Major players on the microbial stage: why archaea are important Free

Abstract

As microbiology undergoes a renaissance, fuelled in part by developments in new sequencing technologies, the massive diversity and abundance of microbes becomes yet more obvious. The Archaea have traditionally been perceived as a minor group of organisms forced to evolve into environmental niches not occupied by their more ‘successful’ and ‘vigorous’ counterparts, the bacteria. Here we outline some of the evidence gathered by an increasingly large and productive group of scientists that demonstrates not only that the Archaea contribute significantly to global nutrient cycling, but also that they compete successfully in ‘mainstream’ environments. Recent data suggest that the Archaea provide the major routes for ammonia oxidation in the environment. Archaea also have huge economic potential that to date has only been fully realized in the production of thermostable polymerases. Archaea have furnished us with key paradigms for understanding fundamentally conserved processes across all domains of life. In addition, they have provided numerous exemplars of novel biological mechanisms that provide us with a much broader view of the forms that life can take and the way in which micro-organisms can interact with other species. That this information has been garnered in a relatively short period of time, and appears to represent only a small proportion of what the Archaea have to offer, should provide further incentives to microbiologists to investigate the underlying biology of this fascinating domain.

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2011-04-01
2024-03-28
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References

  1. Ahmadi M., Yeow J. T. 2011; Fabrication and characterization of a radiation sensor based on bacteriorhodopsin. Biosens Bioelectron 26:2171–2176
    [Google Scholar]
  2. Albers S. V., Birkeland N. K., Driessen A. J., Gertig S., Haferkamp P., Klenk H. P., Kouril T., Manica A., Pham T. K. other authors 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 Trans 37:58–64
    [Google Scholar]
  3. Aravind L., Tatusov R. L., Wolf Y. I., Walker D. R., Koonin E. V. 1998; Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles. Trends Genet 14:442–444
    [Google Scholar]
  4. Armougom F., Henry M., Vialettes B., Raccah D., Raoult D. 2009; Monitoring bacterial community of human gut microbiota reveals an increase in Lactobacillus in obese patients and methanogens in anorexic patients. PLoS ONE 4:e7125
    [Google Scholar]
  5. Auguet J. C., Barberan A., Casamayor E. O. 2010; Global ecological patterns in uncultured Archaea. ISME J 4:182–190
    [Google Scholar]
  6. Bae B., Chen Y. H., Costa A., Onesti S., Brunzelle J. S., Lin Y., Cann I. K., Nair S. K. 2009; Insights into the architecture of the replicative helicase from the structure of an archaeal MCM homolog. Structure 17:211–222
    [Google Scholar]
  7. Baker B. J., Comolli L. R., Dick G. J., Hauser L. J., Hyatt D., Dill B. D., Land M. L., Verberkmoes N. C., Hettich R. L., Banfield J. F. 2010; Enigmatic, ultrasmall, uncultivated Archaea. Proc Natl Acad Sci U S A 107:8806–8811
    [Google Scholar]
  8. Ban N., Nissen P., Hansen J., Moore P. B., Steitz T. A. 2000; The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science 289:905–920
    [Google Scholar]
  9. Barry E. R., McGeoch A. T., Kelman Z., Bell S. D. 2007; Archaeal MCM has separable processivity, substrate choice and helicase domains. Nucleic Acids Res 35:988–998
    [Google Scholar]
  10. Bell S. D., Jackson S. P. 2001; Mechanism and regulation of transcription in archaea. Curr Opin Microbiol 4:208–213
    [Google Scholar]
  11. Bell S. D., Botting C. H., Wardleworth B. N., Jackson S. P., White M. F. 2002; The interaction of Alba, a conserved archaeal chromatin protein, with Sir2 and its regulation by acetylation. Science 296:148–151
    [Google Scholar]
  12. Berg I. A., Kockelkorn D., Ramos-Vera W. H., Say R. F., Zarzycki J., Hügler M., Alber B. E., Fuchs G. 2010; Autotrophic carbon fixation in archaea. Nat Rev Microbiol 8:447–460
    [Google Scholar]
  13. Bettstetter M., Peng X., Garrett R. A., Prangishvili D. 2003; AFV1, a novel virus infecting hyperthermophilic archaea of the genus Acidianus . Virology 315:68–79
    [Google Scholar]
  14. Beveridge T. J., Stewart M., Doyle R. J., Sprott G. D. 1985; Unusual stability of the Methanospirillum hungatei sheath. J Bacteriol 162:728–737
    [Google Scholar]
  15. Beveridge T. J., Sprott G. D., Whippey P. 1991; Ultrastructure, inferred porosity, and Gram-staining character of Methanospirillum hungatei filament termini describe a unique cell permeability for this archaeobacterium. J Bacteriol 173:130–140
    [Google Scholar]
  16. Biles B. D., Connolly B. A. 2004; Low-fidelity Pyrococcus furiosus DNA polymerase mutants useful in error-prone PCR. Nucleic Acids Res 32:e176
    [Google Scholar]
  17. Bini E. 2010; Archaeal transformation of metals in the environment. FEMS Microbiol Ecol 73:1–16
    [Google Scholar]
  18. Bock A., Kandler O. 1985; Antibiotic sensitivity of archaebacteria. In The Bacteria pp 525–544 Edited by Woese C. R., Wolfe R. S. New York: Academic Press;
    [Google Scholar]
  19. Bonneau R., Facciotti M. T., Reiss D. J., Schmid A. K., Pan M., Kaur A., Thorsson V., Shannon P., Johnson M. H., Bare J. C. 2007; A predictive model for transcriptional control of physiology in a free living cell. Cell 131:1354–1365
    [Google Scholar]
  20. Boto L. 2010; Horizontal gene transfer in evolution: facts and challenges. Proc Biol Sci 277:819–827
    [Google Scholar]
  21. Brewster A. S., Wang G., Yu X., Greenleaf W. B., Carazo J. M., Tjajadi M., Klein M. G., Chen X. S. 2008; Crystal structure of a near-full-length archaeal MCM: functional insights for an AAA+ hexameric helicase. Proc Natl Acad Sci U S A 105:20191–20196
    [Google Scholar]
  22. Brochier-Armanet C., Forterre P. 2006; Widespread distribution of archaeal reverse gyrase in thermophilic bacteria suggests a complex history of vertical inheritance and lateral gene transfers. Archaea 2:83–93
    [Google Scholar]
  23. Bruneel O., Pascault N., Egal M., Bancon-Montigny C., Goñi-Urriza M. S., Elbaz-Poulichet F., Personné J. C., Duran R. 2008; Archaeal diversity in a Fe-As rich acid mine drainage at Carnoulès (France. Extremophiles 12:563–571
    [Google Scholar]
  24. Burggraf S., Mayer T., Amann R., Schadhauser S., Woese C. R., Stetter K. O. 1994; Identifying members of the domain Archaea with rRNA-targeted oligonucleotide probes. Appl Environ Microbiol 60:3112–3119
    [Google Scholar]
  25. Burghardt T., Junglas B., Siedler F., Wirth R., Huber H., Rachel R. 2009; The interaction of Nanoarchaeum equitans with Ignicoccus hospitalis : proteins in the contact site between two cells. Biochem Soc Trans 37:127–132
    [Google Scholar]
  26. Burns K. E., Darwin K. H. 2010; Pupylation versus ubiquitylation: tagging for proteasome-dependent degradation. Cell Microbiol 12:424–431
    [Google Scholar]
  27. Burns D. G., Janssen P. H., Itoh T., Kamekura M., Li Z., Jensen G., Rodríguez-Valera F., Bolhuis H., Dyall-Smith M. L. 2007; Haloquadratum walsbyi gen. nov. sp. the square haloarchaeon of Walsby, isolated from saltern crystallizers in Australia and Spain. Int J Syst Evol Microbiol 57:387–392
    [Google Scholar]
  28. Cavalier-Smith T. 2006; Rooting the tree of life by transition analyses. Biol Direct 1:19
    [Google Scholar]
  29. Cavicchioli R. 2011; Archaea – timeline of the third domain. Nat Rev Microbiol 9:51–61
    [Google Scholar]
  30. Cavicchioli R., Curmi P. M., Saunders N., Thomas T. 2003; Pathogenic archaea: do they exist?. Bioessays 25:1119–1128
    [Google Scholar]
  31. Chaban B., Ng S. Y., Jarrell K. F. 2006; Archaeal habitats – from the extreme to the ordinary. Can J Microbiol 52:73–116
    [Google Scholar]
  32. Chastain B. K., Kral T. A. 2010; Approaching Mars-like geochemical conditions in the laboratory: omission of artificial buffers and reductants in a study of biogenic methane production on a smectite clay. Astrobiology 10:889–897
    [Google Scholar]
  33. Chong J. P., Hayashi M. K., Simon M. N., Xu R. M., Stillman B. 2000; A double-hexamer archaeal minichromosome maintenance protein is an ATP-dependent DNA helicase. Proc Natl Acad Sci U S A 97:1530–1535
    [Google Scholar]
  34. Christendat D., Yee A., Dharamsi A., Kluger Y., Savchenko A., Cort J. R., Booth V., Mackereth C. D., Saridakis V. other authors 2000; Structural proteomics of an archaeon. Nat Struct Biol 7:903–909
    [Google Scholar]
  35. Christl S. U., Gibson G. R., Cummings J. H. 1992; Role of dietary sulphate in the regulation of methanogenesis in the human large intestine. Gut 33:1234–1238
    [Google Scholar]
  36. Coker J. A., DasSarma P., Capes M., Wallace T., McGarrity K., Gessler R., Liu J., Xiang H., Tatusov R. other authors 2009; Multiple replication origins of Halobacterium sp. strain NRC-1: properties of the conserved orc7 -dependent oriC1 . J Bacteriol 191:5253–5261
    [Google Scholar]
  37. Comeau A. M., Hatfull G. F., Krisch H. M., Lindell D., Mann N. H., Prangishvili D. 2008; Exploring the prokaryotic virosphere. Res Microbiol 159:306–313
    [Google Scholar]
  38. Comolli L. R., Baker B. J., Downing K. H., Siegerist C. E., Banfield J. F. 2009; Three-dimensional analysis of the structure and ecology of a novel, ultra-small archaeon. ISME J 3:159–167
    [Google Scholar]
  39. Conway de Macario E., Macario A. J. 2009; Methanogenic archaea in health and disease: a novel paradigm of microbial pathogenesis. Int J Med Microbiol 299:99–108
    [Google Scholar]
  40. Costa K. C., Wong P. M., Wang T., Lie T. J., Dodsworth J. A., Swanson I., Burn J. A., Hackett M., Leigh J. A. 2010; Protein complexing in a methanogen suggests electron bifurcation and electron delivery from formate to heterodisulfide reductase. Proc Natl Acad Sci U S A 107:11050–11055
    [Google Scholar]
  41. Cramer P., Bushnell D. A., Kornberg R. D. 2001; Structural basis of transcription: RNA polymerase II at 2.8 Angstrom resolution. Science 292:1863–1876
    [Google Scholar]
  42. Darwin K. H., Hofmann K. 2010; SAMPyling proteins in archaea. Trends Biochem Sci 35:348–351
    [Google Scholar]
  43. DeLong E. F., Pace N. R. 2001; Environmental diversity of bacteria and archaea. Syst Biol 50:470–478
    [Google Scholar]
  44. DeLong E. F., Taylor L. T., Marsh T. L., Preston C. M. 1999; Visualization and enumeration of marine planktonic archaea and bacteria by using polyribonucleotide probes and fluorescent in situ hybridization. Appl Environ Microbiol 65:5554–5563
    [Google Scholar]
  45. DiMarco A. A., Bobik T. A., Wolfe R. S. 1990; Unusual coenzymes of methanogenesis. Annu Rev Biochem 59:355–394
    [Google Scholar]
  46. Ditzel L., Löwe J., Stock D., Stetter K. O., Huber H., Huber R., Steinbacher S. 1998; Crystal structure of the thermosome, the archaeal chaperonin and homolog of CCT. Cell 93:125–138
    [Google Scholar]
  47. Dridi B., Henry M., El Khéchine A., Raoult D., Drancourt M. 2009; High prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae detected in the human gut using an improved DNA detection protocol. PLoS ONE 4:e7063
    [Google Scholar]
  48. Dueber E. L., Corn J. E., Bell S. D., Berger J. M. 2007; Replication origin recognition and deformation by a heterodimeric archaeal Orc1 complex. Science 317:1210–1213
    [Google Scholar]
  49. Eckburg P. B., Lepp P. W., Relman D. A. 2003; Archaea and their potential role in human disease. Infect Immun 71:591–596
    [Google Scholar]
  50. Edmonds C. G., Crain P. F., Gupta R., Hashizume T., Hocart C. H., Kowalak J. A., Pomerantz S. C., Stetter K. O., McCloskey J. A. 1991; Posttranscriptional modification of tRNA in thermophilic archaea (Archaebacteria. J Bacteriol 173:3138–3148
    [Google Scholar]
  51. Edwards K. J., Bond P. L., Gihring T. M., Banfield J. F. 2000; An archaeal iron-oxidizing extreme acidophile important in acid mine drainage. Science 287:1796–1799
    [Google Scholar]
  52. El Oufir L., Flourié B., Bruley des Varannes S., Barry J. L., Cloarec D., Bornet F., Galmiche J. P. 1996; Relations between transit time, fermentation products, and hydrogen consuming flora in healthy humans. Gut 38:870–877
    [Google Scholar]
  53. Ellen A. F., Zolghadr B., Driessen A. M., Albers S. V. 2010; Shaping the archaeal cell envelope. Archaea 2010608243
    [Google Scholar]
  54. Embley T. M., Martin W. 2006; Eukaryotic evolution, changes and challenges. Nature 440:623–630
    [Google Scholar]
  55. Embley T. M., Finlay B. J., Thomas R. H., Dyal P. L. 1992; The use of rRNA sequences and fluorescent probes to investigate the phylogenetic positions of the anaerobic ciliate Metopus palaeformis and its archaeobacterial endosymbiont. J Gen Microbiol 138:1479–1487
    [Google Scholar]
  56. Facciotti M. T., Reiss D. J., Pan M., Kaur A., Vuthoori M., Bonneau R., Shannon P., Srivastava A., Donohoe S. M. other authors 2007; General transcription factor specified global gene regulation in archaea. Proc Natl Acad Sci U S A 104:4630–4635
    [Google Scholar]
  57. Ferrer M., Golyshina O. V., Beloqui A., Golyshin P. N., Timmis K. N. 2007; The cellular machinery of Ferroplasma acidiphilum is iron-protein-dominated. Nature 445:91–94
    [Google Scholar]
  58. Ferry J. G. 2010; How to make a living by exhaling methane. Annu Rev Microbiol 64:453–473
    [Google Scholar]
  59. Fletcher R. J., Bishop B. E., Leon R. P., Sclafani R. A., Ogata C. M., Chen X. S. 2003; The structure and function of MCM from archaeal M. Thermoautotrophicum . Nat Struct Biol 10:160–167
    [Google Scholar]
  60. Formisano V., Atreya S., Encrenaz T., Ignatiev N., Giuranna M. 2004; Detection of methane in the atmosphere of Mars. Science 306:1758–1761
    [Google Scholar]
  61. Forterre P. 2010; Defining life: the virus viewpoint. Orig Life Evol Biosph 40:151–160
    [Google Scholar]
  62. Francis C. A., Beman J. M., Kuypers M. M. 2007; New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation. ISME J 1:19–27
    [Google Scholar]
  63. Gaudier M., Schuwirth B. S., Westcott S. L., Wigley D. B. 2007; Structural basis of DNA replication origin recognition by an ORC protein. Science 317:1213–1216
    [Google Scholar]
  64. Gittel A., Sørensen K. B., Skovhus T. L., Ingvorsen K., Schramm A. 2009; Prokaryotic community structure and sulfate reducer activity in water from high-temperature oil reservoirs with and without nitrate treatment. Appl Environ Microbiol 75:7086–7096
    [Google Scholar]
  65. Golyshina O. V., Timmis K. N. 2005; Ferroplasma and relatives, recently discovered cell wall-lacking archaea making a living in extremely acid, heavy metal-rich environments. Environ Microbiol 7:1277–1288
    [Google Scholar]
  66. Graham D. E., Overbeek R., Olsen G. J., Woese C. R. 2000; An archaeal genomic signature. Proc Natl Acad Sci U S A 97:3304–3308
    [Google Scholar]
  67. Gribaldo S., Poole A. M., Daubin V., Forterre P., Brochier-Armanet C. 2010; The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse?. Nat Rev Microbiol 8:743–752
    [Google Scholar]
  68. Grissa I., Vergnaud G., Pourcel C. 2007; CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 35: (Web Server issue), W52–W57
    [Google Scholar]
  69. Gupta R. S., Shami A. 2011; Molecular signatures for the Crenarchaeota and the Thaumarchaeota. Antonie van Leeuwenhoek 99:133–157
    [Google Scholar]
  70. Gupta R., Woese C. R. 1980; Unusual modification patterns in the transfer ribonucleic acids of archaebacteria. Curr Microbiol 4:245–249
    [Google Scholar]
  71. Hale C. R., Zhao P., Olson S., Duff M. O., Graveley B. R., Wells L., Terns R. M., Terns M. P. 2009; RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex. Cell 139:945–956
    [Google Scholar]
  72. Hallam S. J., Putnam N., Preston C. M., Detter J. C., Rokhsar D., Richardson P. M., DeLong E. F. 2004; Reverse methanogenesis: testing the hypothesis with environmental genomics. Science 305:1457–1462
    [Google Scholar]
  73. Harauz G., Musse A. 2001 Archaeal ribosomes. Encyclopedia of Life Sciences New York: Wiley;
    [Google Scholar]
  74. Häring M., Rachel R., Peng X., Garrett R. A., 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 79:9904–9911
    [Google Scholar]
  75. Hausner W., Wettach J., Hethke C., Thomm M. 1996; Two transcription factors related with the eucaryal transcription factors TATA-binding protein and transcription factor IIB direct promoter recognition by an archaeal RNA polymerase. J Biol Chem 271:30144–30148
    [Google Scholar]
  76. Henderson R., Unwin P. N. 1977; Structure of the purple membrane from Halobacterium halobium . Biophys Struct Mech 3:121
    [Google Scholar]
  77. Hinnebusch B. F., Meng S., Wu J. T., Archer S. Y., Hodin R. A. 2002; The effects of short-chain fatty acids on human colon cancer cell phenotype are associated with histone hyperacetylation. J Nutr 132:1012–1017
    [Google Scholar]
  78. Hogrefe H. H., Hansen C. J., Scott B. R., Nielson K. B. 2002; Archaeal dUTPase enhances PCR amplifications with archaeal DNA polymerases by preventing dUTP incorporation. Proc Natl Acad Sci U S A 99:596–601
    [Google Scholar]
  79. Huber R., Sacher M., Vollmann A., Huber H., Rose D. 2000; Respiration of arsenate and selenate by hyperthermophilic archaea. Syst Appl Microbiol 23:305–314
    [Google Scholar]
  80. Huber H., Hohn M. J., Rachel R., Fuchs T., Wimmer V. C., Stetter K. O. 2002; A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature 417:63–67
    [Google Scholar]
  81. Hugenholtz P., Goebel B. M., Pace N. R. 1998; Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180:4765–4774
    [Google Scholar]
  82. Humbard M. A., Miranda H. V., Lim J. M., Krause D. J., Pritz J. R., Zhou G., Chen S., Wells L., Maupin-Furlow J. A. 2010; Ubiquitin-like small archaeal modifier proteins (SAMPs) in Haloferax volcanii . Nature 463:54–60
    [Google Scholar]
  83. Igura M., Maita N., Kamishikiryo J., Yamada M., Obita T., Maenaka K., Kohda D. 2008; Structure-guided identification of a new catalytic motif of oligosaccharyltransferase. EMBO J 27:234–243
    [Google Scholar]
  84. Jahn U., Gallenberger M., Paper W., Junglas B., Eisenreich W., Stetter K. O., Rachel R., Huber H. 2008; Nanoarchaeum equitans and Ignicoccus hospitalis : new insights into a unique, intimate association of two archaea. J Bacteriol 190:1743–1750
    [Google Scholar]
  85. Jarrell K. F., McBride M. J. 2008; The surprisingly diverse ways that prokaryotes move. Nat Rev Microbiol 6:466–476
    [Google Scholar]
  86. Jarrell K. F., Jones G. M., Kandiba L., Nair D. B., Eichler J. 2010; S-layer glycoproteins and flagellins: reporters of archaeal posttranslational modifications. Archaea 2010612948
    [Google Scholar]
  87. Jenkinson E. R., Chong J. P. 2006; Minichromosome maintenance helicase activity is controlled by N- and C-terminal motifs and requires the ATPase domain helix-2 insert. Proc Natl Acad Sci U S A 103:7613–7618
    [Google Scholar]
  88. Jenney F. E. Jr, Adams M. W. 2008; The impact of extremophiles on structural genomics (and vice versa. Extremophiles 12:39–50
    [Google Scholar]
  89. Junglas B., Briegel A., Burghardt T., Walther P., Wirth R., Huber H., Rachel R. 2008; Ignicoccus hospitalis and Nanoarchaeum equitans : ultrastructure, cell–cell interaction, and 3D reconstruction from serial sections of freeze-substituted cells and by electron cryotomography. Arch Microbiol 190:395–408
    [Google Scholar]
  90. Kandler O., König H. 1978; Chemical composition of the peptidoglycan-free cell walls of methanogenic bacteria. Arch Microbiol 118:141–152
    [Google Scholar]
  91. Kandler O., König H. 1998; Cell wall polymers in Archaea (Archaebacteria. Cell Mol Life Sci 54:305–308
    [Google Scholar]
  92. Kanhere A., Vingron M. 2009; Horizontal Gene Transfers in prokaryotes show differential preferences for metabolic and translational genes. BMC Evol Biol 9:9
    [Google Scholar]
  93. Karginov F. V., Hannon G. J. 2010; The CRISPR system: small RNA-guided defense in bacteria and archaea. Mol Cell 37:7–19
    [Google Scholar]
  94. Kasiviswanathan R., Shin J. H., Melamud E., Kelman Z. 2004; Biochemical characterization of the Methanothermobacter thermautotrophicus minichromosome maintenance (MCM) helicase N-terminal domains. J Biol Chem 279:28358–28366
    [Google Scholar]
  95. Kaster A. K., Moll J., Parey K., Thauer R. K. 2011; Coupling of ferredoxin and heterodisulfide reduction via electron bifurcation in hydrogenotrophic methanogenic archaea. Proc Natl Acad Sci U S A (Epub ahead of print
    [Google Scholar]
  96. Kelman Z., Lee J. K., Hurwitz J. 1999; The single minichromosome maintenance protein of Methanobacterium thermoautotrophicum DeltaH contains DNA helicase activity. Proc Natl Acad Sci U S A 96:14783–14788
    [Google Scholar]
  97. Kendrick M. G., Kral T. A. 2006; Survival of methanogens during desiccation: implications for life on Mars. Astrobiology 6:546–551
    [Google Scholar]
  98. Kim Y. J., Lee H. S., Bae S. S., Jeon J. H., Lim J. K., Cho Y., Nam K. H., Kang S. G., Kim S. J. other authors 2007; Cloning, purification, and characterization of a new DNA polymerase from a hyperthermophilic archaeon, Thermococcus sp. NA1. J Microbiol Biotechnol 17:1090–1097
    [Google Scholar]
  99. Kim Y. J., Ryu Y. G., Lee H. S., Cho Y., Kwon S. T., Lee J. H., Kang S. G. 2008; Characterization of a dITPase from the hyperthermophilic archaeon Thermococcus onnurineus NA1 and its application in PCR amplification. Appl Microbiol Biotechnol 79:571–578
    [Google Scholar]
  100. Knittel K., Boetius A. 2009; Anaerobic oxidation of methane: progress with an unknown process. Annu Rev Microbiol 63:311–334
    [Google Scholar]
  101. König H., Kandler O., Hammes W. 1989; Biosynthesis of pseudomurein: isolation of putative precursors from Methanobacterium thermoautotrophicum . Can J Microbiol 35:176–181
    [Google Scholar]
  102. Könneke M., Bernhard A. E., de la Torre J. R., Walker C. B., Waterbury J. B., Stahl D. A. 2005; Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437:543–546
    [Google Scholar]
  103. Koonin E. V., Wolf Y. I. 2009; Is evolution Darwinian or/and Lamarckian?. Biol Direct 4:42
    [Google Scholar]
  104. Krishnan L., Dicaire C. J., Patel G. B., Sprott G. D. 2000; Archaeosome vaccine adjuvants induce strong humoral, cell-mediated, and memory responses: comparison to conventional liposomes and alum. Infect Immun 68:54–63
    [Google Scholar]
  105. Kulik E. M., Sandmeier H., Hinni K., Meyer J. 2001; Identification of archaeal rDNA from subgingival dental plaque by PCR amplification and sequence analysis. FEMS Microbiol Lett 196:129–133
    [Google Scholar]
  106. Küper U., Meyer C., Müller V., Rachel R., Huber H. 2010; Energized outer membrane and spatial separation of metabolic processes in the hyperthermophilic Archaeon Ignicoccus hospitalis . Proc Natl Acad Sci U S A 107:3152–3156
    [Google Scholar]
  107. Kvaratskhelia M., White M. F. 2000; An archaeal Holliday junction resolving enzyme from Sulfolobus solfataricus exhibits unique properties. J Mol Biol 295:193–202
    [Google Scholar]
  108. Landis G. A. 2001; Martian water: are there extant halobacteria on Mars?. Astrobiology 1:161–164
    [Google Scholar]
  109. Lecompte O., Ripp R., Thierry J. C., Moras D., Poch O. 2002; Comparative analysis of ribosomal proteins in complete genomes: an example of reductive evolution at the domain scale. Nucleic Acids Res 30:5382–5390
    [Google Scholar]
  110. Leigh J. A., Dodsworth J. A. 2007; Nitrogen regulation in bacteria and archaea. Annu Rev Microbiol 61:349–377
    [Google Scholar]
  111. Lessner D. J., Lhu L., Wahal C. S., Ferry J. G. 2010; An engineered methanogenic pathway derived from the domains bacteria and archaea. MBiol 1:e00243–10
    [Google Scholar]
  112. Levitt M. D., Furne J. K., Kuskowski M., Ruddy J. 2006; Stability of human methanogenic flora over 35 years and a review of insights obtained from breath methane measurements. Clin Gastroenterol Hepatol 4:123–129
    [Google Scholar]
  113. Lindås A. C., Karlsson E. A., Lindgren M. T., Ettema T. J., Bernander R. 2008; A unique cell division machinery in the Archaea. Proc Natl Acad Sci U S A 105:18942–18946
    [Google Scholar]
  114. Liu Y., Whitman W. B. 2008; Metabolic, phylogenetic, and ecological diversity of the methanogenic archaea. Ann N Y Acad Sci 1125171–189
    [Google Scholar]
  115. Löwe J., Stock D., Jap B., Zwickl P., Baumeister W., Huber R. 1995; Crystal structure of the 20S proteasome from the archaeon T. acidophilum at 3.4 Å resolution. Science 268:533–539
    [Google Scholar]
  116. Lundgren M., Andersson A., Chen L., Nilsson P., Bernander R. 2004; Three replication origins in Sulfolobus species: synchronous initiation of chromosome replication and asynchronous termination. Proc Natl Acad Sci U S A 101:7046–7051
    [Google Scholar]
  117. Luo X., Schwarz-Linek U., Botting C. H., Hensel R., Siebers B., White M. F. 2007; CC1, a novel crenarchaeal DNA binding protein. J Bacteriol 189:403–409
    [Google Scholar]
  118. Macalady J. L., Jones D. S., Lyon E. H. 2007; Extremely acidic, pendulous cave wall biofilms from the Frasassi cave system, Italy. Environ Microbiol 9:1402–1414
    [Google Scholar]
  119. Magrum L. J., Luehrsen K. R., Woese C. R. 1978; Are extreme halophiles actually “bacteria”?. J Mol Evol 11:1–8
    [Google Scholar]
  120. Mandon E. C., Trueman S. F., Gilmore R. 2009; Translocation of proteins through the Sec61 and SecYEG channels. Curr Opin Cell Biol 21:501–507
    [Google Scholar]
  121. Matsumi R., Atomi H., Driessen A. J., van der Oost J. 2011; Isoprenoid biosynthesis in Archaea – biochemical and evolutionary implications. Res Microbiol 162:39–52
    [Google Scholar]
  122. Maupin-Furlow J. A., Humbard M. A., Kirkland P. A., Li W., Reuter C. J., Wright A. J., Zhou G. 2006; Proteasomes from structure to function: perspectives from Archaea. Curr Top Dev Biol 75:125–169
    [Google Scholar]
  123. McDonald J. P., Hall A., Gasparutto D., Cadet J., Ballantyne J., Woodgate R. 2006; Novel thermostable Y-family polymerases: applications for the PCR amplification of damaged or ancient DNAs. Nucleic Acids Res 34:1102–1111
    [Google Scholar]
  124. McGenity T. J., Gemmell R. T., Grant W. D., Stan-Lotter H. 2000; Origins of halophilic microorganisms in ancient salt deposits. Environ Microbiol 2:243–250
    [Google Scholar]
  125. Mehta M. P., Baross J. A. 2006; Nitrogen fixation at 9 °C by a hydrothermal vent archaeon. Science 314:1783–1786
    [Google Scholar]
  126. Mescher M. F., Strominger J. L. 1976; Purification and characterization of a prokaryotic glucoprotein from the cell envelope of Halobacterium salinarium . J Biol Chem 251:2005–2014
    [Google Scholar]
  127. Mihajlovski A., Alric M., Brugère J. F. 2008; A putative new order of methanogenic Archaea inhabiting the human gut, as revealed by molecular analyses of the mcrA gene. Res Microbiol 159:516–521
    [Google Scholar]
  128. Moissl C., Rachel R., Briegel A., Engelhardt H., Huber R. 2005; The unique structure of archaeal ‘hami’, highly complex cell appendages with nano-grappling hooks. Mol Microbiol 56:361–370
    [Google Scholar]
  129. Moissl-Eichinger C. 2011; Archaea in artificial environments: their presence in global spacecraft clean rooms and impact on planetary protection. ISME J 5:209–219
    [Google Scholar]
  130. Mumma M. J., Villanueva G. L., Novak R. E., Hewagama T., Bonev B. P., Disanti M. A., Mandell A. M., Smith M. D. 2009; Strong release of methane on Mars in northern summer 2003. Science 323:1041–1045
    [Google Scholar]
  131. Myllykallio H., Lopez P., López-García P., Heilig R., Saurin W., Zivanovic Y., Philippe H., Forterre P. 2000; Bacterial mode of replication with eukaryotic-like machinery in a hyperthermophilic archaeon. Science 288:2212–2215
    [Google Scholar]
  132. Naji S., , Grünberg S., Thomm M. 2007; The RPB7 orthologue E′ is required for transcriptional activity of a reconstituted archaeal core enzyme at low temperatures and stimulates open complex formation. J Biol Chem 282:11047–11057
    [Google Scholar]
  133. Naji S., Bertero M. G., Spitalny P., Cramer P., Thomm M. 2008; Structure–function analysis of the RNA polymerase cleft loops elucidates initial transcription, DNA unwinding and RNA displacement. Nucleic Acids Res 36:676–687
    [Google Scholar]
  134. Nelson K. E., Clayton R. A., Gill S. R., Gwinn M. L., Dodson R. J., Haft D. H., Hickey E. K., Peterson J. D., Nelson W. C. other authors 1999; Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima . Nature 399:323–329
    [Google Scholar]
  135. Ng S. Y., Chaban B., Jarrell K. F. 2006; Archaeal flagella, bacterial flagella and type IV pili: a comparison of genes and posttranslational modifications. J Mol Microbiol Biotechnol 11:167–191
    [Google Scholar]
  136. Ng S. Y., Chaban B., VanDyke D. J., Jarrell K. F. 2007; Archaeal signal peptidases. Microbiology 153:305–314
    [Google Scholar]
  137. Ng S. Y., Zolghadr B., Driessen A. J., Albers S. V., Jarrell K. F. 2008; Cell surface structures of archaea. J Bacteriol 190:6039–6047
    [Google Scholar]
  138. Nickell S., Hegerl R., Baumeister W., Rachel R. 2003; Pyrodictium cannulae enter the periplasmic space but do not enter the cytoplasm, as revealed by cryo-electron tomography. J Struct Biol 141:34–42
    [Google Scholar]
  139. Niederberger T. D., Perreault N. N., Tille S., Lollar B. S., Lacrampe-Couloume G., Andersen D., Greer C. W., Pollard W., Whyte L. G. 2010; Microbial characterization of a subzero, hypersaline methane seep in the Canadian High Arctic. ISME J 4:1326–1339
    [Google Scholar]
  140. Norais C., Hawkins M., Hartman A. L., Eisen J. A., Myllykallio H., Allers T. 2007; Genetic and physical mapping of DNA replication origins in Haloferax volcanii . PLoS Genet 3:e77
    [Google Scholar]
  141. Nottebaum S., Tan L., Trzaska D., Carney H. C., Weinzierl R. O. 2008; The RNA polymerase factory: a robotic in vitro assembly platform for high-throughput production of recombinant protein complexes. Nucleic Acids Res 36:245–252
    [Google Scholar]
  142. Obita T., Saksena S., Ghazi-Tabatabai S., Gill D. J., Perisic O., Emr S. D., Williams R. L. 2007; Structural basis for selective recognition of ESCRT-III by the AAA ATPase Vps4. Nature 449:735–739
    [Google Scholar]
  143. Olsen G. J., Lane D. J., Giovannoni S. J., Pace N. R., Stahl D. A. 1986; Microbial ecology and evolution: a ribosomal RNA approach. Annu Rev Microbiol 40:337–365
    [Google Scholar]
  144. Pace N. R. 2006; Time for a change. Nature 441:289
    [Google Scholar]
  145. Paper W., Jahn U., Hohn M. J., Kronner M., Näther D. J., Burghardt T., Rachel R., Stetter K. O., Huber H. 2007; Ignicoccus hospitalis sp. nov., the host of ‘ Nanoarchaeum equitans ’. Int J Syst Evol Microbiol 57:803–808
    [Google Scholar]
  146. Park S. Y., Lee B., Park K. S., Chong Y., Yoon M. Y., Jeon S. J., Kim D. E. 2010; Facilitation of polymerase chain reaction with thermostable inorganic pyrophosphatase from hyperthermophilic archaeon Pyrococcus horikoshii . Appl Microbiol Biotechnol 85:807–812
    [Google Scholar]
  147. Patel G. B., Zhou H., KuoLee R., Chen W. 2004; Archaeosomes as adjuvants for combination vaccines. J Liposome Res 14:191–202
    [Google Scholar]
  148. Podar M., Anderson I., Makarova K. S., Elkins J. G., Ivanova N., Wall M. A., Lykidis A., Mavromatis K., Sun H. other authors 2008; A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans . Genome Biol 9:R158
    [Google Scholar]
  149. Pohlschröder M., Giménez M. I., Jarrell K. F. 2005; Protein transport in Archaea: Sec and twin arginine translocation pathways. Curr Opin Microbiol 8:713–719
    [Google Scholar]
  150. Posner M. G., Upadhyay A., Bagby S., Hough D. W., Danson M. J. 2009; A unique lipoylation system in the Archaea. Lipoylation in Thermoplasma acidophilum requires two proteins. FEBS J 276:4012–4022
    [Google Scholar]
  151. Prangishvili D., Forterre P., Garrett R. A. 2006a; Viruses of the Archaea: a unifying view. Nat Rev Microbiol 4:837–848
    [Google Scholar]
  152. Prangishvili D., Garrett R. A., Koonin E. V. 2006b; Evolutionary genomics of archaeal viruses: unique viral genomes in the third domain of life. Virus Res 117:52–67
    [Google Scholar]
  153. Prosser J. I., Nicol G. W. 2008; Relative contributions of archaea and bacteria to aerobic ammonia oxidation in the environment. Environ Microbiol 10:2931–2941
    [Google Scholar]
  154. Rabl J., Smith D. M., Yu Y., Chang S. C., Goldberg A. L., Cheng Y. 2008; Mechanism of gate opening in the 20S proteasome by the proteasomal ATPases. Mol Cell 30:360–368
    [Google Scholar]
  155. Ranjan N., Damberger F. F., Sutter M., Allain F. H., Weber-Ban E. 2011; Solution structure and activation mechanism of ubiquitin-like small archaeal modifier proteins. J Mol Biol 405:1040–1055
    [Google Scholar]
  156. Reeve J. N. 1999; Archaebacteria then ... Archaes now (are there really no archaeal pathogens?. J Bacteriol 181:3613–3617
    [Google Scholar]
  157. Reher M., Gebhard S., Schönheit P. 2007; Glyceraldehyde-3-phosphate ferredoxin oxidoreductase (GAPOR) and nonphosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN), key enzymes of the respective modified Embden–Meyerhof pathways in the hyperthermophilic crenarchaeota Pyrobaculum aerophilum and Aeropyrum pernix . FEMS Microbiol Lett 273:196–205
    [Google Scholar]
  158. Reher M., Fuhrer T., Bott M., Schönheit P. 2010; The nonphosphorylative Entner-Doudoroff pathway in the thermoacidophilic euryarchaeon Picrophilus torridus involves a novel 2-keto-3-deoxygluconate-specific aldolase. J Bacteriol 192:964–974
    [Google Scholar]
  159. Religa T. L., Sprangers R., Kay L. E. 2010; Dynamic regulation of archaeal proteasome gate opening as studied by TROSY NMR. Science 328:98–102
    [Google Scholar]
  160. Rohwerder T., Sand W. 2007; Oxidation of inorganic sulfur compounds in acidophilic prokaryotes. Eng Life Sci 7:301–309
    [Google Scholar]
  161. Ring G., Eichler J. 2004; Membrane binding of ribosomes occurs at SecYE-based sites in the Archaea Haloferax volcanii . J Mol Biol 336:997–1010
    [Google Scholar]
  162. Roberts E., Sethi A., Montoya J., Woese C. R., Luthey-Schulten Z. 2008; Molecular signatures of ribosomal evolution. Proc Natl Acad Sci U S A 105:13953–13958
    [Google Scholar]
  163. Robertson C. E., Harris J. K., Spear J. R., Pace N. R. 2005; Phylogenetic diversity and ecology of environmental Archaea. Curr Opin Microbiol 8:638–642
    [Google Scholar]
  164. Robinson N. P., Dionne I., Lundgren M., Marsh V. L., Bernander R., Bell S. D. 2004; Identification of two origins of replication in the single chromosome of the archaeon Sulfolobus solfataricus . Cell 116:25–38
    [Google Scholar]
  165. Rother M., Krzycki J. A. 2010; Selenocysteine, pyrrolysine, and the unique energy metabolism of methanogenic archaea. Archaea 2010453642
    [Google Scholar]
  166. Rudolf J., Makrantoni V., Ingledew W. J., Stark M. J., White M. F. 2006; The DNA repair helicases XPD and FancJ have essential iron-sulfur domains. Mol Cell 23:801–808
    [Google Scholar]
  167. Ruschak A. M., Religa T. L., Breuer S., Witt S., Kay L. E. 2010; The proteasome antechamber maintains substrates in an unfolded state. Nature 467:868–871
    [Google Scholar]
  168. Sakuraba H., Goda S., Ohshima T. 2004; Unique sugar metabolism and novel enzymes of hyperthermophilic archaea. Chem Rec 3:281–287
    [Google Scholar]
  169. Samson R. Y., Obita T., Freund S. M., Williams R. L., Bell S. D. 2008; A role for the ESCRT system in cell division in archaea. Science 322:1710–1713
    [Google Scholar]
  170. Samuel B. S., Gordon J. I. 2006; A humanized gnotobiotic mouse model of host–archaeal–bacterial mutualism. Proc Natl Acad Sci U S A 103:10011–10016
    [Google Scholar]
  171. Samuel B. S., Hansen E. E., Manchester J. K., Coutinho P. M., Henrissat B., Fulton R., Latreille P., Kim K., Wilson R. K., Gordon J. I. 2007; Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut. Proc Natl Acad Sci U S A 104:10643–10648
    [Google Scholar]
  172. Samuel B. S., Shaito A., Motoike T., Rey F. E., Backhed F., Manchester J. K., Hammer R. E., Williams S. C., Crowley J. other authors 2008; Effects of the gut microbiota on host adiposity are modulated by the short-chain fatty-acid binding G protein-coupled receptor, Gpr41. Proc Natl Acad Sci U S A 105:16767–16772
    [Google Scholar]
  173. Sanderson K. 2010; Planetary science: a whiff of mystery on Mars. Nature 463:420–421
    [Google Scholar]
  174. Sandman K., Reeve J. N. 2005; Archaeal chromatin proteins: different structures but common function?. Curr Opin Microbiol 8:656–661
    [Google Scholar]
  175. Scanlan P. D., Shanahan F., Marchesi J. R. 2008; Human methanogen diversity and incidence in healthy and diseased colonic groups using mcrA gene analysis. BMC Microbiol 8:79
    [Google Scholar]
  176. Scheller S., Goenrich M., Boecher R., Thauer R. K., Jaun B. 2010; The key nickel enzyme of methanogenesis catalyses the anaerobic oxidation of methane. Nature 465:606–608
    [Google Scholar]
  177. Schleper C. 2010; Ammonia oxidation: different niches for bacteria and archaea?. ISME J 4:1092–1094
    [Google Scholar]
  178. Schleper C., Nicol G. W. 2010; Ammonia-oxidising archaea – physiology, ecology and evolution. Adv Microb Physiol 57:1–41
    [Google Scholar]
  179. Schleper C., Jurgens G., Jonuscheit M. 2005; Genomic studies of uncultivated archaea. Nat Rev Microbiol 3:479–488
    [Google Scholar]
  180. Siebers B., Schönheit P. 2005; Unusual pathways and enzymes of central carbohydrate metabolism in Archaea. Curr Opin Microbiol 8:695–705
    [Google Scholar]
  181. Sleytr U. B., Beveridge T. J. 1999; Bacterial S-layers. Trends Microbiol 7:253–260
    [Google Scholar]
  182. Southam G., Beveridge T. J. 1992; Characterization of novel, phenolsoluble polypeptides which confer rigidity to the sheath of Methanospirillum hungatei GP1. J Bacteriol 174:935–946
    [Google Scholar]
  183. Sprott G. D., Tolson D. L., Patel G. B. 1997; Archaeosomes as novel antigen delivery systems. FEMS Microbiol Lett 154:17–22
    [Google Scholar]
  184. Sprott G. D., Dicaire C. J., Côté J. P., Whitfield D. M. 2008; Adjuvant potential of archaeal synthetic glycolipid mimetics critically depends on the glyco head group structure. Glycobiology 18:559–565
    [Google Scholar]
  185. Srinivasan G., James C. M., Krzycki J. A. 2002; Pyrrolysine encoded by UAG in Archaea: charging of a UAG-decoding specialized tRNA. Science 296:1459–1462
    [Google Scholar]
  186. Stetter K. O. 2006; Hyperthermophiles in the history of life. Philos Trans R Soc Lond B Biol Sci 361:1837–1842
    [Google Scholar]
  187. Strocchi A., Furne J., Ellis C., Levitt M. D. 1994; Methanogens outcompete sulphate reducing bacteria for H2 in the human colon. Gut 35:1098–1101
    [Google Scholar]
  188. Su D., Hohn M. J., Palioura S., Sherrer R. L., Yuan J., , Söll D., O'Donoghue P. 2009; How an obscure archaeal gene inspired the discovery of selenocysteine biosynthesis in humans. IUBMB Life 61:35–39
    [Google Scholar]
  189. Tang T. H., Rozhdestvensky T. S., d'Orval B. C., Bortolin M. L., Huber H., Charpentier B., Branlant C., Bachellerie J. P., Brosius J., Hüttenhofer A. 2002; RNomics in Archaea reveals a further link between splicing of archaeal introns and rRNA processing. Nucleic Acids Res 30:921–930
    [Google Scholar]
  190. Thauer R. K., Kaster A. K., Seedorf H., Buckel W., Hedderich R. 2008; Methanogenic archaea: ecologically relevant differences in energy conservation. Nat Rev Microbiol 6:579–591
    [Google Scholar]
  191. Thavasi V., Lazarova T., Filipek S., Kolinski M., Querol E., Kumar A., Ramakrishna S., , Padrós E., Renugopalakrishnan V. 2009; Study on the feasibility of bacteriorhodopsin as bio-photosensitizer in excitonic solar cell: a first report. J Nanosci Nanotechnol 9:1679–1687
    [Google Scholar]
  192. Thomas N. A., Bardy S. L., Jarrell K. F. 2001; The archaeal flagellum: a different kind of prokaryotic motility structure. FEMS Microbiol Rev 25:147–174
    [Google Scholar]
  193. Tourna M., Freitag T. E., Nicol G. W., Prosser J. I. 2008; Growth, activity and temperature responses of ammonia-oxidizing archaea and bacteria in soil microcosms. Environ Microbiol 10:1357–1364
    [Google Scholar]
  194. Tu J. K., Prangishvilli D., Huber H., Wildgruber G., Zillig W., Stetter K. O. 1982; Taxonomic relations between archaebacteria including 6 novel genera examined by cross hybridization of DNAs and 16S rRNAs. J Mol Evol 18:109–114
    [Google Scholar]
  195. Valentine D. L. 2007; Adaptations to energy stress dictate the ecology and evolution of the Archaea. Nat Rev Microbiol 5:316–323
    [Google Scholar]
  196. van de Vossenberg J. L., Driessen A. J., Konings W. N. 1998; The essence of being extremophilic: the role of the unique archaeal membrane lipids. Extremophiles 2:163–170
    [Google Scholar]
  197. Van den Berg B., Clemons W. M. Jr, Collinson I., Modis Y., Hartmann E., Harrison S. C., Rapoport T. A. 2004; X-ray structure of a protein-conducting channel. Nature 427:36–44
    [Google Scholar]
  198. van der Oost J., Brouns S. J. 2009; RNAi: prokaryotes get in on the act. Cell 139:863–865
    [Google Scholar]
  199. Venter J. C., Remington K., Heidelberg J. F., Halpern A. L., Rusch D., Eisen J. A., Wu D., Paulsen I., Nelson K. E. other authors 2004; Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66–74
    [Google Scholar]
  200. Verhees C. H., Kengen S. W., Tuininga J. E., Schut G. J., Adams M. W., De Vos W. M., Van Der Oost J. 2003; The unique features of glycolytic pathways in Archaea. Biochem J 375:231–246
    [Google Scholar]
  201. Vianna M. E., Conrads G., Gomes B. P., Horz H. P. 2006; Identification and quantification of archaea involved in primary endodontic infections. J Clin Microbiol 44:1274–1282
    [Google Scholar]
  202. Walker C. B., de la Torre J. R., Klotz M. G., Urakawa H., Pinel N., Arp D. J., Brochier-Armanet C., Chain P. S., Chan P. P. other authors 2010; Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea. Proc Natl Acad Sci U S A 107:8818–8823
    [Google Scholar]
  203. Walsby A. E. 2005; Archaea with square cells. Trends Microbiol 13:193–195
    [Google Scholar]
  204. Wang Y. A., Yu X., Ng S. Y., Jarrell K. F., Egelman E. H. 2008; The structure of an archaeal pilus. J Mol Biol 381:456–466
    [Google Scholar]
  205. Wardleworth B. N., Russell R. J., Bell S. D., Taylor G. L., White M. F. 2002; Structure of Alba: an archaeal chromatin protein modulated by acetylation. EMBO J 21:4654–4662
    [Google Scholar]
  206. Waters E., Hohn M. J., Ahel I., Graham D. E., Adams M. D., Barnstead M., Beeson K. Y., Bibbs L., Bolanos R. other authors 2003; The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism. Proc Natl Acad Sci U S A 100:12984–12988
    [Google Scholar]
  207. Weiss D. S., Thauer R. K. 1993; Methanogenesis and the unity of biochemistry. Cell 72:819–822
    [Google Scholar]
  208. Werner F. 2007; Structure and function of archaeal RNA polymerases. Mol Microbiol 65:1395–1404
    [Google Scholar]
  209. Werner F., Weinzierl R. O. 2002; A recombinant RNA polymerase II-like enzyme capable of promoter-specific transcription. Mol Cell 10:635–646
    [Google Scholar]
  210. Williams R. L., Urbé S. 2007; The emerging shape of the ESCRT machinery. Nat Rev Mol Cell Biol 8:355–368
    [Google Scholar]
  211. Winker S., Woese C. R. 1991; A definition of the domains Archaea, Bacteria and Eucarya in terms of small subunit ribosomal RNA characteristics. Syst Appl Microbiol 14:305–310
    [Google Scholar]
  212. Woese C. R. 2004; The archaeal concept and the world it lives in: a retrospective. Photosynth Res 80:361–372
    [Google Scholar]
  213. Woese C. R., Fox G. E. 1977; Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci U S A 74:5088–5090
    [Google Scholar]
  214. Woese C. R., Magrum L. J., Fox G. E. 1978; Archaebacteria. J Mol Evol 11:245–252
    [Google Scholar]
  215. Woese C. R., Kandler O., Wheelis M. L. 1990; Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A 87:4576–4579
    [Google Scholar]
  216. Wuchter C., Abbas B., Coolen M. J., Herfort L., van Bleijswijk J., Timmers P., Strous M., Teira E., Herndl G. J. other authors 2006; Archaeal nitrification in the ocean. Proc Natl Acad Sci U S A 103:12317–12322
    [Google Scholar]
  217. Yamabe K., Maeda H., Kokeguchi S., Tanimoto I., Sonoi N., Asakawa S., Takashiba S. 2008; Distribution of Archaea in Japanese patients with periodontitis and humoral immune response to the components. FEMS Microbiol Lett 287:69–75
    [Google Scholar]
  218. Yao B., Lei M., Ren L., Menke N., Wang Y., Fischer T., Hampp N. 2005a; Polarization multiplexed write-once-read-many optical data storage in bacteriorhodopsin films. Opt Lett 30:3060–3062
    [Google Scholar]
  219. Yao B., Ren Z., Menke N., Wang Y., Zheng Y., Lei M., Chen G., Hampp N. 2005b; Polarization holographic high-density optical data storage in bacteriorhodopsin film. Appl Opt 44:7344–7348
    [Google Scholar]
  220. Yu Y., Smith D. M., Kim H. M., Rodriguez V., Goldberg A. L., Cheng Y. 2010; Interactions of PAN's C-termini with archaeal 20S proteasome and implications for the eukaryotic proteasome–ATPase interactions. EMBO J 29:692–702
    [Google Scholar]
  221. Yuan J., Palioura S., Salazar J. C., Su D., O'Donoghue P., Hohn M. J., Cardoso A. M., Whitman W. B., Söll D. 2006; RNA-dependent conversion of phosphoserine forms selenocysteine in eukaryotes and archaea. Proc Natl Acad Sci U S A 103:18923–18927
    [Google Scholar]
  222. Zaparty M., Tjaden B., Hensel R., Siebers B. 2008; The central carbohydrate metabolism of the hyperthermophilic crenarchaeote Thermoproteus tenax : pathways and insights into their regulation. Arch Microbiol 190:231–245
    [Google Scholar]
  223. Zhang F., Hu M., Tian G., Zhang P., Finley D., Jeffrey P. D., Shi Y. 2009a; Structural insights into the regulatory particle of the proteasome from Methanocaldococcus jannaschii . Mol Cell 34:473–484
    [Google Scholar]
  224. Zhang F., Wu Z., Zhang P., Tian G., Finley D., Shi Y. 2009b; Mechanism of substrate unfolding and translocation by the regulatory particle of the proteasome from Methanocaldococcus jannaschii . Mol Cell 34:485–496
    [Google Scholar]
  225. Zhang J., Baker M. L., Schröder G. F., Douglas N. R., Reissmann S., Jakana J., Dougherty M., Fu C. J., Levitt M. other authors 2010a; Mechanism of folding chamber closure in a group II chaperonin. Nature 463:379–383
    [Google Scholar]
  226. Zhang L. M., Offre P. R., He J. Z., Verhamme D. T., Nicol G. W., Prosser J. I. 2010b; Autotrophic ammonia oxidation by soil thaumarchaea. Proc Natl Acad Sci U S A 107:17240–17245
    [Google Scholar]
  227. Zillig W. 1991; Comparative biochemistry of Archaea and Bacteria. Curr Opin Genet Dev 1:544–551
    [Google Scholar]
  228. Zillig W., Tu J., Holz I. 1981; Thermoproteales – a third order of thermoacidophilic archaebacteria. Nature 293:85–86
    [Google Scholar]
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