메뉴 건너뛰기




Volumn 149, Issue 4, 2003, Pages 855-863

Translational selection is operative for synonymous codon usage in Clostridium perfringens and Clostridium acetobutylicum

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; CYTOSINE; GUANINE; THYMINE;

EID: 0038705152     PISSN: 13500872     EISSN: None     Source Type: Journal    
DOI: 10.1099/mic.0.26063-0     Document Type: Review
Times cited : (26)

References (38)
  • 1
    • 0031738130 scopus 로고    scopus 로고
    • Translational selection and molecular evolution
    • Akashi, H. & 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
  • 3
    • 0022914759 scopus 로고
    • Compositional constraints and genome evolution
    • Bernardi, G. & Bernardi, G. (1986). Compositional constraints and genome evolution. J Mol Evol 24, 1-11.
    • (1986) J. Mol. Evol. , vol.24 , pp. 1-11
    • Bernardi, G.1    Bernardi, G.2
  • 4
    • 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 129, 897-907.
    • (1991) Genetics , vol.129 , pp. 897-907
    • Bulmer, M.1
  • 5
    • 0033921447 scopus 로고    scopus 로고
    • Gene expression, amino acid conservation, and hydrophobicity are the main factors shaping codon preferences in Mycobacterium tuberculosis and Mycobacterium leprae
    • de Miranda, A. B., Alvarez-Valin, F., Jabbari, K., Degrave, W. M. & Bernardi, G. (2000). Gene expression, amino acid conservation, and hydrophobicity are the main factors shaping codon preferences in Mycobacterium tuberculosis and Mycobacterium leprae. J Mol Evol 50, 45-55.
    • (2000) J. Mol. Evol. , vol.50 , pp. 45-55
    • de Miranda, A.B.1    Alvarez-Valin, F.2    Jabbari, K.3    Degrave, W.M.4    Bernardi, G.5
  • 6
  • 7
    • 0030564828 scopus 로고    scopus 로고
    • Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates
    • Dong, H., Nilsson, L. & Kurland, C. G. (1996). Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates. J Mol Biol 260, 649-663.
    • (1996) J. Mol. Biol. , vol.260 , pp. 649-663
    • Dong, H.1    Nilsson, L.2    Kurland, C.G.3
  • 8
    • 0033995545 scopus 로고    scopus 로고
    • Horizontal gene transfer of glycosyl hydrolases of the rumen fungi
    • Garcia-Vallve, S., Romeu, A. & Palau, J. (2000). Horizontal gene transfer of glycosyl hydrolases of the rumen fungi. Mol Biol Evol 17, 352-361.
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 352-361
    • Garcia-Vallve, S.1    Romeu, A.2    Palau, J.3
  • 10
    • 0020491327 scopus 로고
    • Codon usage in bacteria: Correlation with gene expressivity
    • Gouy, M. & Gautier, C. (1982). Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res 10, 7055-7074.
    • (1982) Nucleic Acids Res. , vol.10 , pp. 7055-7074
    • Gouy, M.1    Gautier, C.2
  • 13
    • 0036572274 scopus 로고    scopus 로고
    • Synonymous codon usage in Pseudomonas aeruginosa PAO1
    • Grocock, R. J. & Sharp, P. M. (2002). Synonymous codon usage in Pseudomonas aeruginosa PAO1. Gene 289, 131-139.
    • (2002) Gene , vol.289 , pp. 131-139
    • Grocock, R.J.1    Sharp, P.M.2
  • 14
    • 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 Biol 151, 389-409.
    • (1981) J. Mol. Biol. , vol.151 , pp. 389-409
    • Ikemura, T.1
  • 15
    • 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. & 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
  • 16
    • 0035399931 scopus 로고    scopus 로고
    • Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes
    • Karlin, S. (2001). Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes. Trends Microbiol 9, 335-343.
    • (2001) Trends Microbiol. , vol.9 , pp. 335-343
    • Karlin, S.1
  • 17
    • 0030886877 scopus 로고    scopus 로고
    • Systematic base composition variation around the genome of Mycoplasma genitalium, but not Mycoplasma pneumoniae
    • Kerr, A. R., Peden, J. F. & Sharp, P. M. (1997). Systematic base composition variation around the genome of Mycoplasma genitalium, but not Mycoplasma pneumoniae. Mol Microbiol 25, 1177-1179.
    • (1997) Mol. Microbiol. , vol.25 , pp. 1177-1179
    • Kerr, A.R.1    Peden, J.F.2    Sharp, P.M.3
  • 18
    • 0033118273 scopus 로고    scopus 로고
    • Proteome composition and codon usage in spirochaetes: Species-specific and DNA strand-specific mutational biases
    • Lafay, B., Lloyd, A. T., McLean, M. J., Devine, K. M., Sharp, P. M. & Wolfe, K. H. (1999). Proteome composition and codon usage in spirochaetes: species-specific and DNA strand-specific mutational biases. Nucleic Acids Res 27, 1642-1649.
    • (1999) Nucleic Acids Res. , vol.27 , pp. 1642-1649
    • Lafay, B.1    Lloyd, A.T.2    McLean, M.J.3    Devine, K.M.4    Sharp, P.M.5    Wolfe, K.H.6
  • 19
    • 0034086295 scopus 로고    scopus 로고
    • Absence of translationally selected synonymous codon usage bias in Helicobacter pylori
    • Lafay, B., Atherton, J. C. & Sharp, P. M. (2000). Absence of translationally selected synonymous codon usage bias in Helicobacter pylori. Microbiology 146, 851-860.
    • (2000) Microbiology , vol.146 , pp. 851-860
    • Lafay, B.1    Atherton, J.C.2    Sharp, P.M.3
  • 20
    • 0027403961 scopus 로고
    • Unbiased estimation of the rates of synonymous and nonsynonymous substitution
    • Li, W. H. (1993). Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J Mol Evol 36, 96-99.
    • (1993) J. Mol. Evol. , vol.36 , pp. 96-99
    • Li, W.H.1
  • 21
    • 0029938912 scopus 로고    scopus 로고
    • Origin of replication of Mycoplasma genitalium
    • Lobry, J. R. (1996). Origin of replication of Mycoplasma genitalium. Science 272, 745-746.
    • (1996) Science , vol.272 , pp. 745-746
    • Lobry, J.R.1
  • 22
    • 84975862989 scopus 로고    scopus 로고
    • Prokaryotic genome evolution as assessed by multivariate analysis of codon usage patterns
    • McInerney, J. O. (1997). Prokaryotic genome evolution as assessed by multivariate analysis of codon usage patterns. Microb Comp Genomics 2, 1-10.
    • (1997) Microb. Comp. Genomics , vol.2 , pp. 1-10
    • McInerney, J.O.1
  • 23
    • 0032169578 scopus 로고    scopus 로고
    • Replicational and transcriptional selection on codon usage in Borrelia burgdorferi
    • McInerney, J. O. (1998). Replicational and transcriptional selection on codon usage in Borrelia burgdorferi. Proc Natl Acad Sci U S A 95, 10698-10703.
    • (1998) Proc. Natl. Acad. Sci. U S A , vol.95 , pp. 10698-10703
    • McInerney, J.O.1
  • 24
    • 0033050538 scopus 로고    scopus 로고
    • Synonymous codon choices in the extremely GC-poor genome of Plasmodium falciparum: Compositional constraints and translational selection
    • Musto, H., Romero, H., Zavala, A., Jabbari, K. & Bernardi, G. (1999). Synonymous codon choices in the extremely GC-poor genome of Plasmodium falciparum: compositional constraints and translational selection. J Mol Evol 49, 27-35.
    • (1999) J. Mol. Evol. , vol.49 , pp. 27-35
    • Musto, H.1    Romero, H.2    Zavala, A.3    Jabbari, K.4    Bernardi, G.5
  • 25
    • 0013596021 scopus 로고
    • The guanine and cytosine content of genomic DNA and bacterial evolution
    • Muto, A. & Osawa, S. (1987). The guanine and cytosine content of genomic DNA and bacterial evolution. Proc Natl Acad Sci U S A 84, 166-169.
    • (1987) Proc. Natl. Acad. Sci. U S A , vol.84 , pp. 166-169
    • Muto, A.1    Osawa, S.2
  • 26
    • 0022507362 scopus 로고
    • Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions
    • Nei, M. & Gojobori, T. (1986). Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3, 418-426.
    • (1986) Mol. Biol. Evol. , vol.3 , pp. 418-426
    • Nei, M.1    Gojobori, T.2
  • 27
    • 0034902930 scopus 로고    scopus 로고
    • Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum
    • & 16 other authors
    • Nolling, J., Breton, G., Omelchenko, M. V. & 16 other authors (2001). Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum. J Bacteriol 183, 4823-4838.
    • (2001) J. Bacteriol. , vol.183 , pp. 4823-4838
    • Nolling, J.1    Breton, G.2    Omelchenko, M.V.3
  • 28
    • 17444449538 scopus 로고    scopus 로고
    • Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae
    • Percudani, R., Pavesi, A. & 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
  • 29
    • 0018638965 scopus 로고
    • Nucleotide sequence of the intercistronic region preceding the gene for RNA polymerase subunit alpha in Escherichia coli
    • Post, L. E. & Nomura, M. (1979). Nucleotide sequence of the intercistronic region preceding the gene for RNA polymerase subunit alpha in Escherichia coli. J Biol Chem 254, 10604-10606.
    • (1979) J. Biol. Chem. , vol.254 , pp. 10604-10606
    • Post, L.E.1    Nomura, M.2
  • 30
    • 0034657798 scopus 로고    scopus 로고
    • Codon usage in Chlamydia trachomatis is the result of strand-specific mutational biases and a complex pattern of selective forces
    • Romero, H., Zavala, A. & Musto, H. (2000a). Codon usage in Chlamydia trachomatis is the result of strand-specific mutational biases and a complex pattern of selective forces. Nucleic Acids Res 28, 2084-2090.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 2084-2090
    • Romero, H.1    Zavala, A.2    Musto, H.3
  • 31
    • 0033959348 scopus 로고    scopus 로고
    • Compositional pressure and translational selection determine codon usage in the extremely GC-poor unicellular eukaryote Entamoeba histolytica
    • Romero, H., Zavala, A. & Musto, H. (2000b). Compositional pressure and translational selection determine codon usage in the extremely GC-poor unicellular eukaryote Entamoeba histolytica. Gene 242, 307-311.
    • (2000) Gene , vol.242 , pp. 307-311
    • Romero, H.1    Zavala, A.2    Musto, H.3
  • 32
    • 0022856787 scopus 로고
    • An evolutionary perspective on synonymous codon usage in unicellular organisms
    • Sharp, P. M. & Li, W. H. (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.H.2
  • 33
    • 0023650543 scopus 로고
    • The codon Adaptation Index: A measure of directional synonymous codon usage bias, and its potential applications
    • Sharp, P. M. & Li, W. H. (1987). The codon Adaptation Index: a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 15, 1281-1295.
    • (1987) Nucleic Acids Res. , vol.15 , pp. 1281-1295
    • Sharp, P.M.1    Li, W.H.2
  • 34
    • 0023046874 scopus 로고
    • Codon usage in yeast: Cluster analysis clearly differentiates highly and lowly expressed genes
    • Sharp, P. M., Tuohy, T. M. & 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.2    Mosurski, K.R.3
  • 35
    • 0037154260 scopus 로고    scopus 로고
    • Complete genome sequence of Clostridium perfringens, an anaerobic flesh-eater
    • & 7 other authors
    • Shimizu, T., Ohtani, K., Hirakawa, H. & 7 other authors (2002). Complete genome sequence of Clostridium perfringens, an anaerobic flesh-eater. Proc Natl Acad Sci U S A 99, 996-1001.
    • (2002) Proc. Natl. Acad. Sci. U S A , vol.99 , pp. 996-1001
    • Shimizu, T.1    Ohtani, K.2    Hirakawa, H.3
  • 36
    • 3643052747 scopus 로고
    • On the genetic basis of variation and heterogeneity of DNA base composition
    • Sueoka, N. (1962). On the genetic basis of variation and heterogeneity of DNA base composition. Proc Natl Acad Sci U S A 48, 582-592.
    • (1962) Proc. Natl. Acad. Sci. U S A , vol.48 , pp. 582-592
    • Sueoka, N.1
  • 37
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673-4680.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 38
    • 0036216144 scopus 로고    scopus 로고
    • Trends in codon and amino acid usage in Thermotoga maritima
    • Zavala, A., Naya, H., Romero, H. & Musto, H. (2002). Trends in codon and amino acid usage in Thermotoga maritima. J Mol Evol 54, 563-568.
    • (2002) J. Mol. Evol. , vol.54 , pp. 563-568
    • Zavala, A.1    Naya, H.2    Romero, H.3    Musto, H.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.