Amino acid composition of genomes, lifestyles of organisms, and evolutionary trends: A global picture with correspondence analysis

Gene

Volumn 297, Issue 1-2, 2002, Pages 51-60

  Tekaia, Fredj ^a   Yeramian, Edouard ^a   Dujon, Bernard ^a  

^a INSTITUT PASTEUR   (France)

Author keywords

Amino acid composition; Evolution; Hyperthermophiles; Mesophiles; Multivariate analyses; Thermostability

Indexed keywords

ARGININE; GLUTAMIC ACID; GLUTAMINE; LYSINE; PROTEOME;

AMINO ACID COMPOSITION; ARTICLE; CORRESPONDENCE ANALYSIS; EVOLUTION; GENOME; GLOBAL CHANGE; LIFESTYLE; MULTIVARIATE ANALYSIS; NONHUMAN; ORGANISM SOCIAL GROUP; PREDICTION; PRIORITY JOURNAL; SCALE UP; TEMPERATURE; THERMOSTABILITY;

AMINO ACIDS; ANIMALS; BASE COMPOSITION; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION; GENOME; HUMANS; SPECIES SPECIFICITY; TEMPERATURE;

ARCHAEA; EUKARYOTA;

EID: 0037019808     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0378-1119(02)00871-5     Document Type: Article

References (30)

1. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:1997;3389-3402.
2. Argos P., Rossmann M.G., Grau U.M., Zuber H., Frank G., Tratschin J.D. Structural comparisons of heme binding proteins. Biochemistry. 18:1979;5698-5703.
3. Benzecri J.-P. L'analyse des données. L'Analyse des Correspondances. 1973;Dunod, Paris, France.
4. Cambillau C., Claverie J.M. Structural and genomic correlates of hyperthermostability. J. Biol. Chem. 275:2000;32383-32386.
5. Cole S.T., et al. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature. 393:1998;537-544.
6. Deckert G., et al. The complete genome of the hyperthermophilic bacterium Aquifex aeolicus. Nature. 392:1998;353-358.
7. Deming J.W. Psychrophiles and polar regions. Curr. Opin. Microbiol. 5:2002;301-309.
8. Fellenberg K., Hauser N.C., Brors B., Neutzner A., Hoheisel J.D., Vingron M. Correspondence analysis applied to microarray data. Proc. Natl. Acad. Sci. USA. 98:2001;10781-10786.
9. Forterre P. A hot topic: the origin of hyperthermophiles. Cell. 85:1996;475-480.
10. Galtier N., Tourasse N., Gouy M. A non-hyperthermophilic common ancestor to extant life forms. Science. 283:1999;155-157.
11. Greenacre, M.J., 1984. Theory and Applications of Correspondence Analysis. 1st Edition. Academic press, London, p. 223.
12. Haney P.J., Badger J.H., Buldak G.L., Reich C.I., Woese C.R., Olsen G.J. Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species. Proc. Natl. Acad. Sci. USA. 96:1999;3578-3583.
13. Jaenicke R., Bohm G. Thermostability of proteins from Thermotoga maritima. Methods Enzymol. 334:2001;438-469.
14. Kawarabayasi Y., et al. Complete genome sequence of an aerobic hyper-thermophilic crenarchaeon, Aeropyrum pernix K1. DNA Res. 6:1999;83-101.
15. Kreil D.P., Ouzounis C.A. Identification of thermophilic species by the amino acid compositions deduced from their genomes. Nucleic Acids Res. 468:2001;109-114.
16. Malpertuy A., et al. Genomic exploration of the hemiascomycetous yeasts: ascomycetes-specific genes. FEBS Lett. 487:2000;113-121.
17. McInerney J.O. Replicational and transcriptional selection on codon usage in Borrelia burgdorferi. Proc. Natl. Acad. Sci. USA. 95:1998;10698-10703.
18. Miller S.L., Lazcano A. The origin of life - did it occur at high temperatures? J. Mol. Evol. 41:1995;689-692.
19. Natale D.A., Shankavaram U.T., Galperin M.Y., Wolf Y.I., Aravind L., Koonin E.V. Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs). Genome Biol. 5:2000;1-19.
20. Nelson K.E., et al. Evidence for lateral gene transfer between archaea and bacteria from genome sequence of Thermotoga maritima. Nature. 399:1999;323-329.
21. Rothschild L.J., Mancinelli R.L. Life in extreme environments. Nature. 409:2001;1092-1101.
22. Singer G.A., Hickey D.A. Nucleotide bias causes a genome wide bias in the amino acid composition of proteins. Mol. Biol. Evol. 17:2000;1581-1588.
23. Sterner R., Liebl W. Thermophilic adaptation of proteins. Crit. Rev. Biochem. Mol. Biol. 36:2001;39-106.
24. Tekaia F., Dujon B. Pervasiveness of gene conservation and persistence of duplicates in cellular genomes. J. Mol. Evol. 49:1999;591-600.
25. Tekaia F., Lazcano A., Dujon B. The genomic tree as revealed from whole proteome comparisons. Genome Res. 9:1999;550-557.
26. Tekaia F., et al. Genomic exploration of the hemiascomycetous yeasts: 3. Methods and strategies used for sequence analysis and annotation. FEBS Lett. 487:2000;17-30.
27. Thompson M.J., Eisenberg D. Transproteomic evidence of a loop-deletion mechanism for enhancing protein thermostability. J. Mol. Biol. 290:1999;595-604.
28. Vieille C., Zeikus G.J. Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability. Microbiol. Mol. Biol. Rev. 65:2001;1-43.
29. Wootton J.C., Federhen S. Statistics of local complexity in amino acid sequences and sequence databases. Comput. Chem. 17:1993;149-163.
30. Zhang J. Protein-length distributions for the three domains of life. Trends Genet. 16:2000;107-109.