Skip to main content
SpringerLink
Log in

The impact of genomics on research in diversity and evolution of archaea

  • Review
  • Published:
Biochemistry (Moscow) Aims and scope Submit manuscript

Abstract

Since the definition of archaea as a separate domain of life along with bacteria and eukaryotes, they have become one of the most interesting objects of modern microbiology, molecular biology, and biochemistry. Sequencing and analysis of archaeal genomes were especially important for studies on archaea because of a limited availability of genetic tools for the majority of these microorganisms and problems associated with their cultivation. Fifteen years since the publication of the first genome of an archaeon, more than one hundred complete genome sequences of representatives of different phylogenetic groups have been determined. Analysis of these genomes has expanded our knowledge of biology of archaea, their diversity and evolution, and allowed identification and characterization of new deep phylogenetic lineages of archaea. The development of genome technologies has allowed sequencing the genomes of uncultivated archaea directly from enrichment cultures, metagenomic samples, and even from single cells. Insights have been gained into the evolution of key biochemical processes in archaea, such as cell division and DNA replication, the role of horizontal gene transfer in the evolution of archaea, and new relationships between archaea and eukaryotes have been revealed.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

Abbreviations

FISH:

fluorescent in situ hybridization

kb:

thousand nucleotide pairs

Mb:

million nucleotide pairs

rRNA:

ribosomal RNA

References

  1. Woese, C. R., and Fox, G. E. (1977) Proc. Natl. Acad. Sci. USA, 74, 5088–5090.

    Article  PubMed  CAS  Google Scholar 

  2. Schleper, C., Puehler, G., Holz, I., Gambacorta, A., Janekovic, D., Santarius, U., Klenk, H. P., and Zillig, W. (1995) J. Bacteriol., 177, 7050–7059.

    PubMed  CAS  Google Scholar 

  3. Li, Y., Mandelco, L., and Wiegel, J. (1993) Int. J. Syst. Bacteriol., 43, 450–460.

    Article  Google Scholar 

  4. Blochl, E., Rachel, R., Burggraf, S., Hafenbradl, D., Jannasch, H. W., and Stetter, K. O. (1997) Extremophiles, 1, 14–21.

    Article  PubMed  CAS  Google Scholar 

  5. Kashefi, K., and Lovely, D. R. (2003) Science, 301, 934.

    Article  PubMed  CAS  Google Scholar 

  6. Bintrim, S. B., Donohue, T. J., Handelsman, J., Roberts, G. P., and Goodman, R. M. (1997) Proc. Natl. Acad. Sci. USA, 94, 277–282.

    Article  PubMed  CAS  Google Scholar 

  7. Ochsenreiter, T., Selezi, D., Quaiser, A., Bonch-Osmolovskaya, L., and Schleper, C. (2003) Environ. Microbiol., 5, 787–797.

    Article  PubMed  CAS  Google Scholar 

  8. Galand, P. E., Fritze, H., Conrad, R., and Yrjala, K. (2005) Appl. Environ. Microbiol., 71, 2195–2198.

    Article  PubMed  CAS  Google Scholar 

  9. DeLong, E. F. (1992) Proc. Natl. Acad. Sci. USA, 89, 5685–5689.

    Article  PubMed  CAS  Google Scholar 

  10. Fuhrman, J. A., McCallum, K., and Davis, A. A. (1992) Nature, 356, 148–149.

    Article  PubMed  CAS  Google Scholar 

  11. Boetius, A., Ravenschlag, K., Schubert, C. J., Rickert, D., Widdel, F., Gieseke, A., Amann, R., Jorgensen, B. B., Witte, U., and Pfannkuche, O. (2000) Nature, 407, 623–626.

    Article  PubMed  CAS  Google Scholar 

  12. Orphan, V. J., House, C. H., Hinrichs, K. U., McKeegan, K. D., and DeLong, E. F. (2001) Science, 293, 484–487.

    Article  PubMed  CAS  Google Scholar 

  13. Mills, H. J., Martinez, R. J., Story, S., and Sobecky, P. A. (2005) Appl. Environ. Microbiol., 71, 3235–3247.

    Article  PubMed  CAS  Google Scholar 

  14. MacGregor, B. J., Moser, D. P., Alm, E. W., Nealson, K. H., and Stahl, D. A. (1997) Appl. Environ. Microbiol., 63, 1178–1181.

    PubMed  CAS  Google Scholar 

  15. Keough, B. P., Schmidt, T. M., and Hicks, R. E. (2003) Microb. Ecol., 46, 238–248.

    Article  PubMed  CAS  Google Scholar 

  16. Takai, K., Moser, D. P., DeFlaun, M., Onstott, T. C., and Fredrickson, J. K. (2001) Appl. Environ. Microbiol., 67, 5750–5760.

    Article  PubMed  CAS  Google Scholar 

  17. Lepp, P. W., Brinig, M. M., Ouverney, C. C., Palm, K., Armitage, G. C., and Relman, D. A. (2004) Proc. Natl. Acad. Sci. USA, 101, 6176–6181.

    Article  PubMed  CAS  Google Scholar 

  18. Karner, M. B., DeLong, E. F., and Karl, D. M. (2001) Nature, 409, 507–510.

    Article  PubMed  CAS  Google Scholar 

  19. Konneke, M., Bernhard, A. E., de la Torre, J. R., Walker, C. B., Waterbury, J. B., and Stahl, D. A. (2005) Nature, 437, 543–546.

    Article  PubMed  CAS  Google Scholar 

  20. Leininger, S., Urich, T., Schloter, M., Schwark, L., Qi, J., Nicol, G. W., Prosser, J. I., Schuster, S. C., and Schleper, C. (2006) Nature, 442, 806–809.

    Article  PubMed  CAS  Google Scholar 

  21. Bult, C. J., White, O., Olsen, G. J., Zhou, L., Fleischmann, R. D., Sutton, G. G., Blake, J. A., FitzGerald, L. M., Clayton, R. A., Gocayne, J. D., Kerlavage, A. R., Dougherty, B. A., Tomb, J. F., Adams, M. D., Reich, C. I., Overbeek, R., Kirkness, E. F., Weinstock, K. G., Merrick, J. M., Glodek, A., Scott, J. L., Geoghagen, N. S., and Venter, J. C. (1996) Science, 273, 1058–1073.

    Article  PubMed  CAS  Google Scholar 

  22. Elkins, J. G., Podar, M., Graham, D. E., Makarova, K. S., Wolf, Y., Randau, L., Hedlund, B. P., Brochier-Armanet, C., Kunin, V., Anderson, I., Lapidus, A., Goltsman, E., Barry, K., Koonin, E. V., Hugenholtz, P., Kyrpides, N., Wanner, G., Richardson, P., Keller, M., and Stetter, K. O. (2008) Proc. Natl. Acad. Sci. USA, 105, 8102–8107.

    Article  PubMed  CAS  Google Scholar 

  23. Hallam, S. J., Konstantinidis, K. T., Putnam, N., Schleper, C., Watanabe, Y., Sugahara, J., Preston, C., de la Torre, J., Richardson, P. M., and DeLong, E. F. (2006) Proc. Natl. Acad. Sci. USA, 103, 18296–18301.

    Article  PubMed  CAS  Google Scholar 

  24. Nunoura, T., Takaki, Y., Kakuta, J., Nishi, S., Sugahara, J., Kazama, H., Chee, G. J., Hattori, M., Kanai, A., Atomi, H., Takai, K., and Takami, H. (2011) Nucleic Acids Res., 39, 3204–3223.

    Article  PubMed  CAS  Google Scholar 

  25. 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., and Banfield, J. F. (2010) Proc. Natl. Acad. Sci. USA, 107, 8806–8811.

    Article  PubMed  CAS  Google Scholar 

  26. Meyerdierks, A., Kube, M., Kostadinov, I., Teeling, H., Glockner, F. O., Reinhardt, R., and Amann, R. (2010) Environ. Microbiol., 12, 422–439.

    Article  PubMed  CAS  Google Scholar 

  27. Blainey, P. C., Mosier, A. C., Potanina, A., Francis, C. A., and Quake, S. R. (2011) PLoS One, 6, e16626.

    Article  PubMed  CAS  Google Scholar 

  28. Gribaldo, S., and Brochier-Armanet, C. (2006) Philos. Trans. R. Soc. Lond. B. Biol. Sci., 361, 1007–1022.

    Article  PubMed  CAS  Google Scholar 

  29. Bonch-Osmolovskaya, E. A., and Ravin, N. V. (2010) Vestn. Ros. Akad. Nauk, 80, 977–984.

    CAS  Google Scholar 

  30. Matsunaga, F., Forterre, P., Ishmo, Y., and Myllykallio, H. (2001) Proc. Natl. Acad. Sci. USA, 98, 11152–11157.

    Article  PubMed  CAS  Google Scholar 

  31. Myllykallio, H., Lopez, P., Lopez-Garcia, P., Heilig, R., Saurin, W., Zivanovic, Y., Philippe, H., and Forterre, P. (2000) Science, 288, 2212–2215.

    Article  PubMed  CAS  Google Scholar 

  32. Robinson, N. P., Dionne, I., Lundgren, M., Marsh, V. L., Bernander, R., and Bell, S. D. (2004) Cell, 116, 25–38.

    Article  PubMed  CAS  Google Scholar 

  33. Robinson, N. P., and Bell, S. D. (2007) Proc. Natl. Acad. Sci. USA, 104, 5806–5811.

    Article  PubMed  CAS  Google Scholar 

  34. Forterre, P. (2002) Curr. Opin. Microbiol., 5, 525–532.

    Article  PubMed  CAS  Google Scholar 

  35. Kjems, J., and Garrett, R. A. (1988) Cell, 54, 693–703.

    Article  PubMed  CAS  Google Scholar 

  36. Kjems, J., Leffers, H., Olesen, T., and Garrett, R. A. (1989) J. Biol. Chem., 264, 17834–17837.

    PubMed  CAS  Google Scholar 

  37. Watanabe, Y., Yokobori, S., and Kawarabayasi, Y. (2002) Tanpakushitsu Kakusan Koso, 47, 833–836.

    PubMed  Google Scholar 

  38. She, Q., Singh, R. K., Confalonieri, F., Zivanovic, Y., Allard, G., Awayez, M. J., Chan-Wei her, C. C., Clausen, I. G., Curtis, B. A., De Moors, A., Erauso, G., Fletcher, C., Gordon, P. M., Heikamp-de Jong, I., Jeffries, A. C., Kozera, C. J., Medina, N., Peng, X., Thi-Ngoc, H. P., Redder, P., Schenk, M. E., Thenault, C., Tolstrup, N., Charlebois, R. L., Doolittle, W. F., Duguet, M. T., Gaasterland, R. A., Garrett, M. A., Ragan, C. W., Sensen, C. W., and van der Oost, J. (2001) Proc. Natl. Acad. Sci. USA, 98, 7835–7840.

    Article  PubMed  CAS  Google Scholar 

  39. Chen, L., Brugger, K., Skovgaard, M., Redder, P., She, Q., Torarinsson, E., Greve, B., Awayez, M., Zibat, A., Klenk, H. P., and Garrett, R. A. (2005) J. Bacteriol., 187, 4992–4999.

    Article  PubMed  CAS  Google Scholar 

  40. Jansen, R., Embden, J. D., Gaastra, W., and Schouls, L. M. (2002) Mol. Microbiol., 43, 1565–1575.

    Article  PubMed  CAS  Google Scholar 

  41. Mojica, F. J., Diez-Villasenor, C., Garcia-Martinez, J., and Soria, E. (2005) Mol. Evol., 60, 174–182.

    Article  CAS  Google Scholar 

  42. Lillestol, R. K., Redder, P., Garrett, R. A., and Brugger, K. (2006) Archaea, 2, 59–72.

    Article  PubMed  Google Scholar 

  43. Barrangou, R., Fremaux, C., Deveau, H., Richards, M., Boyaval, P., Moineau, S., Romero, D. A., and Horvath, P. (2007) Science, 315, 1709–1712.

    Article  PubMed  CAS  Google Scholar 

  44. Marraffini, L. A., and Sontheimer, E. J. (2010) Nat. Rev. Genet., 11, 181–190.

    Article  PubMed  CAS  Google Scholar 

  45. Winker, S., and Woese, C. R. (1991) Syst. Appl. Microbiol., 14, 305–310.

    Article  PubMed  CAS  Google Scholar 

  46. Barns, S. M., Delwiche, C. F., Palmer, J. D., and Pace, N. R. (1996) Proc. Natl. Acad. Sci. USA, 93, 9188–9193.

    Article  PubMed  CAS  Google Scholar 

  47. Takai, K., and Horikoshi, K. (1999) Genetics, 152, 1285–1297.

    PubMed  CAS  Google Scholar 

  48. Brochier-Armanet, C., Boussau, B., Gribaldo, S., and Forterre, P. (2008) Nat. Rev. Microbiol., 6, 245–252.

    Article  PubMed  CAS  Google Scholar 

  49. 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., Gollabgir, A., Hemp, J., Hugler, M., Karr, E. A., Konneke, M., Shin, M., Lawton, T. J., Lowe, T., Martens-Habbena, W., Sayavedra-Soto, L. A., Lang, D., Sievert, S. M., Rosenzweig, A. C., Manning, G., and Stahl, D.A. (2010) Proc. Natl. Acad. Sci. USA, 107, 8818–8823.

    Article  PubMed  CAS  Google Scholar 

  50. Spang, A., Hatzenpichler, R., Brochier-Armanet, C., Rattei, T., Tischler, P., Spieck, E., Streit, W., Stahl, D. A., Wagner, M., and Schleper, C. (2010) Trends Microbiol., 18, 331–340.

    Article  PubMed  CAS  Google Scholar 

  51. Woese, C. R., Kandler, O., and Wheelis, M. L. (1990) Proc. Natl. Acad. Sci. USA, 87, 4576–4579.

    Article  PubMed  CAS  Google Scholar 

  52. Brock, T. D., Brock, K. M., Belly, R. T., and Weiss, R. L. (1972) Arch. Microbiol., 84, 54–68.

    CAS  Google Scholar 

  53. Kletzin, A. (2007) in Archaea: Molecular and Cellular Biology (Cavicchioli R., ed.) ASM Press Washington, USA, pp. 14–93.

    Google Scholar 

  54. Stetter, K. O. (1996) FEMS Microbiol. Rev., 18, 149–158.

    Article  CAS  Google Scholar 

  55. Bonch-Osmolovskaya, E. A. (1994) FEMS Microbiol. Rev., 15, 65–77.

    Article  CAS  Google Scholar 

  56. Mardanov, A. V., Gumerov, V. M., Beletsky, A. V., Prokofeva, M. I., Bonch-Osmolovskaya, E. A., Ravin, N. V., and Skryabin, K. G. (2011) J. Bacteriol., 193, 3156–3157.

    Article  PubMed  CAS  Google Scholar 

  57. Siebers, B., Zaparty, M., Raddatz, G., Tjaden, B., Albers, S. V., Bell, S. D., Blombach, F., Kletzin, A., Kyrpides, N., Lanz, C., Plagens, A., Rampp, M., Rosinus, A., von Jan, M., Makarova, K. S., Klenk, H. P., Schuster, S. C., and Hensel, R. (2011) PLoS One, 6, e24222.

    Article  PubMed  CAS  Google Scholar 

  58. Selig, M., and Schonheit, P. (1994) Arch. Microbiol., 162, 286–294.

    Article  CAS  Google Scholar 

  59. Fitz-Gibbon, S. T., Ladner, H., Kim, U. J., Stetter, K. O., Simon, M. I., and Miller, J. H. (2002) Proc. Natl. Acad. Sci. USA, 99, 984–989.

    Article  PubMed  CAS  Google Scholar 

  60. Mardanov, A. V., Gumerov, V. M., Slobodkina, G. B., Beletsky, A. V., Bonch-Osmolovskaya, E. A., Ravin, N. V., and Skryabin, K. G. (2012) J. Bacteriol., 194, 727–728.

    Article  PubMed  CAS  Google Scholar 

  61. Cozen, A. E., Weirauch, M. T., Pollard, K. S., Bernick, D. L., Stuart, J. M., and Lowe, T. M. (2009) J. Bact., 191, 782–794.

    Article  PubMed  CAS  Google Scholar 

  62. Kawarabayasi, Y., Hino, Y., Horikawa, H., Yamazaki, S., Haikawa, Y., Jin-no, K., Takahashi, M., Sekine, M., Baba, S., Ankai, A., Kosugi, H., Hosoyama, A., Fukui, S., Nagai, Y., Nishijima, K., Nakazawa, H., Takamiya, M., Masuda, S., Funahashi, T., Tanaka, T., Kudoh, Y., Yamazaki, J., Kushida, N., Oguchi, A., Aoki, K., Kubota, K., Nakamura, Y., Nomura, N., Sako, Y., and Kikuchi, H. (1999) DNA Res., 6, 83–101.

    Article  PubMed  CAS  Google Scholar 

  63. Ravin, N. V., Mardanov, A. V., Beletsky, A. V., Kublanov, I. V., Kolganova, T. V., Lebedinsky, A. V., Chernyh, N. A., Bonch-Osmolovskaya, E. A., and Skryabin, K. G. (2009) J. Bacteriol., 191, 2371–2379.

    Article  PubMed  CAS  Google Scholar 

  64. Anderson, I. J., Dharmarajan, L., Rodriguez, J., Hooper, S., Porat, I., Ulrich, L. E., Elkins, J. G., Mavromatis, K., Sun, H., Land, M., Lapidus, A., Lucas, S., Barry, K., Huber, H., Zhulin, I. B., Whitman, W. B., Mukhopadhyay, B., Woese, C., Bristow, J., and Kyrpides, N. (2009) BMC Genomics, 10, 145.

    Article  PubMed  CAS  Google Scholar 

  65. Paper, W., Jahn, U., Hohn, M. J., Kronner, M., Nather, D. J., Burghardt, T., Rachel, R., Stetter, K. O., and Huber, H. (2007) Int. J. Syst. Evol. Microbiol., 57, 803–808.

    Article  PubMed  CAS  Google Scholar 

  66. Podar, M., Anderson, I., Makarova, K. S., Elkins, J. G., Ivanova, N., Wall, M. A., Lykidis, A., Mavromatis, K., Sun, H., Hudson, M. E., Chen, W., Deciu, C., Hutchison, D., Eads, J. R., Anderson, A., Fernandes, F., Szeto, E., Lapidus, A., Kyrpides, N. C., Saier, M. H., Jr., Richardson, P. M., Rachel, R., Huber, H., Eisen, J. A., Koonin, E. V., Keller, M., and Stetter, K. O. (2008) Genome Biol., 9, R158.

    Article  PubMed  CAS  Google Scholar 

  67. Prokofeva, M. I., Kostrikina, N. A., Kolganova, T. V., Tourova, T. P., Lysenko, A. M., Lebedinsky, A. V., and Bonch-Osmolovskaya, E. A. (2009) Int. J. Syst. Evol. Microbiol., 59, 3116–3122.

    Article  PubMed  CAS  Google Scholar 

  68. Mardanov, A. V., Svetlitchnyi, V. A., Beletsky, A. V., Prokofeva, M. I., Bonch-Osmolovskaya, E. A., Ravin, N. V., and Skryabin, K. G. (2010) Appl. Environ. Microbiol., 76, 5652–5657.

    Article  PubMed  CAS  Google Scholar 

  69. Brochier-Armanet, C., Forterre, P., and Gribaldo, S. (2011) Curr. Opin. Microbiol., 14, 274–281.

    Article  PubMed  Google Scholar 

  70. Perevalova, A. A., Bidzhieva, S., Kublanov, I. V., Hinrichs, K. U., Liu, X. L., Mardanov, A. V., Lebedinsky, A. V., and Bonch-Osmolovskaya, E. A. (2010) Int. J. Syst. Evol. Microbiol., 60, 2082–2088.

    Article  PubMed  Google Scholar 

  71. Bertoldo, C., and Antranikian, G. (2006) in The Prokaryotes, 3rd Edn (M. Dworkin, S. Falkow, E. Rosenberg, K.-H. Schleifer, and E. Stackebrandt, eds.) Springer-Verlag, New York, Vol. 3, pp. 69–81.

    Chapter  Google Scholar 

  72. Klenk, H. P., Clayton, R. A., Tomb, J. F., White, O., Nelson, K. E., Ketchum, K. A., Dodson, R. J., Gwinn, M., Hickey, E. K., Peterson, J. D., Richardson, D. L., Kerlavage, A. R., Graham, D. E., Kyrpides, N. C., Fleischmann, R. D., Quackenbush, J., Lee, N. H., Sutton, G. G., Gill, S., Kirkness, E. F., Dougherty, B. A., McKenney, K., Adams, M. D., Loftus, B., Peterson, S., Reich, C. I., McNeil, L. K., Badger, J. H., Glodek, A., Zhou, L., Overbeek, R., Gocayne, J. D., Weidman, J. F., McDonald, L., Utterback, T., Cotton, M. D., Spriggs, T., Artiach, P., Kaine, B. P., Sykes, S. M., Sadow, P. W., D’Andrea, K. P., Bowman, C., Fujii, C., Garland, S. A., Mason, T. M., Olsen, G. J., Fraser, C. M., Smith, H. O., Woese, C. R., and Venter, J. C. (1997) Nature, 390, 364–370.

    Article  PubMed  CAS  Google Scholar 

  73. Gumerov, V. M., Mardanov, A. V., Beletsky, A. V., Prokofeva, M. I., Bonch-Osmolovskaya, E. A., Ravin, N. V., and Skryabin, K. G. (2011) J. Bacteriol., 193, 2355–2356.

    Article  PubMed  CAS  Google Scholar 

  74. Kurr, M., Huber, R., Konig, H., Jannasch, H. W., Fricke, H., Trincone, A., Krstjansson, J. K., and Stetter, K. O. (1991) Arch. Microbiol., 156, 239–247.

    Article  CAS  Google Scholar 

  75. Oren, A. (2006) in The Prokaryotes (Dworkin, M., ed.) Springer, 3, 113–164.

  76. Sayeh, R., Birrien, J. L., Alain, K., Barbier, G., Hamdi, M., and Prieur, D. (2010) Extremophiles, 14, 501–514.

    Article  PubMed  CAS  Google Scholar 

  77. Golyshina, O. V., Pivovarova, T. A., Karavaiko, G. I., Kondrat’eva, T. F., Moore, E. R. B., Abraham, W. R., Lunsdorf, H., Timmis, K. N., Yakimov, M. M., and Golyshin, P. N. (2000) Int. J. Syst. Evol. Microbiol., 50, 997–1006.

    Article  PubMed  CAS  Google Scholar 

  78. Sorensen, K. B., and Teske, A. (2006) Appl. Environ. Microbiol., 72, 4596–4603.

    Article  PubMed  CAS  Google Scholar 

  79. Teske, A., and Sorensen, K. B. (2008) ISME J., 2, 3–18.

    Article  PubMed  CAS  Google Scholar 

  80. Schleper, C. (2007) Archaea: Evolution, Physiology, and Molecular Biology (Garrett, R., and Hans-Peter Klenk, H.-P., eds.) Blackwell Publishing Ltd.

  81. Reigstad, L. J., Jorgensen, S. L., and Schleper, C. (2010) ISME J., 4, 346–356.

    Article  PubMed  CAS  Google Scholar 

  82. Gumerov, V. M., Mardanov, A. V., Beletsky, A. V., Bonch-Osmolovskaya, E. A., and Ravin, N. V. (2011) Mikrobiologiya, 80, 258–265.

    CAS  Google Scholar 

  83. Nunoura, T., Hirayama, H., Takami, H., Oida, H., Nishi, S., Shimamura, S., Suzuki, Y., Inagaki, F., Takai, K., Nealson, K. H., and Horikoshi, K. (2005) Environ. Microbiol., 7, 1967–1984.

    Article  PubMed  CAS  Google Scholar 

  84. Kim, B. K., Jung, M. Y., Yu, D. S., Park, S. J., Oh, T. K., Rhee, S. K., and Kim, J. F. (2011) J. Bacteriol., 193, 5539–5540.

    Article  PubMed  CAS  Google Scholar 

  85. Konneke, M., Bernhard, A. E., de la Torre, J. R., Walker, C. B., Waterbury, J. B., and Stahl, D. A. (2005) Nature, 437, 543–546.

    Article  PubMed  CAS  Google Scholar 

  86. Schleper, C., and Nicol, G. W. (2010) Adv. Microb. Physiol., 57, 1–41.

    Article  PubMed  CAS  Google Scholar 

  87. Wuchter, C., Abbas, B., Coolen, M. J., Herfort, L., van Bleijswijk, J., Timmers, P., Strous, M., Teira, E., Herndl, G. J., Middelburg, J. J., Schouten, S., and Sinninghe Damste, J. S. (2006) Proc. Natl. Acad. Sci. USA, 103, 12317–12322.

    Article  PubMed  CAS  Google Scholar 

  88. Hallam, S. J., Putnam, N., Preston, C. M., Detter, J. C., Rokhsar, D., Richardson, P. M., and DeLong, E. F. (2004) Science, 305, 1457–1462.

    Article  PubMed  CAS  Google Scholar 

  89. Reysenbach, A.-L., Liu, Y., Banta, A. B., Beveridge, T. J., Kirshtein, J. D., Schouten, S., Tivey, M. K., von Damm, K. L., and Voytek, M. A. (2006) Nature, 442, 444–447.

    Article  PubMed  CAS  Google Scholar 

  90. Reysenbach, A. L., and Flores, G. E. (2008) Geobiology, 6, 331–336.

    Article  PubMed  CAS  Google Scholar 

  91. Huber, H., Hohn, M. J., Rachel, R., Fuchs, T., Wimmer, V. C., and Stetter, K. O. (2002) Nature, 417, 63–67.

    Article  PubMed  CAS  Google Scholar 

  92. Hohn, M. J., Hedlund, B. P., and Huber, H. (2002) Syst. Appl. Microbiol., 25, 551–554.

    Article  PubMed  CAS  Google Scholar 

  93. McCliment, E. A., Voglesonger, K. M., O’Day, P. A., Dunn, E. E., Holloway, J. R., and Cary, S. C. (2006) Environ. Microbiol., 8, 114–125.

    Article  PubMed  CAS  Google Scholar 

  94. Casanueva, A., Galada, N., Baker, G. C., Grant, W. D., Heaphy, S., Jones, B., Yanhe, M., Ventosa, A., Blamey, J., and Cowan, D. A. (2008) Extremophiles, 12, 651–656.

    Article  PubMed  CAS  Google Scholar 

  95. Waters, E., Hohn, M. J., Ahel, I., Graham, D. E., Adams, M. D., Barnstead, M., Beeson, K. Y., Bibbs, L., Bolanos, R., Keller, M., Kretz, K., Lin, X., Mathur, E., Ni, J., Podar, M., Richardson, T., Sutton, G. G., Simon, M., Soil, D., Stetter, K. O., Short, J. M., and Noordewier, M. (2003) Proc. Natl. Acad. Sci. USA, 100, 12984–12988.

    Article  PubMed  CAS  Google Scholar 

  96. Di Giulio, M. (2007) Gene, 401, 108–113.

    Article  PubMed  CAS  Google Scholar 

  97. Makarova, K. S., and Koonin, E. V. (2005) Curr. Opin. Microbiol., 117, 52–67.

    Google Scholar 

  98. Brochier, C., Forterre, P., and Gribaldo, S. (2005) BMC Evol. Biol., 5, 36.

    Article  PubMed  CAS  Google Scholar 

  99. Forterre, P., Gribaldo, S., and Brochier-Armanet, C. (2009) J. Biol., 8, 7.

    Article  PubMed  CAS  Google Scholar 

  100. Fujishima, K., Sugahara, J., Kikuta, K., Hirano, R., Sato, A., Tomita, M., and Kanai, A. (2009) Proc. Natl. Acad. Sci. USA, 106, 2683–2687.

    Article  PubMed  CAS  Google Scholar 

  101. Baker, B. J., Tyson, G. W., Webb, R. I., Flanagan, J., Hugenholtz, P., Allen, E. E., and Banfield, J. F. (2006) Science, 314, 1933–1935.

    Article  PubMed  CAS  Google Scholar 

  102. Narasingarao, P., Podell, S., Ugalde, J. A., Brochier-Armanet, C., Emerson, J. B., Brocks, J. J., Heidelberg, K. B., Banfield, J. F., and Allen, E. E. (2012) ISME J., 6, 81–93.

    Article  PubMed  CAS  Google Scholar 

  103. Cohen, G. N., Barbe, V., Flament, D., Galperin, M., Heilig, R., Lecompte, O., Poch, O., Prieur, D., Querellou, J., Ripp, R., Thierry, J. C., van der Oost, J., Weissenbach, J., Zivanovic, Y., and Forterre, P. (2003) Mol. Microbiol., 47, 1495–1512.

    Article  PubMed  CAS  Google Scholar 

  104. Kawarabayasi, Y., Sawada, M., Horikawa, H., Haikawa, Y., Hino, Y., Yamamoto, S., Sekine, M., Baba, S., Kosugi, H., Hosoyama, A., Nagai, Y., Sakai, M., Ogura, K., Otsuka, R., Nakazawa, H., Takamiya, M., Ohfuku, Y., Funahashi, T., Tanaka, T., Kudoh, Y., Yamazaki, J., Kushida, N., Oguchi, A., Aoki, K., and Kikuchi, H. (1998) DNA Res., 5, 147–155.

    Article  PubMed  CAS  Google Scholar 

  105. Zivanovic, Y., Lopez, P., Philippe, H., and Forterre, P. (2002) Nucleic Acids Res., 30, 1902–1910.

    Article  PubMed  CAS  Google Scholar 

  106. Brugger, K., Torarinsson, E., Redder, P., Chen, L., and Garrett, R. A. (2004) Biochem. Soc. Trans., 32, 179–183.

    Article  PubMed  CAS  Google Scholar 

  107. Robb, F. T., Maeder, D. L., Brown, J. R., DiRuggiero, J., Stump, M. D., Yeh, R. K., Weiss, R. B., and Dunn, D. M. (2001) Methods Enzymol., 330, 134–157.

    Article  PubMed  CAS  Google Scholar 

  108. Lake, J. A., Henderson, E., Oakes, M., and Clark, M. W. (1984) Proc. Natl. Acad. Sci. USA, 81, 3786–3790.

    Article  PubMed  CAS  Google Scholar 

  109. Makarova, K. S., Aravind, L., Galperin, M. Y., Grishin, N. V., Tatusov, R. L., Wolf, Y. I., and Koonin, E. V. (1999) Genome Res., 9, 608–628.

    PubMed  CAS  Google Scholar 

  110. Galagan, J. E., Nusbaum, C., Roy, A., Endrizzi, M. G., Macdonald, P., FitzHugh, W., Calvo, S., Engels, R., Smirnov, S., Atnoor, D., Brown, A., Allen, N., Naylor, J., Stange-Thomann, N., DeArellano, K., Johnson, R., Linton, L., McEwan, P., McKernan, K., Talamas, J., Tirrell, A., Ye, W., Zimmer, A., Barber, R. D., Cann, I., Graham, D. E., Grahame, D. A., Guss, A. M., Hedderich, R., Ingram-Smith, C., Kuettner, H. C., Krzycki, J. A., Leigh, J. A., Li, W., Liu, J., Mukhopadhyay, B., Reeve, J. N., Smith, K., Springer, T. A., Umayam, L. A., White, O., White, R. H., Conway de Macario, E., Ferry, J. G., Jarrell, K. F., Jing, H., Macario, A. J., Paulsen, I., Pritchett, M., Sowers, K. R., Swanson, R. V., Zinder, S. H., Lander, E., Metcalf, W. W., and Birren, B. (2002) Genome Res., 12, 532–542.

    Article  PubMed  CAS  Google Scholar 

  111. Diruggiero, J., Dunn, D., Maeder, D. L., Holley-Shanks, R., Chatard, J., Horlacher, R., Robb, F. T., Boos, W., and Weiss, R. B. (2000) Mol. Microbiol., 38, 684–693.

    Article  PubMed  CAS  Google Scholar 

  112. Mardanov, A. V., Ravin, N. V., Svetlitchnyi, V. A., Beletsky, A. V., Miroshnichenko, M. L., Bonch-Osmolovskaya, E. A., and Skryabin, K. G. (2009) Appl. Environ. Microbiol., 75, 4580–4588.

    Article  PubMed  CAS  Google Scholar 

  113. Futterer, O., Angelov, A., Liesegang, H., Gottschalk, G., Schleper, C., Schepers, B., Dock, C., Antranikian, G., and Liebl, W. (2004) Proc. Natl. Acad. Sci. USA, 101, 9091–9096.

    Article  PubMed  CAS  Google Scholar 

  114. Ruepp, A., Graml, W., Santos-Martinez, M. L., Koretke, K. K., Volker, C., Mewes, H. W., Frishman, D., Stocker, S., Lupas, A. N., and Baumeister, W. (2000) Nature, 407, 508–513.

    Article  PubMed  CAS  Google Scholar 

  115. Pina, M., Bize, A., Forterre, P., and Prangishvili, D. (2011) FEMS Microbiol. Rev., 35, 1035–1054.

    Article  PubMed  CAS  Google Scholar 

  116. Haring, M., Peng, X., Brugger, K., Rachel, R., Stetter, K. O., Garrett, R. A., and Prangishvili, D. (2004) Virology, 323, 233–242.

    Article  PubMed  CAS  Google Scholar 

  117. Cortez, D., Forterre, P., and Gribaldo, S. (2009) Genome Biol., 10, 65.

    Article  CAS  Google Scholar 

  118. Lindas, A. C., Karlsson, E. A., Lindgren, M. T., Ettema, T. J., and Bernander, R. (2008) Proc. Natl. Acad. Sci. USA, 105, 18942–18946.

    Article  PubMed  CAS  Google Scholar 

  119. Csuros, M., and Miklos, I. (2009) Mol. Biol. Evol., 26, 2087–2095.

    Article  PubMed  CAS  Google Scholar 

  120. Leigh, J. A., Albers, S. V., Atomi, H., and Allers, T. (2011) FEMS Microbiol. Rev., 35, 577–608.

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Laboratory of Molecular Cloning, Centre “Bioengineering”, Russian Academy of Sciences, pr. 60-let Oktyabrya 7-1, 117312, Moscow, Russia

    A. V. Mardanov & N. V. Ravin

Authors
  1. A. V. Mardanov
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. N. V. Ravin
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to N. V. Ravin.

Additional information

Original Russian Text © A. V. Mardanov, N. V. Ravin, 2012, published in Biokhimiya, 2012, Vol. 77, No. 8, pp. 965–980.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Mardanov, A.V., Ravin, N.V. The impact of genomics on research in diversity and evolution of archaea. Biochemistry Moscow 77, 799–812 (2012). https://doi.org/10.1134/S0006297912080019

Download citation

  • Received:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1134/S0006297912080019

Key words

Search

Navigation