The genome of Nanoarchaeum equitans: Insights into early archaeal evolution and derived parasitism

Proceedings of the National Academy of Sciences of the United States of America

Volumn 100, Issue 22, 2003, Pages 12984-12988

  Waters, Elizabeth ^a,b   Hohn, Michael J ^c   Ahel, Ivan ^e   Graham, David E ^f   Adams, Mark D ^d   Barnstead, Mary ^d   Beeson, Karen Y ^d   Bibbs, Lisa ^a   Bolanos, Randall ^d   Keller, Martin ^a   Kretz, Keith ^a   Lin, Xiaoying ^d   Mathur, Eric ^a   Ni, Jingwei ^d   Podar, Mircea ^a   Richardson, Toby ^a   Sutton, Granger G ^d   Simon, Melvin ^a   Söll, Dieter ^e   Stetter, Karl O ^a,c   Short, Jay M ^a   Noordewier, Michiel ^a   more..

^a DIVERSA CORPORATION   (United States)

^b SAN DIEGO STATE UNIVERSITY   (United States)

^c UNIVERSITY OF REGENSBURG   (Germany)

^d CELERA GENOMICS   (United States)

^e YALE UNIVERSITY   (United States)

^f UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; BACTERIAL DNA; BACTERIAL RNA; LIPID; NUCLEOTIDE; RIBOSOME PROTEIN; RIBOSOME RNA;

AMINO ACID SYNTHESIS; ARCHAEBACTERIUM; ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; BASE PAIRING; CATABOLISM; COCULTURE; CRENARCHAEOTA; DNA SEQUENCE; GENETIC CODE; GENOME SIZE; IGNICOCCUS; MOLECULAR EVOLUTION; NANOARCHAEOTA; NANOARCHAEUM EQUITANS; NONHUMAN; NUCLEOTIDE METABOLISM; PARASITE; PARASITISM; PHYLOGENY; PREDICTION; PRIORITY JOURNAL; PSEUDOGENE; SYMBIONT; SYMBIOSIS;

NON-PROGRAMMATIC;

ARABIDOPSIS; ARCHAEA; DNA, ARCHAEAL; EVOLUTION; GENE LIBRARY; GENOME, ARCHAEAL; PHYLOGENY;

ARCHAEA; BACTERIA (MICROORGANISMS); CRENARCHAEOTA; IGNICOCCUS; NANOARCHAEOTA; NANOARCHAEUM EQUITANS;

EID: 0242300069     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.1735403100     Document Type: Article

References (53)

1. Huber, H., Hohn, M. J., Rachel, R., Fuchs, T., Wimmer, V. C. & Stetter, K. O. (2002) Nature 417, 63-67.
2. Boucher, Y. & Doolittle, W. F. (2002) Nature 417, 27-28.
3. Huber, H., Hohn, M. J., Stetter, K. O. & Rachel, R. (2003) Res. Microbiol. 154, 165-171.
4. Silva, F. J., Latorre, A. & Moya, A. (2001) Trends Genet. 17, 615-618.
5. Ochman, H., Lawrence, J. G. & Groisman, E. A. (2000) Nature 405, 299-304.
6. Zhou, J., Bruns, M. A. & Tiedje, J. M. (1996) Appl. Environ. Microbiol. 62, 316-322.
7. Robertson, D. E., Mathur, E. M., Swanson, R. V., Marrs, B. L. & Short, J. M. (1996) Soc. Indust. Microbiol. News 46, 3-8.
8. Short, J. M. (1997) Nat. Biotechnol. 15, 1322-1323.
9. Adams, M. D., Celniker, S. E., Holt, R. A., Evans, C. A., Gocayne, J. D., Amanatides, P. G., Scherer, S. E., Li, P. W., Hoskins, R. A., Galle, R. F., et al. (2000) Science 287, 2185-2195.
10. Myers, E. W., Sutton, G. G., Delcher, A. L., Dew, I. M., Fasulo, D. P., Flanigan, M. J., Kravitz, S. A., Mobarry, C. M., Reinert, K. H., Remington, K. A., et al. (2000) Science 287, 2196-2204.
11. Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., Holt, R. A., et al. (2001) Science 291, 1304-1351.
12. Delcher, A. L., Harmon, D., Kasif, S., White, O. & Salzberg, S. L. (1999) Nucleic Acids Res. 27, 4636-4641.
13. Badger, J. H. & Olsen, G. J. (1998) Mol. Biol. Evol. 16, 512-524.
14. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. (1997) Nucleic Acids Res. 25, 3389-3402.
15. Apweiler, R., Attwood, T. K., Bairoch, A., Bateman, A., Birney, E., Biswas, M., Bucher, P., Cerutti, L., Corpet, F., Croning, M. D., et al. (2001) Nucleic Acids Res. 29, 37-40.
16. Tatusov, R. L., Natale, D. A., Garkavtsev, I. V., Tatusova, T. A., Shankavaram, U. T., Rao, B. S., Kiryutin, B., Galperin, M. Y., Fedorova, N. D. & Koonin, E. V. (2001) Nucleic Acids Res. 29, 22-28.
17. Perler, F. B. (2002) Nucleic Acids Res. 30, 383-384.
18. Lowe, T. M. & Eddy, S. R. (1997) Nucleic Acids Res. 25, 955-964.
19. Tsui, V., Macke, T. & Case, D. A. (2003) RNA 9, 507-517.
20. Eddy, S. R. (2003) HMMER (Washington University, St. Louis), Version 2.3.1.
21. Omer, A. D., Lowe, T. M., Russell, A. G., Ebhardt, H., Eddy, S. R. & Dennis, P. P. (2000) Science 288, 517-522.
22. Ahel, I., Stathopoulos, C., Ambrogelly, A., Sauerwald, A., Toogood, H., Hartsch, T. & Söll, D. (2002) J. Biol. Chem. 277, 34743-34748.
23. Matte-Tailliez, O., Brochier, C., Forterre, P. & Philippe, H. (2002) Mol. Biol. Evol. 19, 631-639.
24. Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994) Nucleic Acids Res. 22, 4673-4680.
25. Hall, T. (1999) Nucleic Acids Symp. Ser. 41, 95-98.
26. Lyons-Weiler, J., Hoelzer, G. A. & Tausch, R. J. (1996) Mol. Biol. Evol. 13, 749-757.
27. Felsenstein, J. (2001) PHYLIP: Phylogeny Inference Package (Department of Genetics, University of Washington, Seattle), Version 3.6a2.1.
28. Huelsenbeck, J. P. & Ronquist, F. (2001) Bioinformatics 17, 754-755.
29. Swofford, D. (1996) PAUP*: Phylogenic Analysis Using Parsimony (* and Other Methods) (Sinauer, Sunderland, MA), Version 4.0b.
30. Tareas, I., Klasson, L., Canback, B., Näslund, A. K., Eriksson, A.-S., Wernegreen, J. J., Sandström, J. P., Moran, N. A. & Andersson, S. G. E. (2002) Science 296, 2376-2379.
31. Graham, D. E., Overbeek, R., Olsen, G. J. & Woese, C. R. (2000) Proc. Natl. Acad. Sci. USA 97, 3304-3308.
32. Klein, R. J., Misulovin, Z. & Eddy, S. R. (2002) Proc. Natl. Acad. Sci. USA 99, 7542-7547.
33. Wächtershäuser, G. (1998) Syst. Appl. Microbiol. 187, 483-494.
34. Lingl, A., Huber, H., Stetter, K. O., Mayer, F., Kellermann, J. & Müller, V. (2003) Extremophiles 7, 249-257.
35. Tumbula, D. L., Becker, H. D., Chang, W.-Z. & Söll, D. (2000) Nature 407, 106-110.
36. Huber, H., Burggraf, S., Mayer, T., Wyschkony, I., Rachel, R. & Stetter, K. O. (2000) Int. J. Syst. Evol. Microbiol. 50, 2093-2100.
37. Moran, N. A. (1996) Proc. Natl. Acad. Sci. USA 93, 2873-2878.
38. Lykke-Andersen, J. & Garrett, R. A. (1997) EMBO J. 16, 6290-6300.
39. Kleman-Leyer, K., Armbruster, D. W. & Daniels, C. J. (1997) Cell 89, 839-847.
40. Andachi, Y., Yamao, F., Muto, A. & Osawa, S. (1989) J. Mol. Biol. 209, 37-54.
41. Burbaum, J. J. & Schimmel, P. (1991) Biochemistry 30, 319-324.
42. Wu, H., Hu, Z. & Liu, X.-Q. (1998) Proc. Natl. Acad. Sci. USA 95, 9226-9231.
43. Krah, R., Kozyavkin, S., Slesarev, A. & Gellert, M. (1996) Proc. Natl. Acad. Sci. USA 93, 106-110.
44. Forterre, P. (2002) Trends Genet. 18, 236-237.
45. Forterre, P., de la Tour, C. B., Philippe, H. & Duguet, M. (2000) Trends Genet. 16, 152-154.
46. Stetter, K. O. (1997) in Commentarii Pontificia Academica Scientiarium (Vatican City), Vol. IV, pp. 261-283.
47. Doolittle, W. F. (1978) Nature 272, 581-582.
48. Gilbert, W. (1987) Cold Spring Harbor Symp. Quant. Biol. 52, 901-905.
49. Stoltzfus, A., Logsdon, J. M., Jr., Palmer, J. D. & Doolittle, W. F. (1997) Proc. Natl. Acad. Sci. USA 94, 10739-10744.
50. Ogata, H., Audic, S., Renesto-Audiffren, P., Fournier, P.-E., Barbe, V., Samson, D., Roux, V., Cossart, P., Weissenbach, J., Claverie, J.-M., et al. (2001) Science 293, 2093-2098.
51. Andersson, J. O. & Andersson, S. G. E. (2001) Mol. Biol. Evol. 18, 829-839.
52. Hohn, M. J., Hedlund, B. P. & Huber, H. (2002) Syst. Appl. Microbiol. 25, 551-554.
53. Woese, C. (1998) Proc. Natl. Acad. Sci. USA 95, 6854-6859.