Correspondence analysis of amino acid usage within the family Bacillaceae

Biochemical and Biophysical Research Communications

Volumn 325, Issue 4, 2004, Pages 1252-1257

  Naya, Hugo ^a   Zavala, Alejandro ^a   Romero, Héctor ^a,b   Rodríguez Maseda, Helena ^c   Musto, Héctor ^a  

^a Facultad de Ciencias   (Uruguay)

^b Avda Italia Hosp Clinicas M   (Uruguay)

^c Facultad de Medicina   (Uruguay)

Author keywords

Genome evolution; Genomic GC; Multivariate analysis; Optimal growth temperature; Proteome

Indexed keywords

AMINO ACID; CYSTEINE; CYTOSINE; GUANINE;

AMINO ACID ANALYSIS; ARTICLE; BACILLUS; CONTROLLED STUDY; CORRESPONDENCE ANALYSIS; HYDROPHOBICITY; NONHUMAN; PRIORITY JOURNAL; TEMPERATURE;

AMINO ACIDS; BACILLACEAE; BASE COMPOSITION; EVOLUTION, MOLECULAR; GENE FREQUENCY; GENOME, BACTERIAL; MULTIVARIATE ANALYSIS; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY; SPECIES SPECIFICITY; TEMPERATURE;

BACILLACEAE; PROKARYOTA;

EID: 8844280220     PISSN: 0006291X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbrc.2004.10.170     Document Type: Article

References (23)

1. H. Naya, H. Romero, A. Zavala, B. Alvarez, and H. Musto Aerobiosis increases the genomic guanine plus cytosine content (GC%) in prokaryotes J. Mol. Evol. 55 2002 260 264
2. E.P. Rocha, and A. Danchin Base composition bias might result from competition for metabolic resources Trends Genet. 18 2002 291 294
3. N. Galtier, and J.R. Lobry Relationships between genomic G + C content, RNA secondary structures, and optimal growth temperature in prokaryotes J. Mol. Evol. 44 1997 632 636
4. L.D. Hurst, and A.R. Merchant High guanine-cytosine content is not an adaptation to high temperature: a comparative analysis amongst prokaryotes Proc. R. Soc. Lond B. 268 2001 493 497
5. H. Musto, H. Naya, A. Zavala, H. Romero, F. Alvarez-Valin, and G. Bernardi Correlations between genomic GC levels and optimal growth temperatures in prokaryotes FEBS Lett. 573 2004 73 77
6. D.J. Lynn, G.A. Singer, and D.A. Hickey Synonymous codon usage is subject to selection in thermophilic bacteria Nucleic Acids Res. 30 2002 4272 4277
7. J.R. Lobry, and D. Chessel Internal correspondence analysis of codon and amino-acid usage in thermophilic bacteria J. Appl. Genet. 44 2003 235 261
8. G.A. Singer, and D.A. Hickey Thermophilic prokaryotes have characteristic patterns of codon usage, amino acid composition and nucleotide content Gene 317 2003 39 47
9. C. Cambillau, and J.M. Claverie Structural and genomic correlates of hyperthermostability J. Biol. Chem. 275 2000 32383 32386
10. D.P. Kreil, and C.A. Ouzounis Identification of thermophilic species by the amino acid compositions deduced from their genomes Nucleic Acids Res. 29 2001 1608 1615
11. K. Suhre, and J.M. Claverie Genomic correlates of hyperthermostability, an update J. Biol. Chem. 278 2003 17198 17202
12. P.J. Haney, J.H. Badger, G.L. Buldak, C.I. Reich, C.R. Woese, and G.J. Olsen 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. J.H. McDonald, A.M. Grasso, and L.K. Rejto Patterns of temperature adaptation in proteins from Methanococcus and Bacillus Mol. Biol. Evol. 16 1999 1785 1790
14. Y. Nishio, Y. Nakamura, Y. Kawarabayasi, Y. Usuda, E. Kimura, S. Sugimoto, K. Matsui, A. Yamagishi, H. Kikuchi, K. Ikeo, and T. Gojobori Comparative complete genome sequence analysis of the amino acid replacements responsible for the thermostability of Corynebacterium efficiens Genome Res. 13 2003 1572 1579
15. N. Sueoka Correlation between base composition of deoxyribonucleic acid and amino acid composition of protein Proc. Natl. Acad. Sci. USA 47 1961 1141 1149
16. G. Bernardi, and G. Bernardi Compositional constraints and genome evolution J. Mol. Evol. 24 1986 1 11
17. A. Muto, and S. Osawa The guanine and cytosine content of genomic DNA and bacterial evolution Proc. Natl. Acad. Sci. USA 84 1987 166 169
18. F. Tekaia, E. Yeramian, and B. Dujon Amino acid composition of genomes, lifestyles of organisms, and evolutionary trends: a global picture with correspondence analysis Gene 297 2002 51 60
19. G. Perriere, and J. Thioulouse Use and misuse of correspondence analysis in codon usage studies Nucleic Acids Res. 30 2002 4548 4555
20. S.B. Hedges The origin and evolution of model organisms Nat. Rev. Genet. 3 2002 838 849
21. A. Zavala, H. Naya, H. Romero, and H. Musto Trends in codon and amino acid usage in Thermotoga maritima J. Mol. Evol. 54 2002 563 568
22. J.R. Lobry, and C. Gautier Hydrophobicity, expressivity and aromaticity are the major trends of amino-acid usage in 999 Escherichia coli chromosome-encoded genes Nucleic Acids Res 22 1994 3174 3180
23. B. Garat, and H. Musto Trends of amino acid usage in the proteins from the unicellular parasite Giardia lamblia Biochem. Biophys. Res. Commun. 279 2000 996 1000