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Annual Review of Virology

Volume 1, 2014

Archaeal Viruses: Diversity, Replication, and Structure

Abstract

The Archaea—and their viruses—remain the most enigmatic of life's three domains. Once thought to inhabit only extreme environments, archaea are now known to inhabit diverse environments. Even though the first archaeal virus was described over 40 years ago, only 117 archaeal viruses have been discovered to date. Despite this small number, these viruses have painted a portrait of enormous morphological and genetic diversity. For example, research centered around the various steps of the archaeal virus life cycle has led to the discovery of unique mechanisms employed by archaeal viruses during replication, maturation, and virion release. In many instances, archaeal virus proteins display very low levels of sequence homology to other proteins listed in the public database, and therefore, structural characterization of these proteins has played an integral role in functional assignment. These structural studies have not only provided insights into structure-function relationships but have also identified links between viruses across all three domains of life.

Keyword(s): Crenarchaea virus, Euryarchaea virus, viral assembly, virus proteins
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2014-09-29
2024-04-16
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Literature Cited

  1. Torsvik T, Dundas ID. 1.  1974. Bacteriophage of Halobacterium salinarium. Nature 248:680–81 [Google Scholar]
  2. Ackermann HW, Prangishvili D. 2.  2012. Prokaryote viruses studied by electron microscopy. Arch. Virol. 157:1843–49 [Google Scholar]
  3. Janekovic D, Wunderl S, Holz I, Zillig W, Gierl A, Neumann H. 3.  1983. TTV1, TTV2 and TTV3, a family of viruses of the extremely thermophilic, anaerobic, sulfur reducing archaebacterium Thermoproteus tenax. Mol. Gen. Genet. 192:39–45 [Google Scholar]
  4. Pina M, Bize A, Forterre P, Prangishvili D. 4.  2011. The archeoviruses. FEMS Microbiol. Rev. 35:1035–54 [Google Scholar]
  5. Pietilä MK, Demina TA, Atanasova NS, Oksanen HM, Bamford DH. 5.  2014. Archaeal viruses and bacteriophages: comparisons and contrasts. Trends Microbiol. 22334–44
  6. Prangishvili D. 6.  2013. The wonderful world of archaeal viruses. Annu. Rev. Microbiol. 67:565–85 [Google Scholar]
  7. Krupovič M, White MF, Forterre P, Prangishvili D. 7.  2012. Postcards from the edge: structural genomics of archaeal viruses. Adv. Virus Res. 82:33–62 [Google Scholar]
  8. King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ. 8.  2012. Virus Taxonomy: Ninth Report of the International Committee on Taxonomy of Viruses San Diego, CA: Academic
  9. Arnold HP, Ziese U, Zillig W. 9.  2000. SNDV, a novel virus of the extremely thermophilic and acidophilic archaeon Sulfolobus. Virology 272:409–16 [Google Scholar]
  10. Häring M, Rachel R, Peng X, Garrett RA, Prangishvili D. 10.  2005. Viral diversity in hot springs of Pozzuoli, Italy, and characterization of a unique archaeal virus, Acidianus bottle-shaped virus, from a new family, the Ampullaviridae. J. Virol. 79:9904–11 [Google Scholar]
  11. Häring M, Vestergaard G, Rachel R, Chen L, Garrett RA, Prangishvili D. 11.  2005. Virology: independent virus development outside a host. Nature 436:1101–2 [Google Scholar]
  12. Atanasova NS, Roine E, Oren A, Bamford DH, Oksanen HM. 12.  2012. Global network of specific virus-host interactions in hypersaline environments. Environ. Microbiol. 14:426–40 [Google Scholar]
  13. Pietilä MK, Laurinmäki P, Russell DA, Ko CC, Jacobs-Sera D. 13.  et al. 2013. Insights into head-tailed viruses infecting extremely halophilic archaea. J. Virol. 87:3248–60 [Google Scholar]
  14. Porter K, Tang SL, Chen CP, Chiang PW, Hong MJ, Dyall-Smith M. 14.  2013. PH1: an archaeovirus of Haloarcula hispanica related to SH1 and HHIV-2. Archaea 2013:456318 [Google Scholar]
  15. Ahn DG, Kim SI, Rhee JK, Kim KP, Pan JG, Oh JW. 15.  2006. TTSV1, a new virus-like particle isolated from the hyperthermophilic crenarchaeote Thermoproteus tenax. Virology 351:280–90 [Google Scholar]
  16. Arnold HP, Zillig W, Ziese U, Holz I, Crosby M. 16.  et al. 2000. A novel lipothrixvirus, SIFV, of the extremely thermophilic crenarchaeon Sulfolobus. Virology 267:252–66 [Google Scholar]
  17. Bize A, Peng X, Prokofeva M, Maclellan K, Lucas S. 17.  et al. 2008. Viruses in acidic geothermal environments of the Kamchatka Peninsula. Res. Microbiol. 159:358–66 [Google Scholar]
  18. Erdmann S, Shah SA, Garrett RA. 18.  2013. SMV1 virus-induced CRISPR spacer acquisition from the conjugative plasmid pMGB1 in Sulfolobus solfataricus P2. Biochem. Soc. Trans. 41:1449–58 [Google Scholar]
  19. Mochizuki T, Yoshida T, Tanaka R, Forterre P, Sako Y, Prangishvili D. 19.  2010. Diversity of viruses of the hyperthermophilic archaeal genus Aeropyrum, and isolation of the Aeropyrum pernix bacilliform virus 1, APBV1, the first representative of the family Clavaviridae. Virology 402:347–54 [Google Scholar]
  20. Rachel R, Bettstetter M, Hedlund BP, Häring M, Kessler A. 20.  et al. 2002. Remarkable morphological diversity of viruses and virus-like particles in hot terrestrial environments. Arch. Virol. 147:2419–29 [Google Scholar]
  21. Roine E, Kukkaro P, Paulin L, Laurinavičius S, Domanska A. 21.  et al. 2010. New, closely related haloarchaeal viral elements with different nucleic acid types. J. Virol. 84:3682–89 [Google Scholar]
  22. Vestergaard G, Aramayo R, Basta T, Häring M, Peng X. 22.  et al. 2008. Structure of the Acidianus filamentous virus 3 and comparative genomics of related archaeal lipothrixviruses. J. Virol. 82:371–81 [Google Scholar]
  23. Vestergaard G, Häring M, Peng X, Rachel R, Garrett RA, Prangishvili D. 23.  2005. A novel rudivirus, ARV1, of the hyperthermophilic archaeal genus Acidianus. Virology 336:83–92 [Google Scholar]
  24. Vestergaard G, Shah SA, Bize A, Reitberger W, Reuter M. 24.  et al. 2008. Stygiolobus rod-shaped virus and the interplay of crenarchaeal rudiviruses with the CRISPR antiviral system. J. Bacteriol. 190:6837–45 [Google Scholar]
  25. Zillig W, Kletzin A, Schleper C, Holz I, Janekovic D. 25.  et al. 1994. Screening for Sulfolobales, their plasmids and their viruses in Icelandic solfataras. Syst. Appl. Microbiol. 16:609–28 [Google Scholar]
  26. Bertani G, Baresi L. 26.  1986. Looking for gene transfer mechanisms in methanogenic bacteria. Archaeabacteria ‘85 O Kandler, W Zillig 398 Stuttgart, Ger.: Gustav Fisher [Google Scholar]
  27. Daniels LL, Wais AC. 27.  1984. Restriction and modification of halophage S45 in Halobacterium. Curr. Microbiol. 10:133–36 [Google Scholar]
  28. Daniels LL, Wais AC. 28.  1998. Virulence in phage populations infecting Halobacterium cutirubrum. FEMS Microbiol. Ecol. 25:129–34 [Google Scholar]
  29. Eiserling F, Pushkin A, Gingery M, Bertani G. 29.  1999. Bacteriophage-like particles associated with the gene transfer agent of Methanococcus voltae PS. J. Gen. Virol. 80:3305–8 [Google Scholar]
  30. Jordan M, Meile L, Leisinger T. 30.  1989. Organization of Methanobacterium thermoautotrophicum bacteriophage ψM1 DNA. Mol. Gen. Genet. 220:161–64 [Google Scholar]
  31. Knox MR, Harris JE. 31.  1986. Isolation and characterization of a bacteriophage of Methanobrevibacter smithii. Abstr. XIV Int. Congress Microbiol Manchester, UK: IUMS [Google Scholar]
  32. Meile L, Jenal U, Studer D, Jordan M, Leisinger T. 32.  1989. Characterization of ψM1, a virulent phage of Methanobacterium thermoautotrophicum Marburg. Arch. Microbiol. 152:105–10 [Google Scholar]
  33. Nölling J, Groffen A, de Vos WM. 33.  1993. ϕF1 and ϕF3, two novel virulent, archaeal phages infecting different thermophilic strains of the genus Methanobacterium. J. Gen. Microbiol. 139:2511–16 [Google Scholar]
  34. Stolt P, Zillig W. 34.  1994. Transcription of the halophage ϕH repressor gene is abolished by transcription from an inversely oriented lytic promoter. FEBS Lett. 344:125–28 [Google Scholar]
  35. Torsvik T. 35.  1982. Characterization of four bacteriophages for Halobacterium, with a special emphasis on phage Hs1. Archaebacteria O Kandler. Stuttgart, Ger.: Gustav Fischer [Google Scholar]
  36. Vogelsang-Wenke H, Oesterheld D. 36.  1988. Isolation of a halobacterial phage with a fully cytosine-methylated genome. Mol. Gen. Genet. 211:407–14 [Google Scholar]
  37. Valentine DL. 37.  2007. Adaptations to energy stress dictate the ecology and evolution of the Archaea. Nat. Rev. Microbiol. 5:316–23 [Google Scholar]
  38. Chaban B, Ng SY, Jarrell KF. 38.  2006. Archaeal habitats—from the extreme to the ordinary. Can. J. Microbiol. 52:73–116 [Google Scholar]
  39. DeLong EF. 39.  1992. Archaea in coastal marine environments. Proc. Natl. Acad. Sci. USA 89:5685–89 [Google Scholar]
  40. Fuhrman JA, McCallum K, Davis AA. 40.  1992. Novel major archaebacterial group from marine plankton. Nature 356:148–49 [Google Scholar]
  41. Mochizuki T, Krupovič M, Pehau-Arnaudet G, Sako Y, Forterre P, Prangishvili D. 41.  2012. Archaeal virus with exceptional virion architecture and the largest single-stranded DNA genome. Proc. Natl. Acad. Sci. USA 109:13386–91 [Google Scholar]
  42. Webb JS, Lau M, Kjelleberg S. 42.  2004. Bacteriophage and phenotypic variation in Pseudomonas aeruginosa biofilm development. J. Bacteriol. 186:8066–73 [Google Scholar]
  43. Xiang X, Chen L, Huang X, Luo Y, She Q, Huang L. 43.  2005. Sulfolobus tengchongensis spindle-shaped virus STVS1: virus-host interactions and genomic features. J. Virol. 79:8677–86 [Google Scholar]
  44. Erdmann S, Chen B, Huang X, Deng L, Liu C. 44.  et al. 2014. A novel single-tailed fusiform Sulfolobus virus STSV2 infecting model Sulfolobus species. Extremophiles 18:51–60 [Google Scholar]
  45. Mochizuki T, Sako Y, Prangishvili D. 45.  2011. Provirus induction in hyperthermophilic archaea: characterization of Aeropyrum pernix spindle-shaped virus 1 and Aeropyrum pernix ovoid virus 1. J. Bacteriol. 193:5412–19 [Google Scholar]
  46. Geslin C, Le Romancer M, Erauso G, Gaillard M, Perrot G, Prieur D. 46.  2003. PAV1, the first virus-like particle isolated from a hyperthermophilic euryarchaeote, “Pyrococcus abyssi.”. J. Bacteriol. 185:3888–94 [Google Scholar]
  47. Gorlas A, Koonin EV, Bienvenu N, Prieur D, Geslin C. 47.  2012. TPV1, the first virus isolated from the hyperthermophilic genus Thermococcus. Environ. Microbiol. 14:503–16 [Google Scholar]
  48. Porter K, Kukkaro P, Bamford JK, Bath C, Kivelä HM. 48.  et al. 2005. SH1: a novel, spherical halovirus isolated from an Australian hypersaline lake. Virology 335:22–33 [Google Scholar]
  49. Jaakkola ST, Penttinen RK, Vilén ST, Jalasvuori M, Rönnholm G. 49.  et al. 2012. Closely related archaeal Haloarcula hispanica icosahedral viruses HHIV-2 and SH1 have nonhomologous genes encoding host recognition functions. J. Virol. 86:4734–42 [Google Scholar]
  50. Mei Y, Chen J, Sun D, Chen D, Yang Y. 50.  et al. 2007. Induction and preliminary characterization of a novel halophage SNJ1 from lysogenic Natrinema sp. F5. Can. J. Microbiol. 53:1106–10 [Google Scholar]
  51. Jäälinoja HT, Roine E, Laurinmäki P, Kivelä HM, Bamford DH, Butcher SJ. 51.  2008. Structure and host-cell interaction of SH1, a membrane-containing, halophilic euryarchaeal virus. Proc. Natl. Acad. Sci. USA 105:8008–13 [Google Scholar]
  52. Zhang Z, Liu Y, Wang S, Yang D, Cheng Y. 52.  et al. 2012. Temperate membrane-containing halophilic archaeal virus SNJ1 has a circular dsDNA genome identical to that of plasmid pHH205. Virology 434:233–41 [Google Scholar]
  53. Pietilä MK, Roine E, Paulin L, Kalkkinen N, Bamford DH. 53.  2009. An ssDNA virus infecting archaea: a new lineage of viruses with a membrane envelope. Mol. Microbiol. 72:307–19 [Google Scholar]
  54. Pietilä MK, Atanasova NS, Manole V, Liljeroos L, Butcher SJ. 54.  et al. 2012. Virion architecture unifies globally distributed pleolipoviruses infecting halophilic archaea. J. Virol. 86:5067–79 [Google Scholar]
  55. Bath C, Cukalac T, Porter K, Dyall-Smith ML. 55.  2006. His1 and His2 are distantly related, spindle-shaped haloviruses belonging to the novel virus group, Salterprovirus. Virology 350:228–39 [Google Scholar]
  56. Sencilo A, Paulin L, Kellner S, Helm M, Roine E. 56.  2012. Related haloarchaeal pleomorphic viruses contain different genome types. Nucleic Acids Res. 40:5523–34 [Google Scholar]
  57. Dyall-Smith M, Tang SL, Bath C. 57.  2003. Haloarchaeal viruses: How diverse are they?. Res. Microbiol. 154:309–13 [Google Scholar]
  58. Porter K, Russ BE, Dyall-Smith ML. 58.  2007. Virus-host interactions in salt lakes. Curr. Opin. Microbiol. 10:418–24 [Google Scholar]
  59. Santos F, Meyerdierks A, Pena A, Rossello-Mora R, Amann R, Anton J. 59.  2007. Metagenomic approach to the study of halophages: the environmental halophage 1. Environ. Microbiol. 9:1711–23 [Google Scholar]
  60. Sime-Ngando T, Lucas S, Robin A, Tucker KP, Colombet J. 60.  et al. 2011. Diversity of virus-host systems in hypersaline Lake Retba, Senegal. Environ. Microbiol. 13:1–17 [Google Scholar]
  61. Tang SL, Nuttall S, Dyall-Smith M. 61.  2004. Haloviruses HF1 and HF2: evidence for a recent and large recombination event. J. Bacteriol. 186:2810–17 [Google Scholar]
  62. Tang SL, Nuttall S, Ngui K, Fisher C, Lopez P, Dyall-Smith M. 62.  2002. HF2: a double-stranded DNA tailed haloarchaeal virus with a mosaic genome. Mol. Microbiol. 44:283–96 [Google Scholar]
  63. Pietilä MK, Laurinmäki P, Russell DA, Ko CC, Jacobs-Sera D. 63.  et al. 2013. Structure of the archaeal head-tailed virus HSTV-1 completes the HK97 fold story. Proc. Natl. Acad. Sci. USA 110:10604–9 [Google Scholar]
  64. Wikoff WR, Liljas L, Duda RL, Tsuruta H, Hendrix RW, Johnson JE. 64.  2000. Topologically linked protein rings in the bacteriophage HK97 capsid. Science 289:2129–33 [Google Scholar]
  65. Baker ML, Jiang W, Rixon FJ, Chiu W. 65.  2005. Common ancestry of herpesviruses and tailed DNA bacteriophages. J. Virol. 79:14967–70 [Google Scholar]
  66. Effantin G, Boulanger P, Neumann E, Letellier L, Conway JF. 66.  2006. Bacteriophage T5 structure reveals similarities with HK97 and T4 suggesting evolutionary relationships. J. Mol. Biol. 361:993–1002 [Google Scholar]
  67. Zillig W, Prangishvili D, Schleper C, Elferink M, Holz I. 67.  et al. 1996. Viruses, plasmids and other genetic elements of thermophilic and hyperthermophilic Archaea. FEMS Microbiol. Rev. 18:225–36 [Google Scholar]
  68. Bolduc B, Shaughnessy DP, Wolf YI, Koonin EV, Roberto FF, Young M. 68.  2012. Identification of novel positive-strand RNA viruses by metagenomic analysis of archaea-dominated Yellowstone hot springs. J. Virol. 86:5562–73 [Google Scholar]
  69. Weinbauer MG. 69.  2004. Ecology of prokaryotic viruses. FEMS Microbiol. Rev. 28:127–81 [Google Scholar]
  70. Palm P, Schleper C, Grampp B, Yeats S, McWilliam P. 70.  et al. 1991. Complete nucleotide sequence of the virus SSV1 of the archaebacterium Sulfolobus shibatae. Virology 185:242–50 [Google Scholar]
  71. Prangishvili D, Arnold HP, Gotz D, Ziese U, Holz I. 71.  et al. 1999. A novel virus family, the Rudiviridae: structure, virus-host interactions and genome variability of the Sulfolobus viruses SIRV1 and SIRV2. Genetics 152:1387–96 [Google Scholar]
  72. Rice G, Tang L, Stedman K, Roberto F, Spuhler J. 72.  et al. 2004. 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. USA 101:7716–20 [Google Scholar]
  73. Witte A, Baranyi U, Klein R, Sulzner M, Luo C, Wanner G. 73.  et al. 1997. Characterization of Natronobacterium magadii phage ϕCh1, a unique archaeal phage containing DNA and RNA. Mol. Microbiol. 23:603–16 [Google Scholar]
  74. Daniels LL, Wais AC. 74.  1990. Ecophysiology of bacteriophage S5100 infecting Halobacterium cutirubrum. Appl. Environ. Microbiol. 56:3605–8 [Google Scholar]
  75. Kukkaro P, Bamford DH. 75.  2009. Virus-host interactions in environments with a wide range of ionic strengths. Environ. Microbiol. Rep. 1:71–77 [Google Scholar]
  76. Pauling C. 76.  1982. Bacteriophages of Halobacterium halobium: isolation from fermented fish sauce and primary characterization. Can. J. Microbiol. 28:916–21 [Google Scholar]
  77. Torsvik T, Dundas ID. 77.  1980. Persisting phage infection in Halobacterium salinarium str. 1. J. Gen. Virol. 47:29–36 [Google Scholar]
  78. Klein R, Rossler N, Iro M, Scholz H, Witte A. 78.  2012. Haloarchaeal myovirus ϕCh1 harbours a phase variation system for the production of protein variants with distinct cell surface adhesion specificities. Mol. Microbiol. 83:137–50 [Google Scholar]
  79. Quemin ERJ, Lucas S, Daum B, Quax TEF, Kühlbrandt W. 79.  et al. 2013. First insights into the entry process of hyperthermophilic archaeal viruses. J. Virol. 87:13379–85 [Google Scholar]
  80. Erdmann S, Scheele U, Garrett RA. 80.  2011. AAA ATPase p529 of Acidianus two-tailed virus ATV and host receptor recognition. Virology 421:61–66 [Google Scholar]
  81. Menon SK, Maaty WS, Corn GJ, Kwok SC, Eilers BJ. 81.  et al. 2008. Cysteine usage in Sulfolobus spindle-shaped virus 1 and extension to hyperthermophilic viruses in general. Virology 376:270–78 [Google Scholar]
  82. Redder P, Peng X, Brügger K, Shah SA, Roesch F. 82.  et al. 2009. Four newly isolated fuselloviruses from extreme geothermal environments reveal unusual morphologies and a possible interviral recombination mechanism. Environ. Microbiol. 11:2849–62 [Google Scholar]
  83. Steinmetz NF, Bize A, Findlay KC, Lomonossoff GP, Manchester M. 83.  et al. 2008. Site-specific and spatially controlled addressability of a new viral nanobuilding block: Sulfolobus islandicus rod-shaped virus 2. Adv. Funct. Mater. 18:3478–86 [Google Scholar]
  84. Bettstetter M, Peng X, Garrett RA, Prangishvili D. 84.  2003. AFV1, a novel virus infecting hyperthermophilic archaea of the genus Acidianus. Virology 315:68–79 [Google Scholar]
  85. Bath C, Dyall-Smith ML. 85.  1998. His1, an archaeal virus of the Fuselloviridae family that infects Haloarcula hispanica. J. Virol. 72:9392–95 [Google Scholar]
  86. Hanhijärvi KJ, Ziedaite G, Pietilä MK, Hæggström E, Bamford DH. 86.  2013. DNA ejection from an archaeal virus—a single-molecule approach. Biophys. J. 104:2264–72 [Google Scholar]
  87. Häring M, Peng X, Brügger K, Rachel R, Stetter KO. 87.  et al. 2004. Morphology and genome organization of the virus PSV of the hyperthermophilic archaeal genera Pyrobaculum and Thermoproteus: a novel virus family, the Globuloviridae. Virology 323:233–42 [Google Scholar]
  88. Prangishvili D, Forterre P, Garrett RA. 88.  2006. Viruses of the Archaea: a unifying view. Nat. Rev. Microbiol. 4:837–48 [Google Scholar]
  89. Fu CY, Johnson JE. 89.  2012. Structure and cell biology of archaeal virus STIV. Curr. Opin. Virol. 2:122–27 [Google Scholar]
  90. Fu CY, Wang K, Gan L, Lanman J, Khayat R. 90.  et al. 2010. In vivo assembly of an archaeal virus studied with whole-cell electron cryotomography. Structure 18:1579–86 [Google Scholar]
  91. Khayat R, Fu CY, Ortmann AC, Young MJ, Johnson JE. 91.  2010. The architecture and chemical stability of the archaeal Sulfolobus turreted icosahedral virus. J. Virol. 84:9575–83 [Google Scholar]
  92. Pietilä MK, Atanasova NS, Oksanen HM, Bamford DH. 92.  2013. Modified coat protein forms the flexible spindle-shaped virion of haloarchaeal virus His1. Environ. Microbiol. 15:1674–86 [Google Scholar]
  93. Pietilä MK, Laurinavičius S, Sund J, Roine E, Bamford DH. 93.  2010. The single-stranded DNA genome of novel archaeal virus Halorubrum pleomorphic virus 1 is enclosed in the envelope decorated with glycoprotein spikes. J. Virol. 84:788–98 [Google Scholar]
  94. Krupovič M, Gribaldo S, Bamford DH, Forterre P. 94.  2010. The evolutionary history of archaeal MCM helicases: a case study of vertical evolution combined with hitchhiking of mobile genetic elements. Mol. Biol. Evol. 27:2716–32 [Google Scholar]
  95. Pagaling E, Haigh RD, Grant WD, Cowan DA, Jones BE. 95.  et al. 2007. Sequence analysis of an archaeal virus isolated from a hypersaline lake in Inner Mongolia, China. BMC Genomics 8:410 [Google Scholar]
  96. Oke M, Kerou M, Liu H, Peng X, Garrett RA. 96.  et al. 2011. A dimeric Rep protein initiates replication of a linear archaeal virus genome: implications for Rep mechanism and viral replication. J. Virol. 85:925–31 [Google Scholar]
  97. Peng X, Blum H, She Q, Mallok S, Brügger K. 97.  et al. 2001. Sequences and replication of genomes of the archaeal rudiviruses SIRV1 and SIRV2: relationships to the archaeal lipothrixvirus SIFV and some eukaryal viruses. Virology 291:226–34 [Google Scholar]
  98. Baroudy BM, Moss B. 98.  1982. Sequence homologies of diverse length tandem repetitions near ends of vaccinia virus genome suggest unequal crossing over. Nucleic Acids Res. 10:5673–79 [Google Scholar]
  99. Blum H, Zillig W, Mallok S, Domdey H, Prangishvili D. 99.  2001. The genome of the archaeal virus SIRV1 has features in common with genomes of eukaryal viruses. Virology 281:6–9 [Google Scholar]
  100. Prangishvili D. 100.  2003. Evolutionary insights from studies on viruses of hyperthermophilic archaea. Res. Microbiol. 154:289–94 [Google Scholar]
  101. Birkenbihl RP, Neef K, Prangishvili D, Kemper B. 101.  2001. Holliday junction resolving enzymes of archaeal viruses SIRV1 and SIRV2. J. Mol. Biol. 309:1067–76 [Google Scholar]
  102. Bamford DH, Grimes JM, Stuart DI. 102.  2005. What does structure tell us about virus evolution?. Curr. Opin. Struct. Biol. 15:655–63 [Google Scholar]
  103. Happonen LJ, Oksanen E, Liljeroos L, Goldman A, Kajander T, Butcher SJ. 103.  2013. The structure of the NTPase that powers DNA packaging into Sulfolobus turreted icosahedral virus 2. J. Virol. 87:8388–98 [Google Scholar]
  104. Happonen LJ, Redder P, Peng X, Reigstad LJ, Prangishvili D, Butcher SJ. 104.  2010. Familial relationships in hyperthermo- and acidophilic archaeal viruses. J. Virol. 84:4747–54 [Google Scholar]
  105. Veesler D, Ng TS, Sendamarai AK, Eilers BJ, Lawrence CM. 105.  et al. 2013. Atomic structure of the 75 MDa extremophile Sulfolobus turreted icosahedral virus determined by cryoEM and X-ray crystallography. Proc. Natl. Acad. Sci. USA 110:5504–9 [Google Scholar]
  106. Khayat R, Tang L, Larson ET, Lawrence CM, Young M, Johnson JE. 106.  2005. Structure of an archaeal virus capsid protein reveals a common ancestry to eukaryotic and bacterial viruses. Proc. Natl. Acad. Sci. USA 102:18944–49 [Google Scholar]
  107. Iyer LM, Makarova KS, Koonin EV, Aravind L. 107.  2004. Comparative genomics of the FtsK-HerA superfamily of pumping ATPases: implications for the origins of chromosome segregation, cell division and viral capsid packaging. Nucleic Acids Res. 32:5260–79 [Google Scholar]
  108. Maaty WS, Ortmann AC, Dlakić M, Schulstad K, Hilmer JK. 108.  et al. 2006. 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. 80:7625–35 [Google Scholar]
  109. Snyder JC, Samson RY, Brumfield SK, Bell SD, Young MJ. 109.  2013. Functional interplay between a virus and the ESCRT machinery in Archaea. Proc. Natl. Acad. Sci. USA 110:10783–87 [Google Scholar]
  110. Santos F, Yarza P, Parro V, Briones C, Anton J. 110.  2010. The metavirome of a hypersaline environment. Environ. Microbiol. 12:2965–76 [Google Scholar]
  111. Snyder JC, Stedman K, Rice G, Wiedenheft B, Spuhler J, Young MJ. 111.  2003. Viruses of hyperthermophilic Archaea. Res. Microbiol. 154:474–82 [Google Scholar]
  112. Häring M, Vestergaard G, Brügger K, Rachel R, Garrett RA, Prangishvili D. 112.  2005. Structure and genome organization of AFV2, a novel archaeal lipothrixvirus with unusual terminal and core structures. J. Bacteriol. 187:3855–58 [Google Scholar]
  113. Peng X. 113.  2008. Evidence for the horizontal transfer of an integrase gene from a fusellovirus to a pRN-like plasmid within a single strain of Sulfolobus and the implications for plasmid survival. Microbiology 154:383–91 [Google Scholar]
  114. Stedman KM, She Q, Phan H, Arnold HP, Holz I. 114.  et al. 2003. Relationships between fuselloviruses infecting the extremely thermophilic archaeon Sulfolobus: SSV1 and SSV2. Res. Microbiol. 154:295–302 [Google Scholar]
  115. Wiedenheft B, Stedman K, Roberto F, Willits D, Gleske AK. 115.  et al. 2004. Comparative genomic analysis of hyperthermophilic archaeal Fuselloviridae viruses. J. Virol. 78:1954–61 [Google Scholar]
  116. Brumfield SK, Ortmann AC, Ruigrok V, Suci P, Douglas T, Young MJ. 116.  2009. Particle assembly and ultrastructural features associated with replication of the lytic archaeal virus Sulfolobus turreted icosahedral virus (STIV). J. Virol. 83:5964–70 [Google Scholar]
  117. Snyder JC, Brumfield SK, Kerchner KM, Quax TEF, Prangishvili D, Young MJ. 117.  2013. Insights into a novel viral lytic pathway operating in multiple archaeal virus-host systems. J. Virol. 87:2186–92 [Google Scholar]
  118. Snyder JC, Brumfield SK, Peng N, She Q, Young MJ. 118.  2011. Sulfolobus turreted icosahedral virus c92 protein responsible for formation of pyramid-like cellular lysis structures. J. Virol. 85:6287–92 [Google Scholar]
  119. Bize A, Karlsson EA, Ekefjärd K, Quax TEF, Pina M. 119.  et al. 2009. A unique virus release mechanism in the Archaea. Proc. Natl. Acad. Sci. USA 106:11306–11 [Google Scholar]
  120. Daum B, Quax TEF, Sachse M, Mills DJ, Reimann J. 120.  et al. 2014. Self-assembly of the general membrane-remodeling protein PVAP into sevenfold virus-associated pyramids. Proc. Natl. Acad. Sci. USA 111:3829–34 [Google Scholar]
  121. Quax TEF, Krupovič M, Lucas S, Forterre P, Prangishvili D. 121.  2010. The Sulfolobus rod-shaped virus 2 encodes a prominent structural component of the unique virion release system in Archaea. Virology 404:1–4 [Google Scholar]
  122. Quax TEF, Lucas S, Reimann J, Pehau-Arnaudet G, Prevost MC. 122.  et al. 2011. Simple and elegant design of a virion egress structure in Archaea. Proc. Natl. Acad. Sci. USA 108:3354–59 [Google Scholar]
  123. Prangishvili D, Vestergaard G, Häring M, Aramayo R, Basta T. 123.  et al. 2006. Structural and genomic properties of the hyperthermophilic archaeal virus ATV with an extracellular stage of the reproductive cycle. J. Mol. Biol. 359:1203–16 [Google Scholar]
  124. Brenner SE, Levitt M. 124.  2000. Expectations from structural genomics. Protein Sci. 9:197–200 [Google Scholar]
  125. Koppensteiner WA, Lackner P, Wiederstein M, Sippl MJ. 125.  2000. Characterization of novel proteins based on known protein structures. J. Mol. Biol. 296:1139–52 [Google Scholar]
  126. Saqi MA, Wild DL. 126.  2005. Expectations from structural genomics revisited: an analysis of structural genomics targets. Am. J. Pharmacogenomics 5:339–42 [Google Scholar]
  127. Leulliot N, Quevillon-Cheruel S, Graille M, Geslin C, Flament D. 127.  et al. 2013. Crystal structure of PAV1-137: a protein from the virus PAV1 that infects Pyrococcus abyssi. Arch. Int. Microbiol. J. 2013:568053 [Google Scholar]
  128. Aravind L, Anantharaman V, Balaji S, Babu MM, Iyer LM. 128.  2005. The many faces of the helix-turn-helix domain: transcription regulation and beyond. FEMS Microbiol. Rev. 29:231–62 [Google Scholar]
  129. Gomis-Ruth FX, Sola M, Acebo P, Parraga A, Guasch A. 129.  et al. 1998. The structure of plasmid-encoded transcriptional repressor CopG unliganded and bound to its operator. EMBO J. 17:7404–15 [Google Scholar]
  130. Guillière F, Peixeiro N, Kessler A, Raynal B, Desnoues N. 130.  et al. 2009. Structure, function, and targets of the transcriptional regulator SvtR from the hyperthermophilic archaeal virus SIRV1. J. Biol. Chem. 284:22222–37 [Google Scholar]
  131. Peixeiro N, Keller J, Collinet B, Leulliot N, Campanacci V. 131.  et al. 2013. Structure and function of AvtR, a novel transcriptional regulator from a hyperthermophilic archaeal lipothrixvirus. J. Virol. 87:124–36 [Google Scholar]
  132. Schlenker C, Goel A, Tripet BP, Menon S, Willi T. 132.  et al. 2012. Structural studies of E73 from a hyperthermophilic archaeal virus identify the “RH3” domain, an elaborated ribbon-helix-helix motif involved in DNA recognition. Biochemistry 51:2899–910 [Google Scholar]
  133. Brennan RG. 133.  1993. The winged-helix DNA-binding motif—another helix-turn-helix takeoff. Cell 74:773–76 [Google Scholar]
  134. Kraft P, Kummel D, Oeckinghaus A, Gauss GH, Wiedenheft B. 134.  et al. 2004. 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. 78:7438–42 [Google Scholar]
  135. Larson ET, Eilers B, Menon S, Reiter D, Ortmann A. 135.  et al. 2007. A winged-helix protein from Sulfolobus turreted icosahedral virus points toward stabilizing disulfide bonds in the intracellular proteins of a hyperthermophilic virus. Virology 368:249–61 [Google Scholar]
  136. Menon SK, Eilers BJ, Young MJ, Lawrence CM. 136.  2010. The crystal structure of D212 from Sulfolobus spindle-shaped virus ragged hills reveals a new member of the PD-(D/E)XK nuclease superfamily. J. Virol. 84:5890–97 [Google Scholar]
  137. Ibarra JA, Pérez-Rueda E, Carroll RK, Shaw LN. 137.  2013. Global analysis of transcriptional regulators in Staphylococcus aureus. BMC Genomics 14:126 [Google Scholar]
  138. Manna A, Cheung AL. 138.  2001. Characterization of sarR, a modulator of sar expression in Staphylococcus aureus. Infect. Immun. 69:885–96 [Google Scholar]
  139. Oke M, Carter LG, Johnson KA, Liu H, McMahon SA. 139.  et al. 2010. The Scottish Structural Proteomics Facility: targets, methods and outputs. J. Struct. Funct. Genomics 11:167–80 [Google Scholar]
  140. Wolfe SA, Nekludova L, Pabo CO. 140.  2000. DNA recognition by Cys2His2 zinc finger proteins. Annu. Rev. Biophys. Biomol. Struct. 29:183–212 [Google Scholar]
  141. Guillière F, Danioux C, Jaubert C, Desnoues N, Delepierre M. 141.  et al. 2013. Solution structure of an archaeal DNA binding protein with an eukaryotic zinc finger fold. PLoS ONE 8:e5 2908
  142. Eilers BJ, Young MJ, Lawrence CM. 142.  2012. The structure of an archaeal viral integrase reveals an evolutionarily conserved catalytic core yet supports a mechanism of DNA cleavage in trans. J. Virol. 86:8309–13 [Google Scholar]
  143. Zhan Z, Ouyang S, Liang W, Zhang Z, Liu ZJ, Huang L. 143.  2012. Structural and functional characterization of the C-terminal catalytic domain of SSV1 integrase. Acta Crystallogr. D 68:659–70 [Google Scholar]
  144. Chen Y, Narendra U, Iype LE, Cox MM, Rice PA. 144.  2000. Crystal structure of a Flp recombinase–Holliday junction complex: assembly of an active oligomer by helix swapping. Mol. Cell 6:885–97 [Google Scholar]
  145. Larson ET, Reiter D, Young M, Lawrence CM. 145.  2006. Structure of A197 from Sulfolobus turreted icosahedral virus: a crenarchaeal viral glycosyltransferase exhibiting the GT-A fold. J. Virol. 80:7636–44 [Google Scholar]
  146. Goulet A, Pina M, Redder P, Prangishvili D, Vera L. 146.  et al. 2010. ORF157 from the archaeal virus Acidianus filamentous virus 1 defines a new class of nuclease. J. Virol. 84:5025–31 [Google Scholar]
  147. Richardson JS. 147.  1981. The anatomy and taxonomy of protein structure. Adv. Protein Chem. 34:167–339 [Google Scholar]
  148. Benson SD, Bamford JK, Bamford DH, Burnett RM. 148.  1999. Viral evolution revealed by bacteriophage PRD1 and human adenovirus coat protein structures. Cell 98:825–33 [Google Scholar]
  149. Nandhagopal N, Simpson AA, Gurnon JR, Yan X, Baker TS. 149.  et al. 2002. The structure and evolution of the major capsid protein of a large, lipid-containing DNA virus. Proc. Natl. Acad. Sci. USA 99:14758–63 [Google Scholar]
  150. Stromsten NJ, Bamford DH, Bamford JK. 150.  2005. In vitro DNA packaging of PRD1: a common mechanism for internal-membrane viruses. J. Mol. Biol. 348:617–29 [Google Scholar]
  151. Keller J, Leulliot N, Cambillau C, Campanacci V, Porciero S. 151.  et al. 2007. Crystal structure of AFV3-109, a highly conserved protein from crenarchaeal viruses. Virol. J. 4:12 [Google Scholar]
  152. Larson ET, Eilers BJ, Reiter D, Ortmann AC, Young MJ, Lawrence CM. 152.  2007. A new DNA binding protein highly conserved in diverse crenarchaeal viruses. Virology 363:387–96 [Google Scholar]
  153. Goulet A, Blangy S, Redder P, Prangishvili D, Felisberto-Rodrigues C. 153.  et al. 2009. Acidianus filamentous virus 1 coat proteins display a helical fold spanning the filamentous archaeal viruses lineage. Proc. Natl. Acad. Sci. USA 106:21155–60 [Google Scholar]
  154. Szymczyna BR, Taurog RE, Young MJ, Snyder JC, Johnson JE, Williamson JR. 154.  2009. Synergy of NMR, computation, and X-ray crystallography for structural biology. Structure 17:499–507 [Google Scholar]
  155. Orengo CA, Jones DT, Thornton JM. 155.  1994. Protein superfamilies and domain superfolds. Nature 372:631–34 [Google Scholar]
  156. Wais AC, Kon M, MacDonald RE, Stollar BD. 156.  1975. Salt-dependent bacteriophage infecting Halobacterium cutirubrum and H. halobium. Nature 256:314–15 [Google Scholar]
/content/journals/10.1146/annurev-virology-031413-085357
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Archaeal Viruses: Diversity, Replication, and Structure
Annual Review of Virology 1, 399 (2014); https://doi.org/10.1146/annurev-virology-031413-085357
/content/journals/10.1146/annurev-virology-031413-085357
/content/journals/10.1146/annurev-virology-031413-085357
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Supplementary Data

  • Download Supplemental Table 1: Overview of all archaeal viral protein structures deposited in the PDB (PDF).

  • Article Type: Review Article

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