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Volumn 60, Issue 1, 2005, Pages 27-35

Universal biases in protein composition of model prokaryotes

Author keywords

Amino acids; Aromaticity; GC content; Hydrophobicity; Multivariate analysis; Orphans

Indexed keywords

AMINO ACID; MEMBRANE PROTEIN; PROTEOME;

EID: 19544363942     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20475     Document Type: Article
Times cited : (26)

References (46)
  • 1
    • 0030867609 scopus 로고    scopus 로고
    • Sequence analysis of the AAA protein family
    • Beyer A. Sequence analysis of the AAA protein family. Protein Sci 1997;6:2043-2058.
    • (1997) Protein Sci , vol.6 , pp. 2043-2058
    • Beyer, A.1
  • 2
    • 0035366379 scopus 로고    scopus 로고
    • Protein functional epitopes: Hot spots, dynamics and combinatorial libraries
    • Ma B, Wolfson HJ, Nussinov R. Protein functional epitopes: hot spots, dynamics and combinatorial libraries. Curr Opin Struct Biol 2001;11:364-369.
    • (2001) Curr Opin Struct Biol , vol.11 , pp. 364-369
    • Ma, B.1    Wolfson, H.J.2    Nussinov, R.3
  • 3
    • 0034888796 scopus 로고    scopus 로고
    • Ongoing evolution of strand composition in bacterial genomes
    • Rocha EP, Danchin A. Ongoing evolution of strand composition in bacterial genomes. Mol Biol Evol 2001;18:1789-1799.
    • (2001) Mol Biol Evol , vol.18 , pp. 1789-1799
    • Rocha, E.P.1    Danchin, A.2
  • 4
    • 0024322762 scopus 로고
    • Selection and neutrality in lactose operons of Escherichia coli
    • Dean AM. Selection and neutrality in lactose operons of Escherichia coli. Genetics 1989;123:441-454.
    • (1989) Genetics , vol.123 , pp. 441-454
    • Dean, A.M.1
  • 5
    • 0037133671 scopus 로고    scopus 로고
    • Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis
    • Akashi H, Gojobori T. Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis. Proc Natl Acad Sci USA 2002;99:3695-3700.
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 3695-3700
    • Akashi, H.1    Gojobori, T.2
  • 6
    • 0031593216 scopus 로고    scopus 로고
    • Influence of genomic G+C content on average amino-acid composition of proteins from 59 bacterial species
    • Lobry JR. Influence of genomic G+C content on average amino-acid composition of proteins from 59 bacterial species. Gene 1997;205:309-316.
    • (1997) Gene , vol.205 , pp. 309-316
    • Lobry, J.R.1
  • 7
    • 0036730186 scopus 로고    scopus 로고
    • A strong effect of at mutational bias on amino acid usage in Buchnera is mitigated at high-expression genes
    • Palacios C, Wernegreen JJ. A strong effect of AT mutational bias on amino acid usage in Buchnera is mitigated at high-expression genes. Mol Biol Evol 2002;19:1575-1584.
    • (2002) Mol Biol Evol , vol.19 , pp. 1575-1584
    • Palacios, C.1    Wernegreen, J.J.2
  • 8
    • 0031592733 scopus 로고    scopus 로고
    • Using codon usage to predict genes origin: Is the Escherichia coli outer membrane a patchwork of products from different genomes?
    • Guerdoux-Jamet P, Henaut A, Nitschke P, Risler JL, Danchin A. Using codon usage to predict genes origin: is the Escherichia coli outer membrane a patchwork of products from different genomes? DNA Res 1997;4:257-265.
    • (1997) DNA Res , vol.4 , pp. 257-265
    • Guerdoux-Jamet, P.1    Henaut, A.2    Nitschke, P.3    Risler, J.L.4    Danchin, A.5
  • 9
    • 0028088517 scopus 로고
    • Hydrophobicity, expressivity and aromaticity are the major trends of amino-acid usage in 999 Escherichia coli chromosome-encoded genes
    • Lobry JR, Gautier C. Hydrophobicity, expressivity and aromaticity are the major trends of amino-acid usage in 999 Escherichia coli chromosome-encoded genes. Nucleic Acids Res 1994;22:3174-3180.
    • (1994) Nucleic Acids Res , vol.22 , pp. 3174-3180
    • Lobry, J.R.1    Gautier, C.2
  • 10
    • 0037179524 scopus 로고    scopus 로고
    • Asymmetric directional mutation pressures in bacteria
    • Lobry JR, Sueoka N. Asymmetric directional mutation pressures in bacteria. Genome Biol 2002;3(10).
    • (2002) Genome Biol , vol.3 , Issue.10
    • Lobry, J.R.1    Sueoka, N.2
  • 12
    • 0035312933 scopus 로고    scopus 로고
    • Identification of thermophilic species by the amino acid compositions deduced from their genomes
    • Kreil DP, Ouzounis CA. Identification of thermophilic species by the amino acid compositions deduced from their genomes. Nucleic Acids Res 2001;29:1608-1615.
    • (2001) Nucleic Acids Res , vol.29 , pp. 1608-1615
    • Kreil, D.P.1    Ouzounis, C.A.2
  • 13
    • 0037019808 scopus 로고    scopus 로고
    • Amino acid composition of genomes, lifestyles of organisms, and evolutionary trends: A global picture with correspondence analysis
    • 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.
    • (2002) Gene , vol.297 , pp. 51-60
    • Tekaia, F.1    Yeramian, E.2    Dujon, B.3
  • 14
    • 12244283680 scopus 로고    scopus 로고
    • Modeling the percolation of annotation errors in a database of protein sequences
    • Gilks WR, Audit B, De Angelis D, Tsoka S, Ouzounis CA. Modeling the percolation of annotation errors in a database of protein sequences. Bioinformatics 2002;18:1641-1649.
    • (2002) Bioinformatics , vol.18 , pp. 1641-1649
    • Gilks, W.R.1    Audit, B.2    De Angelis, D.3    Tsoka, S.4    Ouzounis, C.A.5
  • 16
    • 0037109119 scopus 로고    scopus 로고
    • Use and misuse of correspondence analysis in codon usage studies
    • Perrière G, Thioulouse J. Use and misuse of correspondence analysis in codon usage studies. Nucleic Acids Res 2002;30:4548-4555.
    • (2002) Nucleic Acids Res , vol.30 , pp. 4548-4555
    • Perrière, G.1    Thioulouse, J.2
  • 18
    • 0020475449 scopus 로고
    • A simple method for displaying the hydropathic character of a protein
    • Kyte J, Doolittle RF. A simple method for displaying the hydropathic character of a protein. J Mol Biol 1982;157:105-132.
    • (1982) J Mol Biol , vol.157 , pp. 105-132
    • Kyte, J.1    Doolittle, R.F.2
  • 19
    • 0033198729 scopus 로고    scopus 로고
    • Translation in Bacillus subtilis: Roles and trends of initiation and termination, insights from a genome analysis
    • Rocha EP, Danchin A, Viari A. Translation in Bacillus subtilis: roles and trends of initiation and termination, insights from a genome analysis. Nucleic Acids Res 1999;27:3567-3576.
    • (1999) Nucleic Acids Res , vol.27 , pp. 3567-3576
    • Rocha, E.P.1    Danchin, A.2    Viari, A.3
  • 21
    • 17544393481 scopus 로고    scopus 로고
    • Extracting biological information from DNA arrays: An unexpected link between arginine and methionine metabolism in Bacillus subtilis
    • Sekowska A, Robin S, Daudin JJ, Henaut A, Danchin A. Extracting biological information from DNA arrays: an unexpected link between arginine and methionine metabolism in Bacillus subtilis. Genome Biol 2001;2(6).
    • (2001) Genome Biol , vol.2 , Issue.6
    • Sekowska, A.1    Robin, S.2    Daudin, J.J.3    Henaut, A.4    Danchin, A.5
  • 22
    • 0347135951 scopus 로고    scopus 로고
    • Mutational and selective pressures on codon and amino acid usage in Buchnera, endosymbiotic bacteria of aphids
    • Rispe C, Delmotte F, van Ham RC, Moya A. Mutational and selective pressures on codon and amino acid usage in Buchnera, endosymbiotic bacteria of aphids. Genome Res 2004;14:44-53.
    • (2004) Genome Res , vol.14 , pp. 44-53
    • Rispe, C.1    Delmotte, F.2    Van Ham, R.C.3    Moya, A.4
  • 23
    • 0036155782 scopus 로고    scopus 로고
    • The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification
    • Cavalier-Smith T. The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. Int J Syst Evol Microbiol 2002;52:7-76.
    • (2002) Int J Syst Evol Microbiol , vol.52 , pp. 7-76
    • Cavalier-Smith, T.1
  • 24
    • 0033557175 scopus 로고    scopus 로고
    • Major structural determinants of transmembrane proteins identified by principal component analysis
    • Koshi JM, Bruno WJ. Major structural determinants of transmembrane proteins identified by principal component analysis. Proteins 1999;34:333-340.
    • (1999) Proteins , vol.34 , pp. 333-340
    • Koshi, J.M.1    Bruno, W.J.2
  • 25
    • 0035795721 scopus 로고    scopus 로고
    • Amino acid distributions in integral membrane protein structures
    • Ulmschneider MB, Sansom MS. Amino acid distributions in integral membrane protein structures. Biochim Biophys Acta 2001;1512:1-14.
    • (2001) Biochim Biophys Acta , vol.1512 , pp. 1-14
    • Ulmschneider, M.B.1    Sansom, M.S.2
  • 27
    • 0036147641 scopus 로고    scopus 로고
    • Toward genomic identification of beta-barrel membrane proteins: Composition and architecture of known structures
    • Wimley WC. Toward genomic identification of beta-barrel membrane proteins: composition and architecture of known structures. Protein Sci 2002;11:301-312.
    • (2002) Protein Sci , vol.11 , pp. 301-312
    • Wimley, W.C.1
  • 28
    • 0038648028 scopus 로고    scopus 로고
    • Quantifying the species-specificity in genomic signatures, synonymous codon choice, amino acid usage and G+C content
    • Sandberg R, Branden CI, Ernberg I, Coster J. Quantifying the species-specificity in genomic signatures, synonymous codon choice, amino acid usage and G+C content. Gene 2003;311:35-42.
    • (2003) Gene , vol.311 , pp. 35-42
    • Sandberg, R.1    Branden, C.I.2    Ernberg, I.3    Coster, J.4
  • 29
    • 0036796799 scopus 로고    scopus 로고
    • Synonymous codon usage is subject to selection in thermophilic bacteria
    • Lynn DJ, Singer GA, Hickey DA. Synonymous codon usage is subject to selection in thermophilic bacteria. Nucleic Acids Res 2002;30:4272-4277.
    • (2002) Nucleic Acids Res , vol.30 , pp. 4272-4277
    • Lynn, D.J.1    Singer, G.A.2    Hickey, D.A.3
  • 30
    • 0023650543 scopus 로고
    • The Codon Adaptation Index-a measure of directional synonymous codon usage bias, and its potential applications
    • Sharp PM, Li WH. The Codon Adaptation Index-a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 1987;15:1281-1295.
    • (1987) Nucleic Acids Res , vol.15 , pp. 1281-1295
    • Sharp, P.M.1    Li, W.H.2
  • 31
    • 0032700253 scopus 로고    scopus 로고
    • The role of the codon first letter in the relationship between genomic GC content and protein amino acid composition
    • Wilquet V, Van de Casteele M. The role of the codon first letter in the relationship between genomic GC content and protein amino acid composition. Res Microbiol 1999;150:21-32.
    • (1999) Res Microbiol , vol.150 , pp. 21-32
    • Wilquet, V.1    Van De Casteele, M.2
  • 32
    • 0036606915 scopus 로고    scopus 로고
    • Base composition bias might result from competition for metabolic resources
    • Rocha EP, Danchin A. Base composition bias might result from competition for metabolic resources. Trends Genet 2002;18:291-294.
    • (2002) Trends Genet , vol.18 , pp. 291-294
    • Rocha, E.P.1    Danchin, A.2
  • 33
    • 1242317029 scopus 로고    scopus 로고
    • Intimate evolution of proteins: Proteome atomic content correlates with genome base composition
    • Baudouin-Cornu P, Schuerer K, Marliere P, Thomas D. Intimate evolution of proteins: proteome atomic content correlates with genome base composition. J Biol Chem 2004;279:5421-5428.
    • (2004) J Biol Chem , vol.279 , pp. 5421-5428
    • Baudouin-Cornu, P.1    Schuerer, K.2    Marliere, P.3    Thomas, D.4
  • 34
    • 0025344222 scopus 로고
    • A sensitive genetic assay for the detection of cytosine deamination: Determination of rate constants and the activation energy
    • Frederico LA, Kunkel TA, Shaw BR. A sensitive genetic assay for the detection of cytosine deamination: determination of rate constants and the activation energy. Biochemistry 1990;29:2532-2537.
    • (1990) Biochemistry , vol.29 , pp. 2532-2537
    • Frederico, L.A.1    Kunkel, T.A.2    Shaw, B.R.3
  • 35
    • 0032884548 scopus 로고    scopus 로고
    • Evolutionary changes reflected by the cellular amino acid composition
    • Sorimachi K. Evolutionary changes reflected by the cellular amino acid composition. Amino Acids 1999;17:207-226.
    • (1999) Amino Acids , vol.17 , pp. 207-226
    • Sorimachi, K.1
  • 36
    • 0032737311 scopus 로고    scopus 로고
    • Patterns of temperature adaptation in proteins from Methanococcus and Bacillus
    • McDonald JH, Grasso AM, Rejto LK. Patterns of temperature adaptation in proteins from Methanococcus and Bacillus. Mol Biol Evol 1999;16:1785-1790.
    • (1999) Mol Biol Evol , vol.16 , pp. 1785-1790
    • McDonald, J.H.1    Grasso, A.M.2    Rejto, L.K.3
  • 37
    • 0036606927 scopus 로고    scopus 로고
    • Evidence for cysteine clustering in thermophilic proteomes
    • Rosato V, Pucello N, Giuliano G. Evidence for cysteine clustering in thermophilic proteomes. Trends Genet 2002;18:278-281.
    • (2002) Trends Genet , vol.18 , pp. 278-281
    • Rosato, V.1    Pucello, N.2    Giuliano, G.3
  • 38
    • 0037115872 scopus 로고    scopus 로고
    • Comparative analysis of ribosomal proteins in complete genomes: An example of reductive evolution at the domain scale
    • Lecompte O, Ripp R, Thierry JC, Moras D, Poch O. Comparative analysis of ribosomal proteins in complete genomes: an example of reductive evolution at the domain scale. Nucleic Acids Res 2002;30: 5382-5390.
    • (2002) Nucleic Acids Res , vol.30 , pp. 5382-5390
    • Lecompte, O.1    Ripp, R.2    Thierry, J.C.3    Moras, D.4    Poch, O.5
  • 39
    • 0036606072 scopus 로고    scopus 로고
    • Conserved codon composition of ribosomal protein coding genes in Escherichia coli, Mycobacterium tuberculosis and Saccharomyces cerevisiae: Lessons from supervised machine learning in functional genomics
    • Lin K, Kuang Y, Joseph JS, Kolatkar PR. Conserved codon composition of ribosomal protein coding genes in Escherichia coli, Mycobacterium tuberculosis and Saccharomyces cerevisiae: lessons from supervised machine learning in functional genomics. Nucleic Acids Res 2002;30:2599-2607.
    • (2002) Nucleic Acids Res , vol.30 , pp. 2599-2607
    • Lin, K.1    Kuang, Y.2    Joseph, J.S.3    Kolatkar, P.R.4
  • 40
    • 0036463713 scopus 로고    scopus 로고
    • Increased frequency of cysteine, tyrosine, and phenylalanine residues since the last universal ancestor
    • Brooks DJ, Fresco JR. Increased frequency of cysteine, tyrosine, and phenylalanine residues since the last universal ancestor. Mol Cell Proteomics 2002;1:125-131.
    • (2002) Mol Cell Proteomics , vol.1 , pp. 125-131
    • Brooks, D.J.1    Fresco, J.R.2
  • 41
    • 0036721415 scopus 로고    scopus 로고
    • Aromatic side-chain interactions in proteins: II. Near- And far-sequence Phe-X pairs
    • Thomas A, Meurisse R, Brasseur R. Aromatic side-chain interactions in proteins: II. Near- and far-sequence Phe-X pairs. Proteins 2002;48:635-644.
    • (2002) Proteins , vol.48 , pp. 635-644
    • Thomas, A.1    Meurisse, R.2    Brasseur, R.3
  • 42
    • 0036721382 scopus 로고    scopus 로고
    • Aromatic side-chain interactions in proteins: I. Main structural features
    • Thomas A, Meurisse R, Charloteaux B, Brasseur R. Aromatic side-chain interactions in proteins: I. Main structural features. Proteins 2002;48:628-634.
    • (2002) Proteins , vol.48 , pp. 628-634
    • Thomas, A.1    Meurisse, R.2    Charloteaux, B.3    Brasseur, R.4
  • 43
    • 0025878347 scopus 로고
    • Pi-pi interactions: The geometry and energetics of phenylalanine- phenylalanine interactions in proteins
    • Hunter CA, Singh J, Thornton JM. Pi-pi interactions: the geometry and energetics of phenylalanine-phenylalanine interactions in proteins. J Mol Biol 1991;218:837-846.
    • (1991) J Mol Biol , vol.218 , pp. 837-846
    • Hunter, C.A.1    Singh, J.2    Thornton, J.M.3
  • 44
    • 0142028990 scopus 로고    scopus 로고
    • An evolutionary analysis of orphan genes in Drosophila
    • Domazet-Loso T, Tautz D. An evolutionary analysis of orphan genes in Drosophila. Genome Res 2003;13:2213-2219.
    • (2003) Genome Res , vol.13 , pp. 2213-2219
    • Domazet-Loso, T.1    Tautz, D.2
  • 45
    • 3042569657 scopus 로고    scopus 로고
    • Bacterial genomes as new gene homes: The genealogy of ORFans in E. coli
    • Daubin V, Ochman H. Bacterial genomes as new gene homes: the genealogy of ORFans in E. coli. Genome Res 2004;14:1036-1042.
    • (2004) Genome Res , vol.14 , pp. 1036-1042
    • Daubin, V.1    Ochman, H.2


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