hatfull G.F., Pedulla M.L., Jacobs-Sera D., Cichon P.M., Foley A., Ford M.E., Gonda R.M., Houtz J.M., Hryckowian A.J., Kelchner V.A., Namburi S., Pajcini K.V., Popovich M.G., Schleicher D.T., Simanek B.Z., Smith A.L., Zdanowicz G.M., Kumar V., Peebles C.L., Jacobs W.R., Lawrence J.G., Hendrix R.W. Exploring the mycobacteriophage metaproteome: phage genomics as an educational platform. PLoS Genet. 2006, 2(6):835-847.
22. Hendrix R.W. Bacteriophages: evolution of the majority. Theor. Popul. Biol. 2002, 61(4):471-480.
23. Hendrix R.W. Bacteriophage genomics. Curr. Opin. Microbiol. 2003, 6(5):506-511.
24. Heymann J.B., Cheng N.Q., Newcomb W.W., Trus B.L., Brown J.C., Steven A.C. Dynamics of herpes simplex virus capsid maturation visualized by time-lapse cryo-electron microscopy. Nat. Struct. Biol. 2003, 10(5):334-341.
25. Hildebrand A., Remmert M., Biegert A., Soding J. Fast and accurate automatic structure prediction with HHpred. Proteins Struct. Funct. Bioinf. 2009, 77:128-132.
26. Jiang S.C., Paul J.H. Gene transfer by transduction in the marine environment. Appl. Environ. Microbiol. 1998, 64(8):2780-2787.
27. Juhala R.J., Ford M.E., Duda R.L., Youlton A., Hatfull G.F., Hendrix R.W. Genomic sequences of bacteriophages HK97 and HK022: pervasive genetic mosaicism in the lambdoid bacteriophages. J. Mol. Biol. 2000, 299(1):27-51.
28. Kelley L.A., Sternberg M.J.E. Protein structure prediction on the Web: a case study using the Phyre server. Nat. Protoc. 2009, 4(3):363-371.
29. Kiefer F., Arnold K., Kunzli M., Bordoli L., Schwede T. The SWISS-MODEL repository and associated resources. Nucleic Acids Res. 2009, 37:D387-D392.
30. Kraft P., Kummel D., Oeckinghaus A., Gauss G.H., Wiedenheft B., Young M., 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. 2004, 78(14):7438-7442.
31. Kraft P., Oeckinghaus A., Kummel D., Gauss G.H., Gilmore J., Wiedenheft B., Young M., Lawrence C.M. Crystal structure of F-93 from Sulfolobus spindle-shaped virus 1, a winged-helix DNA binding protein. J. Virol. 2004, 78(21):11544-11550.
32. Krupovic M., Forterre P., Bamford D.H. Comparative analysis of the mosaic genomes of tailed archaeal viruses and proviruses suggests common themes for virion architecture and assembly with tailed viruses of bacteria. J. Mol. Biol. 2010, 397(1):144-160.
33. Larson E.T., Reiter D., Young M., Lawrence C.M. Structure of A197 from Sulfolobus turreted icosahedral virus: a crenarchaeal viral glycosyltransferase exhibiting the GT-A fold. J. Virol. 2006, 80(15):7636-7644.
34. Lawrence C.M., Menon S., Eilers B.J., Bothner B., Khayat R., Douglas T., Young M.J. Structural and functional studies of archaeal viruses. J. Biol. Chem. 2009, 284(19):12599-12603.
35. Lin G.G., Li J.M. Sequence identity between the genomes of humans and viruses. Intervirology 2009, 52(4):196-200.
36. Maaty W.S.A., Ortmann A.C., Dlakic M., Schulstad K., Hilmer J.K., Liepold L., Weidenheft B., Khayat R., Douglas T., Young M.J., Bothner B. Characterization of the archaeal thermophile Sulfolobus turreted icosahedral virus validates an evolutionary link among double-stranded DNA viruses from all domains of life. J. Virol. 2006, 80(15):7625-7635.
37. Moreira D. Multiple independent horizontal transfers of informational genes from bacteria to plasmids and phages: implications for the origin of bacterial replication machinery. Mol. Microbiol. 2000, 35(1):1-5.
38. Mosig G., Gewin J., Luder A., Colowick N., Vo D. Two recombination-dependent DNA replication pathways of bacteriophage T4, and their roles in mutagenesis and horizontal gene transfer. Proc. Natl. Acad. Sci. U.S.A. 2001, 98(15):8306-8311.
39. Muche A.A., Levin R.E. Repression of Uv induction of lambda-prophage by caffeine. Mutat. Res. 1983, 119(1):1-6.
40. Namba K., Hagiwara K., Tanaka H., Nakaishi Y., Chong K.T., Yamashita E., Armah G.E., Ono Y., Ishino Y., Omura T., Tsukihara T., Nakagawa A. Expression and molecular characterization of spherical particles derived from the genome of the hyperthermophilic euryarchaeote Pyrococcus furiosus. J. Biochem. 2005, 138(2):193-199.
41. Newcomb W.W., Homa F.L., Thomsen D.R., Brown J.C. In vitro assembly of the herpes simplex virus procapsid: formation of small procapsids at reduced scaffolding protein concentration. J. Struct. Biol. 2001, 133(1):23-31.
42. Osterhout R.E., Figueroa I.A., Keasling J.D., Arkin A.P. Global analysis of host response to induction of a latent bacteriophage. BMC Microbiol. 2007, 7.
43. Prangishvili D., Stedman K., Zillig W. Viruses of the extremely thermophilic archaeon Sulfolobus. Trends Microbiol. 2001, 9(1):39-43.
44. Prangishvili D., Vestergaard G., Haring M., Aramayo R., Basta T., Rachel R., Garrett R.A. Structural and genomic properties of the hyperthermophilic archaeal virus ATV with an extracellular stage of the reproductive cycle. J. Mol. Biol. 2006, 359(5):1203-1216.
45. Prangishvill D., Garrett R.A., Koonin E.V. Evolutionary genomics of archaeal viruses: unique viral genomes in the third domain of life. Virus Res. 2006, 117(1):52-67.
46. Rao V.B., Feiss M. The bacteriophage DNA packaging motor. Annu. Rev. Genet. 2008, 42:647-681.
47. Reiter W.D., Palm P. Identification and characterization of a defective Ssv1 genome integrated into a transfer-RNA gene in the archaebacterium Sulfolobus Sp B12. Mol. Gen. Genet. 1990, 221(1):65-71.
48. Rice G., Tang L., Stedman K., Roberto F., Spuhler J., Gillitzer E., Johnson J.E., Douglas T., Young M. The structure of a thermophilic archaeal virus shows a double-stranded DNA viral capsid type that spans all domains of life. Proc. Natl. Acad. Sci. U.S.A. 2004, 101(20):7716-7720.
49. Rokyta D.R., Burch C.L., Caudle S.B., Wichman H.A. Horizontal gene transfer and the evolution of microvirid coliphage genomes. J. Bacteriol. 2006, 188(3):1134-1142.
50. Schwartz D.H., Viscidi R., Laeyendecker O., Song H.F., Ray S.C., Michael N. Predominance of defective proviral sequences in an HIV plus long-term non-progressor. Immunol. Lett. 1996, 51(1-2):3-6.
51. Shah A.R., Oehmen C.S., Webb-Robertson B.J. SVM-HUSTLE-an iterative semi-supervised machine learning approach for pairwise protein remote homology detection. Bioinformatics 2008, 24(6):783-790.
52. Soding J., Biegert A., Lupas A.N. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res. 2005, 33:W244-W248.
53. Sutter M., Boehringer D., Gutmann S., Guenther S., Prangishvili D., Loessner M.J., Stetter K.O., Weber-Ban E., Ban N. Structural basis of enzyme encapsulation into a bacterial nanocompartment. Nat. Struct. Mol. Biol. 2008, 15(9):939-947.
54. Suttle C.A. Viruses in the sea. Nature 2005, 437(7057):356-361.
55. Takebe H., Ichikawa H., Iwo K., Kondo S. Phage induction by ultraviolet radiation in strains of Escherichia Coli possessing and lacking dark repair capacity. Virology 1967, 33(4):638-649.
56. Tipper C.H., Bencsics C.E., Coffin J.A. Characterization of Hortulanus endogenous murine leukemia virus, an endogenous provirus that encodes an infectious murine leukemia virus of a novel subgroup. J. Virol. 2005, 79(13):8316-8329.
57. Trautner T.A., Pawlek B., Gunthert U., Canosi U., Jentsch S., Freund M. Restriction and modification in bacillus-subtilis-identification of a gene in the temperate phage Spbeta coding for a Bsur specific modification methyltransferase. Mol. Gen. Genet. 1980, 180(2):361-367.
58. Varani A.D., Souza R.C., Nakaya H.I., de Lima W.C., de Almeida L.G.P., Kitajima E.W., Chen J., Civerolo E., Vasconcelos A.T.R., Van Sluys M.A. Origins of the Xylella fastidiosa prophage-like regions and their impact in genome differentiation. PLoS One 2008, 3(12).
59. Wiedenheft B., Mosolf J., Willits D., Yeager M., Dryden K.A., Young M., Douglas T. An archaeal antioxidant: characterization of a Dps-like protein from Sulfolobus solfataricus. Proc. Natl. Acad. Sci. U.S.A. 2005, 102(30):10551-10556.
60. Wiederstein M., Sippl M.J. ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res. 2007, 35:W407-W410.
61. Wikoff W.R., Liljas L., Duda R.L., Tsuruta H., Hendrix R.W., Johnson J.E. Topologically linked protein rings in the bacteriophage HK97 capsid. Science 2000, 289(5487):2129-2133.
62. Woese C.R. Interpreting the universal phylogenetic tree. Proc. Natl. Acad. Sci. U.S.A. 2000, 97(15):8392-8396.
63. Yamada T., Iwamoto A. Comparison of proviral accessory genes between long-term nonprogressors and progressors of human immunodeficiency virus type 1 infection. Arch. Virol. 2000, 145(5):1021-1027.