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Volumn 31, Issue 23, 2003, Pages 6976-6985

Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; MESSENGER RNA; THYMINE;

EID: 0344237338     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg897     Document Type: Review
Times cited : (193)

References (52)
  • 1
    • 0018849680 scopus 로고
    • DNA sequences from the str operon of Escherichia coli
    • Post,L.E. and Nomura,M. (1980) DNA sequences from the str operon of Escherichia coli. J. Biol. Chem., 255, 4660-4666.
    • (1980) J. Biol. Chem. , vol.255 , pp. 4660-4666
    • Post, L.E.1    Nomura, M.2
  • 2
    • 0019474499 scopus 로고
    • Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes
    • Ikemura,T. (1981) Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes. J. Mol. Biol., 146, 1-21.
    • (1981) J. Mol. Biol. , vol.146 , pp. 1-21
    • Ikemura, T.1
  • 3
    • 0019824131 scopus 로고
    • Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: A proposal for a synonymous codon choice that is optimal for the E. coli translational system
    • Ikemura,T. (1981) Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system. J. Mol. Evol., 151, 389-409.
    • (1981) J. Mol. Evol. , vol.151 , pp. 389-409
    • Ikemura, T.1
  • 4
    • 0022856787 scopus 로고
    • An evolutionary perspective on synonymous codon usage in unicellular organisms
    • Sharp,P.M. and Li,W. (1986) An evolutionary perspective on synonymous codon usage in unicellular organisms. J. Mol. Evol., 24, 28-38.
    • (1986) J. Mol. Evol. , vol.24 , pp. 28-38
    • Sharp, P.M.1    Li, W.2
  • 5
    • 0025297285 scopus 로고
    • Codon preferences in free-living microorganisms
    • Anderson,S.G.E. and Kurland,C.G. (1990) Codon preferences in free-living microorganisms. Microbiol. Rev., 54, 198-210.
    • (1990) Microbiol. Rev. , vol.54 , pp. 198-210
    • Anderson, S.G.E.1    Kurland, C.G.2
  • 6
    • 0020024572 scopus 로고
    • Codon selection in yeast
    • Bennetzen,J.L. and Hall,B.D. (1982) Codon selection in yeast. J. Biol. Chem., 257, 3026-3031.
    • (1982) J. Biol. Chem. , vol.257 , pp. 3026-3031
    • Bennetzen, J.L.1    Hall, B.D.2
  • 7
    • 0025941139 scopus 로고
    • The selection-mutation-drift theory of synonymous codon usage
    • Bulmer,M. (1991) The selection-mutation-drift theory of synonymous codon usage. Genetics, 149, 897-907.
    • (1991) Genetics , vol.149 , pp. 897-907
    • Bulmer, M.1
  • 8
    • 0027715731 scopus 로고
    • Codon usage: Mutational bias, translational selection, or both?
    • Sharp,P.M., Stenico,M., Peden,J.F. and Lloyd,A.T. (1993) Codon usage: mutational bias, translational selection, or both? Biochem. Soc. Trans, 21, 835-841.
    • (1993) Biochem. Soc. Trans. , vol.21 , pp. 835-841
    • Sharp, P.M.1    Stenico, M.2    Peden, J.F.3    Lloyd, A.T.4
  • 9
    • 0036889468 scopus 로고    scopus 로고
    • Evolution of synonymous codon usage in metazoans
    • Laurent,D. (2002) Evolution of synonymous codon usage in metazoans. Curr. Opin. Genet. Dev., 12, 640-649.
    • (2002) Curr. Opin. Genet. Dev. , vol.12 , pp. 640-649
    • Laurent, D.1
  • 10
    • 0028359705 scopus 로고
    • Codon usage in Caenorhabditis elegans: Delineation of translational selection and mutational bias
    • Stenico,M., Lloyd,A.T. and Sharp,P.M. (1994) Codon usage in Caenorhabditis elegans: delineation of translational selection and mutational bias. Nucleic Acids Res., 22, 2437-2446.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 2437-2446
    • Stenico, M.1    Lloyd, A.T.2    Sharp, P.M.3
  • 11
    • 0033551151 scopus 로고    scopus 로고
    • Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila and Arabidopsis
    • Duret,L. and Mouchiroud,D. (1999) Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila and Arabidopsis. Proc. Natl Acad. Sci. USA, 96, 4482-4487.
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 4482-4487
    • Duret, L.1    Mouchiroud, D.2
  • 12
    • 0031738130 scopus 로고    scopus 로고
    • Translational selection and molecular evolution
    • Akashi,H. and Eyre-Walker,A. (1998) Translational selection and molecular evolution. Curr. Opin. Genet. Dev., 8, 688-693.
    • (1998) Curr. Opin. Genet. Dev. , vol.8 , pp. 688-693
    • Akashi, H.1    Eyre-Walker, A.2
  • 13
    • 0035546157 scopus 로고    scopus 로고
    • Gene expression and molecular evolution
    • Akashi,H. (2001) Gene expression and molecular evolution. Curr. Opin. Genet. Dev., 11, 660-666.
    • (2001) Curr. Opin. Genet. Dev. , vol.11 , pp. 660-666
    • Akashi, H.1
  • 14
    • 0034666040 scopus 로고    scopus 로고
    • Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae
    • Coghlan,A. and Wolfe,K.H. (2000) Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae. Yeast, 16, 1131-1145.
    • (2000) Yeast , vol.16 , pp. 1131-1145
    • Coghlan, A.1    Wolfe, K.H.2
  • 15
    • 0036098278 scopus 로고    scopus 로고
    • Genome evolution and developmental constraint in Caenorhabditis elegans
    • Castillo-Davis,C.I. and Hartl,D.L. (2002) Genome evolution and developmental constraint in Caenorhabditis elegans. Mol. Biol. Evol., 19, 728-735.
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 728-735
    • Castillo-Davis, C.I.1    Hartl, D.L.2
  • 18
    • 0036224939 scopus 로고    scopus 로고
    • Over 1000 genes are involved in the DNA damage response of Escherichia coli
    • Khil,P.P. and Camerini-Otero,R.D. (2002) Over 1000 genes are involved in the DNA damage response of Escherichia coli. Mol. Microbiol., 44, 89-105.
    • (2002) Mol. Microbiol. , vol.44 , pp. 89-105
    • Khil, P.P.1    Camerini-Otero, R.D.2
  • 19
    • 0037162469 scopus 로고    scopus 로고
    • Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-colour fluorescent DNA microarrays
    • Bernstein,J.A., Khodursky,A.B., Lin,P.H., Lin-Chao,S. and Cohen,S.N. (2002) Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-colour fluorescent DNA microarrays. Proc. Natl Acad. Sci. USA, 99, 9697-9702.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 9697-9702
    • Bernstein, J.A.1    Khodursky, A.B.2    Lin, P.H.3    Lin-Chao, S.4    Cohen, S.N.5
  • 20
    • 0025286203 scopus 로고
    • The effect of context on synonymous codon usage in genes with low codon usage bias
    • Bulmer,M. (1990) The effect of context on synonymous codon usage in genes with low codon usage bias. Nucleic Acids Res., 18, 2869-2873.
    • (1990) Nucleic Acids Res. , vol.18 , pp. 2869-2873
    • Bulmer, M.1
  • 21
    • 0344898766 scopus 로고
    • Evidence for use of rare codons in the danG gene and other regulatory genes of Escherichia coli
    • Kronigsberg,W. and Codson,G.N. (1983) Evidence for use of rare codons in the danG gene and other regulatory genes of Escherichia coli. Proc. Natl Acad. Sci. USA, 80, 687-691.
    • (1983) Proc. Natl. Acad. Sci. USA , vol.80 , pp. 687-691
    • Kronigsberg, W.1    Codson, G.N.2
  • 22
    • 0022856787 scopus 로고
    • Codon usage in regulatory genes in Escherichia coli does not reflect selection for 'rare' codons
    • Sharp,P.M. and Li,W. (1986) Codon usage in regulatory genes in Escherichia coli does not reflect selection for 'rare' codons. Nucleic Acids Res., 24, 28-38.
    • (1986) Nucleic Acids Res. , vol.24 , pp. 28-38
    • Sharp, P.M.1    Li, W.2
  • 24
    • 0023650543 scopus 로고
    • The codon adaptation index - A measure of directional synonymous codon usage bias and its potential applications
    • Sharp,P.M. and Li,W. (1986) The codon adaptation index - a measure of directional synonymous codon usage bias and its potential applications. Nucleic Acids Res., 15, 1281-1295.
    • (1986) Nucleic Acids Res. , vol.15 , pp. 1281-1295
    • Sharp, P.M.1    Li, W.2
  • 25
    • 0025318864 scopus 로고
    • The 'effective number of codons' used in a gene
    • Wright,F. (1990) The 'effective number of codons' used in a gene. Gene, 87, 23-29.
    • (1990) Gene , vol.87 , pp. 23-29
    • Wright, F.1
  • 26
    • 0020475449 scopus 로고
    • A simple method for displaying the hydropathic character of a protein
    • Kyte,J. and Doolittle,R.F. (1982) A simple method for displaying the hydropathic character of a protein. J. Mol. Biol., 157, 105-132.
    • (1982) J. Mol. Biol. , vol.157 , pp. 105-132
    • Kyte, J.1    Doolittle, R.F.2
  • 27
    • 0037109119 scopus 로고    scopus 로고
    • Use and misuse of correspondence analysis in codon usage studies
    • Perrière,G. and Thioulouse,J. (2002) Use and misuse of correspondence analysis in codon usage studies. Nucleic Acids Res., 30, 4548-4555.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 4548-4555
    • Perrière, G.1    Thioulouse, J.2
  • 30
    • 0030854739 scopus 로고    scopus 로고
    • tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence
    • Lowe,T.M. and Eddy,S.R. (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res., 25, 955-964.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 955-964
    • Lowe, T.M.1    Eddy, S.R.2
  • 31
    • 0027762486 scopus 로고
    • Major codon preference: Theme and variations
    • Kurland,C.G., (1993) Major codon preference: theme and variations. Biochem. Soc. Trans, 22, 841-846.
    • (1993) Biochem. Soc. Trans. , vol.22 , pp. 841-846
    • Kurland, C.G.1
  • 32
    • 0032882170 scopus 로고    scopus 로고
    • Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAs: Gene expression level and species-specific diversity of codon usage based on multivariate analysis
    • Kanaya,S., Yamada,Y., Kudo,Y. and Ikemura,T. (1999) Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAs: gene expression level and species-specific diversity of codon usage based on multivariate analysis. Gene, 238, 143-155.
    • (1999) Gene , vol.238 , pp. 143-155
    • Kanaya, S.1    Yamada, Y.2    Kudo, Y.3    Ikemura, T.4
  • 34
    • 0031694427 scopus 로고    scopus 로고
    • An evaluation of measures of synonymous codon usage bias
    • Comeron,J.M. and Aguadé,M. (1998) An evaluation of measures of synonymous codon usage bias. J. Mol. Evol., 47, 268-274.
    • (1998) J. Mol. Evol. , vol.47 , pp. 268-274
    • Comeron, J.M.1    Aguadé, M.2
  • 35
    • 0028088517 scopus 로고
    • Hydrophobicity, expressivity and aromaticity are the major trends of amino-acid usage in 999 Escherichia coli chromosome-encoded genes
    • 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.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 3174-3180
    • Lobry, J.R.1    Gautier, C.2
  • 37
    • 0026332291 scopus 로고
    • Evidence for horizontal gene transfer in Escherichia coli speciation
    • Médigue,C., Rouxel,T., Vigier,P., Hénaut,A. and Danchin,A. (1991) Evidence for horizontal gene transfer in Escherichia coli speciation. J. Mol. Evol., 222, 851-856.
    • (1991) J. Mol. Evol. , vol.222 , pp. 851-856
    • Médigue, C.1    Rouxel, T.2    Vigier, P.3    Hénaut, A.4    Danchin, A.5
  • 38
    • 0000526062 scopus 로고    scopus 로고
    • Phylogenetics and the amelioration of bacterial genomes
    • Neidhardt,F.C. (ed.), ASM Press, Washington, DC
    • Ochman,H. and Lawrence,J.G. (1996) Phylogenetics and the amelioration of bacterial genomes. In Neidhardt,F.C. (ed.), Escherichia coli and Salmonella, Cellular and Molecular Biology. ASM Press, Washington, DC, Vol. II, pp. 2627-2637.
    • (1996) Escherichia Coli and Salmonella, Cellular and Molecular Biology , vol.2 , pp. 2627-2637
    • Ochman, H.1    Lawrence, J.G.2
  • 39
    • 0001620789 scopus 로고    scopus 로고
    • Genetic variation and evolutionary processes in natural populations of Escherichia coli
    • Neidhardt,F.C. (ed.), ASM Press, Washington, DC
    • Whittam,T.S. (1996) Genetic variation and evolutionary processes in natural populations of Escherichia coli. In Neidhardt,F.C. (ed.), Escherichia coli and Salmonella, Cellular and Molecular Biology. ASM Press, Washington, DC, Vol. II, pp. 2708-2720.
    • (1996) Escherichia Coli and Salmonella, Cellular and Molecular Biology , vol.2 , pp. 2708-2720
    • Whittam, T.S.1
  • 40
    • 0032482924 scopus 로고    scopus 로고
    • Molecular archaeology of the Escherichia coli genome
    • Lawrence,J.G. and Ochman,H. (1998) Molecular archaeology of the Escherichia coli genome. Proc. Natl Acad. Sci. USA, 95, 9413-9417.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 9413-9417
    • Lawrence, J.G.1    Ochman, H.2
  • 41
    • 0033670249 scopus 로고    scopus 로고
    • Horizontal gene transfer in bacterial and archaeal complete genomes
    • Garcia-Vallve,S., Romeu,A. and Palau,J. (2000) Horizontal gene transfer in bacterial and archaeal complete genomes. Genome Res., 10, 1719-1725.
    • (2000) Genome Res. , vol.10 , pp. 1719-1725
    • Garcia-Vallve, S.1    Romeu, A.2    Palau, J.3
  • 42
    • 0034888743 scopus 로고    scopus 로고
    • Characterizations of highly expressed genes of four fast-growing bacteria
    • Karlin,S., Mrázek,J., Campbell,A. and Kaiser,D. (2001) Characterizations of highly expressed genes of four fast-growing bacteria. J. Bacteriol., 187, 5025-5040.
    • (2001) J. Bacteriol. , vol.187 , pp. 5025-5040
    • Karlin, S.1    Mrázek, J.2    Campbell, A.3    Kaiser, D.4
  • 43
    • 0029931535 scopus 로고    scopus 로고
    • Synonymous codon bias is related to gene length in Escherichia coli: Selection for translational accuracy?
    • Eyre-Walker,A. (1996) Synonymous codon bias is related to gene length in Escherichia coli: selection for translational accuracy? Mol. Biol. Evol., 13, 864-872.
    • (1996) Mol. Biol. Evol. , vol.13 , pp. 864-872
    • Eyre-Walker, A.1
  • 44
    • 0019188794 scopus 로고
    • Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type
    • Grantham,R., Gautier,C. and Gouy,M. (1980) Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type. Nucleic Acids Res., 8, 1893-1912.
    • (1980) Nucleic Acids Res. , vol.8 , pp. 1893-1912
    • Grantham, R.1    Gautier, C.2    Gouy, M.3
  • 46
    • 0023046874 scopus 로고
    • Codon usage in yeast: Cluster analysis clearly differentiates highly and lowly expressed genes
    • Sharp,P.M., Tuohy,T.M.F. and Mosurski,K.R. (1986) Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Res., 14, 5125-5143.
    • (1986) Nucleic Acids Res. , vol.14 , pp. 5125-5143
    • Sharp, P.M.1    Tuohy, T.M.F.2    Mosurski, K.R.3
  • 48
    • 17444449538 scopus 로고    scopus 로고
    • Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae
    • Percudani,R., Pavesi,A. and Ottonello,S. (1997) Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae. J. Mol. Biol., 268, 322-330.
    • (1997) J. Mol. Biol. , vol.268 , pp. 322-330
    • Percudani, R.1    Pavesi, A.2    Ottonello, S.3
  • 49
    • 0034237669 scopus 로고    scopus 로고
    • tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes
    • Duret,L. (2000) tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes. Trends Genet., 16, 287-289.
    • (2000) Trends Genet. , vol.16 , pp. 287-289
    • Duret, L.1
  • 50
    • 0000908762 scopus 로고    scopus 로고
    • Analysis and predictions from Escherichia coli sequences, or E. coli in silico
    • Neidhardt,F.C. (ed.), ASM Press, Washington, DC
    • Hénaut,A. and Danchin,A. (1996) Analysis and predictions from Escherichia coli sequences, or E. coli in silico. In Neidhardt,F.C. (ed.), Escherichia coli and Salmonella, Cellular and Molecular Biology. ASM Press, Washington, DC, Vol. II, pp. 2047-2066.
    • (1996) Escherichia Coli and Salmonella, Cellular and Molecular Biology , vol.2 , pp. 2047-2066
    • Hénaut, A.1    Danchin, A.2
  • 51
    • 0023645180 scopus 로고
    • Structure-function studies on bacteriorhodopsin
    • Nassal,M., Mogi,T., Karnik,S.S. and Khorana,H.G. (1987) Structure-function studies on bacteriorhodopsin. J. Biol. Chem., 262, 9264-9270.
    • (1987) J. Biol. Chem. , vol.262 , pp. 9264-9270
    • Nassal, M.1    Mogi, T.2    Karnik, S.S.3    Khorana, H.G.4
  • 52
    • 0036133146 scopus 로고    scopus 로고
    • Correlations between mRNA expression levels and GC contents of coding and untranslated regions of genes in rodents
    • Konu,Ö. and Li,M.D. (2002) Correlations between mRNA expression levels and GC contents of coding and untranslated regions of genes in rodents. J. Mol. Evol., 54, 35-41.
    • (2002) J. Mol. Evol. , vol.54 , pp. 35-41
    • Konu, Ö.1    Li, M.D.2


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