Quantitative exploration of the occurence of lateral gene transfer by using nitrogen fixation gene as a case study

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

Volumn 103, Issue 25, 2006, Pages 9584-9589

  Kechris, Katherina J ^a,c   Lin, Jason C ^b   Bickel, Peter J ^b   Glazer, Alexander N ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF COLORADO   (United States)

Author keywords

Blast; Codon usage; Horizontal gene transfer; Phylogeny

Indexed keywords

AMMONIA; NITROGENASE; RNA 16S;

ARTICLE; CODON; ENZYME MECHANISM; GENE IDENTIFICATION; GENE LOSS; GENOME; HORIZONTAL GENE TRANSFER; MOLECULAR EVOLUTION; NITROGEN FIXATION; NONHUMAN; PHYLOGENETIC TREE; PRIORITY JOURNAL; PROKARYOTE; QUANTITATIVE ANALYSIS; BIOLOGY; GENETICS; PHYLOGENY;

LANGAT VIRUS; PROKARYOTA;

CODON; COMPUTATIONAL BIOLOGY; GENE TRANSFER, HORIZONTAL; NITROGEN FIXATION; PHYLOGENY; RNA, RIBOSOMAL, 16S;

EID: 33745447005     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0603534103     Document Type: Article

References (39)

1. Koonin, E. V., Makarova, K. S. & Aravind, L. (2001) Annu. Rev. Microbiol. 55, 709-742.
2. Syvanen, M. & Kado, C. I., eds. (2002) Horizontal Gene Transfer (Academic, London), 2nd Ed.
3. Kurland, C. G., Canback, B. & Berg, O. G. (2003) Proc. Natl. Acad. Sci. USA 100, 9658-9662.
4. Kurland, C. G. (2005) BioEssays 27, 741-747.
5. Eisen, J. A. (2000) Curr. Opin. Genet. Dev. 10, 606-611.
6. Raymond, J., Zhaxybayeva, O., Gogarten, J. P., Gerdes, S. & Blankenship, R. E. (2002) Science 298, 1616-1620.
7. Archibald, J. M., Rogers, M., Toop, M., Ishida, K. & Keeling, P. J. (2003) Proc. Natl. Acad. Sci. USA 100, 7678-7683.
8. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. (1990) J. Mol. Biol. 215, 403-410.
9. Rivera, M. C., Jain, R., Moore, J. E. & Lake, J. A. (1998) Proc. Natl. Acad. Sci. USA 95, 6239-6244.
10. 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., Ketchum, K. A., et al. (1999) Nature 399, 323-329.
11. Mrazek, J. & Karlin, S. (1999) Ann. N.Y. Acad. Sci. 18, 314-329.
12. Young, J. P. W. (1999) in Nitrogen Fixation: From Molecules to Crop Productivity, eds. Pedrosa, F. O., Hungria, M., Yates, M. G. & Newton, W. E. (Kluwer-Academic, London), pp. 161-164.
13. Leigh, J. A. (2000) Curr. Issues. Mol. Biol. 2, 125-131.
14. Boucher, Y., Christophe, J., Douady, R., Papke, T., Walsh, D. A., Boudreau, M. R., Nesbø, C. L., Case, R. J. & Doolittle, W. F. (2003) Annu. Rev. Genet. 37, 283-328.
15. Genereux, D. P. & Logsdon, J. M. (2003) Trends Genet. 19, 191-195.
16. Koski, L. B. & Golding, G. B. (2001) J. Mol. Evol. 52, 540-542.
17. Dzidic, S. & Bedekovic, V. (2003) Acta Pharmacol. Sin. 24, 519-526.
18. Bonnet, R. (2004) Antimicrob. Agents Chemother. 48, 1-14.
19. Jain, R., Rivera, M. C. & Lake, J. A. (1999) Proc. Natl. Acad. Sci. USA 96, 3801-3806.
20. Woese, C. R. (1990) Science 247, 789.
21. Farahi, K., Pusch, G. D., Overbeek, R. & Whitman, W. B. (2004) J. Mol. Evol. 58, 615-631.
22. Woese, C. R., Kandler, O. & Wheelis, M. L. (1990) Proc. Natl. Acad. Sci. USA 87, 4576-4579.
23. Doolittle, W. F. (1999) Science 286, 2124-2128.
24. Gutell, R. R., Lee, J. C. & Cannone, J. J. (2002) Curr. Opin. Struct. Biol. 12, 301-310.
25. Wolf, Y. I., Rogozin, I. B., Grishin, N. V., Tatusov, R. L. & Koonin, E. V. (2001) BMC Evol. Biol. 1, 8.
26. van Berkum, P., Terefework, Z., Paulin, L., Suomalainen, S., Lindstrom, K. & Eardly, B. D. (2003) J. Bacteriol. 185, 2988-2998.
27. Breiman, L. (2001) Mach. Learn. 45, 5-32.
28. Bickel, P. J., Kechris, K. J., Spector, P. C., Wedemayer, G. J. & Glazer, A. N. (2002) Proc. Natl. Acad. Sci. USA 99, 14764-14771.
29. Eady, R. R. (1996) Chem. Rev. 96, 3013-3030.
30. Howard, J. B. & Rees, D. C. (1996) Chem. Rev. 96, 2965-2982.
31. Raymond, J., Siefert, J., Staples, C. & Blankenship, R. E. (2004) Mol. Biol. Evol. 21, 541-554.
32. Rubio, L. M. & Ludden, P. W. (2005) J. Bacteriol. 187, 405-414.
33. Anbar, A. D. & Knoll, A. H. (2002) Science 297, 1137-1142.
34. Newton, W. (2000) in Prokaryotic Nitrogen Fixation: A Model System for the Analysis of a Biological Process, ed. Triplett, W. (Springer, New York), pp. 3-8.
35. Miller, R. V. & Day, M. J., eds. (2004) Microbial Evolution: Gene Establishment, Survival, and Exchange (Am. Soc. Microbiol., Washington, DC).
36. Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994) Nucleic Acids Res. 22, 4673-4680.
37. Peden, J. (1999) Ph.D. thesis (Univ. of Nottingham, Nottingham, U.K.).
38. Sharp, P. M., Tuohy, T. M. F. & Mosurski, K. R. (1986) Nucleic Acids Res. 14, 5125-5143.
39. Felsenstein, J. (1989) Cladistics 5, 164-166.