References
- Allen, E. E. and J. F. Banfield (2005) Community genomics in microbial ecology and evolution. Nat. Rev. Microbiol. 3: 489-498. https://doi.org/10.1038/nrmicro1157
- Allers, T. and M. Mevarech (2005) Archaeal genetics -The third way. Nat. Rev. Genet. 6: 58-73. https://doi.org/10.1038/nrg1504
- Berg, I. A., D. Kockelkorn, W. Buckel, and G. Fuchs (2007) A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in archaea. Science 318: 1782-1786. https://doi.org/10.1126/science.1149976
- Bleichert, F., K. T. Gagnon, B. A. Brown, E. S. Maxwell, A. E. Leschziner, V. M. Unger, and S. J. Baserga (2009) A dimeric structure for archaeal box C/D small ribonucleoproteins. Science 325: 1384-1387. https://doi.org/10.1126/science.1176099
- Dong, X. C., M. Y. Zhou, C. Zhong, B. Yang, N. Shen, and J. P. Ding (2010) Crystal structure of Pyrococcus horikoshii tryptophany1-tRNA synthetase and strueture-based phylogenetic analysis suggest an archaeal origin of tryptophany1-tRNA synthetase. Nucleic Acids Res. 38: 1401-1412. https://doi.org/10.1093/nar/gkp1053
- Dore, J. E., R. Lukas, D. W. Sadler, M. J. Church, and D. M. Karl (2009) Physical and biogeochemical modulation of ocean acidification in the central North Pacific. Proc. Natl. Acad. Sci. 106: 12235-12240. https://doi.org/10.1073/pnas.0906044106
- Ferber, D. (2004) Synthetic biology: Microbes made to order. Science 303: 158-161. https://doi.org/10.1126/science.303.5655.158
- Gaasterland, T. (1999) Archaeal genomics. Curr. Opin. Microbiol. 2: 542-547. https://doi.org/10.1016/S1369-5274(99)00014-4
- Gibson, D. G., J. I. Glass, C. Lartigue, V. N. Noskov, R. Y. Chuang, M. A. Algire, G. A. Benders, M. G. Montague, L. Ma, M. M. Moodie, C. Merryman, S. Vashee, R. Krishnakumar, N. AssadGarcia, C. Andrews-Pfannkoch, E. A. Denisova, L. Young, Z. Q. Qi, T. H. Segall-Shapiro, C. H. Calvey, P. P. Parmar, C. A. Hutehison, H. O. Smith, and J. C. Venter (2010) Creation of a bacterial cell controlled by a ehemically synthesized genome. Science 329: 52-56. https://doi.org/10.1126/science.1190719
- Gil, R, F. J. Silva, J. Pereto, and A. Moya (2004) Determination of the core of a minimal bacterial gene set. Microbiol. Mol. Biol. Rev. 68: 518-537. https://doi.org/10.1128/MMBR.68.3.518-537.2004
- Glass, J. I., N. Assad-Gareia, N. Alperovieh, S. Yooseph, M. R. Lewis, M. Maruf, C. A. Hutchison, H. O. Smith, and J. C. Venter (2006) Essential genes of a minimal bacterium. Proc. Natl. Acad. Sci. 103: 425-430. https://doi.org/10.1073/pnas.0510013103
- Han, S. S., J. Y. Lee, W. H. Kim, H. J. Shin, and G. J. Kim (2008) Screening of promoters from metagenomic DNA and their use for the construetion of expression vectors. J. Microbiol. Biotechnol. 18: 1634-1640.
- Herndl, G. J., T. Reinthaler, E. Teira, H. van Aken, C. Veth, A. Pemthaler, and J. Pemthaler (2005) Contribution of Archaea to total prokaryotie production in the deep Atlantic Ocean. Appl. Environ. Microbiol. 71: 2303-2309. https://doi.org/10.1128/AEM.71.5.2303-2309.2005
- Humbard,M. A., H. V. Miranda,J. M. Lim, D. J. Krause, J. R. Pritz, G. Y. Zhou, S. X. Chen, L. Wells, and J. A. Maupin-Furlow (2010) Ubiquitin-like small archaeal modifier proteins (SAMPs) in Haloferax volcanii. Nature 463: 54-60. https://doi.org/10.1038/nature08659
- Khomyakova, M., O. Bukmez, L. K. Thomas, T. J. Erb, and I. A. Berg (2011) A methylaspartate cycle in haloarchaea. Science 331: 334-337. https://doi.org/10.1126/science.1196544
- Konneke, M., A. E. Bernhard, J. R. de la Torre, C. B. Walker, J. B. Waterbury, and D. A. Stahl (2005) Isolation of an autotrophic ammonia-oxidizing marine arehaeon. Nature 437: 543-546. https://doi.org/10.1038/nature03911
- McDaniel, L. D., E. Young, J. Delaney, F. Ruhnau, K. B. Ritchie, and J. H. Paul (2010) High frequency of horizontal gene transfer in the oceans. Science 330: 50. https://doi.org/10.1126/science.1192243
- Mincer, T. J., M. J. Church, L. T. Taylor, C. Preston, D. M. Kar, and E. F. DeLong (2007) Quantitative distribution of presumptive archaeal and bacterial nitrifiers in Monterey Bay and the North Pacific Subtropical Gyre. Environ. Microbiol. 9: 1162-1175. https://doi.org/10.1111/j.1462-2920.2007.01239.x
- 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. https://doi.org/10.1038/ismej.2010.124
- Mushegian, A. R. and E. V. Koonin (1996) A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc. Natl. Acad. Sci. 93: 10268-10273. https://doi.org/10.1073/pnas.93.19.10268
- Nather, D. J. and R Rachel (2004) The outer membrane of the hyperthermophilic archaeon ignicoccus: dynamics, ultrastructure and composition. Biochem. Soc. Trans. 32: 199-203. https://doi.org/10.1042/BST0320199
- Orengo, C. A. and J. M. Thornton (2005) Protein families and their evolution - A structural perspective. Ann. Rev. Biochem. 74: 867-900. https://doi.org/10.1146/annurev.biochem.74.082803.133029
- Park, B. J., S. J. Park, D. N. Yoon, S. Schouten, J. S. S. Damste, and S. K. Rhee (2010) Cultivation of autotrophic ammoniaoxidizing arehaea from marine sediments in coculture with sulfur-oxidizing bacteria. Appl. Environ. Microbiol. 76: 7575-7587. https://doi.org/10.1128/AEM.01478-10
- Schleper, C., I. Holz, D. Janekovic, J. Murphy, and W. Zillig (1995) A muIticopy plasmid of the extremely thermophilic archaeon Sulfolobus effects its transfer to recipients by mating. J. Bacteriol. 177: 4417-4426.
- Spang, A., R. Hatzenpichler, C. Brochier-Armanet, T. Rattei, P. Tischler, E. Spieck, W. Streit, D. A. Stahl, M. Wagner, and C. Schleper (2010) Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota. Trends Microbiol. 18: 331-340. https://doi.org/10.1016/j.tim.2010.06.003
- Thomas, N. A., S. L. Bardy, and K. F. Jarrell (2001) The archaeal flagellum: a different kind of prokaryotic motility structure. FEMS Microbiol. Rev. 25: 147-174. https://doi.org/10.1111/j.1574-6976.2001.tb00575.x
- Venter, J. C., K. Remington, J. F. Heidelberg, A. L. Halpern, D. Rusch, J. A. Eisen, D. Y. Wu, I. Paulsen, K. E. Nelson, W. Nelson, D. E. Fouts, S. Levy, A. H. Knap, M. W. Lomas, K. Nealson, O. White, J. Peterson, J. Hoffman, R. Parsons, H. Baden-Tillson, C. Pfannkoch, Y. H. Rogers, and H. O. Smith (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66-74. https://doi.org/10.1126/science.1093857
- Walker, C. B., J. R. de la Torre, M. G. Klotz, H. Urakawa, N. Pinel, D. J. Arp, C. Brochier-Armanet, P. S. G. Chain, P. P. Chan, A. Gollabgir, J. Hemp, M. Hugler, E. A. Karr, M. Konneke, M. Shin, T. J. Lawton, T. Lowe, W. Martens-Habbena, L. A. Sayavedra-Soto, D. Lang, S. M. Sievert, A. C. Rosenzweig, G. Manning, and D. A. Stahl (2010) Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and auto trophy in globally distributed marine crenarchaea. Proc. Natl. Acad. Sci. 107: 8818-8823. https://doi.org/10.1073/pnas.0913533107
- Woese, C. R. and G. E. Fox (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc. Natl. Acad. Sci. 74: 5088-5090. https://doi.org/10.1073/pnas.74.11.5088
- Wuchter, C., B. Abbas, M. J. L. Coolen, L. Heffort, J. van Bleijswijk, P. Timmers, M. Strous, E. Teira, G. J. Herndl, J. J. Middelburg, S. Schouten, and J. S. S. Damste (2006) Archaeal nitrification in the ocean. Proc. Natl. Acad. Sci. 103: 12317-12322. https://doi.org/10.1073/pnas.0600756103