Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins

Nature

Volumn 425, Issue 6955, 2003, Pages 285-288

  Gaucher, Eric A ^a   Thomson, J Michael ^b,d   Burgan, Michelle F ^c   Benner, Steven A ^a,b,c  

^a UNIVERSITY OF FLORIDA   (United States)

^b UNIVERSITY OF FLORIDA COLLEGE OF MEDICINE   (United States)

^c NONE   (United States)

^d UNIVERSITY OF NORTH CAROLINA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIOLOGY; GENETIC ENGINEERING; PROTEINS; RNA;

MESOPHILES;

BIOCHEMISTRY;

BACTERIAL PROTEIN; CYTOSINE; ELONGATION FACTOR; ELONGATION FACTOR TU; GUANINE; RIBOSOME RNA;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENE; BACTERIUM; GENE CONSTRUCT; GEOLOGY; MOLECULAR CLOCK; MOLECULAR CLONING; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PALEOENVIRONMENT; PHYLOGENY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN FUNCTION; SEQUENCE ANALYSIS; TEMPERATURE DEPENDENCE; THERMOPHILIC BACTERIUM;

BACTERIA; BACTERIAL PROTEINS; BASE COMPOSITION; ENVIRONMENT; ENZYME STABILITY; GUANOSINE DIPHOSPHATE; MOLECULAR SEQUENCE DATA; PEPTIDE ELONGATION FACTOR TU; PHYLOGENY; PROTEIN BINDING; RNA, RIBOSOMAL; TEMPERATURE; TIME FACTORS;

BACTERIA (MICROORGANISMS);

EID: 0141828152     PISSN: 00280836     EISSN: None     Source Type: Journal    
DOI: 10.1038/nature01977     Document Type: Article

References (30)

1. Malcolm, B. A., Wilson, K. P., Matthews, B. W., Kirsch, J. F. & Wilson, A. C. Ancestral lysozymes reconstructed, neutrality tested, and thermostability linked to hydrocarbon packing. Nature 345, 86-89 (1990).
2. Stackhouse, J., Presnell, S. R., McGeehan, G. M., Nambiar, K. P. & Benner, S. A. The ribonuclease from an extinct bovid. FEBS Lett. 262, 104-106 (1990).
3. Adey, N. B., Tollefsbol, T. O., Sparks, A. B., Edgell, M. H. & Hutchison, C. A. Molecular resurrection of an extinct ancestral promoter for mouse L1. Proc. Natl Acad. Sci. USA 91, 1569-1573 (1994).
4. Jermann, T. M., Opitz, J. G., Stackhouse, J. & Benner, S. A. Reconstructing the evolutionary history of the artiodactyl ribonuclease superfamily. Nature 374, 57-59 (1995).
5. Chandrasekharan, U. M., Sanker, S., Glynias, M. J., Karnik, S. S. & Husain, A. Angiotensin II forming activity in a reconstructed ancestral chymase. Science 271, 502-505 (1996).
6. Golding, G. B. & Dean, A. M. The structural basis of molecular adaptation. Mol. Biol. Evol. 15, 355-369 (1998).
7. Miyazaki, J. et al. Ancestral residues stabilizing 3-isopropylmalate dehydrogenase of an extreme thermophile: Experimental evidence supporting the thermophilic common ancestor hypothesis. J. Biochem. 129, 777-782 (2001).
8. Chang, B. S., Jonsson, K., Kazmi, M. A., Donoghue, M. J. & Sakmar, T. P. Recreating a functional ancestral archosaur visual pigment. Mol. Biol. Evol. 19, 1483-1489 (2002).
9. Zhang, J. Z. & Rosenberg, H. F. Complementary advantageous substitutions in the evolution of an antiviral RNase of higher primates. Proc. Natl Acad. Sci. USA 99, 5486-5491 (2002).
10. Woese, C. R. Bacterial evolution. Microbiol. Rev. 51, 221-271 (1987).
11. Hugenholtz, P., Goebel, B. M. & Pace, N. R. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 180, 4765-4774 (1998).
12. Galtier, N., Tourasse, N. & Gouy, M. A nonhyperthermophilic common ancestor to extant life forms. Science 283, 220-221 (1999).
13. Cavalier-Smith, T. The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. Int. J. Syst. Evol. Microbiol. 52, 7-76 (2002).
14. Pauling, L. & Zuckerkandl, E. Chemical paleogenetics: molecular "restoration studies" of extinct forms of life. Acta Chem. Scand. A 17, S9-S16 (1963).
15. Benner, S. A., Caraco, M. D., Thomson, J. M. & Gaucher, E. A. Planetary biology-paleontological, geological, and molecular histories of life. Science 296, 864-868 (2002).
16. Arai, K.-I., Kawakita, M. & Kaziro, Y. Studies on polypeptide elongation factors from Escherichia coli. J. Biol. Chem. 37, 7029-7037 (1972).
17. Nock, S. et al. Properties of isolated domains of the elongation factor Tu from Thermus thermophilus HB8. Eur. J. Biochem. 234, 132-139 (1995).
18. Sanangelantoni, A. M., Cammarano, R. & Tiboni, O. Manipulation of the tuf gene provides clues to the localization of sequence element(s) involved in the thermal stability of Thermotoga maritima elongation factor Tu. Microbiol. 142, 2525-2532 (1996).
19. Gromiha, M. M., Oobatake, M. & Sarai, A. Important amino acid properties for enhanced thermostability from mesophilic to thermophilic proteins. Biophys. Chem. 82, 51-67 (1999).
20. Gaucher, E. A., Miyamoto, M. M. & Benner, S. A. Function-structure analysis of proteins using covarion-based evolutionary approaches: Elongation factors. Proc. Natl Acad. Sci. USA 98, 548-552 (2001).
21. Yang, Z. H., Kumar, S. & Nei, M. A new method of inference of ancestral nucleotide and amino acid sequences. Genetics 141, 1641-1650 (1995).
22. Brochier, C. & Philippe, H. Phylogeny: a non-hyperthermophilic ancestor for bacteria. Nature 417, 244 (2002).
23. Gaschen, B. et al. Diversity considerations in HIV-1 vaccine selection. Science 296, 2354-2360 (2002).
24. Kumar, S., Tamura, K. & Nei, M. MEGA-Molecular evolutionary genetics analysis software for microcomputers. Comput. Appl. Biosci. 10, 189-191 (1994).
25. Swofford, D. L. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods) Version 4.10 (Sinauer Associates, Sunderland, Massachusetts, 2002).
26. Adachi, J. & Hasegawa, M. MOLPHY version 2.3: programs for molecular phylogenetics based on maximum likelihood. Comput. Sci. Monogr. 28, 1-150 (1996).
27. Yang, Z. PAML: a program package for phylogenetic analyses by maximum likelihood. Comput. Appl. Biosci. 13, 555-556 (1999).
28. Jones, D. T., Taylor, W. R. & Thornton, J. M. The rapid generation of mutation data matrices from protein sequence. Comput. Appl. Biosci. 8, 275-282 (1992).
29. Dayhoff, M. O., Schwartz, R. M. & Orcutt, B. C. Atlas of Protein Sequence and Structure 345-358 (National Biomedical Research Foundation, Washington DC, 1978).
30. Whelan, S. & Goldman, N. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol. Biol. Evol. 18, 691-699 (2001).