Evolution of proteomes: Fundamental signatures and global trends in amino acid compositions

BMC Genomics

Volumn 7, Issue , 2006, Pages

  Tekaia, Fredj ^a   Yeramian, Edouard ^b  

^a SORBONNE UNIVERSITÉ   (France)

^b INSTITUT PASTEUR   (France)

Author keywords

[No Author keywords available]

Indexed keywords

CYSTEINE; GLYCINE; PROTEOME;

AMINO ACID ANALYSIS; AMINO ACID COMPOSITION; ARTICLE; CHRONOLOGY; CONTROLLED STUDY; CORRELATION ANALYSIS; EUKARYOTE EVOLUTION; GENETIC CODE; HYPERTHERMOPHILE; LIFESTYLE; MESOPHILE; MOLECULAR EVOLUTION; PHYLOGENY; PROKARYOTE; PROTEIN DETERMINATION; PROTEIN DOMAIN; PSYCHROPHILE; TEMPERATURE MEASUREMENT;

AMINO ACIDS; ARCHAEA; BACTERIA; BASE COMPOSITION; EUKARYOTIC CELLS; EVOLUTION, MOLECULAR; GENOME; PHYLOGENY; PROTEOME; SPECIES SPECIFICITY; TEMPERATURE;

EUKARYOTA; PROKARYOTA;

EID: 33846536849     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-7-307     Document Type: Article

References (26)

1. Hickey DA Singer GA Genomic and proteomic adaptations to growth at high temperature Genome Biol 2004 5 117 Epub 2004. 545586 15461805 10.1186/ gb-2004-5-10-117
2. Cavicchioli R Cold-adapted archaea Nature Reviews Microbiology 2006 4 331-343 10.1038/nrmicro1390 16715049
3. Karlin S Global dinucleotide signatures and analysis of genomic heterogeneity Curr Opin Microbiol 1998 1 598-610 10.1016/ S1369-5274(98)80095-7 10066522
4. Eyre-Walker A Hurst LD The evolution of isochores Nat Rev Genet 2001 2 549-55 10.1038/35080577 11433361
5. Brocchieri L Environmental signatures in proteome properties Proc Natl Acad Sci USA 2004 101 8257-8 420380 15159533 10.1073/pnas.0402797101
6. Kreil DP Ouzounis CA Identification of thermophilic species by the amino acid compositions deduced from their genomes Nucleic Acids Res 2001 29 1608-1615 31282 11266564 10.1093/nar/29.7.1608
7. Tekaia F Yeramian E Dujon B Amino acid composition of genomes, lifestyles of organisms, and evolutionary trends: A global picture with Correspondence analysis Gene 2002 297 51-60 10.1016/ S0378-1119(02)00871-5 12384285
8. Suhre K Claverie JM Genomic correlates of hyperthermostability, an update J Biol Chem 2003 278 17198-17202 10.1074/jbc.M301327200 12600994
9. Jordan IK Kondrashov FA Adzhubei IA Wolf YI Koonin EV Kondrashov AS Sunyaev S A universal trend of amino acid gain and loss in protein evolution Nature 2005 433 633-638 10.1038/nature03306 15660107
10. Trifonov EN The triplet code from first principles J Biomol Struct & Dyn 2004 22 1-11 15214800
11. Tekaia F Yeramian E Genome Trees from Conservation Profiles PLoS Comput Biol 2005 1 7 e75 1314884 16362074 10.1371/journal.pcbi.0010075
12. Green P Lipman D Hillier L Waterston R States D Claverie JM Ancient conserved regions in new gene sequences and the protein databases Science 1993 259 1711-6 10.1126/science.8456298 8456298
13. Miller SL A production of amino acids under possible primitive earth conditions Science 1953 117 528-529 10.1126/science.117.3046.528 13056598
14. Miller SL Which organic compounds could have occurred on the prebiotic earth? Cold Spring Harb Symp Quant Biol 1987 52 17-27 3454260
15. Cronin JR Pizzarello S Amino acids in meteorites Adv Space Res 1983 3 5-18 10.1016/0273-1177(83)90036-4 11542462
16. Goldstein RA Pollock DD Observations of Amino Acid Gain and Loss during Protein Evolution Are Explained by Statistical Bias Mol Biol Evol 2006 23 1444-1449 10.1093/molbev/msl010 16698770
17. Hurst LD Feil EJ Rocha EP Protein evolution: Causes of trends in amino-acid gain and loss Nature 2006 442 E11-2 10.1038/nature05137 16929253
18. McDonald JH Apparent trends of amino Acid gain and loss in protein evolution due to nearly neutral variation Mol Biol Evol 2006 23 240-4 10.1093/molbev/msj026 16195487
19. Pace NR A molecular view of microbial diversity and the biosphere Science 1997 276 734-740 10.1126/science.276.5313.734 9115194
20. The ncbi Entrez Genome Project http://www.ncbi.nlm.nih.gov/entrez/ query.fcgi?db=genomeprj
21. Benzecri JP L'analyse des données: L'analyse des correspondances Dunod, Paris 1973 2
22. Beh EJ Simple Correspondence analysis: A bibliographic review Internat Statist Rev 2004 72 257-284
23. Murtagh F Correspondence Analysis And Data Coding With Java And R Chapman & Hall/CRC 2005
24. McInerney JO Replicational and transcriptional selection on codon usage in Borrelia burgdorferi Proc Natl Acad Sci USA 1998 95 10698-10703 27958 9724767 10.1073/pnas.95.18.10698
25. Tekaia F Lazcano A Dujon B The genomic tree as revealed from whole proteome comparisons Genome Research 1999 9 550-557 310764 10400922
26. Fellenberg K Hauser NC Brors B Neutzner A Hoheisel JD Vingron M Correspondence analysis applied to microarray data Proc Natl Acad Sci USA 2001 98 10781-6 58552 11535808 10.1073/pnas.181597298