Navegar

Colección

Datos Estadísticas

Artículo

Krick, T.; Verstraete, N.; Alonso, L.G.; Shub, D.A.; Ferreiro, D.U.; Shub, M.; Sánchez, I.E. "Amino acid metabolism conflicts with protein diversity" (2014) Molecular Biology and Evolution. 31(11):2905-2912
Estamos trabajando para incorporar este artículo al repositorio
Consulte el artículo en la página del editor
Consulte la política de Acceso Abierto del editor

Abstract:

The 20 protein-coding amino acids are found in proteomes with different relative abundances. The most abundant amino acid, leucine, is nearly an order of magnitude more prevalent than the least abundant amino acid, cysteine. Amino acid metabolic costs differ similarly, constraining their incorporation into proteins. On the other hand, a diverse set of protein sequences is necessary to build functional proteomes. Here, we present a simple model for a cost-diversity trade-off postulating that natural proteomes minimize amino acid metabolic flux while maximizing sequence entropy. The model explains the relative abundances of amino acids across a diverse set of proteomes. We found that the data are remarkably well explained when the cost function accounts for amino acid chemical decay. More than 100 organisms reach comparable solutions to the trade-off by different combinations of proteome cost and sequence diversity. Quantifying the interplay between proteome size and entropy shows that proteomes can get optimally large and diverse. © 2014 The Author.

Registro:

Documento: Artículo
Título:Amino acid metabolism conflicts with protein diversity
Autor:Krick, T.; Verstraete, N.; Alonso, L.G.; Shub, D.A.; Ferreiro, D.U.; Shub, M.; Sánchez, I.E.
Filiación:Departamento de Matemática, Facultad de Ciencias Exactas y Naturales and IMAS, Universidad de Buenos Aires, Buenos Aires, Argentina
Protein Physiology Laboratory, Departamento de Química Biológica, Universidad de Buenos Aires, Buenos Aires, Argentina
Fundación Instituto Leloir - IIBBA CONICET, Buenos Aires, Argentina
Department of Biological Sciences, University at Albany, State University of New York, United States
IMAS, CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
Palabras clave:amino acid decay; amino acid metabolism; information theory; maximum entropy; proteomics; adenosine triphosphate; nonessential amino acid; proteome; amino acid; proteome; amino acid composition; amino acid metabolism; amino acid sequence; Article; biodiversity; biosynthesis; codon; correlation analysis; DNA base composition; DNA sequence; energy cost; entropy; genetic code; metabolic flux analysis; nucleophilicity; protein synthesis; proteomics; theoretical model; biological model; chemistry; genetic variability; genetics; genome; metabolism; molecular genetics; regression analysis; Adenosine Triphosphate; Amino Acid Sequence; Amino Acids; Entropy; Genome; Genomic Structural Variation; Least-Squares Analysis; Models, Biological; Molecular Sequence Data; Protein Biosynthesis; Proteome
Año:2014
Volumen:31
Número:11
Página de inicio:2905
Página de fin:2912
DOI: http://dx.doi.org/10.1093/molbev/msu228
Título revista:Molecular Biology and Evolution
Título revista abreviado:Mol. Biol. Evol.
ISSN:07374038
CODEN:MBEVE
CAS:adenosine triphosphate, 15237-44-2, 56-65-5, 987-65-5; amino acid, 65072-01-7; Adenosine Triphosphate; Amino Acids; Proteome
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_07374038_v31_n11_p2905_Krick

Referencias:

  • Akashi, H., Gojobori, T., Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis (2002) Proc Natl Acad Sci USA., 99 (6), pp. 3695-3700
  • Alves, R., Savageau, M.A., Evidence of selection for low cognate amino acid bias in amino acid biosynthetic enzymes (2005) Mol Microbiol., 56 (4), pp. 1017-1034
  • Barton, M.D., Delneri, D., Oliver, S.G., Rattray, M., Bergman, C.M., Evolutionary systems biology of amino acid biosynthetic cost in yeast (2010) PLoS One, 5 (8), p. e11935
  • Beeby, M., O'Connor, B.D., Ryttersgaard, C., Boutz, D.R., Perry, L.J., Yeates, T.O., The genomics of disulfide bonding and protein stabilization in thermophiles (2005) PLoS Biol., 3, p. e309
  • Bryngelson, J.D., Wolynes, P.G., Spin glasses and the statistical mechanics of protein folding (1987) Proc Natl Acad Sci USA., 84 (21), pp. 7524-7528
  • Creighton, T.E., (1983) Proteins: Structures and Molecular Properties, , Oxford W. H. Freeman and Co
  • Dtf, D., Thomson, A.R., White, J.H., How much of protein sequence space has been explored by life on Earth? (2008) J Roy Soc Interface, 5 (25), pp. 953-956
  • Dyer, F.K., The quiet revolution: A new synthesis of biological knowledge (1971) J Biol Educ., 5, pp. 15-24
  • Gupta, P.K., (2005) Molecular Biology and Genetic Engineering, , New Delhi (India): Rastogi Publications
  • Heizer, E.M., Raymer, M.L., Krane, D.E., Amino acid biosynthetic cost and protein conservation (2011) J Mol Evol., 72 (5-6), pp. 466-473
  • Kryukov, K., Sumiyama, K., Ikeo, K., Gojobori, T., Saitou, N., A new database (GCD) on genome com position for eukaryote and prokaryote genome sequences and their initial analyses (2012) Genome Biol Evol., 4 (4), pp. 501-512
  • Lightfield, J., Fram, N.R., Ely, B., Across bacterial phyla, distantly-related genomes with similar genomic GC content have similar patterns of amino acid usage (2011) PLoS One, 6, p. e17677
  • Lotka, A.J., Contribution to the energetics of evolution (1922) Proc Natl Acad Sci USA., 8 (6), pp. 147-151
  • Moskovitz, J., Berlett, B.S., Poston, J.M., Stadtman, E.R., The yeast peptide-methionine sulfoxide reductase functions as an antioxidant in vivo (1997) Proc Natl Acad Sci USA., 94 (18), pp. 9585-9589
  • Per Lstein, E.O., De Bivort, B.L., Kunes, S., Schreiber, S.L., Evolutionarily conserved optimization of amino acid biosynthesis (2007) J Mol Evol., 65 (2), pp. 186-196
  • Raiford, D.W., Heizer, E.M., Miller, R.V., Akashi, H., Raymer, M.L., Krane, D.E., Do amino acid biosynthetic costs constrain protein evolution in Saccharomyces cerevisiae? (2008) J Mol Evol., 67 (6), pp. 621-630
  • Raiford, D.W., Heizer, E.M., Miller, R.V., Doom, T.E., Raymer, M.L., Krane, D.E., Metabolic and translational efficiency in microbial organisms (2012) J Mol Evol., 74 (3-4), pp. 206-216
  • Reissner, K.J., Aswad, D.W., Deamidation and isoaspartate formation in proteins: Unwanted alterations or surreptitious signals? (2003) Cell Mol Life Sci., 60 (7), pp. 1281-1295
  • Seligmann, H., Cost-minimization of amino acid usage (2003) J Mol Evol., 56 (2), pp. 151-161
  • Shakhnovich, E.I., Protein design: A perspective from simple tractable models (1998) Fold Des., 3 (3), pp. R45-R58
  • Shannon, C., A mathematical theory of communication (1948) Bell Syst Tech J., 27, pp. 379-423
  • Shannon, C.E., Weaver, W., (1949) The Mathematical Theory of Communication., 27. , Illinois University of Illinois Press
  • Smith, D.R., Chapman, M.R., Economical evolution: Microbes reduce the synthetic cost of extracellular proteins (2010) MBio, 1 (3), pp. e00131-e00210
  • Sokal, R.R., Rohlf, F.J., (1995) Biometry: The Principles and Practice of Statistics in Biological Research, , New York WH Freeman
  • Stadtman, E.R., Protein oxidation and aging (2006) Free Radic Res., 40 (12), pp. 1250-1258
  • Stroher, E., Millar, A.H., The biological roles of glutaredoxins (2012) Biochem J., 446 (3), pp. 333-348
  • Subramanyam, M.B., Gnanamani, M., Ramachandran, S., Simple sequence proteins in prokaryotic proteomes (2006) BMC Genomics, 7, p. 141
  • Swire, J., Selection on synthesis cost affects interprotein amino acid usage in all three domains of life (2007) J Mol Evol., 64 (5), pp. 558-571
  • Tekaia, F., Yeramian, E., Evolution of proteomes: Fundamental signatures and global trends in amino acid compositions (2006) BMC Genomics, 7, p. 307
  • Update on activities at the Universal Protein Resource (UniProt) in 2013 (2013) Nucleic Acids Res., 41, pp. D43-D47. , Database issue
  • Wang, M., Weiss, M., Simonovic, M., Haertinger, G., Schrimpf, S.P., Hengartner, M.O., Von Mering, C., PaxDb, a database of protein abundance averages across a ll three domains of life (2012) Mol Cell Proteomics., 11 (8), pp. 492-500
  • Weiss, O., Jim-Enez-Montaño, M.A., Herzel, H., Information content of protein sequences (2000) J Theor Biol., 206 (3), pp. 379-386
  • Wolynes, P., As simple as can be? (1997) Nat Struct Mol Biol., 4, pp. 871-874

Citas:

---------- APA ----------
Krick, T., Verstraete, N., Alonso, L.G., Shub, D.A., Ferreiro, D.U., Shub, M. & Sánchez, I.E. (2014) . Amino acid metabolism conflicts with protein diversity. Molecular Biology and Evolution, 31(11), 2905-2912.
http://dx.doi.org/10.1093/molbev/msu228
---------- CHICAGO ----------
Krick, T., Verstraete, N., Alonso, L.G., Shub, D.A., Ferreiro, D.U., Shub, M., et al. "Amino acid metabolism conflicts with protein diversity" . Molecular Biology and Evolution 31, no. 11 (2014) : 2905-2912.
http://dx.doi.org/10.1093/molbev/msu228
---------- MLA ----------
Krick, T., Verstraete, N., Alonso, L.G., Shub, D.A., Ferreiro, D.U., Shub, M., et al. "Amino acid metabolism conflicts with protein diversity" . Molecular Biology and Evolution, vol. 31, no. 11, 2014, pp. 2905-2912.
http://dx.doi.org/10.1093/molbev/msu228
---------- VANCOUVER ----------
Krick, T., Verstraete, N., Alonso, L.G., Shub, D.A., Ferreiro, D.U., Shub, M., et al. Amino acid metabolism conflicts with protein diversity. Mol. Biol. Evol. 2014;31(11):2905-2912.
http://dx.doi.org/10.1093/molbev/msu228