Evidence of selection for low cognate amino acid bias in amino acid biosynthetic enzymes

Molecular Microbiology

Volumn 56, Issue 4, 2005, Pages 1017-1034

  Alves, Rui ^a,b   Savageau, Michael A ^a  

^a University of California   (United States)

^b UNIVERSITY OF LLEIDA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; CELL PROTEIN;

AMINO ACID COMPOSITION; AMINO ACID SYNTHESIS; ARTICLE; BACILLUS SUBTILIS; EFFECTOR CELL; ENZYME SYNTHESIS; ESCHERICHIA COLI; HYPOTHESIS; NATURAL SELECTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN STRUCTURE; SALMONELLA TYPHIMURIUM; SIGNAL TRANSDUCTION;

AMINO ACIDS; BACILLUS SUBTILIS; BACTERIAL PROTEINS; ENZYMES; ESCHERICHIA COLI; GENE EXPRESSION REGULATION, BACTERIAL; MATHEMATICS; MODELS, GENETIC; SALMONELLA TYPHIMURIUM; SELECTION (GENETICS); STATISTICS;

BACILLUS SUBTILIS; ESCHERICHIA COLI; SALMONELLA TYPHIMURIUM; TYPHIMURIUM;

EID: 18444379063     PISSN: 0950382X     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1365-2958.2005.04566.x     Document Type: Article

References (43)

1. Akashi, H., and Gojobori, T. (2002) Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis. Proc Natl Acad Sci USA 99: 3695-3700.
2. Altschul, S.F., Madden, T.L., Schaffet, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
3. Baudouin-Cornu, P., Surdin-Kerjan, Y., Marliere, P., and Thomas, D. (2001) Molecular evolution of protein atomic composition. Science 293: 297-300.
4. Boeckmann, B., Bairoch, A., Apweiler, R., Blatter, M.-C., Estreicher, A., Gasteiger, E., et al. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res 31: 365-370.
5. Chenna, R., Sugawara, H., Koike, T., Lopez, R., Gibson, T.J., Higgins, D.G., and Thompson, J.D. (2003) Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 31: 3497-3500.
6. Cohen, L., and Holliday, M. (1998) Statistics for the Social Scientists. New York: Addison-Wesley.
7. Cootes, A.P., Curmi, P.M., Cunningham, R., Donnelly, C., and Torda, A.E. (1998) The dependence of amino acid pair correlation on structural environment. Proteins: Struct Function Genet 32: 175-189.
8. Dufton, M.J. (1997) Genetic code synonym quotas and amino acid complexity: cutting the cost of proteins? J Theor Biol 187: 165-173.
9. Elf, J., Nilsson, D., Tenson, T., and Ehrenberg, M. (2003) Selective charging of tRNA isoacceptors explains patterns of codon usage. Science 300: 1718-1722.
10. Foster, J.W., and Spector, M.P. (1995) How Salmonella survive against the odds. Ann Rev Microbiol 49: 145-174.
11. Frey, P.A. (2001) Radical mechanisms of enzymatic catalysis. Ann Rev Biochem 70: 121-148.
12. Herrmann, K.M., and Somerville, R.L. (1983) Amino Acids: Biosynthesis and Genetic Regulation. Reading, MA: Addison-Wesley Publishing.
13. Jansen, R., and Gerstein, M. (2000) Analysis of the yeast transcriptome with structural and functional categories: characterizing highly expressed proteins. Nucleic Acids Res 28: 1481-1488.
14. Kanehisa, M., Goto, S., Sato, K., Fijibuchi, W., and Nakaya, A. (2002) The KEGG database at Genomenet. Nucleic Acids Res 30: 42-46.
15. Karlin, S., and Bucher, P. (1992) Correlation analysis of amino acid usage in protein classes. Proc Natl Acad Sci USA 89: 12165-12169.
16. Karp, P.D., Riley, M., Saier, M., Paulsen, I.T., Paley, S., and Pellegrini-Toole, A. (2002) The Ecocyc Database. Nucleic Acids Res 30: 56-58.
17. Khodursky, A.B., Peter, B.J., Cozzarelli, N.R., Botstein, D., Brown, P.O., and Yanofsky, C. (2000) DNA microarray analysis of gene expression in response to physiological and genetic changes that affect tryptophan metabolism in Escherichia coli. Proc Natl Acad Sci USA 97: 12170-12175.
18. King, J.L., and Jukes, T.H. (1969) Non darwinian evolution. Science 164: 788-798.
19. Li, W.-H. (1997) Molecular Evolution. New York: Sinauer Associates.
20. Lobry, J.R. (1997) Influence of genomic G+C content on average amino acid composition of proteins from 59 bacterial species. Gene 205: 309-316.
21. Lobry, J.R., and Gautier, C. (1994) Hydrophobicity, expressivity and aromaticity are the major trends of amino-acid usage in 999 Escherichia coli chromosome-encoded genes. Nucleic Acids Res 22: 3174-3180.
22. Maaøoe, O., and Kjeldgaard, N.O. (1966) Control of Macromolecular Synthesis; a Study of DNA, RNA, and Protein Synthesis in Bacteria. New York: W.A. Benjamin.
23. Magnusson, L.U., Nystrom, T., and Farewell, A. (2003) Underproduction of sigma 70 mimics a stringent response. A proteome approach. J Biol Chem 278: 968-973.
24. Matin, A. (1991) The molecular basis of carbon-starvation-induced general resistance in Escherichia coli. Mol Microbiol 5:3-10.
25. Mazel, D., and Marliere, P. (1989) Adaptive eradication of methionine and cysteine from cyanobacterial light-harvesting-proteins. Nature 341: 245-248.
26. Neidhardt, F.C. (1999) Escherichia coli and Salmonella: Cellular and Molecular Biology. Washington, DC: American Society for Microbiology.
27. Neidhardt, F.C., Ingraham, J.L., and Schaechter, M. (1990) Physiology of the Bacterial Cell: A Molecular Approach. Sunderland, MA: Sinauer Ass.
28. Nystrom, T. (2004) Stationary-phase physiology. Ann Rev Microbiol 58: 161-181.
29. Overbeek, R., Larsen, N., Pusch, G., D'Souza, M., Selkov, E., Jr, Kyrpides, N., et al. (2000) WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction. Nucleic Acids Res 28: 123-125.
30. Pedersen, J.Z., and Finazzi-Agro, A. (1993) Protein-radical enzymes. FEBS Lett 325: 53-58.
31. Pramanik, J., and Keasling, J.D. (1998) Effect of Escherichia coli biomass composition on central metabolic fluxes prodicted by a stoichiometric model. Biotech Bioeng 60: 230-238.
32. Reeve, C.A., Bockman, A.T., and Matin, A. (1984) Role of protein degradation in the survival of carbon-starved Escherichia coli and Salmonella typhimurium. J Bacteriol 157: 758-763.
33. Richmond, R.C. (1970) Non darwinian evolution: a critique. Nature 225: 1025-1028.
34. Rogers, M.S., and Dooley, D.M. (2003) Copper-tyrosyl radical enzymes. Curr Opin Chem Biol 7: 189-196.
35. Sauer, U., Hatzimanikatis, V., Hohmann, H.P., Manneberg, M., van Loon, A.P., and Bailey, J.E. (1996) Physiology and metabolic fluxes of wild-type and riboflavin-producing Bacillus subtilis. Appl Environ Microbiol 62: 3687-3696.
36. Savageau, M.A. (1983) Escherichia coli habitats, cell types, and molecular mechanisms of gene control. Am Nat 122: 732-744.
37. Seligmman, H. (2003) Cost-minimization of amino acid usage. J Mol Evol 56: 151-161.
38. Singer, G.A., and Mickey, D.A. (2000) Nucleotide bias causes a genomewide bias in the amino acid composition of proteins. Mol Biol Evol 17: 1581-1588.
39. Trifonov, E.N. (1987) Translation framing code and frame-monitoring mechanism as suggested by the analysis of mRNA and 16 S rRNA nucleotide sequences. J Mol Biol 194: 643-652.
40. Voit, E.O., and Ferreira, A.E.N. (2000) Computational Analysis of Biochemical Systems, a Practical Guide for Biochemists and Molecular Biologists. Cambridge, UK: Cambridge University Press.
41. Weichart, D., Querfurth, N., Dreger, M., and Hengge-Aronis, R. (2003) Global role for ClpP-containing proteases in stationary phase adaptation of Escherichia coli. J Bacteriol 185: 115-125.
42. Wolfram, S. (1999) The Mathematica Book. New York: Cambridge University Press.
43. Xiu, Z-L., Chang, Z.-Y., and Zeng, A.-P. (2002) Nonlinear dynamics of regulation of bacterial trp operon: model analysis of integrated effects of repression, feedback inhibition, and attenuation. Biotechnol Prog 18: 686-693.