Archaeal viruses: Diversity, replication, and structure

Annual Review of Virology

Volumn 1, Issue 1, 2014, Pages 399-426

  Dellas, Nikki ^a   Snyder, Jamie C ^a   Bolduc, Benjamin ^a   Young, Mark J ^a  

^a MONTANA STATE UNIVERSITY   (United States)

Author keywords

Crenarchaea virus; Euryarchaea virus; Viral assembly; Virus proteins

Indexed keywords

CROSSOVER JUNCTION ENDODEOXYRIBONUCLEASE; DNA POLYMERASE; GENOMIC DNA; SINGLE STRANDED DNA;

ARCHAEAL VIRUS; ARTICLE; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; DNA BINDING MOTIF; DNA PACKAGING; DNA REPLICATION; DNA SYNTHESIS; FUSELLOVIRIDAE; GENE REPLICATION; GENE SEQUENCE; GENE STRUCTURE; GENETIC VARIABILITY; GENOME ANALYSIS; GUTTAVIRIDAE; INVERTED TERMINAL REPEAT; LIFE CYCLE; LIPOTHRIXVIRIDAE; METAGENOMICS; MICROBIAL DIVERSITY; NONHUMAN; NUCLEOTIDE METABOLISM; PRIORITY JOURNAL; PROTEIN STRUCTURE; RNA PROCESSING; RUDIVIRIDAE; SEQUENCE HOMOLOGY; STRUCTURE ACTIVITY RELATION; VIRION; VIRUS ASSEMBLY; VIRUS GENOME; VIRUS MORPHOLOGY; VIRUS REPLICATION;

ARCHAEA; CRENARCHAEOTA; EURYARCHAEOTA;

EID: 85017028734     PISSN: 2327056X     EISSN: 23270578     Source Type: Journal    
DOI: 10.1146/annurev-virology-031413-085357     Document Type: Article

References (156)

1. Torsvik T, Dundas ID. 1974. Bacteriophage of Halobacterium salinarium. Nature 248:680-81
2. Ackermann HW, Prangishvili D. 2012. Prokaryote viruses studied by electron microscopy. Arch. Virol. 157:1843-49
3. Janekovic D, Wunderl S, Holz I, Zillig W, Gierl A, Neumann H. 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
4. Pina M, Bize A, Forterre P, Prangishvili D. 2011. The archeoviruses. FEMS Microbiol. Rev. 35:1035-54
5. Pietilä MK, Demina TA, Atanasova NS, Oksanen HM, Bamford DH. 2014. Archaeal viruses and bacteriophages: comparisons and contrasts. Trends Microbiol. 22:334-44
6. Prangishvili D. 2013. The wonderful world of archaeal viruses. Annu. Rev. Microbiol. 67:565-85
7. KrupovičM,White MF, Forterre P, Prangishvili D. 2012. Postcards from the edge: structural genomics of archaeal viruses. Adv. Virus Res. 82:33-62
8. King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ, eds. 2012. Virus Taxonomy: Ninth Report of the International Committee on Taxonomy of Viruses. San Diego, CA: Academic
9. Arnold HP, Ziese U, Zillig W. 2000. SNDV, a novel virus of the extremely thermophilic and acidophilic archaeon Sulfolobus. Virology 272:409-16
10. HäringM, Rachel R, Peng X, Garrett RA, Prangishvili D. 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
11. HäringM, Vestergaard G, Rachel R, Chen L, Garrett RA, Prangishvili D. 2005. Virology: independent virus development outside a host. Nature 436:1101-2
12. Atanasova NS, RoineE,OrenA, Bamford DH,OksanenHM.2012. Global network of specific virus-host interactions in hypersaline environments. Environ. Microbiol. 14:426-40
13. Pietilä MK, Laurinmäki P, Russell DA, Ko CC, Jacobs-Sera D, et al. 2013. Insights into head-tailed viruses infecting extremely halophilic archaea. J. Virol. 87:3248-60
14. Porter K, Tang SL, Chen CP, Chiang PW, Hong MJ, Dyall-Smith M. 2013. PH1: an archaeovirus of Haloarcula hispanica related to SH1 and HHIV-2. Archaea 2013:456318
15. Ahn DG, Kim SI, Rhee JK, Kim KP, Pan JG, Oh JW. 2006. TTSV1, a new virus-like particle isolated from the hyperthermophilic crenarchaeote Thermoproteus tenax. Virology 351:280-90
16. Arnold HP, Zillig W, Ziese U, Holz I, Crosby M, et al. 2000. A novel lipothrixvirus, SIFV, of the extremely thermophilic crenarchaeon Sulfolobus. Virology 267:252-66
17. Bize A, Peng X, Prokofeva M, Maclellan K, Lucas S, et al. 2008. Viruses in acidic geothermal environments of the Kamchatka Peninsula. Res. Microbiol. 159:358-66
18. Erdmann S, Shah SA, Garrett RA. 2013. SMV1 virus-induced CRISPR spacer acquisition from the conjugative plasmid pMGB1 in Sulfolobus solfataricus P2. Biochem. Soc. Trans. 41:1449-58
19. Mochizuki T, Yoshida T, Tanaka R, Forterre P, Sako Y, Prangishvili D. 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
20. Rachel R, Bettstetter M, Hedlund BP, Häring M, Kessler A, et al. 2002. Remarkable morphological diversity of viruses and virus-like particles in hot terrestrial environments. Arch. Virol. 147:2419-29
21. Roine E, Kukkaro P, Paulin L, Laurinavičius S, Domanska A, et al. 2010. New, closely related haloarchaeal viral elements with different nucleic acid types. J. Virol. 84:3682-89
22. VestergaardG,Aramayo R, BastaT,HäringM, PengX, et al. 2008. Structure of the Acidianus filamentous virus 3 and comparative genomics of related archaeal lipothrixviruses. J. Virol. 82:371-81
23. Vestergaard G, Häring M, Peng X, Rachel R, Garrett RA, Prangishvili D. 2005. A novel rudivirus, ARV1, of the hyperthermophilic archaeal genus Acidianus. Virology 336:83-92
24. Vestergaard G, Shah SA, Bize A, Reitberger W, Reuter M, et al. 2008. Stygiolobus rod-shaped virus and the interplay of crenarchaeal rudiviruses with the CRISPR antiviral system. J. Bacteriol. 190:6837-45
25. Zillig W, Kletzin A, Schleper C, Holz I, Janekovic D, et al. 1994. Screening for Sulfolobales, their plasmids and their viruses in Icelandic solfataras. Syst. Appl. Microbiol. 16:609-28
26. Bertani G, Baresi L. 1986. Looking for gene transfer mechanisms in methanogenic bacteria. In Archaeabacteria '85, ed. O Kandler,WZillig, p. 398. Stuttgart, Ger.: Gustav Fisher
27. Daniels LL, Wais AC. 1984. Restriction and modification of halophage S45 in Halobacterium. Curr. Microbiol. 10:133-36
28. Daniels LL, Wais AC. 1998. Virulence in phage populations infecting Halobacterium cutirubrum. FEMS Microbiol. Ecol. 25:129-34
29. Eiserling F, Pushkin A, Gingery M, Bertani G. 1999. Bacteriophage-like particles associated with the gene transfer agent of Methanococcus voltae PS. J. Gen. Virol. 80:3305-8
30. Jordan M, Meile L, Leisinger T. 1989. Organization of Methanobacterium thermoautotrophicum bacteriophage ψM1 DNA. Mol. Gen. Genet. 220:161-64
31. Knox MR, Harris JE. 1986. Isolation and characterization of a bacteriophage of Methanobrevibacter smithii. In Abstr. XIV Int. Congress Microbiol. Manchester, UK: IUMS
32. Meile L, Jenal U, Studer D, Jordan M, Leisinger T. 1989. Characterization of ψM1, a virulent phage of Methanobacterium thermoautotrophicum Marburg. Arch. Microbiol. 152:105-10
33. Nölling J, Groffen A, de Vos WM. 1993. PdblF1 and PdblF3, two novel virulent, archaeal phages infecting different thermophilic strains of the genus Methanobacterium. J. Gen. Microbiol. 139:2511-16
34. Stolt P, Zillig W. 1994. Transcription of the halophagePdblH repressor gene is abolished by transcription from an inversely oriented lytic promoter. FEBS Lett. 344:125-28
35. Torsvik T. 1982. Characterization of four bacteriophages for Halobacterium, with a special emphasis on phage Hs1. In Archaebacteria, ed. O Kandler. Stuttgart, Ger.: Gustav Fischer
36. Vogelsang-Wenke H, Oesterheld D. 1988. Isolation of a halobacterial phage with a fully cytosinemethylated genome. Mol. Gen. Genet. 211:407-14
37. Valentine DL. 2007. Adaptations to energy stress dictate the ecology and evolution of the Archaea. Nat. Rev. Microbiol. 5:316-23
38. Chaban B, Ng SY, Jarrell KF. 2006. Archaeal habitats-from the extreme to the ordinary. Can. J. Microbiol. 52:73-116
39. DeLong EF. 1992. Archaea in coastal marine environments. Proc. Natl. Acad. Sci. USA 89:5685-89
40. Fuhrman JA, McCallum K, Davis AA. 1992. Novel major archaebacterial group from marine plankton. Nature 356:148-49
41. Mochizuki T, KrupovičM, Pehau-Arnaudet G, Sako Y, Forterre P, Prangishvili D. 2012. Archaeal virus with exceptional virion architecture and the largest single-stranded DNA genome. Proc. Natl. Acad. Sci. USA 109:13386-91
42. Webb JS, Lau M, Kjelleberg S. 2004. Bacteriophage and phenotypic variation in Pseudomonas aeruginosa biofilm development. J. Bacteriol. 186:8066-73
43. Xiang X, Chen L,Huang X, Luo Y, She Q, Huang L. 2005. Sulfolobus tengchongensis spindle-shaped virus STVS1: virus-host interactions and genomic features. J. Virol. 79:8677-86
44. Erdmann S, Chen B,Huang X, Deng L, Liu C, et al. 2014. A novel single-tailed fusiform Sulfolobus virus STSV2 infecting model Sulfolobus species. Extremophiles 18:51-60
45. Mochizuki T, Sako Y, Prangishvili D. 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
46. Geslin C, Le Romancer M, Erauso G, Gaillard M, Perrot G, Prieur D. 2003. PAV1, the first virus-like particle isolated from a hyperthermophilic euryarchaeote, "Pyrococcus abyssi." J. Bacteriol. 185:3888-94
47. Gorlas A, Koonin EV, Bienvenu N, Prieur D, Geslin C. 2012. TPV1, the first virus isolated from the hyperthermophilic genus Thermococcus. Environ. Microbiol. 14:503-16
48. Porter K, Kukkaro P, Bamford JK, Bath C, Kivelä HM, et al. 2005. SH1: a novel, spherical halovirus isolated from an Australian hypersaline lake. Virology 335:22-33
49. Jaakkola ST, Penttinen RK, Vilén ST, Jalasvuori M, Rönnholm G, 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
50. Mei Y, Chen J, Sun D, Chen D, Yang Y, et al. 2007. Induction and preliminary characterization of a novel halophage SNJ1 from lysogenic Natrinema sp. F5. Can. J. Microbiol. 53:1106-10
51. Jäälinoja HT, Roine E, Laurinmäki P, Kivelä HM, Bamford DH, Butcher SJ. 2008. Structure and hostcell interaction of SH1, a membrane-containing, halophilic euryarchaeal virus. Proc. Natl. Acad. Sci. USA 105:8008-13
52. Zhang Z, Liu Y, Wang S, Yang D, Cheng Y, et al. 2012. Temperate membrane-containing halophilic archaeal virus SNJ1 has a circulardsDNAgenome identical to that of plasmid pHH205. Virology 434:233-41
53. Pietilä MK, Roine E, Paulin L, Kalkkinen N, Bamford DH. 2009. An ssDNA virus infecting archaea: a new lineage of viruses with a membrane envelope. Mol. Microbiol. 72:307-19
54. Pietilä MK, Atanasova NS, Manole V, Liljeroos L, Butcher SJ, et al. 2012. Virion architecture unifies globally distributed pleolipoviruses infecting halophilic archaea. J. Virol. 86:5067-79
55. Bath C, Cukalac T, Porter K, Dyall-SmithML. 2006. His1 andHis2 are distantly related, spindle-shaped haloviruses belonging to the novel virus group, Salterprovirus. Virology 350:228-39
56. Sencilo A, Paulin L, Kellner S, Helm M, Roine E. 2012. Related haloarchaeal pleomorphic viruses contain different genome types. Nucleic Acids Res. 40:5523-34
57. Dyall-Smith M, Tang SL, Bath C. 2003. Haloarchaeal viruses: How diverse are they? Res. Microbiol. 154:309-13
58. Porter K, Russ BE, Dyall-Smith ML. 2007. Virus-host interactions in salt lakes. Curr. Opin. Microbiol. 10:418-24
59. Santos F, Meyerdierks A, Pena A, Rossello-Mora R, Amann R, Anton J. 2007. Metagenomic approach to the study of halophages: the environmental halophage 1. Environ. Microbiol. 9:1711-23
60. Sime-Ngando T, Lucas S, Robin A, Tucker KP, Colombet J, et al. 2011. Diversity of virus-host systems in hypersaline Lake Retba, Senegal. Environ. Microbiol. 13:1-17
61. Tang SL, Nuttall S, Dyall-Smith M. 2004. Haloviruses HF1 and HF2: evidence for a recent and large recombination event. J. Bacteriol. 186:2810-17
62. Tang SL, Nuttall S, Ngui K, Fisher C, Lopez P, Dyall-Smith M. 2002. HF2: a double-stranded DNA tailed haloarchaeal virus with a mosaic genome. Mol. Microbiol. 44:283-96
63. Pietilä MK, Laurinmäki P, Russell DA, Ko CC, Jacobs-Sera D, 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
64. Wikoff WR, Liljas L, Duda RL, Tsuruta H, Hendrix RW, Johnson JE. 2000. Topologically linked protein rings in the bacteriophage HK97 capsid. Science 289:2129-33
65. Baker ML, Jiang W, Rixon FJ, Chiu W. 2005. Common ancestry of herpesviruses and tailed DNA bacteriophages. J. Virol. 79:14967-70
66. Effantin G, Boulanger P,Neumann E, Letellier L, Conway JF. 2006. Bacteriophage T5 structure reveals similarities with HK97 and T4 suggesting evolutionary relationships. J. Mol. Biol. 361:993-1002
67. Zillig W, Prangishvili D, Schleper C, Elferink M, Holz I, et al. 1996. Viruses, plasmids and other genetic elements of thermophilic and hyperthermophilic Archaea. FEMS Microbiol. Rev. 18:225-36
68. Bolduc B, Shaughnessy DP,Wolf YI, Koonin EV, Roberto FF, Young M. 2012. Identification of novel positive-strand RNA viruses by metagenomic analysis of archaea-dominated Yellowstone hot springs. J. Virol. 86:5562-73
69. Weinbauer MG. 2004. Ecology of prokaryotic viruses. FEMS Microbiol. Rev. 28:127-81
70. Palm P, Schleper C, Grampp B, Yeats S, McWilliam P, et al. 1991. Complete nucleotide sequence of the virus SSV1 of the archaebacterium Sulfolobus shibatae. Virology 185:242-50
71. Prangishvili D, Arnold HP, Gotz D, Ziese U, Holz I, 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
72. Rice G, Tang L, Stedman K, Roberto F, Spuhler J, 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
73. Witte A, Baranyi U, Klein R, Sulzner M, Luo C, Wanner G, et al. 1997. Characterization of Natronobacterium magadii phagePdblCh1, a unique archaeal phage containing DNA and RNA. Mol. Microbiol. 23:603-16
74. Daniels LL, Wais AC. 1990. Ecophysiology of bacteriophage S5100 infecting Halobacterium cutirubrum. Appl. Environ. Microbiol. 56:3605-8
75. Kukkaro P, Bamford DH. 2009. Virus-host interactions in environments with a wide range of ionic strengths. Environ. Microbiol. Rep. 1:71-77
76. Pauling C. 1982. Bacteriophages of Halobacterium halobium: isolation from fermented fish sauce and primary characterization. Can. J. Microbiol. 28:916-21
77. Torsvik T, Dundas ID. 1980. Persisting phage infection in Halobacterium salinarium str. 1. J. Gen. Virol. 47:29-36
78. Klein R, Rossler N, Iro M, Scholz H, Witte A. 2012. Haloarchaeal myovirus PdblCh1 harbours a phase variation system for the production of protein variants with distinct cell surface adhesion specificities. Mol. Microbiol. 83:137-50
79. Quemin ERJ, Lucas S, Daum B, Quax TEF, Kühlbrandt W, et al. 2013. First insights into the entry process of hyperthermophilic archaeal viruses. J. Virol. 87:13379-85
80. Erdmann S, Scheele U, Garrett RA. 2011. AAA ATPase p529 of Acidianus two-tailed virus ATV and host receptor recognition. Virology 421:61-66
81. Menon SK, MaatyWS, Corn GJ, Kwok SC, Eilers BJ, et al. 2008. Cysteine usage in Sulfolobus spindleshaped virus 1 and extension to hyperthermophilic viruses in general. Virology 376:270-78
82. Redder P, Peng X, Brügger K, Shah SA, Roesch F, 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
83. Steinmetz NF, Bize A, Findlay KC, Lomonossoff GP, Manchester M, 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
84. BettstetterM,PengX,Garrett RA,Prangishvili D. 2003. AFV1, a novel virus infecting hyperthermophilic archaea of the genus Acidianus. Virology 315:68-79
85. Bath C, Dyall-SmithML. 1998. His1, an archaeal virus of the Fuselloviridae family that infects Haloarcula hispanica. J. Virol. 72:9392-95
86. Hanhijärvi KJ, Ziedaite G, Pietilä MK, Hæggström E, Bamford DH. 2013. DNA ejection from an archaeal virus-a single-molecule approach. Biophys. J. 104:2264-72
87. HäringM, Peng X, Brügger K, Rachel R, Stetter KO, 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
88. Prangishvili D, Forterre P, Garrett RA. 2006. Viruses of the Archaea: a unifying view. Nat. Rev. Microbiol. 4:837-48
89. Fu CY, Johnson JE. 2012. Structure and cell biology of archaeal virus STIV. Curr. Opin. Virol. 2:122-27
90. Fu CY,Wang K, Gan L, Lanman J, Khayat R, et al. 2010. In vivo assembly of an archaeal virus studied with whole-cell electron cryotomography. Structure 18:1579-86
91. Khayat R, Fu CY, Ortmann AC, Young MJ, Johnson JE. 2010. The architecture and chemical stability of the archaeal Sulfolobus turreted icosahedral virus. J. Virol. 84:9575-83
92. Pietilä MK, Atanasova NS, Oksanen HM, Bamford DH. 2013. Modified coat protein forms the flexible spindle-shaped virion of haloarchaeal virus His1. Environ. Microbiol. 15:1674-86
93. Pietilä MK, Laurinavičius S, Sund J, Roine E, Bamford DH. 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
94. Krupovič M, Gribaldo S, Bamford DH, Forterre P. 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
95. Pagaling E, Haigh RD, GrantWD, Cowan DA, Jones BE, et al. 2007. Sequence analysis of an archaeal virus isolated from a hypersaline lake in Inner Mongolia, China. BMC Genomics 8:410
96. OkeM, Kerou M, Liu H, Peng X, Garrett RA, 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
97. Peng X, Blum H, She Q, Mallok S, Brügger K, 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
98. Baroudy BM, Moss B. 1982. Sequence homologies of diverse length tandem repetitions near ends of vaccinia virus genome suggest unequal crossing over. Nucleic Acids Res. 10:5673-79
99. Blum H, Zillig W, Mallok S,DomdeyH, Prangishvili D. 2001. The genome of the archaeal virus SIRV1 has features in common with genomes of eukaryal viruses. Virology 281:6-9
100. Prangishvili D. 2003. Evolutionary insights from studies on viruses of hyperthermophilic archaea. Res. Microbiol. 154:289-94
101. Birkenbihl RP,Neef K, Prangishvili D, Kemper B. 2001. Holliday junction resolving enzymes of archaeal viruses SIRV1 and SIRV2. J. Mol. Biol. 309:1067-76
102. Bamford DH, Grimes JM, Stuart DI. 2005. What does structure tell us about virus evolution? Curr. Opin. Struct. Biol. 15:655-63
103. Happonen LJ, Oksanen E, Liljeroos L, Goldman A, Kajander T, Butcher SJ. 2013. The structure of the NTPase that powers DNA packaging into Sulfolobus turreted icosahedral virus 2. J. Virol. 87:8388-98
104. Happonen LJ, Redder P, Peng X, Reigstad LJ, Prangishvili D, Butcher SJ. 2010. Familial relationships in hyperthermo-and acidophilic archaeal viruses. J. Virol. 84:4747-54
105. VeeslerD,NgTS, Sendamarai AK, Eilers BJ, LawrenceCM, et al. 2013. Atomic structure of the 75MDa extremophile Sulfolobus turreted icosahedral virus determined by cryoEM andX-ray crystallography. Proc. Natl. Acad. Sci. USA 110:5504-9
106. Khayat R, Tang L, Larson ET, Lawrence CM, Young M, Johnson JE. 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
107. Iyer LM,Makarova KS, Koonin EV, Aravind L. 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
108. MaatyWS, Ortmann AC, DlakićM, Schulstad K, Hilmer JK, 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
109. Snyder JC, Samson RY, Brumfield SK, Bell SD, Young MJ. 2013. Functional interplay between a virus and the ESCRT machinery in Archaea. Proc. Natl. Acad. Sci. USA 110:10783-87
110. Santos F, Yarza P, Parro V, Briones C, Anton J. 2010. The metavirome of a hypersaline environment. Environ. Microbiol. 12:2965-76
111. Snyder JC, StedmanK, Rice G, Wiedenheft B, Spuhler J, YoungMJ. 2003. Viruses of hyperthermophilic Archaea. Res. Microbiol. 154:474-82
112. Häring M, Vestergaard G, Brügger K, Rachel R, Garrett RA, Prangishvili D. 2005. Structure and genome organization of AFV2, a novel archaeal lipothrixvirus with unusual terminal and core structures. J. Bacteriol. 187:3855-58
113. Peng X. 2008. Evidence for the horizontal transfer of an integrase gene from a fusellovirus to a pRNlike plasmid within a single strain of Sulfolobus and the implications for plasmid survival. Microbiology 154:383-91
114. Stedman KM, She Q, Phan H, Arnold HP, Holz I, et al. 2003. Relationships between fuselloviruses infecting the extremely thermophilic archaeon Sulfolobus: SSV1 and SSV2. Res. Microbiol. 154:295-302
115. Wiedenheft B, Stedman K, Roberto F,Willits D, Gleske AK, et al. 2004. Comparative genomic analysis of hyperthermophilic archaeal Fuselloviridae viruses. J. Virol. 78:1954-61
116. Brumfield SK, Ortmann AC, Ruigrok V, Suci P, Douglas T, Young MJ. 2009. Particle assembly and ultrastructural features associated with replication of the lytic archaeal virus Sulfolobus turreted icosahedral virus (STIV). J. Virol. 83:5964-70
117. Snyder JC, Brumfield SK, Kerchner KM, Quax TEF, Prangishvili D, Young MJ. 2013. Insights into a novel viral lytic pathway operating in multiple archaeal virus-host systems. J. Virol. 87:2186-92
118. Snyder JC, Brumfield SK, Peng N, She Q, Young MJ. 2011. Sulfolobus turreted icosahedral virus c92 protein responsible for formation of pyramid-like cellular lysis structures. J. Virol. 85:6287-92
119. Bize A, Karlsson EA, Ekefjärd K, Quax TEF, Pina M, et al. 2009. A unique virus release mechanism in the Archaea. Proc. Natl. Acad. Sci. USA 106:11306-11
120. Daum B, Quax TEF, Sachse M, Mills DJ, Reimann J, et al. 2014. Self-assembly of the general membraneremodeling protein PVAP into sevenfold virus-associated pyramids. Proc. Natl. Acad. Sci. USA 111:3829-34
121. Quax TEF, Krupovič M, Lucas S, Forterre P, Prangishvili D. 2010. The Sulfolobus rod-shaped virus 2 encodes a prominent structural component of the unique virion release system in Archaea. Virology 404:1-4
122. Quax TEF, Lucas S, Reimann J, Pehau-Arnaudet G, Prevost MC, et al. 2011. Simple and elegant design of a virion egress structure in Archaea. Proc. Natl. Acad. Sci. USA 108:3354-59
123. Prangishvili D, Vestergaard G, Häring M, Aramayo R, Basta T, 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
124. Brenner SE, Levitt M. 2000. Expectations from structural genomics. Protein Sci. 9:197-200
125. Koppensteiner WA, Lackner P, Wiederstein M, Sippl MJ. 2000. Characterization of novel proteins based on known protein structures. J. Mol. Biol. 296:1139-52
126. Saqi MA, Wild DL. 2005. Expectations from structural genomics revisited: an analysis of structural genomics targets. Am. J. Pharmacogenomics 5:339-42
127. LeulliotN,Quevillon-Cheruel S,Graille M, Geslin C, FlamentD, et al. 2013. Crystal structure of PAV1-137: a protein from the virus PAV1 that infects Pyrococcus abyssi. Arch. Int. Microbiol. J. 2013:568053
128. Aravind L, Anantharaman V, Balaji S, Babu MM, Iyer LM. 2005. The many faces of the helix-turn-helix domain: transcription regulation and beyond. FEMS Microbiol. Rev. 29:231-62
129. Gomis-Ruth FX, Sola M, Acebo P, Parraga A, Guasch A, et al. 1998. The structure of plasmid-encoded transcriptional repressor CopG unliganded and bound to its operator. EMBO J. 17:7404-15
130. Guillière F, Peixeiro N, Kessler A, Raynal B, Desnoues N, et al. 2009. Structure, function, and targets of the transcriptional regulator SvtR from the hyperthermophilic archaeal virus SIRV1. J. Biol. Chem. 284:22222-37
131. Peixeiro N, Keller J, Collinet B, Leulliot N, Campanacci V, et al. 2013. Structure and function of AvtR, a novel transcriptional regulator from a hyperthermophilic archaeal lipothrixvirus. J. Virol. 87:124-36
132. Schlenker C, Goel A, Tripet BP, Menon S, Willi T, 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
133. Brennan RG. 1993. The winged-helix DNA-binding motif-another helix-turn-helix takeoff. Cell 74:773-76
134. Kraft P, Kummel D, Oeckinghaus A, Gauss GH, Wiedenheft B, 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
135. Larson ET, Eilers B, Menon S, Reiter D, Ortmann A, 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
136. Menon SK, Eilers BJ, Young MJ, Lawrence CM. 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
137. Ibarra JA, Pérez-Rueda E, Carroll RK, Shaw LN. 2013. Global analysis of transcriptional regulators in Staphylococcus aureus. BMC Genomics 14:126
138. Manna A, Cheung AL. 2001. Characterization of sarR, a modulator of sar expression in Staphylococcus aureus. Infect. Immun. 69:885-96
139. OkeM, Carter LG, Johnson KA, Liu H, McMahon SA, et al. 2010. The Scottish Structural Proteomics Facility: targets, methods and outputs. J. Struct. Funct. Genomics 11:167-80
140. Wolfe SA, Nekludova L, Pabo CO. 2000. DNA recognition by Cys2His2 zinc finger proteins. Annu. Rev. Biophys. Biomol. Struct. 29:183-212
141. Guillière F, Danioux C, Jaubert C, Desnoues N, Delepierre M, 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. 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
143. Zhan Z, Ouyang S, LiangW,Zhang Z, LiuZJ, HuangL. 2012. Structural and functional characterization of the C-terminal catalytic domain of SSV1 integrase. Acta Crystallogr. D 68:659-70
144. Chen Y, Narendra U, Iype LE, CoxMM,Rice PA. 2000. Crystal structure of a Flp recombinase-Holliday junction complex: assembly of an active oligomer by helix swapping. Mol. Cell 6:885-97
145. Larson ET, Reiter D, YoungM, Lawrence CM. 2006. Structure of A197 from Sulfolobus turreted icosahedral virus: a crenarchaeal viral glycosyltransferase exhibiting the GT-A fold. J. Virol. 80:7636-44
146. Goulet A, Pina M, Redder P, Prangishvili D, Vera L, et al. 2010. ORF157 from the archaeal virus Acidianus filamentous virus 1 defines a new class of nuclease. J. Virol. 84:5025-31
147. Richardson JS. 1981. The anatomy and taxonomy of protein structure. Adv. Protein Chem. 34:167-339
148. Benson SD, Bamford JK, Bamford DH, Burnett RM. 1999. Viral evolution revealed by bacteriophage PRD1 and human adenovirus coat protein structures. Cell 98:825-33
149. Nandhagopal N, Simpson AA, Gurnon JR, Yan X, Baker TS, 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
150. Stromsten NJ, Bamford DH, Bamford JK. 2005. In vitro DNA packaging of PRD1: a common mechanism for internal-membrane viruses. J. Mol. Biol. 348:617-29
151. Keller J, LeulliotN,Cambillau C, Campanacci V, Porciero S, et al. 2007. Crystal structure of AFV3-109, a highly conserved protein from crenarchaeal viruses. Virol. J. 4:12
152. Larson ET, Eilers BJ, Reiter D, Ortmann AC, Young MJ, Lawrence CM. 2007. A new DNA binding protein highly conserved in diverse crenarchaeal viruses. Virology 363:387-96
153. Goulet A, Blangy S, Redder P, Prangishvili D, Felisberto-Rodrigues C, 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
154. Szymczyna BR, Taurog RE, YoungMJ, Snyder JC, Johnson JE,Williamson JR. 2009. Synergy ofNMR, computation, and X-ray crystallography for structural biology. Structure 17:499-507
155. Orengo CA, Jones DT, Thornton JM. 1994. Protein superfamilies and domain superfolds. Nature 372:631-34
156. Wais AC, Kon M, MacDonald RE, Stollar BD. 1975. Salt-dependent bacteriophage infecting Halobacterium cutirubrum and H. halobium. Nature 256:314-15