Amino acid biosynthetic cost and protein conservation

Journal of Molecular Evolution

Volumn 72, Issue 5-6, 2011, Pages 466-473

  Heizer Jr , Esley M ^a   Raymer, Michael L ^b   Krane, Dan E ^a  

^a WRIGHT STATE UNIVERSITY   (United States)

^b Wright State University   (United States)

Author keywords

Amino acid; Bioinformatics; Biosynthetic cost; Conservation; CpG islands; Metabolic efficiency; Substitution

Indexed keywords

AMINO ACID; PROTEIN;

AMINO ACID SUBSTITUTION; ANIMAL; ARTICLE; BIOSYNTHESIS; CATTLE; CHEMISTRY; CPG ISLAND; DNA BASE COMPOSITION; DOG; GENETICS; HUMAN; MOUSE;

AMINO ACID SUBSTITUTION; AMINO ACIDS; ANIMALS; BASE COMPOSITION; CATTLE; CPG ISLANDS; DOGS; HUMANS; MICE; PROTEINS;

ARTIODACTYLA; MAMMALIA; PRIMATES; RODENTIA;

EID: 79961026752     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-011-9445-4     Document Type: Article

References (31)

1. S Aerts G Thijs M Dabrowski Y Moreau B De Moor 2004 Comprehensive analysis of the base composition around the transcription start site in Metazoa BMC Genomics 34 43
2. H Akashi T Gojobori 2002 Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis PNAS USA 3695 3700
3. DR Caffrey S Somaroo JD Hughes J Mintseris ES Huang 2004 Are protein-protein interfaces more conserved in sequence than the rest of the protein surface? Protein Sci 190 202
4. CL Craig RS Weber 1998 Selection costs of amino acid substitutions in ColE1 and ColIa gene clusters harbored by Escherichia coli Mol Biol Evol 774 776
5. Dayhoff MO (1978) Atlas of protein sequence and structure Volume 5 supplement 3. National Biomedical Research Foundation, Silver Spring, Maryland, pp 345-352
6. Ensembl (2010) BioMart. http://uswest.ensembl.org/biomart/martview/ f9e42e0a6d868fb83e5e2add8f503225. Accessed 31 Jan 2010
7. A Eyre-Walker 1996 Synonymous codon bias is related to gene length in Escherichia coli: selection for translational accuracy? Mol Biol Evol 13 864 872 8754221 1:CAS:528:DyaK28XktFygsrc%3D (Pubitemid 26240090)
8. M Guharoy P Chakrabarti 2005 Conservation and relative importance of residues across protein-protein interfaces PNAS USA 15447 15452
9. BM Hallstrom A Janke 2010 Mammalian evolution may not be strictly bifurcating Mol Biol Evol 27 2804 2816 20591845 10.1093/molbev/msq166
10. EM Heizer DW Raiford ML Raymer TE Doom RV Miller DE Krane 2006 Amino acid cost and codon-usage biases in 6 prokaryotic genomes: a whole-genome analysis Mol Biol Evol 1670 1680
11. S Karlin L Brocchieri 1996 Evolutionary conservation of RecA genes in relation to protein structure and function J Bacteriol 1881 1894
12. MJ Lawson L Zhang 2008 Housekeeping and tissue-specific genes differ in simple sequence repeats in the 5′-UTR region Gene 407 54 62 17964742 10.1016/j.gene.2007.09.017 1:CAS:528:DC%2BD2sXhsVejtr3F (Pubitemid 350251654)
13. MJ Lercher AO Urrutia A Pavlicek LD Hurst 2003 A unification of mosaic structures in the human genome Hum Mol Genet 12 2411 2415 12915446 10.1093/hmg/ddg251 1:CAS:528:DC%2BD3sXnsVekt74%3D (Pubitemid 37220406)
14. S Liang C Zhang S Liu Y Zhou 2006 Protein binding site prediction using an empirical scoring function Nucleic Acids Res 3698 3707
15. TJ Magliery L Regan 2005 Sequence variation in ligand binding sites in proteins BMC Bioinformatics 240 251
16. W Miller K Rosenbloom, et al. 2007 28-way vertebrate alignment and conservation track in the UCSC Genome Browser Genome Res 17 12 1797 1808 17984227 10.1101/gr.6761107 1:CAS:528:DC%2BD2sXhsVGhsLnN (Pubitemid 351360004)
17. J Mintseris Z Weng 2005 Structure, function, and evolution of transient and obligate protein-protein interactions PNAS USA 10930 10935
18. NCBI (2009a) Homologene. http://www.ncbi.nlm.nih.gov/homologene. Accessed 3 Nov 2009
19. NCBI (2009b) COBALT. ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/cobalt/. Accessed 6 Nov 2009
20. M Nei T Gojobori 1986 Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions Mol Biol Evol 3 418 426 3444411 1:CAS:528:DyaL28Xmt1aisbs%3D (Pubitemid 16010523)
21. SL Pond SD Frost 2005 A genetic algorithm approach to detecting lineage-specific variation in selection pressure Mol Biol Evol 478 485
22. AB Prasad NISC Allard MW ComparativeSequencing Program ED Green 2008 Confirming the phylogeny of mammals by use of large comparative sequence data sets Mol Biol Evol 25 9 1795 1808 18453548 10.1093/molbev/msn104 1:CAS:528:DC%2BD1cXhtV2it7rI
23. DW Raiford EM Heizer Jr RV Miller H Akashi ML Raymer DE Krane 2008 Do amino acid biosynthetic costs constrain protein evolution in Saccharomyces cerevisiae? J Mol Evol 621 630
24. P Rice I Longden A Bleasby 2000 EMBOSS: the European molecular biology open software suite Trends Genet 16 6 276 277 10827456 10.1016/S0168-9525(00) 02024-2 1:CAS:528:DC%2BD3cXjvVygsbs%3D
25. H Seligmann 2003 Cost-minimization of amino acid usage J Mol Evol 56 151 161 12574861 10.1007/s00239-002-2388-z 1:CAS:528:DC%2BD3sXhtFKltr0%3D (Pubitemid 36169683)
26. BD Smith RT Raines 2006 Genetic selection for critical residues in ribonucleases J Mol Biol 459 478
27. C Spearman 1904 General intelligence objectively determined and measured Am J Psychol 201 293
28. J Suckow P Markiewicz LG Kleina J Miller B Kisters-Woike B Muller-Hill 1996 Genetic studies of the Lac repressor. XV: 4000 single amino acid substitutions and analysis of the resulting phenotypes on the basis of the protein structure J Mol Biol 509 523
29. J Swire 2007 Selection on synthesis cost affects interprotein amino acid usage in all three domains of life J Mol Evol 558 571
30. A Varriale G Bernardi 2010 Distribution of DNA methylation, CpGs, and CpG islands in human isochores Genomics 95 25 28 19800400 10.1016/j.ygeno.2009.09. 006 1:CAS:528:DC%2BD1MXhsFOrurjJ
31. A Wagner 2005 Energy constraints on the evolution of gene expression Mol Biol Evol 1365 1374