Model organisms for genetics in the domain Archaea: Methanogens, halophiles, Thermococcales and Sulfolobales

FEMS Microbiology Reviews

Volumn 35, Issue 4, 2011, Pages 577-608

  Leigh, John A ^a   Albers, Sonja Verena ^b   Atomi, Haruyuki ^c   Allers, Thorsten ^d  

^a UNIVERSITY OF WASHINGTON   (United States)

^b MAX PLANCK INSTITUTE FOR TERRESTRIAL MICROBIOLOGY   (Germany)

^c KYOTO UNIVERSITY   (Japan)

^d UNIVERSITY OF NOTTINGHAM   (United Kingdom)

Author keywords

Archaea; Genetics; Halophiles; Methanogens; Sulfolobales; Thermococcales

Indexed keywords

BETA GALACTOSIDASE; BETA GLUCURONIDASE; BETA GLYCOSIDASE; GLYCOSIDASE; GREEN FLUORESCENT PROTEIN; UNCLASSIFIED DRUG;

ARCHAEAL GENOME; ARTICLE; CRENARCHAEOTA; ECOSYSTEM; EURYARCHAEOTA; GENE DISRUPTION; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENE INACTIVATION; GENE INSERTION; GENE OVEREXPRESSION; GENE TARGETING; HALOBACTERIUM SALINARUM; HALOFERAX VOLCANII; HALOPHILE; INTRODUCED SPECIES; METHANOCOCCUS; METHANOGEN; METHANOGENESIS; METHANOSARCINA; NONHUMAN; PHYLOGENETIC TREE; PYROCOCCUS ABYSSI; PYROCOCCUS FURIOSUS; REPORTER GENE; SHUTTLE VECTOR; SPECIES CULTIVATION; SULFOLOBALES; SULFOLOBUS; SULFOLOBUS ACIDOCALDARIUS; SULFOLOBUS ISLANDICUS; SULFOLOBUS SOLFATARICUS; THERMOCOCCALES; THERMOCOCCUS KODAKARENSIS; TRANSPOSON;

ARCHAEA; BIOCHEMISTRY; CRENARCHAEOTA; EURYARCHAEOTA; GENE EXPRESSION REGULATION, ARCHAEAL; GENETIC TECHNIQUES; GENETICS, MICROBIAL; MODELS, GENETIC; PHYLOGENY;

ARCHAEA; CRENARCHAEOTA; EUKARYOTA; EURYARCHAEOTA; SULFOLOBALES; THERMOCOCCALES;

EID: 79958073627     PISSN: 01686445     EISSN: 15746976     Source Type: Journal    
DOI: 10.1111/j.1574-6976.2011.00265.x     Document Type: Article

References (369)

1. Aagaard C, Leviev I, Aravalli RN, Forterre P, Prieur D & Garrett RA (1996) General vectors for archaeal hyperthermophiles: strategies based on a mobile intron and a plasmid. FEMS Microbiol Rev 18: 93-104.
2. Albers SV & Driessen AJM (2008) Conditions for gene disruption by homologous recombination of exogenous DNA into the Sulfolobus solfataricus genome. Archaea 2: 145-149.
3. Albers SV, Koning SM, Konings WN & Driessen AJ (2004) Insights into ABC transport in archaea. J Bioenerg Biomembr 36: 5-15.
4. Albers SV, Jonuscheit M, Dinkelaker S et al. (2006) Production of recombinant and tagged proteins in the hyperthermophilic archaeon Sulfolobus solfataricus. Appl Environ Microb 72: 102-111.
5. Albers SV, Birkeland NK, Driessen AJ et al. (2009) SulfoSYS (Sulfolobus Systems Biology): towards a silicon cell model for the central carbohydrate metabolism of the archaeon Sulfolobus solfataricus under temperature variation. Biochem Soc T 37: 58-64.
6. Allers T & Mevarech M (2005) Archaeal genetics - the third way. Nat Rev Genet 6: 58-73.
7. Allers T, Ngo HP, Mevarech M & Lloyd RG (2004) Development of additional selectable markers for the halophilic archaeon Haloferax volcanii based on the leuB and trpA genes. Appl Environ Microb 70: 943-953.
8. Allers T, Barak S, Liddell S, Wardell K & Mevarech M (2010) Improved strains and plasmid vectors for conditional overexpression of His-tagged proteins in Haloferax volcanii. Appl Environ Microb 76: 1759-1769.
9. Amend JP & Shock EL (2001) Energetics of overall metabolic reactions of thermophilic and hyperthermophilic Archaea and bacteria. FEMS Microbiol Rev 25: 175-243.
10. Aravalli RN & Garrett RA (1997) Shuttle vectors for hyperthermophilic archaea. Extremophiles 1: 183-191.
11. Argyle JL, Tumbula DL & Leigh JA (1996) Neomycin resistance as a selectable marker in Methanococcus maripaludis. Appl Environ Microb 62: 4233-4237.
12. Arndt JW, Hao B, Ramakrishnan V, Cheng T, Chan SI & Chan MK (2002) Crystal structure of a novel carboxypeptidase from the hyperthermophilic archaeon Pyrococcus furiosus. Structure 10: 215-224.
13. Arnott MA, Michael RA, Thompson CR, Hough DW & Danson MJ (2000) Thermostability and thermoactivity of citrate synthases from the thermophilic and hyperthermophilic archaea, Thermoplasma acidophilum and Pyrococcus furiosus. J Mol Biol 304: 657-668.
14. Atomi H (2005) Recent progress towards the application of hyperthermophiles and their enzymes. Curr Opin Chem Biol 9: 166-173.
15. Atomi H, Fukui T, Kanai T, Morikawa M & Imanaka T (2004a) Description of Thermococcus kodakaraensis sp. nov., a well studied hyperthermophilic archaeon previously reported as Pyrococcus sp. KOD1. Archaea 1: 263-267.
16. Atomi H, Matsumi R & Imanaka T (2004b) Reverse gyrase is not a prerequisite for hyperthermophilic life. J Bacteriol 186: 4829-4833.
17. Aucelli T, Contursi P, Girfoglio M, Rossi M & Cannio R (2006) A spreadable, non-integrative and high copy number shuttle vector for Sulfolobus solfataricus based on the genetic element pSSVx from Sulfolobus islandicus. Nucleic Acids Res 34: e114.
18. Balch WE, Fox GE, Magrum LJ, Woese CR & Wolfe RS (1979) Methanogens: reevaluation of a unique biological group. Microbiol Rev 43: 260-296.
19. Baliga NS, Bjork SJ, Bonneau R et al. (2004) Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1. Genome Res 14: 1025-1035.
20. Ban N, Nissen P, Hansen J, Moore PB & Steitz TA (2000) The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science 289: 905-920.
21. Bauer MW, Bylina EJ, Swanson RV & Kelly RM (1996) Comparison of a β-glucosidase and a β-mannosidase from the hyperthermophilic archaeon Pyrococcus furiosus. Purification, characterization, gene cloning, and sequence analysis. J Biol Chem 271: 23749-23755.
22. Beneke S, Bestgen H & Klein A (1995) Use of the Escherichia coli uidA gene as a reporter in Methanococcus voltae for the analysis of the regulatory function of the intergenic region between the operons encoding selenium-free hydrogenases. Mol Gen Genet 248: 225-228.
23. Berkner S & Lipps G (2008) Genetic tools for Sulfolobus spp.: vectors and first applications. Arch Microbiol 190: 217-230.
24. Berkner S, Grogan D, Albers SV & Lipps G (2007) Small multicopy, non-integrative shuttle vectors based on the plasmid pRN1 for Sulfolobus acidocaldarius and Sulfolobus solfataricus, model organisms of the (cren-)archaea. Nucleic Acids Res 35: e88.
25. Berkner S, Wlodkowski A, Albers SV & Lipps G (2010) Inducible and constitutive promoters for genetic systems in Sulfolobus acidocaldarius. Extremophiles 14: 249-259.
26. Bernander R (2007) The cell cycle of Sulfolobus. Mol Microbiol 66: 557-562.
27. Berquist BR, Muller JA & Dassarma S (2006) Genetic systems for halophilic archaea. Methods in Microbiology: Extremophiles (Rainey F & Oren A, eds), pp. 649-680. Elsevier/Academic Press, Amsterdam.
28. Berquist BR, DasSarma P & DasSarma S (2007) Essential and non-essential DNA replication genes in the model halophilic Archaeon, Halobacterium sp. NRC-1. BMC Genet 8: 31.
29. Bertani G & Baresi L (1987) Genetic transformation in the methanogen Methanococcus voltae PS. J Bacteriol 169: 2730-2738.
30. Bidle KA, Hanson TE, Howell K & Nannen J (2007) HMG-CoA reductase is regulated by salinity at the level of transcription in Haloferax volcanii. Extremophiles 11: 49-55.
31. Bidle KA, Kirkland PA, Nannen JL & Maupin-Furlow JA (2008) Proteomic analysis of Haloferax volcanii reveals salinity-mediated regulation of the stress response protein PspA. Microbiology 154: 1436-1443.
32. Bidle KA, Haramaty L, Baggett N, Nannen J & Bidle KD (2010) Tantalizing evidence for caspase-like protein expression and activity in the cellular stress response of Archaea. Environ Microbiol 12: 1161-1172.
33. Bitan-Banin G, Ortenberg R & Mevarech M (2003) Development of a gene knockout system for the halophilic archaeon Haloferax volcanii by use of the pyrE gene. J Bacteriol 185: 772-778.
34. Blank CE, Kessler PS & Leigh JA (1995) Genetics in methanogens: transposon insertion mutagenesis of a Methanococcus maripaludis nifH gene. J Bacteriol 177: 5773-5777.
35. Blaseio U & Pfeifer F (1990) Transformation of Halobacterium halobium: development of vectors and investigation of gas vesicle synthesis. P Natl Acad Sci USA 87: 6772-6776.
36. Blumentals II, Brown SH, Schicho RN, Skaja AK, Costantino HR & Kelly RM (1990) The hyperthermophilic archaebacterium, Pyrococcus furiosus. Development of culturing protocols, perspectives on scaleup, and potential applications. Ann NY Acad Sci 589: 301-314.
37. Boccazzi P, Zhang JK & Metcalf WW (2000) Generation of dominant selectable markers for resistance to pseudomonic acid by cloning and mutagenesis of the ileS gene from the archaeon Methanosarcina barkeri fusaro. J Bacteriol 182: 2611-2618.
38. Bolhuis H, Palm P, Wende A et al. (2006) The genome of the square archaeon Haloquadratum walsbyi: life at the limits of water activity. BMC Genomics 7: 169.
39. Bonneau R, Facciotti MT, Reiss DJ et al. (2007) A predictive model for transcriptional control of physiology in a free living cell. Cell 131: 1354-1365.
40. Boucher Y, Douady CJ, Papke RT et al. (2003) Lateral gene transfer and the origins of prokaryotic groups. Annu Rev Genet 37: 283-328.
41. Breuert S, Allers T, Spohn G & Soppa J (2006) Regulated polyploidy in halophilic archaea. PLoS ONE 1: e92.
42. Britton KL, Baker PJ, Fisher M et al. (2006) Analysis of protein solvent interactions in glucose dehydrogenase from the extreme halophile Haloferax mediterranei. P Natl Acad Sci USA 103: 4846-4851.
43. Brock TD, Brock KM, Belly RT & Weiss RL (1972) Sulfolobus: a new genus of sulfur-oxidizing bacteria living at low pH and high temperature. Arch Mikrobiol 84: 54-68.
44. Brugger K, Redder P, She Q, Confalonieri F, Zivanovic Y & Garrett RA (2002) Mobile elements in archaeal genomes. FEMS Microbiol Lett 206: 131-141.
45. Bult CJ, White O, Olsen GJ et al. (1996) Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273: 1058-1073.
46. Calo D, Kaminski L & Eichler J (2010) Protein glycosylation in Archaea: sweet and extreme. Glycobiology 20: 1065-1076.
47. Cannio R, Contursi P, Rossi M & Bartolucci S (1998) An autonomously replicating transforming vector for Sulfolobus solfataricus. J Bacteriol 180: 3237-3240.
48. Chaban B, Ng SY, Kanbe M, Saltzman I, Nimmo G, Aizawa S & Jarrell KF (2007) Systematic deletion analyses of the fla genes in the flagella operon identify several genes essential for proper assembly and function of flagella in the archaeon, Methanococcus maripaludis. Mol Microbiol 66: 596-609.
49. Charlebois RL, Lam WL, Cline SW & Doolittle WF (1987) Characterization of pHV2 from Halobacterium volcanii and its use in demonstrating transformation of an archaebacterium. P Natl Acad Sci USA 84: 8530-8534.
50. Charlebois RL, Schalkwyk LC, Hofman JD & Doolittle WF (1991) Detailed physical map and set of overlapping clones covering the genome of the archaebacterium Haloferax volcanii DS2. J Mol Biol 222: 509-524.
51. Christian JH & Waltho JA (1962) Solute concentrations within cells of halophilic and non-halophilic bacteria. Biochim Biophys Acta 65: 506-508.
52. Clay MD, Cosper CA, Jenney FE Jr, Adams MW & Johnson MK (2003) Nitric oxide binding at the mononuclear active site of reduced Pyrococcus furiosus superoxide reductase. P Natl Acad Sci USA 100: 3796-3801.
53. Cline SW & Doolittle WF (1987) Efficient transfection of the archaebacterium Halobacterium halobium. J Bacteriol 169: 1341-1344.
54. Cline SW & Doolittle WF (1992) Transformation of members of the genus Haloarcula with shuttle vectors based on Halobacterium halobium and Haloferax volcanii plasmid replicons. J Bacteriol 174: 1076-1080.
55. Cline SW, Lam WL, Charlebois RL, Schalkwyk LC & Doolittle WF (1989) Transformation methods for halophilic archaebacteria. Can J Microbiol 35: 148-152.
56. Cohen A, Lam WL, Charlebois RL, Doolittle WF & Schalkwyk LC (1992) Localizing genes on the map of the genome of Haloferax volcanii, one of the Archaea. P Natl Acad Sci USA 89: 1602-1606.
57. Cohen GN, Barbe V, Flament D et al. (2003) An integrated analysis of the genome of the hyperthermophilic archaeon Pyrococcus abyssi. Mol Microbiol 47: 1495-1512.
58. Coker JA, DasSarma P, Kumar J, Muller JA & DasSarma S (2007) Transcriptional profiling of the model Archaeon Halobacterium sp. NRC-1: responses to changes in salinity and temperature. Saline Systems 3: 6.
59. Costa KC, Wong PM, Wang T et al. (2010) Protein complexing in a methanogen suggests electron bifurcation and electron delivery from formate to heterodisulfide reductase. P Natl Acad Sci USA 107: 11050-11055.
60. Crowley DJ, Boubriak I, Berquist BR et al. (2006) The uvrA, uvrB and uvrC genes are required for repair of ultraviolet light induced DNA photoproducts in Halobacterium sp. NRC-1. Saline Systems 2: 11.
61. Daniel RM, Peterson ME, Danson MJ et al. (2010) The molecular basis of the effect of temperature on enzyme activity. Biochem J 425: 353-360.
62. Danner S & Soppa J (1996) Characterization of the distal promoter element of halobacteria in vivo using saturation mutagenesis and selection. Mol Microbiol 19: 1265-1276.
63. Danno A, Fukuda W, Yoshida M et al. (2008) Expression profiles and physiological roles of two types of prefoldins from the hyperthermophilic archaeon Thermococcus kodakaraensis. J Mol Biol 382: 298-311.
64. DasSarma S (1995) Natural plasmids and plasmid vectors of halophiles. Archaea: A Laboratory Manual, Vol. Halophiles (DasSarma S & Fleischmann EM, eds), pp. 241-252. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
65. DasSarma S, Berquist BR, Coker JA, DasSarma P & Muller JA (2006) Post-genomics of the model haloarchaeon Halobacterium sp. NRC-1. Saline Systems 2: 3.
66. Delfosse V, Girard E, Birck C et al. (2009) Structure of the archaeal pab87 peptidase reveals a novel self-compartmentalizing protease family. PLoS One 4: e4712.
67. Delmas S, Shunburne L, Ngo HP & Allers T (2009) Mre11-Rad50 promotes rapid repair of DNA damage in the polyploid archaeon Haloferax volcanii by restraining homologous recombination. PLoS Genet 5: e1000552.
68. DeLong EF (1998) Everything in moderation: archaea as 'non-extremophiles'. Curr Opin Genet Dev 8: 649-654.
69. Deng L, Zhu H, Chen Z, Liang YX & She Q (2009) Unmarked gene deletion and host-vector system for the hyperthermophilic crenarchaeon Sulfolobus islandicus. Extremophiles 13: 735-746.
70. Dodsworth JA & Leigh JA (2006) Regulation of nitrogenase by 2-oxoglutarate-reversible, direct binding of a PII-like nitrogen sensor protein to dinitrogenase. P Natl Acad Sci USA 103: 9779-9784.
71. Dodsworth JA, Cady NC & Leigh JA (2005) 2-Oxoglutarate and the PII homologues NifI1 and NifI2 regulate nitrogenase activity in cell extracts of Methanococcus maripaludis. Mol Microbiol 56: 1527-1538.
72. Dodsworth JA, Li L, Wei S, Hedlund BP, Leigh JA & de Figueiredo P (2010) Interdomain conjugal transfer of DNA from bacteria to archaea. Appl Environ Microb 76: 5644-5647.
73. Dong G, Vieille C, Savchenko A & Zeikus JG (1997a) Cloning, sequencing, and expression of the gene encoding extracellular α-amylase from Pyrococcus furiosus and biochemical characterization of the recombinant enzyme. Appl Environ Microb 63: 3569-3576.
74. Dong G, Vieille C & Zeikus JG (1997b) Cloning, sequencing, and expression of the gene encoding amylopullulanase from Pyrococcus furiosus and biochemical characterization of the recombinant enzyme. Appl Environ Microb 63: 3577-3584.
75. Doolittle WF & Zhaxybayeva O (2009) On the origin of prokaryotic species. Genome Res 19: 744-756.
76. Driskill LE, Bauer MW & Kelly RM (1999) Synergistic interactions among β-laminarinase, β-1, 4-glucanase, and β-glucosidase from the hyperthermophilic archaeon Pyrococcus furiosus during hydrolysis of β-1, 4-, β-1, 3-, and mixed-linked polysaccharides. Biotechnol Bioeng 66: 51-60.
77. Du X, Choi IG, Kim R, Wang W, Jancarik J, Yokota H & Kim SH (2000) Crystal structure of an intracellular protease from Pyrococcus horikoshii at 2Å resolution. P Natl Acad Sci USA 97: 14079-14084.
78. Duggin IG, McCallum SA & Bell SD (2008) Chromosome replication dynamics in the archaeon Sulfolobus acidocaldarius. P Natl Acad Sci USA 105: 16737-16742.
79. Dura MA, Rosenbaum E, Larabi A, Gabel F, Vellieux FM & Franzetti B (2009) The structural and biochemical characterizations of a novel TET peptidase complex from Pyrococcus horikoshii reveal an integrated peptide degradation system in hyperthermophilic Archaea. Mol Microbiol 72: 26-40.
80. Dyall-Smith M (2009) The Halohandbook - Protocols for haloarchaeal genetics. Available at
81. Dyall-Smith M, Tang SL & Bath C (2003) Haloarchaeal viruses: how diverse are they? Res Microbiol 154: 309-313.
82. Dyall-Smith ML & Doolittle WF (1994) Construction of composite transposons for halophilic Archaea. Can J Microbiol 40: 922-929.
83. Egorova K & Antranikian G (2005) Industrial relevance of thermophilic Archaea. Curr Opin Microbiol 8: 649-655.
84. Elazari-Volcani B (1936) Life in the Dead Sea. Nature 138: 467.
85. Elferink MG, de Wit JG, Demel R, Driessen AJ & Konings WN (1992) Functional reconstitution of membrane proteins in monolayer liposomes from bipolar lipids of Sulfolobus acidocaldarius. J Biol Chem 267: 1375-1381.
86. Elferink MG, Albers SV, Konings WN & Driessen AJ (2001) Sugar transport in Sulfolobus solfataricus is mediated by two families of binding protein-dependent ABC transporters. Mol Microbiol 39: 1494-1503.
87. Ellen AF, Albers SV & Driessen AJ (2010) Comparative study of the extracellular proteome of Sulfolobus species reveals limited secretion. Extremophiles 14: 87-98.
88. El Yacoubi B, Phillips G, Blaby IK, Haas CE, Cruz Y, Greenberg J & de Crecy-Lagard V (2009) A Gateway platform for functional genomics in Haloferax volcanii: deletion of three tRNA modification genes. Archaea 2: 211-219.
89. Facciotti MT, Reiss DJ, Pan M et al. (2007) General transcription factor specified global gene regulation in archaea. P Natl Acad Sci USA 104: 4630-4635.
90. Falb M, Muller K, Konigsmaier L et al. (2008) Metabolism of halophilic archaea. Extremophiles 12: 177-196.
91. Fiala G & Stetter KO (1986) Pyrococcus furiosus sp. nov. represents a novel genus of marine heterotrophic archaebacteria growing optimally at 100°C. Arch Microbiol 145: 56-61.
92. Fields S & Johnston M (2005) Cell biology. Whither model organism research? Science 307: 1885-1886.
93. Fox GE, Magrum LJ, Balch WE, Wolfe RS & Woese CR (1977) Classification of methanogenic bacteria by 16S ribosomal RNA characterization. P Natl Acad Sci USA 74: 4537-4541.
94. Frols S, Ajon M, Wagner M et al. (2008) UV-inducible cellular aggregation of the hyperthermophilic archaeon Sulfolobus solfataricus is mediated by pili formation. Mol Microbiol 70: 938-952.
95. Fujiwara S, Aki R, Yoshida M, Higashibata H, Imanaka T & Fukuda W (2008) Expression profiles and physiological roles of two types of molecular chaperonins from the hyperthermophilic archaeon Thermococcus kodakarensis. Appl Environ Microb 74: 7306-7312.
96. Fukuda W, Morimoto N, Imanaka T & Fujiwara S (2008) Agmatine is essential for the cell growth of Thermococcus kodakaraensis. FEMS Microbiol Lett 287: 113-120.
97. Fukui T, Atomi H, Kanai T, Matsumi R, Fujiwara S & Imanaka T (2005) Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes. Genome Res 15: 352-363.
98. Galperin MY, Aravind L & Koonin EV (2000) Aldolases of the DhnA family: a possible solution to the problem of pentose and hexose biosynthesis in archaea. FEMS Microbiol Lett 183: 259-264.
99. Gardner WL & Whitman WB (1999) Expression vectors for Methanococcus maripaludis: overexpression of acetohydroxyacid synthase and beta-galactosidase. Genetics 152: 1439-1447.
100. Garrett RA & Klenk HP (2007) Archaea: Evolution, Physiology and Molecular Biology. Blackwell Publishing, Oxford.
101. Geiduschek EP & Ouhammouch M (2005) Archaeal transcription and its regulators. Mol Microbiol 56: 1397-1407.
102. Gernhardt P, Possot O, Foglino M, Sibold L & Klein A (1990) Construction of an integration vector for use in the archaebacterium Methanococcus voltae and expression of a eubacterial resistance gene. Mol Gen Genet 221: 273-279.
103. Giladi M, Bitan-Banin G, Mevarech M & Ortenberg R (2002) Genetic evidence for a novel thymidylate synthase in the halophilic archaeon Halobacterium salinarum and in Campylobacter jejuni. FEMS Microbiol Lett 216: 105-109.
104. Goede B, Naji S, von Kampen O, Ilg K & Thomm M (2006) Protein-protein interactions in the archaeal transcriptional machinery: binding studies of isolated RNA polymerase subunits and transcription factors. J Biol Chem 281: 30581-30592.
105. Gonzalez JM, Sheckells D, Viebahn M, Krupatkina D, Borges KM & Robb FT (1999) Thermococcus waiotapuensis sp. nov., an extremely thermophilic archaeon isolated from a freshwater hot spring. Arch Microbiol 172: 95-101.
106. Greve B, Jensen S, Brugger K, Zillig W & Garrett RA (2004) Genomic comparison of archaeal conjugative plasmids from Sulfolobus. Archaea 1: 231-239.
107. Grogan DW (1989) Phenotypic characterization of the archaebacterial genus Sulfolobus: comparison of five wild-type strains. J Bacteriol 171: 6710-6719.
108. Gueguen Y, Voorhorst WG, van der Oost J & de Vos WM (1997) Molecular and biochemical characterization of an endo-β-1, 3- glucanase of the hyperthermophilic archaeon Pyrococcus furiosus. J Biol Chem 272: 31258-31264.
109. Guss AM, Rother M, Zhang JK, Kulkarni G & Metcalf WW (2008) New methods for tightly regulated gene expression and highly efficient chromosomal integration of cloned genes for Methanosarcina species. Archaea 2: 193-203.
110. Hale CR, Zhao P, Olson S et al. (2009) RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex. Cell 139: 945-956.
111. Halio SB, Blumentals II, Short SA, Merrill BM & Kelly RM (1996) Sequence, expression in Escherichia coli, and analysis of the gene encoding a novel intracellular protease (PfpI) from the hyperthermophilic archaeon Pyrococcus furiosus. J Bacteriol 178: 2605-2612.
112. Harrison FC & Kennedy ME (1922) The red discoloration of cured cod fish. T Roy Soc Can Sect V 16: 101-152.
113. Hartman AL, Norais C, Badger JH et al. (2010) The complete genome sequence of Haloferax volcanii DS2, a model archaeon. PLoS ONE 5: e9605.
114. Hasenohrl D, Lombo T, Kaberdin V, Londei P & Blasi U (2008) Translation initiation factor a/eIF2(-gamma) counteracts 5' to 3' mRNA decay in the archaeon Sulfolobus solfataricus. P Natl Acad Sci USA 105: 2146-2150.
115. Hashimoto H, Inoue T, Nishioka M, Fujiwara S, Takagi M, Imanaka T & Kai Y (1999) Hyperthermostable protein structure maintained by intra-and inter-helix ion-pairs in archaeal O6-methylguanine-DNA methyltransferase. J Mol Biol 292: 707-716.
116. Hashimoto Y, Yamamoto T, Fujiwara S, Takagi M & Imanaka T (2001) Extracellular synthesis, specific recognition, and intracellular degradation of cyclomaltodextrins by the hyperthermophilic archaeon Thermococcus sp. strain B1001. J Bacteriol 183: 5050-5057.
117. Haydock AK, Porat I, Whitman WB & Leigh JA (2004) Continuous culture of Methanococcus maripaludis under defined nutrient conditions. FEMS Microbiol Lett 238: 85-91.
118. Hechler T & Pfeifer F (2009) Anaerobiosis inhibits gas vesicle formation in halophilic Archaea. Mol Microbiol 71: 132-145.
119. Hendrickson EL & Leigh JA (2008) Roles of coenzyme F420-reducing hydrogenases and hydrogen- and F420-dependent methylenetetrahydromethanopterin dehydrogenases in reduction of F420 and production of hydrogen during methanogenesis. J Bacteriol 190: 4818-4821.
120. Hendrickson EL, Haydock AK, Moore BC, Whitman WB & Leigh JA (2007) Functionally distinct genes regulated by hydrogen limitation and growth rate in methanogenic Archaea. P Natl Acad Sci USA 104: 8930-8934.
121. Hendrickson EL, Liu Y, Rosas-Sandoval G, Porat I, Soll D, Whitman WB & Leigh JA (2008) Global responses of Methanococcus maripaludis to specific nutrient limitations and growth rate. J Bacteriol 190: 2198-2205.
122. Hering O, Brenneis M, Beer J, Suess B & Soppa J (2009) A novel mechanism for translation initiation operates in haloarchaea. Mol Microbiol 71: 1451-1463.
123. Hilpert R, Winter J, Hammes W & Kandler O (1981) The sensitivity of archaebacteria to antibiotics. Zbl Bakt Hyg I C 2: 11-20.
124. Hirata A, Kanai T, Santangelo TJ et al. (2008a) Archaeal RNA polymerase subunits E and F are not required for transcription in vitro, but a Thermococcus kodakarensis mutant lacking subunit F is temperature-sensitive. Mol Microbiol 70: 623-633.
125. Hirata A, Klein BJ & Murakami KS (2008b) The X-ray crystal structure of RNA polymerase from Archaea. Nature 451: 851-854.
126. Holden JF, Takai K, Summit M, Bolton S, Zyskowski J & Baross JA (2001) Diversity among three novel groups of hyperthermophilic deep-sea Thermococcus species from three sites in the northeastern Pacific Ocean. FEMS Microbiol Ecol 36: 51-60.
127. Holmes M, Pfeifer F & Dyall-Smith M (1994) Improved shuttle vectors for Haloferax volcanii including a dual-resistance plasmid. Gene 146: 117-121.
128. Holmes ML & Dyall-Smith ML (1991) Mutations in DNA gyrase result in novobiocin resistance in halophilic archaebacteria. J Bacteriol 173: 642-648.
129. Holmes ML & Dyall-Smith ML (2000) Sequence and expression of a halobacterial beta-galactosidase gene. Mol Microbiol 36: 114-122.
130. Hopkins BB & Paull TT (2008) The P. furiosus mre11/rad50 complex promotes 5' strand resection at a DNA double-strand break. Cell 135: 250-260.
131. Hovey R, Lentes S, Ehrenreich A et al. (2005) DNA microarray analysis of Methanosarcina mazei Go1 reveals adaptation to different methanogenic substrates. Mol Genet Genomics 273: 225-239.
132. Huber G & Stetter KO (1991) Sulfolobus metallicus, sp. nov., a novel strictly chemolithotrophic thermophilic archaeal species of metal-mobilizers. Syst Appl Microbiol 14: 372-378.
133. Huet J, Schnabel R, Sentenac A & Zillig W (1983) Archaebacteria and eukaryotes possess DNA-dependent RNA polymerases of a common type. EMBO J 2: 1291-1294.
134. Hugenholtz P, Goebel BM & Pace NR (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180: 4765-4774.
135. Humbard MA, Miranda HV, Lim JM et al. (2010) Ubiquitin-like small archaeal modifier proteins (SAMPs) in Haloferax volcanii. Nature 463: 54-60.
136. Hura GL, Menon AL, Hammel M et al. (2009) Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS). Nat Methods 6: 606-612.
137. Hutcheon GW & Bolhuis A (2003) The archaeal twin-arginine translocation pathway. Biochem Soc T 31: 686-689.
138. Imanaka H, Fukui T, Atomi H & Imanaka T (2002) Gene cloning and characterization of fructose-1, 6-bisphosphate aldolase from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. J Biosci Bioeng 94: 237-243.
139. Imanaka H, Yamatsu A, Fukui T, Atomi H & Imanaka T (2006) Phosphoenolpyruvate synthase plays an essential role for glycolysis in the modified Embden-Meyerhof pathway in Thermococcus kodakarensis. Mol Microbiol 61: 898-909.
140. Jager D, Sharma CM, Thomsen J, Ehlers C, Vogel J & Schmitz RA (2009) Deep sequencing analysis of the Methanosarcina mazei Go1 transcriptome in response to nitrogen availability. P Natl Acad Sci USA 106: 21878-21882.
141. Jarrell KF, Jones GM, Kandiba L, Nair DB & Eichler J (2010) S-layer glycoproteins and flagellins: reporters of archaeal posttranslational modifications. Archaea 2010 pii: 612948.
142. Jenney FE Jr, Verhagen MF, Cui X & Adams MW (1999) Anaerobic microbes: oxygen detoxification without superoxide dismutase. Science 286: 306-309.
143. Jeon BS, Taguchi H, Sakai H, Ohshima T, Wakagi T & Matsuzawa H (1997) 4-α-glucanotransferase from the hyperthermophilic archaeon Thermococcus litoralis- enzyme purification and characterization, and gene cloning, sequencing and expression in Escherichia coli. Eur J Biochem 248: 171-178.
144. Jonuscheit M, Martusewitsch E, Stedman KM & Schleper C (2003) A reporter gene system for the hyperthermophilic archaeon Sulfolobus solfataricus based on a selectable and integrative shuttle vector. Mol Microbiol 48: 1241-1252.
145. Kanai T, Akerboom J, Takedomi S et al. (2007) A global transcriptional regulator in Thermococcus kodakaraensis controls the expression levels of both glycolytic and gluconeogenic enzyme-encoding genes. J Biol Chem 282: 33659-33670.
146. Kanai T, Takedomi S, Fujiwara S, Atomi H & Imanaka T (2010) Identification of the Phr-dependent heat shock regulon in the hyperthermophilic archaeon, Thermococcus kodakaraensis. J Biochem 147: 361-370.
147. Kanzaki T, Iizuka R, Takahashi K et al. (2008) Sequential action of ATP-dependent subunit conformational change and interaction between helical protrusions in the closure of the built-in lid of group II chaperonins. J Biol Chem 283: 34773-34784.
148. Karner MB, DeLong EF & Karl DM (2001) Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature 409: 507-510.
149. Kasting JF & Siefert JL (2002) Life and the evolution of Earth's atmosphere. Science 296: 1066-1068.
150. Kaur A, Pan M, Meislin M, Facciotti MT, El-Gewely R & Baliga NS (2006) A systems view of haloarchaeal strategies to withstand stress from transition metals. Genome Res 16: 841-854.
151. Kawarabayasi Y, Sawada M, Horikawa H et al. (1998) Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3. DNA Res 5: 55-76.
152. Keese AM, Schut GJ, Ouhammouch M, Adams MW & Thomm M (2010) Genome-wide identification of targets for the archaeal heat shock regulator phr by cell-free transcription of genomic DNA. J Bacteriol 192: 1292-1298.
153. Kengen SW, Luesink EJ, Stams AJ & Zehnder AJ (1993) Purification and characterization of an extremely thermostable β-glucosidase from the hyperthermophilic archaeon Pyrococcus furiosus. Eur J Biochem 213: 305-312.
154. Kengen SW, de Bok FA, van Loo ND, Dijkema C, Stams AJ & de Vos WM (1994) Evidence for the operation of a novel Embden-Meyerhof pathway that involves ADP-dependent kinases during sugar fermentation by Pyrococcus furiosus. J Biol Chem 269: 17537-17541.
155. Kengen SW, Tuininga JE, de Bok FA, Stams AJ & de Vos WM (1995) Purification and characterization of a novel ADP-dependent glucokinase from the hyperthermophilic archaeon Pyrococcus furiosus. J Biol Chem 270: 30453-30457.
156. Kennedy SP, Ng WV, Salzberg SL, Hood L & DasSarma S (2001) Understanding the adaptation of Halobacterium species NRC-1 to its extreme environment through computational analysis of its genome sequence. Genome Res 11: 1641-1650.
157. Kida H, Sugano Y, Iizuka R, Fujihashi M, Yohda M & Miki K (2008) Structural and molecular characterization of the prefoldin beta subunit from Thermococcus strain KS-1. J Mol Biol 383: 465-474.
158. Kim YJ, Lee HS, Kim ES et al. (2010) Formate-driven growth coupled with H(2) production. Nature 467: 352-355.
159. Kirkland PA, Gil MA, Karadzic IM & Maupin-Furlow JA (2008) Genetic and proteomic analyses of a proteasome-activating nucleotidase A mutant of the haloarchaeon Haloferax volcanii. J Bacteriol 190: 193-205.
160. Kiyonari S, Tahara S, Uchimura M, Shirai T, Ishino S & Ishino Y (2009) Studies on the base excision repair (BER) complex in Pyrococcus furiosus. Biochem Soc T 37: 79-82.
161. Knittel K & Boetius A (2009) Anaerobic oxidation of methane: progress with an unknown process. Annu Rev Microbiol 63: 311-334.
162. Konneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB & Stahl DA (2005) Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437: 543-546.
163. Korkhin Y, Unligil UM, Littlefield O et al. (2009) Evolution of complex RNA polymerases: the complete Archaeal RNA polymerase structure. PLoS Biol 7: e102.
164. Krebs MP, Hauss T, Heyn MP, RajBhandary UL & Khorana HG (1991) Expression of the bacterioopsin gene in Halobacterium halobium using a multicopy plasmid. P Natl Acad Sci USA 88: 859-863.
165. Kulkarni G, Kridelbaugh DM, Guss AM & Metcalf WW (2009) Hydrogen is a preferred intermediate in the energy-conserving electron transport chain of Methanosarcina barkeri. P Natl Acad Sci USA 106: 15915-15920.
166. Kuo YP, Thompson DK, St Jean A, Charlebois RL & Daniels CJ (1997) Characterization of two heat shock genes from Haloferax volcanii: a model system for transcription regulation in the Archaea. J Bacteriol 179: 6318-6324.
167. Kurosawa N & Grogan DW (2005) Homologous recombination of exogenous DNA with the Sulfolobus acidocaldarius genome: properties and uses. FEMS Microbiol Lett 253: 141-149.
168. Ladapo J & Whitman WB (1990) Method for isolation of auxotrophs in the methanogenic archaebacteria: role of the acetyl-CoA pathway of autotrophic CO2 fixation in Methanococcus maripaludis. P Natl Acad Sci USA 87: 5598-5602.
169. Laderman KA, Asada K, Uemori T, Mukai H, Taguchi Y, Kato I & Anfinsen CB (1993) α-amylase from the hyperthermophilic archaebacterium Pyrococcus furiosus. Cloning and sequencing of the gene and expression in Escherichia coli. J Biol Chem 268: 24402-24407.
170. Laksanalamai P & Robb FT (2004) Small heat shock proteins from extremophiles: a review. Extremophiles 8: 1-11.
171. Lam WL & Doolittle WF (1989) Shuttle vectors for the archaebacterium Halobacterium volcanii. P Natl Acad Sci USA 86: 5478-5482.
172. Lam WL & Doolittle WF (1992) Mevinolin-resistant mutations identify a promoter and the gene for a eukaryote-like 3-hydroxy-3-methylglutaryl-coenzyme A reductase in the archaebacterium Haloferax volcanii. J Biol Chem 267: 5829-5834.
173. Lanyi JK (1974) Salt-dependent properties of proteins from extremely halophilic bacteria. Bacteriol Rev 38: 272-290.
174. Large A, Stamme C, Lange C, Duan Z, Allers T, Soppa J & Lund PA (2007) Characterization of a tightly controlled promoter of the halophilic archaeon Haloferax volcanii and its use in the analysis of the essential cct1 gene. Mol Microbiol 66: 1092-1106.
175. Lee HS, Shockley KR, Schut GJ et al. (2006) Transcriptional and biochemical analysis of starch metabolism in the hyperthermophilic archaeon Pyrococcus furiosus. J Bacteriol 188: 2115-2125.
176. Lee HS, Kang SG, Bae SS et al. (2008) The complete genome sequence of Thermococcus onnurineus NA1 reveals a mixed heterotrophic and carboxydotrophic metabolism. J Bacteriol 190: 7491-7499.
177. Lee SJ, Moulakakis C, Koning SM, Hausner W, Thomm M & Boos W (2005) TrmB, a sugar sensing regulator of ABC transporter genes in Pyrococcus furiosus exhibits dual promoter specificity and is controlled by different inducers. Mol Microbiol 57: 1797-1807.
178. Lee SJ, Surma M, Seitz S, Hausner W, Thomm M & Boos W (2007) Characterization of the TrmB-like protein, PF0124, a TGM-recognizing global transcriptional regulator of the hyperthermophilic archaeon Pyrococcus furiosus. Mol Microbiol 65: 305-318.
179. 2 to methane in CO-grown Methanosarcina acetivorans revealed by proteomics. P Natl Acad Sci USA 103: 17921-17926.
180. Lestini R, Duan Z & Allers T (2010) The archaeal Xpf/Mus81/FANCM homolog Hef and the Holliday junction resolvase Hjc define alternative pathways that are essential for cell viability in Haloferax volcanii. DNA Repair (Amst) 9: 994-1002.
181. Levin I, Giladi M, Altman-Price N, Ortenberg R & Mevarech M (2004) An alternative pathway for reduced folate biosynthesis in bacteria and halophilic archaea. Mol Microbiol 54: 1307-1318.
182. Li Q, Li L, Rejtar T, Karger BL & Ferry JG (2005a) Proteome of Methanosarcina acetivorans Part I: an expanded view of the biology of the cell. J Proteome Res 4: 112-128.
183. Li Q, Li L, Rejtar T, Karger BL & Ferry JG (2005b) Proteome of Methanosarcina acetivorans Part II: comparison of protein levels in acetate- and methanol-grown cells. J Proteome Res 4: 129-135.
184. Lie TJ & Leigh JA (2002) Regulatory response of Methanococcus maripaludis to alanine, an intermediate nitrogen source. J Bacteriol 184: 5301-5306.
185. Lie TJ & Leigh JA (2003) A novel repressor of nif and glnA expression in the methanogenic archaeon Methanococcus maripaludis. Mol Microbiol 47: 235-246.
186. Lie TJ & Leigh JA (2007) Genetic screen for regulatory mutations in Methanococcus maripaludis and its use in identification of induction-deficient mutants of the euryarchaeal repressor NrpR. Appl Environ Microb 73: 6595-6600.
187. Lie TJ, Wood GE & Leigh JA (2005) Regulation of nif expression in Methanococcus maripaludis: roles of the euryarchaeal repressor NrpR, 2-oxoglutarate, and two operators. J Biol Chem 280: 5236-5241.
188. Lindas AC, Karlsson EA, Lindgren MT, Ettema TJ & Bernander R (2008) A unique cell division machinery in the Archaea. P Natl Acad Sci USA 105: 18942-18946.
189. Lipscomb GL, Stirrett K, Schut GJ, Yang F, Jenney FE Jr, Scott RA, Michael WW & Westpheling J (2011) Natural competence in the hyperthermophilic archaeon Pyrococcus furiosus facilitates genetic manipulation: construction of multiple markerless deletions of genes encoding the two cytoplasmic hydrogenases. Appl Environ Microbiol (in press).
190. Liu H, Rudolf J, Johnson KA et al. (2008) Structure of the DNA repair helicase XPD. Cell 133: 801-812.
191. Liu Y & Whitman WB (2008) Metabolic, phylogenetic, and ecological diversity of the methanogenic archaea. Ann NY Acad Sci 1125: 171-189.
192. Lopez-Garcia P, St Jean A, Amils R & Charlebois RL (1995) Genomic stability in the archaea Haloferax volcanii and Haloferax mediterranei. J Bacteriol 177: 1405-1408.
193. Lucas S, Toffin L, Zivanovic Y et al. (2002) Construction of a shuttle vector for, and spheroplast transformation of, the hyperthermophilic archaeon Pyrococcus abyssi. Appl Environ Microb 68: 5528-5536.
194. Lundgren M, Malandrin L, Eriksson S, Huber H & Bernander R (2008) Cell cycle characteristics of crenarchaeota: unity among diversity. J Bacteriol 190: 5362-5367.
195. Maaty WS, Wiedenheft B, Tarlykov P et al. (2009) Something old, something new, something borrowed; how the thermoacidophilic archaeon Sulfolobus solfataricus responds to oxidative stress. PLoS One 4: e6964.
196. Mahapatra A, Patel A, Soares JA, Larue RC, Zhang JK, Metcalf WW & Krzycki JA (2006) Characterization of a Methanosarcina acetivorans mutant unable to translate UAG as pyrrolysine. Mol Microbiol 59: 56-66.
197. Mahapatra A, Srinivasan G, Richter KB et al. (2007) Class I and class II lysyl-tRNA synthetase mutants and the genetic encoding of pyrrolysine in Methanosarcina spp. Mol Microbiol 64: 1306-1318.
198. Maher MJ, Ghosh M, Grunden AM, Menon AL, Adams MW, Freeman HC & Guss JM (2004) Structure of the prolidase from Pyrococcus furiosus. Biochemistry 43: 2771-2783.
199. Mardanov AV, Ravin NV, Svetlitchnyi VA, Beletsky AV, Miroshnichenko ML, Bonch-Osmolovskaya EA & Skryabin KG (2009) Metabolic versatility and indigenous origin of the archaeon Thermococcus sibiricus, isolated from a siberian oil reservoir, as revealed by genome analysis. Appl Environ Microb 75: 4580-4588.
200. Marg BL, Schweimer K, Sticht H & Oesterhelt D (2005) A two-alpha-helix extra domain mediates the halophilic character of a plant-type ferredoxin from halophilic archaea. Biochemistry 44: 29-39.
201. Margesin R & Schinner F (2001) Potential of halotolerant and halophilic microorganisms for biotechnology. Extremophiles 5: 73-83.
202. Martusewitsch E, Sensen CW & Schleper C (2000) High spontaneous mutation rate in the hyperthermophilic archaeon Sulfolobus solfataricus is mediated by transposable elements. J Bacteriol 182: 2574-2581.
203. Matsui I, Sakai Y, Matsui E, Kikuchi H, Kawarabayasi Y & Honda K (2000) Novel substrate specificity of a membrane-bound β-glycosidase from the hyperthermophilic archaeon Pyrococcus horikoshii. FEBS Lett 467: 195-200.
204. Matsumi R, Manabe K, Fukui T, Atomi H & Imanaka T (2007) Disruption of a sugar transporter gene cluster in a hyperthermophilic archaeon using a host-marker system based on antibiotic resistance. J Bacteriol 189: 2683-2691.
205. Mayanagi K, Kiyonari S, Saito M, Shirai T, Ishino Y & Morikawa K (2009) Mechanism of replication machinery assembly as revealed by the DNA ligase-PCNA-DNA complex architecture. P Natl Acad Sci USA 106: 4647-4652.
206. McCready S & Marcello L (2003) Repair of UV damage in Halobacterium salinarum. Biochem Soc T 31: 694-698.
207. McCready S, Muller JA, Boubriak I, Berquist BR, Ng WL & Dassarma S (2005) UV irradiation induces homologous recombination genes in the model archaeon, Halobacterium sp. NRC-1. Saline Systems 1: 3.
208. Menon AL, Poole FL II, Cvetkovic A et al. (2009) Novel multiprotein complexes identified in the hyperthermophilic archaeon Pyrococcus furiosus by non-denaturing fractionation of the native proteome. Mol Cell Proteomics 8: 735-751.
209. Metcalf WW, Zhang JK, Apolinario E, Sowers KR & Wolfe RS (1997) A genetic system for Archaea of the genus Methanosarcina: liposome-mediated transformation and construction of shuttle vectors. P Natl Acad Sci USA 94: 2626-2631.
210. Meuer J, Kuettner HC, Zhang JK, Hedderich R & Metcalf WW (2002) Genetic analysis of the archaeon Methanosarcina barkeri Fusaro reveals a central role for Ech hydrogenase and ferredoxin in methanogenesis and carbon fixation. P Natl Acad Sci USA 99: 5632-5637.
211. Mevarech M & Werczberger R (1985) Genetic transfer in Halobacterium volcanii. J Bacteriol 162: 461-462.
212. Mevarech M, Frolow F & Gloss LM (2000) Halophilic enzymes: proteins with a grain of salt. Biophys Chem 86: 155-164.
213. Mizanur RM, Griffin AK & Pohl NL (2008) Recombinant production and biochemical characterization of a hyperthermostable α-glucan/maltodextrin phosphorylase from Pyrococcus furiosus. Archaea 2: 169-176.
214. Moll R & Schäfer G (1988) Chemiosmotic H+ cycling across the plasma membrane of the thermoacidophilic archaebacterium Sulfolobus acidocaldarius. FEBS Lett 232: 359-363.
215. Moore BC & Leigh JA (2005) Markerless mutagenesis in Methanococcus maripaludis demonstrates roles for alanine dehydrogenase, alanine racemase, and alanine permease. J Bacteriol 187: 972-979.
216. Morikawa M, Izawa Y, Rashid N, Hoaki T & Imanaka T (1994) Purification and characterization of a thermostable thiol protease from a newly isolated hyperthermophilic Pyrococcus sp. Appl Environ Microb 60: 4559-4566.
217. Mueller M, Takemasa R, Schwarz A, Atomi H & Nidetzky B (2009) "Short-chain" alpha-1, 4-glucan phosphorylase having a truncated N-terminal domain: functional expression and characterization of the enzyme from Sulfolobus solfataricus. Biochim Biophys Acta 1794: 1709-1714.
218. Mukund S & Adams MW (1995) Glyceraldehyde-3-phosphate ferredoxin oxidoreductase, a novel tungsten-containing enzyme with a potential glycolytic role in the hyperthermophilic archaeon Pyrococcus furiosus. J Biol Chem 270: 8389-8392.
219. Mullakhanbhai MF & Larsen H (1975) Halobacterium volcanii spec. nov., a Dead Sea halobacterium with a moderate salt requirement. Arch Microbiol 104: 207-214.
220. Muller JA & DasSarma S (2005) Genomic analysis of anaerobic respiration in the archaeon Halobacterium sp. strain NRC-1: dimethyl sulfoxide and trimethylamine N-oxide as terminal electron acceptors. J Bacteriol 187: 1659-1667.
221. Murakami T, Kanai T, Takata H, Kuriki T & Imanaka T (2006) A novel branching enzyme of the GH-57 family in the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. J Bacteriol 188: 5915-5924.
222. Neves C, da Costa MS & Santos H (2005) Compatible solutes of the hyperthermophile Palaeococcus ferrophilus: osmoadaptation and thermoadaptation in the order thermococcales. Appl Environ Microb 71: 8091-8098.
223. Ng SY, Chaban B & Jarrell KF (2006) Archaeal flagella, bacterial flagella and type IV pili: a comparison of genes and posttranslational modifications. J Mol Microb Biotech 11: 167-191.
224. Ng WV, Kennedy SP, Mahairas GG et al. (2000) Genome sequence of Halobacterium species NRC-1. P Natl Acad Sci USA 97: 12176-12181.
225. Nishida H, Mayanagi K, Kiyonari S, Sato Y, Oyama T, Ishino Y & Morikawa K (2009) Structural determinant for switching between the polymerase and exonuclease modes in the PCNA-replicative DNA polymerase complex. P Natl Acad Sci USA 106: 20693-20698.
226. Nomura S & Harada Y (1998) Functional expression of green fluorescent protein derivatives in Halobacterium salinarum. FEMS Microbiol Lett 167: 287-293.
227. Norais C, Hawkins M, Hartman AL, Eisen JA, Myllykallio H & Allers T (2007) Genetic and physical mapping of DNA replication origins in Haloferax volcanii. PLoS Genet 3: e77.
228. Oesterhelt D & Stoeckenius W (1971) Rhodopsin-like protein from the purple membrane of Halobacterium halobium. Nat New Biol 233: 149-152.
229. Olsen GJ & Woese CR (1996) Lessons from an Archaeal genome: what are we learning from Methanococcus jannaschii? Trends Genet 12: 377-379.
230. Oren A (1999) Bioenergetic aspects of halophilism. Microbiol Mol Biol R 63: 334-348.
231. Oren A (2008) Microbial life at high salt concentrations: phylogenetic and metabolic diversity. Saline Systems 4: 2.
232. Oren A (2010) Industrial and environmental applications of halophilic microorganisms. Environ Technol 31: 825-834.
233. Oren A, Heldal M, Norland S & Galinski EA (2002) Intracellular ion and organic solute concentrations of the extremely halophilic bacterium Salinibacter ruber. Extremophiles 6: 491-498.
234. Oren A, Arahal DR & Ventosa A (2009) Emended descriptions of genera of the family Halobacteriaceae. Int J Syst Evol Micr 59: 637-642.
235. Orita I, Sato T, Yurimoto H, Kato N, Atomi H, Imanaka T & Sakai Y (2006) The ribulose monophosphate pathway substitutes for the missing pentose phosphate pathway in the archaeon Thermococcus kodakaraensis. J Bacteriol 188: 4698-4704.
236. Orphan VJ, Taylor LT, Hafenbradl D & Delong EF (2000) Culture-dependent and culture-independent characterization of microbial assemblages associated with high-temperature petroleum reservoirs. Appl Environ Microb 66: 700-711.
237. Papke RT, Koenig JE, Rodriguez-Valera F & Doolittle WF (2004) Frequent recombination in a saltern population of Halorubrum. Science 306: 1928-1929.
238. Papke RT, Zhaxybayeva O, Feil EJ, Sommerfeld K, Muise D & Doolittle WF (2007) Searching for species in haloarchaea. P Natl Acad Sci USA 104: 14092-14097.
239. Patenge N, Haase A, Bolhuis H & Oesterhelt D (2000) The gene for a halophilic beta-galactosidase (bgaH) of Haloferax alicantei as a reporter gene for promoter analyses in Halobacterium salinarum. Mol Microbiol 36: 105-113.
240. Peck RF, Dassarma S & Krebs MP (2000) Homologous gene knockout in the archaeon Halobacterium salinarum with ura3 as a counterselectable marker. Mol Microbiol 35: 667-676.
241. Peeters E, Albers SV, Vassart A, Driessen AJ & Charlier D (2009) Ss-LrpB, a transcriptional regulator from Sulfolobus solfataricus, regulates a gene cluster with a pyruvate ferredoxin oxidoreductase-encoding operon and permease genes. Mol Microbiol 71: 972-988.
242. Peng N, Xia Q, Chen Z, Liang YX & She Q (2009) An upstream activation element exerting differential transcriptional activation on an archaeal promoter. Mol Microbiol 74: 928-939.
243. Peng X, Holz I, Zillig W, Garrett RA & She Q (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.
244. Pfeifer F & Betlach M (1985) Genome organization in Halobacterium halobium: a 70 kb island of more (AT) rich DNA in the chromosome. Mol Gen Genet 198: 449-455.
245. Pfeifer F, Gregor D, Hofacker A, Plosser P & Zimmermann P (2002) Regulation of gas vesicle formation in halophilic archaea. J Mol Microb Biotech 4: 175-181.
246. Pfeiffer F, Broicher A, Gillich T, Klee K, Mejia J, Rampp M & Oesterhelt D (2008a) Genome information management and integrated data analysis with HaloLex. Arch Microbiol 190: 281-299.
247. Pfeiffer F, Schuster SC, Broicher A et al. (2008b) Evolution in the laboratory: the genome of Halobacterium salinarum strain R1 compared to that of strain NRC-1. Genomics 91: 335-346.
248. Pfluger K, Ehrenreich A, Salmon K, Gunsalus RP, Deppenmeier U, Gottschalk G & Muller V (2007) Identification of genes involved in salt adaptation in the archaeon Methanosarcina mazei Go1 using genome-wide gene expression profiling. FEMS Microbiol Lett 277: 79-89.
249. Porat I & Whitman WB (2009) Tryptophan auxotrophs were obtained by random transposon insertions in the Methanococcus maripaludis tryptophan operon. FEMS Microbiol Lett 297: 250-254.
250. Porat I, Kim W, Hendrickson EL et al. (2006) Disruption of the operon encoding Ehb hydrogenase limits anabolic CO2 assimilation in the archaeon Methanococcus maripaludis. J Bacteriol 188: 1373-1380.
251. Prangishvili D, Albers SV, Holz I et al. (1998) Conjugation in archaea: frequent occurrence of conjugative plasmids in Sulfolobus. Plasmid 40: 190-202.
252. Prangishvili D, Forterre P & Garrett RA (2006) Viruses of the Archaea: a unifying view. Nat Rev Microbiol 4: 837-848.
253. Prangishvili DA, Vashakidze RP, Chelidze MG & Gabriadze I (1985) A restriction endonuclease SuaI from the thermoacidophilic archaebacterium Sulfolobus acidocaldarius. FEBS Lett 192: 57-60.
254. Pritchett MA, Zhang JK & Metcalf WW (2004) Development of a markerless genetic exchange method for Methanosarcina acetivorans C2A and its use in construction of new genetic tools for methanogenic archaea. Appl Environ Microb 70: 1425-1433.
255. Rahman RN, Fujiwara S, Nakamura H, Takagi M & Imanaka T (1998) Ion pairs involved in maintaining a thermostable structure of glutamate dehydrogenase from a hyperthermophilic archaeon. Biochem Bioph Res Co 248: 920-926.
256. Rashid N, Cornista J, Ezaki S, Fukui T, Atomi H & Imanaka T (2002a) Characterization of an archaeal cyclodextrin glucanotransferase with a novel C-terminal domain. J Bacteriol 184: 777-784.
257. Rashid N, Imanaka H, Kanai T, Fukui T, Atomi H & Imanaka T (2002b) A novel candidate for the true fructose-1, 6-bisphosphatase in archaea. J Biol Chem 277: 30649-30655.
258. Redder P & Garrett RA (2006) Mutations and rearrangements in the genome of Sulfolobus solfataricus P2. J Bacteriol 188: 4198-4206.
259. Reilly MS & Grogan DW (2001) Characterization of intragenic recombination in a hyperthermophilic archaeon via conjugational DNA exchange. J Bacteriol 183: 2943-2946.
260. Reno ML, Held NL, Fields CJ, Burke PV & Whitaker RJ (2009) Biogeography of the Sulfolobus islandicus pan-genome. P Natl Acad Sci USA 106: 8605-8610.
261. Reuter CJ & Maupin-Furlow J (2004) Analysis of proteasome-dependent proteolysis in Haloferax volcanii cells, using short-lived green fluorescent proteins. Appl Environ Microb 70: 7530-7538.
262. Rice DW, Yip KS, Stillman TJ et al. (1996) Insights into the molecular basis of thermal stability from the structure determination of Pyrococcus furiosus glutamate dehydrogenase. FEMS Microbiol Rev 18: 105-117.
263. Rivera MC, Jain R, Moore JE & Lake JA (1998) Genomic evidence for two functionally distinct gene classes. P Natl Acad Sci USA 95: 6239-6244.
264. Robb FT, Maeder DL, Brown JR et al. (2001) Genomic sequence of hyperthermophile, Pyrococcus furiosus: implications for physiology and enzymology. Method Enzymol 330: 134-157.
265. Robertson CE, Harris JK, Spear JR & Pace NR (2005) Phylogenetic diversity and ecology of environmental Archaea. Curr Opin Microbiol 8: 638-642.
266. Robinson JL, Pyzyna B, Atrasz RG et al. (2005) Growth kinetics of extremely halophilic archaea (family halobacteriaceae) as revealed by arrhenius plots. J Bacteriol 187: 923-929.
267. Rodrigues MV, Borges N, Henriques M et al. (2007) Bifunctional CTP:inositol-1-phosphate cytidylyltransferase/CDP-inositol:inositol-1-phosphate transferase, the key enzyme for di-myo-inositol-phosphate synthesis in several (hyper)thermophiles. J Bacteriol 189: 5405-5412.
268. Rose RW, Bruser T, Kissinger JC & Pohlschroder M (2002) Adaptation of protein secretion to extremely high-salt conditions by extensive use of the twin-arginine translocation pathway. Mol Microbiol 45: 943-950.
269. Rosenshine I, Tchelet R & Mevarech M (1989) The mechanism of DNA transfer in the mating system of an archaebacterium. Science 245: 1387-1389.
270. Rother M & Metcalf WW (2005) Genetic technologies for Archaea. Curr Opin Microbiol 8: 745-751.
271. Rother M, Resch A, Gardner WL, Whitman WB & Bock A (2001) Heterologous expression of archaeal selenoprotein genes directed by the SECIS element located in the 3' non-translated region. Mol Microbiol 40: 900-908.
272. Russell RJ, Ferguson JM, Hough DW, Danson MJ & Taylor GL (1997) The crystal structure of citrate synthase from the hyperthermophilic archaeon Pyrococcus furiosus at 1.9 A resolution. Biochemistry 36: 9983-9994.
273. Samson RY, Obita T, Freund SM, Williams RL & Bell SD (2008) A role for the ESCRT system in cell division in archaea. Science 322: 1710-1713.
274. Santangelo TJ, Cubonova L, James CL & Reeve JN (2007) TFB1 or TFB2 is sufficient for Thermococcus kodakaraensis viability and for basal transcription in vitro. J Mol Biol 367: 344-357.
275. Santangelo TJ, Cubonova L, Matsumi R, Atomi H, Imanaka T & Reeve JN (2008a) Polarity in archaeal operon transcription in Thermococcus kodakaraensis. J Bacteriol 190: 2244-2248.
276. Santangelo TJ, Cubonova L & Reeve JN (2008b) Shuttle vector expression in Thermococcus kodakaraensis: contributions of cis elements to protein synthesis in a hyperthermophilic archaeon. Appl Environ Microb 74: 3099-3104.
277. Santangelo TJ, Cubonova L, Skinner KM & Reeve JN (2009) Archaeal intrinsic transcription termination in vivo. J Bacteriol 191: 7102-7108.
278. Santangelo TJ, Cubonova L & Reeve JN (2010) Thermococcus kodakarensis genetics: TK1827-encoded β-glycosidase, new positive-selection protocol, and targeted and repetitive deletion technology. Appl Environ Microb 76: 1044-1052.
279. Sapienza C, Rose MR & Doolittle WF (1982) High-frequency genomic rearrangements involving archaebacterial repeat sequence elements. Nature 299: 182-185.
280. Sapra R, Bagramyan K & Adams MW (2003) A simple energy-conserving system: proton reduction coupled to proton translocation. P Natl Acad Sci USA 100: 7545-7550.
281. Sato T, Fukui T, Atomi H & Imanaka T (2003) Targeted gene disruption by homologous recombination in the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. J Bacteriol 185: 210-220.
282. Sato T, Imanaka H, Rashid N, Fukui T, Atomi H & Imanaka T (2004) Genetic evidence identifying the true gluconeogenic fructose-1, 6-bisphosphatase in Thermococcus kodakaraensis and other hyperthermophiles. J Bacteriol 186: 5799-5807.
283. Sato T, Fukui T, Atomi H & Imanaka T (2005) Improved and versatile transformation system allowing multiple genetic manipulations of the hyperthermophilic archaeon Thermococcus kodakaraensis. Appl Environ Microb 71: 3889-3899.
284. Sato T, Atomi H & Imanaka T (2007) Archaeal type III RuBisCOs function in a pathway for AMP metabolism. Science 315: 1003-1006.
285. Sauerwald A, Zhu W, Major TA et al. (2005) RNA-dependent cysteine biosynthesis in archaea. Science 307: 1969-1972.
286. Schelert J, Dixit V, Hoang V, Simbahan J, Drozda M & Blum P (2004) Occurrence and characterization of mercury resistance in the hyperthermophilic archaeon Sulfolobus solfataricus by use of gene disruption. J Bacteriol 186: 427-437.
287. Schelert J, Drozda M, Dixit V, Dillman A & Blum P (2006) Regulation of mercury resistance in the crenarchaeote Sulfolobus solfataricus. J Bacteriol 188: 7141-7150.
288. Schinzel R & Burger KJ (1986) A site-specific endonuclease activity in Halobacterium halobium. FEMS Microbiol Lett 37: 325-329.
289. Schleper C, Kubo K & Zillig W (1992) The particle SSV1 from the extremely thermophilic archaeon Sulfolobus is a virus: demonstration of infectivity and of transfection with viral DNA. P Natl Acad Sci USA 89: 7645-7649.
290. Schleper C, Jurgens G & Jonuscheit M (2005) Genomic studies of uncultivated archaea. Nat Rev Microbiol 3: 479-488.
291. Schlesner M, Miller A, Streif S et al. (2009) Identification of Archaea-specific chemotaxis proteins which interact with the flagellar apparatus. BMC Microbiol 9: 56.
292. Schut GJ, Brehm SD, Datta S & Adams MW (2003) Whole-genome DNA microarray analysis of a hyperthermophile and an archaeon: Pyrococcus furiosus grown on carbohydrates or peptides. J Bacteriol 185: 3935-3947.
293. She Q, Singh RK, Confalonieri F et al. (2001) The complete genome of the crenarchaeon Sulfolobus solfataricus P2. P Natl Acad Sci USA 98: 7835-7840.
294. She Q, Zhang C, Deng L, Peng N, Chen Z & Liang YX (2009) Genetic analyses in the hyperthermophilic archaeon Sulfolobus islandicus. Biochem Soc T 37: 92-96.
295. Shimoyama T, Kato S, Ishii S & Watanabe K (2009) Flagellum mediates symbiosis. Science 323: 1574.
296. Siebers B & Schönheit P (2005) Unusual pathways and enzymes of central carbohydrate metabolism in Archaea. Curr Opin Microbiol 8: 695-705.
297. Siebers B, Brinkmann H, Dorr C, Tjaden B, Lilie H, van der Oost J & Verhees CH (2001) Archaeal fructose-1, 6-bisphosphate aldolases constitute a new family of archaeal type class I aldolase. J Biol Chem 276: 28710-28718.
298. Simsek M, DasSarma S, RajBhandary UL & Khorana HG (1982) A transposable element from Halobacterium halobium which inactivates the bacteriorhodopsin gene. P Natl Acad Sci USA 79: 7268-7272.
299. Sisignano M, Morbitzer D, Gatgens J, Oldiges M & Soppa J (2010) A 2-oxoacid dehydrogenase complex of Haloferax volcanii is essential for growth on isoleucine but not on other branched-chain amino acids. Microbiology 156: 521-529.
300. Sollner S, Berkner S & Lipps G (2006) Characterisation of the novel restriction endonuclease SuiI from Sulfolobus islandicus. Extremophiles 10: 629-634.
301. Soppa J (2006) From genomes to function: haloarchaea as model organisms. Microbiology 152: 585-590.
302. Soppa J & Oesterhelt D (1989) Bacteriorhodopsin mutants of Halobacterium sp. GRB. I. The 5-bromo-2'-deoxyuridine selection as a method to isolate point mutants in halobacteria. J Biol Chem 264: 13043-13048.
303. Soppa J, Baumann A, Brenneis M, Dambeck M, Hering O & Lange C (2008) Genomics and functional genomics with haloarchaea. Arch Microbiol 190: 197-215.
304. Sowers KR, Boone JE & Gunsalus RP (1993) Disaggregation of Methanosarcina spp. and growth as single cells at elevated osmolarity. Appl Environ Microb 59: 3832-3839.
305. Spanheimer R & Muller V (2008) The molecular basis of salt adaptation in Methanosarcina mazei Go1. Arch Microbiol 190: 271-279.
306. Stathopoulos C, Kim W, Li T et al. (2001) Cysteinyl-tRNA synthetase is not essential for viability of the archaeon Methanococcus maripaludis. P Natl Acad Sci USA 98: 14292-14297.
307. Stedman KM, Schleper C, Rumpf E & Zillig W (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.
308. Stock T, Selzer M & Rother M (2010) In vivo requirement of selenophosphate for selenoprotein synthesis in archaea. Mol Microbiol 75: 149-160.
309. Story SV, Shah C, Jenney FE Jr & Adams MW (2005) Characterization of a novel zinc-containing, lysine-specific aminopeptidase from the hyperthermophilic archaeon Pyrococcus furiosus. J Bacteriol 187: 2077-2083.
310. Sun J & Klein A (2004) A lysR-type regulator is involved in the negative regulation of genes encoding selenium-free hydrogenases in the archaeon Methanococcus voltae. Mol Microbiol 52: 563-571.
311. Suzuki T, Iwasaki T, Uzawa T et al. (2002) Sulfolobus tokodaii sp. nov. (f. Sulfolobus sp. strain 7), a new member of the genus Sulfolobus isolated from Beppu Hot Springs, Japan. Extremophiles 6: 39-44.
312. Szabo Z, Sani M, Groeneveld M et al. (2007) Flagellar motility and structure in the hyperthermoacidophilic archaeon Sulfolobus solfataricus. J Bacteriol 189: 4305-4309.
313. Tachibana Y, Kuramura A, Shirasaka N et al. (1999) Purification and characterization of an extremely thermostable cyclomaltodextrin glucanotransferase from a newly isolated hyperthermophilic archaeon, a Thermococcus sp. Appl Environ Microb 65: 1991-1997.
314. Tadeo X, Lopez-Mendez B, Trigueros T, Lain A, Castano D & Millet O (2009) Structural basis for the aminoacid composition of proteins from halophilic archea. PLoS Biol 7: e1000257.
315. Takai K, Sugai A, Itoh T & Horikoshi K (2000) Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney. Int J Syst Evol Micr 50: 489-500.
316. Tchelet R & Mevarech M (1994) Interspecies genetic transfer in halophilic archaebacteria. Syst Appl Microbiol 15: 578-581.
317. Thauer RK, Kaster AK, Seedorf H, Buckel W & Hedderich R (2008) Methanogenic archaea: ecologically relevant differences in energy conservation. Nat Rev Microbiol 6: 579-591.
318. Trauger SA, Kalisak E, Kalisiak J et al. (2008) Correlating the transcriptome, proteome, and metabolome in the environmental adaptation of a hyperthermophile. J Proteome Res 7: 1027-1035.
319. Tu D, Blaha G, Moore PB & Steitz TA (2005) Gene replacement in Haloarcula marismortui: construction of a strain with two of its three chromosomal rRNA operons deleted. Extremophiles 9: 427-435.
320. Tuininga JE, Verhees CH, van der Oost J, Kengen SW, Stams AJ & de Vos WM (1999) Molecular and biochemical characterization of the ADP-dependent phosphofructokinase from the hyperthermophilic archaeon Pyrococcus furiosus. J Biol Chem 274: 21023-21028.
321. Tumbula DL & Whitman WB (1999) Genetics of Methanococcus: possibilities for functional genomics in Archaea. Mol Microbiol 33: 1-7.
322. Tumbula DL, Makula RA & Whitman WB (1994) Transformation of Methanococcus maripaludis and identification of a PstI-like restriction system. FEMS Microbiol Lett 121: 309-314.
323. Tumbula DL, Bowen TL & Whitman WB (1997) Characterization of pURB500 from the archaeon Methanococcus maripaludis and construction of a shuttle vector. J Bacteriol 179: 2976-2986.
324. Twellmeyer J, Wende A, Wolfertz J et al. (2007) Microarray analysis in the archaeon Halobacterium salinarum strain R1. PLoS ONE 2: e1064.
325. van der Oost J, Schut G, Kengen SW, Hagen WR, Thomm M & de Vos WM (1998) The ferredoxin-dependent conversion of glyceraldehyde-3-phosphate in the hyperthermophilic archaeon Pyrococcus furiosus represents a novel site of glycolytic regulation. J Biol Chem 273: 28149-28154.
326. van de Vossenberg JL, Ubbink-Kok T, Elferink MG, Driessen AJ & Konings WN (1995) Ion permeability of the cytoplasmic membrane limits the maximum growth temperature of bacteria and archaea. Mol Microbiol 18: 925-932.
327. Veit K, Ehlers C, Ehrenreich A et al. (2006) Global transcriptional analysis of Methanosarcina mazei strain Go1 under different nitrogen availabilities. Mol Genet Genomics 276: 41-55.
328. Verhees CH, Kengen SW, Tuininga JE, Schut GJ, Adams MW, De Vos WM & Van Der Oost J (2003) The unique features of glycolytic pathways in Archaea. Biochem J 375: 231-246.
329. Vetriani C, Maeder DL, Tolliday N et al. (1998) Protein thermostability above 100°C: a key role for ionic interactions. P Natl Acad Sci USA 95: 12300-12305.
330. Vierke G, Engelmann A, Hebbeln C & Thomm M (2003) A novel archaeal transcriptional regulator of heat shock response. J Biol Chem 278: 18-26.
331. Voorhorst WG, Eggen RI, Luesink EJ & de Vos WM (1995) Characterization of the celB gene coding for β-glucosidase from the hyperthermophilic archaeon Pyrococcus furiosus and its expression and site-directed mutation in Escherichia coli. J Bacteriol 177: 7105-7111.
332. Voorhorst WG, Eggen RI, Geerling AC, Platteeuw C, Siezen RJ & Vos WM (1996) Isolation and characterization of the hyperthermostable serine protease, pyrolysin, and its gene from the hyperthermophilic archaeon Pyrococcus furiosus. J Biol Chem 271: 20426-20431.
333. Waege I, Schmid G, Thumann S, Thomm M & Hausner W (2010) Shuttle vector-based transformation system for Pyrococcus furiosus. Appl Environ Microb 76: 3308-3313.
334. Wagner M, Berkner S, Ajon M, Driessen AJ, Lipps G & Albers SV (2009) Expanding and understanding the genetic toolbox of the hyperthermophilic genus Sulfolobus. Biochem Soc T 37: 97-101.
335. Walters AD & Chong JP (2009) Methanococcus maripaludis: an archaeon with multiple functional MCM proteins? Biochem Soc T 37: 1-6.
336. Wanner C & Soppa J (1999) Genetic identification of three ABC transporters as essential elements for nitrate respiration in Haloferax volcanii. Genetics 152: 1417-1428.
337. Ward DE, Shockley KR, Chang LS, Levy RD, Michel JK, Conners SB & Kelly RM (2002) Proteolysis in hyperthermophilic microorganisms. Archaea 1: 63-74.
338. Welander PV & Metcalf WW (2008) Mutagenesis of the C1 oxidation pathway in Methanosarcina barkeri: new insights into the Mtr/Mer bypass pathway. J Bacteriol 190: 1928-1936.
339. Wende A, Furtwangler K & Oesterhelt D (2009) Phosphate-dependent behavior of the archaeon Halobacterium salinarum strain R1. J Bacteriol 191: 3852-3860.
340. Whitaker RJ, Grogan DW & Taylor JW (2005) Recombination shapes the natural population structure of the hyperthermophilic archaeon Sulfolobus islandicus. Mol Biol Evol 22: 2354-2361.
341. Whitehead K, Kish A, Pan M et al. (2006) An integrated systems approach for understanding cellular responses to gamma radiation. Mol Syst Biol 2: 47.
342. Whitman WB, Boone DR, Koga Y & Keswani J (2001) Taxonomy of methanogenic Archaea. Bergey's Manual of Systematic Bacteriology, Vol. 1 (Boone DR & Castenholz RW, eds), pp. 211-294. Springer-Verlag, New York.
343. Williams RS, Moncalian G, Williams JS et al. (2008) Mre11 dimers coordinate DNA end bridging and nuclease processing in double-strand-break repair. Cell 135: 97-109.
344. Woese CR & Fox GE (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. P Natl Acad Sci USA 74: 5088-5090.
345. Woese CR, Kandler O & Wheelis ML (1990) Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. P Natl Acad Sci USA 87: 4576-4579.
346. Wolfe RS (1996) 1776-1996: alessandro volta's combustible air. ASM News 62: 529-534.
347. Woods WG & Dyall-Smith ML (1997) Construction and analysis of a recombination-deficient (radA) mutant of Haloferax volcanii. Mol Microbiol 23: 791-797.
348. Woods WG, Ngui K & Dyall-Smith ML (1999) An improved transposon for the halophilic archaeon Haloarcula hispanica. J Bacteriol 181: 7140-7142.
349. Worthington P, Hoang V, Perez-Pomares F & Blum P (2003) Targeted disruption of the alpha-amylase gene in the hyperthermophilic archaeon Sulfolobus solfataricus. J Bacteriol 185: 482-488.
350. Wright DB, Banks DD, Lohman JR, Hilsenbeck JL & Gloss LM (2002) The effect of salts on the activity and stability of Escherichia coli and Haloferax volcanii dihydrofolate reductases. J Mol Biol 323: 327-344.
351. Wurtzel O, Sapra R, Chen F, Zhu Y, Simmons BA & Sorek R (2010) A single-base resolution map of an archaeal transcriptome. Genome Res 20: 133-141.
352. Xia Q, Hendrickson EL, Zhang Y et al. (2006) Quantitative proteomics of the archaeon Methanococcus maripaludis validated by microarray analysis and real time PCR. Mol Cell Proteomics 5: 868-881.
353. Xia Q, Wang T, Hendrickson EL, Lie TJ, Hackett M & Leigh JA (2009) Quantitative proteomics of nutrient limitation in the hydrogenotrophic methanogen Methanococcus maripaludis. BMC Microbiol 9: 149.
354. Yip KS, Stillman TJ, Britton KL et al. (1995) The structure of Pyrococcus furiosus glutamate dehydrogenase reveals a key role for ion-pair networks in maintaining enzyme stability at extreme temperatures. Structure 3: 1147-1158.
355. Yip KS, Britton KL, Stillman TJ et al. (1998) Insights into the molecular basis of thermal stability from the analysis of ion-pair networks in the glutamate dehydrogenase family. Eur J Biochem 255: 336-346.
356. Yokooji Y, Tomita H, Atomi H & Imanaka T (2009) Pantoate kinase and phosphopantothenate synthetase, two novel enzymes necessary for CoA biosynthesis in the Archaea. J Biol Chem 284: 28137-28145.
357. Yokoyama H, Matsui E, Akiba T, Harata K & Matsui I (2006) Molecular structure of a novel membrane protease specific for a stomatin homolog from the hyperthermophilic archaeon Pyrococcus horikoshii. J Mol Biol 358: 1152-1164.
358. Yoshimochi T, Fujikane R, Kawanami M, Matsunaga F & Ishino Y (2008) The GINS complex from Pyrococcus furiosus stimulates the MCM helicase activity. J Biol Chem 283: 1601-1609.
359. Yuan J, Palioura S, Salazar JC et al. (2006) RNA-dependent conversion of phosphoserine forms selenocysteine in eukaryotes and archaea. P Natl Acad Sci USA 103: 18923-18927.
360. Yutin N, Makarova KS, Mekhedov SL, Wolf YI & Koonin EV (2008) The deep archaeal roots of eukaryotes. Mol Biol Evol 25: 1619-1630.
361. Zaigler A, Schuster SC & Soppa J (2003) Construction and usage of a onefold coverage shotgun DNA microarray to characterize the metabolism of the archaeon Haloferax volcanii. Mol Microbiol 48: 1089-1105.
362. Zaparty M, Esser D, Gertig S et al. (2010) "Hot standards" for the thermoacidophilic archaeon Sulfolobus solfataricus. Extremophiles 14: 119-142.
363. Zhang JK, Pritchett MA, Lampe DJ, Robertson HM & Metcalf WW (2000) In vivo transposon mutagenesis of the methanogenic archaeon Methanosarcina acetivorans C2A using a modified version of the insect mariner-family transposable element Himar1. P Natl Acad Sci USA 97: 9665-9670.
364. Zillig W, Stetter KO, Wunderl S, Schulz W, Priess H & Scholz I (1980) The Sulfolobus-"Caldariella" group: taxonomy on the basis of the structure of DNA-dependent RNA polymerases. Arch Microbiol 125: 259-269.
365. Zillig W, Holz I, Janekovic D, Schäfer W & Reiter WD (1983) The archaebacterium Thermococcus celer represents, a novel genus within the thermophilic branch of the archaebacteria. Syst Appl Microbiol 4: 88-94.
366. Zillig W, Prangishvilli D, Schleper C et al. (1996) Viruses, plasmids and other genetic elements of thermophilic and hyperthermophilic Archaea. FEMS Microbiol Rev 18: 225-236.
367. Zivanovic Y, Armengaud J, Lagorce A et al. (2009) Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea. Genome Biol 10: R70.
368. Zolghadr B, Weber S, Szabo Z, Driessen AJ & Albers SV (2007) Identification of a system required for the functional surface localization of sugar binding proteins with class III signal peptides in Sulfolobus solfataricus. Mol Microbiol 64: 795-806.
369. Zolghadr B, Klingl A, Koerdt A, Driessen AJ, Rachel R & Albers SV (2010) Appendage-mediated surface adherence of Sulfolobus solfataricus. J Bacteriol 192: 104-110.