메뉴 건너뛰기




Volumn 86, Issue 2, 2004, Pages 135-147

Bioinformatic analysis of the link between gene composition and expressivity in Saccharomyces cerevisiae and Schizosaccharomyces pombe

Author keywords

Codon optimization; Codon usage; DNA composition; Expression levels; Yeast

Indexed keywords

ALANINE; ARGININE; ASPARAGINE; ASPARTIC ACID; CYSTEINE; GLUTAMIC ACID; GLUTAMINE; GLYCINE; HISTIDINE; ISOLEUCINE; LEUCINE; LYSINE; METHIONINE; NUCLEOTIDE; PHENYLALANINE; PROLINE; SERINE; THREONINE; TRYPTOPHAN; TYROSINE; VALINE;

EID: 4043074964     PISSN: 00036072     EISSN: None     Source Type: Journal    
DOI: 10.1023/B:ANTO.0000036119.00001.3b     Document Type: Article
Times cited : (9)

References (43)
  • 1
    • 0036389792 scopus 로고    scopus 로고
    • Improvement of human interferon HUIFNalpha2 and HCV core protein expression levels in Escherichia coli but not of HUIFNalpha8 by using the tRNA(AGA/AGG)
    • Acosta-Rivero N., Sanchez J.C. and Morales J. 2002. Improvement of human interferon HUIFNalpha2 and HCV core protein expression levels in Escherichia coli but not of HUIFNalpha8 by using the tRNA(AGA/AGG). Biochem. Biophys. Res. Commun. 296: 1303-1309.
    • (2002) Biochem. Biophys. Res. Commun. , vol.296 , pp. 1303-1309
    • Acosta-Rivero, N.1    Sanchez, J.C.2    Morales, J.3
  • 2
    • 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
  • 4
    • 0029153552 scopus 로고
    • The efficiency of translation termination is determined by a synergistic interplay between upstream and downstream sequences in Saccharomyces cerevisiae
    • Bonetti B., Fu L., Moon J. and Bedwell D.M. 1995. The efficiency of translation termination is determined by a synergistic interplay between upstream and downstream sequences in Saccharomyces cerevisiae. J. Mol. Biol. 251: 334-345.
    • (1995) J. Mol. Biol. , vol.251 , pp. 334-345
    • Bonetti, B.1    Fu, L.2    Moon, J.3    Bedwell, D.M.4
  • 5
    • 0023126266 scopus 로고
    • Coevolution of codon usage and transfer RNA abundance
    • Bulmer M. 1987. Coevolution of codon usage and transfer RNA abundance. Nature 325: 728-730.
    • (1987) Nature , vol.325 , pp. 728-730
    • Bulmer, M.1
  • 6
    • 0023813828 scopus 로고
    • Codon usage and intragenic position
    • Bulmer M. 1988. Codon usage and intragenic position. J. Theor. Biol. 133: 67-71.
    • (1988) J. Theor. Biol. , vol.133 , pp. 67-71
    • Bulmer, M.1
  • 8
    • 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
  • 9
    • 0031694427 scopus 로고    scopus 로고
    • An evaluation of measures of synonymous codon usage bias
    • Comeron J.M. and Aguade M. 1998. An evaluation of measures of synonymous codon usage bias. J. Mol. Evol. 48: 268-274.
    • (1998) J. Mol. Evol. , vol.48 , pp. 268-274
    • Comeron, J.M.1    Aguade, M.2
  • 10
    • 0028181116 scopus 로고
    • Human interferon-beta, expressed in Saccharomyces cerevisiae, is predominantly directed to the vacuoles. Influence of modified co-expression of secretion factors and chaperones
    • Demolder J., Fiers W. and Contreras R. 1994. Human interferon-beta, expressed in Saccharomyces cerevisiae, is predominantly directed to the vacuoles. Influence of modified co-expression of secretion factors and chaperones. J. Biotechnol. 32: 179-189.
    • (1994) J. Biotechnol. , vol.32 , pp. 179-189
    • Demolder, J.1    Fiers, W.2    Contreras, R.3
  • 11
    • 0033551151 scopus 로고    scopus 로고
    • Expression pattern and, surprisingly, gene length, shape codon usage in Caeenorhabditis, Drosophila and Arabidopsis
    • Duret L. and Mouchiroud D. 1999. Expression pattern and, surprisingly, gene length, shape codon usage in Caeenorhabditis, Drosophila and Arabidopsis. Proc. Natl. Acad. Sci. 96: 4482-4487.
    • (1999) Proc. Natl. Acad. Sci. , vol.96 , pp. 4482-4487
    • Duret, L.1    Mouchiroud, D.2
  • 12
    • 0033977618 scopus 로고    scopus 로고
    • Determinants of substitution rates in mammalian genes: Expression pattern affects selection intensity but not mutation rate
    • Duret L. and Mouchiroud D. 2000. Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate. Mol. Biol. Evol. 17: 68-74.
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 68-74
    • Duret, L.1    Mouchiroud, D.2
  • 13
    • 0026016564 scopus 로고
    • Quantitation of readthrough of termination codons in yeast using a novel gene fusion assay
    • Firoozan M., Grant C.M., Duarte J.A. and Tuite M.F. 1991. Quantitation of readthrough of termination codons in yeast using a novel gene fusion assay. Yeast 7: 173-183.
    • (1991) Yeast , vol.7 , pp. 173-183
    • Firoozan, M.1    Grant, C.M.2    Duarte, J.A.3    Tuite, M.F.4
  • 14
    • 0242267013 scopus 로고    scopus 로고
    • Association of the x nucleotide to codon bias, amino acid usage and expressivity: Differences between Bacillus subtilis and Escherichia coli
    • Fuglsang A. 2003. Association of the x nucleotide to codon bias, amino acid usage and expressivity: differences between Bacillus subtilis and Escherichia coli. APMIS 111: 926-930.
    • (2003) APMIS , vol.111 , pp. 926-930
    • Fuglsang, A.1
  • 15
    • 0037428283 scopus 로고    scopus 로고
    • Non-randomness in Shine-Dalgarno regions: Links to gene characteristics
    • Fuglsang A. and Engberg J. 2003. Non-randomness in Shine-Dalgarno regions: links to gene characteristics. Biochem. Bopphys. Res. Comm. 302: 296-301.
    • (2003) Biochem. Bopphys. Res. Comm. , vol.302 , pp. 296-301
    • Fuglsang, A.1    Engberg, J.2
  • 16
    • 0020491327 scopus 로고
    • Codon usage in bacteria: Correlation with gene expressivity
    • Gouy M. and Gautier G. 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, G.2
  • 17
    • 0030151989 scopus 로고    scopus 로고
    • Specific replacement of consecutive AGG codons results in high-level expression of human cardiac troponin T in Escherichia coli
    • Hu X., Shi Q., Yang T. and Jackowski G. 1996. Specific replacement of consecutive AGG codons results in high-level expression of human cardiac troponin T in Escherichia coli. Protein Expr. Purif. 7: 289-293.
    • (1996) Protein Expr. Purif. , vol.7 , pp. 289-293
    • Hu, X.1    Shi, Q.2    Yang, T.3    Jackowski, G.4
  • 18
    • 0021958933 scopus 로고
    • Codon usage and tRNA content in unicellular and multicellular organisms
    • Ikemura T. 1985. Codon usage and tRNA content in unicellular and multicellular organisms. Mol. Biol. Evol. 2: 13-34.
    • (1985) Mol. Biol. Evol. , vol.2 , pp. 13-34
    • Ikemura, T.1
  • 19
    • 0020262659 scopus 로고
    • Codon usage and transfer RNA contents: Organism-specific codon-choice patterns in reference to the isoacceptor contents
    • Ikemura T. and Ozeki H. 1983. Codon usage and transfer RNA contents: organism-specific codon-choice patterns in reference to the isoacceptor contents. Cold Spring Harb. Symp. Quant. Biol. 47: 1087-1097.
    • (1983) Cold Spring Harb. Symp. Quant. Biol. , vol.47 , pp. 1087-1097
    • Ikemura, T.1    Ozeki, H.2
  • 21
    • 0034821884 scopus 로고    scopus 로고
    • Codon usage and tRNA genes in eukaryotes: Correlation of codon usage diversity with translation efficiency and with CG-dinucleotide usage as assessed by multivariate analysis
    • Kanaya S., Yamada Y., Kinouchi M., Kudo Y. and Ikemura T. 2001. Codon usage and tRNA genes in eukaryotes: correlation of codon usage diversity with translation efficiency and with CG-dinucleotide usage as assessed by multivariate analysis. J. Mol Evol. 53: 290-298.
    • (2001) J. Mol. Evol. , vol.53 , pp. 290-298
    • Kanaya, S.1    Yamada, Y.2    Kinouchi, M.3    Kudo, Y.4    Ikemura, T.5
  • 22
    • 0033061571 scopus 로고    scopus 로고
    • Initiation of translation in prokaryotes and eukaryotes
    • Kozak M. 1999. Initiation of translation in prokaryotes and eukaryotes. Gene 234 (1999) 187-208.
    • (1999) Gene , vol.234 , Issue.1999 , pp. 187-208
    • Kozak, M.1
  • 23
    • 0037121050 scopus 로고    scopus 로고
    • Publishing the limits of the scanning mechanism for initiation of translation
    • Kozak M. 2002. Publishing the limits of the scanning mechanism for initiation of translation. Gene 299: 1-34.
    • (2002) Gene , vol.299 , pp. 1-34
    • Kozak, M.1
  • 24
    • 0023134450 scopus 로고
    • Translation rate modification by preferential codon usage: Intragenic position effects
    • Liljenstrom H. and von Heijne G. 1987. Translation rate modification by preferential codon usage: intragenic position effects. J. Theor. Biol. 124: 43-55.
    • (1987) J. Theor. Biol. , vol.124 , pp. 43-55
    • Liljenstrom, H.1    von Heijne, G.2
  • 25
    • 0027183708 scopus 로고
    • Influence of the three nucleotides upstream of the initiation codon on expression of the Escherichia coli LacZ gene in Saccharomyces cerevisiae
    • Looman A.C. and Kuivenhoven J.A. 1993. Influence of the three nucleotides upstream of the initiation codon on expression of the Escherichia coli LacZ gene in Saccharomyces cerevisiae. Nucleic Acids Res. 21: 4268-4271.
    • (1993) Nucleic Acids Res. , vol.21 , pp. 4268-4271
    • Looman, A.C.1    Kuivenhoven, J.A.2
  • 26
    • 0026032130 scopus 로고
    • Influence of the codon following the initiation codon on the expression of the lacZ gene in Saccharomyces cerevisiae
    • Looman A.C., Laude M. and Stahl U. 1991. Influence of the codon following the initiation codon on the expression of the lacZ gene in Saccharomyces cerevisiae. Yeast 7: 157-165.
    • (1991) Yeast , vol.7 , pp. 157-165
    • Looman, A.C.1    Laude, M.2    Stahl, U.3
  • 27
    • 0032189779 scopus 로고    scopus 로고
    • The influence of 5′ codon context on translation termination in Saccharomyces cerevisiae
    • Mottagui-Tabar S., Tuite M.F. and Isaksson L.A. 1998. The influence of 5′ codon context on translation termination in Saccharomyces cerevisiae. Eur. J. Biochem. 257: 249-254.
    • (1998) Eur. J. Biochem. , vol.257 , pp. 249-254
    • Mottagui-Tabar, S.1    Tuite, M.F.2    Isaksson, L.A.3
  • 28
    • 0034779875 scopus 로고    scopus 로고
    • Impact of the six nucleotides downstream of the stop codon on translation termination
    • Namy O., Hatin I. and Rousset J.P. 2000. Impact of the six nucleotides downstream of the stop codon on translation termination. EMBO Rep. 2: 787-793.
    • (2000) EMBO Rep. , vol.2 , pp. 787-793
    • Namy, O.1    Hatin, I.2    Rousset, J.P.3
  • 29
    • 0036447572 scopus 로고    scopus 로고
    • Effect of tandem rare codon substitution and vector-host combinations on the expression of the EBV gp110 C-terminal domain in Escherichia coli
    • Park S.J., Lee S.K. and Lee B.J. 2002. Effect of tandem rare codon substitution and vector-host combinations on the expression of the EBV gp110 C-terminal domain in Escherichia coli. Protein Expr. Purif. 24: 470-480.
    • (2002) Protein Expr. Purif. , vol.24 , pp. 470-480
    • Park, S.J.1    Lee, S.K.2    Lee, B.J.3
  • 30
    • 0032736056 scopus 로고    scopus 로고
    • Selection at the wobble position of codons read by the same tRNA in Saccharomyces cerevisiae
    • Percudani R. and Ottonello S. 1999. Selection at the wobble position of codons read by the same tRNA in Saccharomyces cerevisiae. Mol. Biol. Evol. 16: 1752-1762.
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 1752-1762
    • Percudani, R.1    Ottonello, S.2
  • 31
    • 0023915972 scopus 로고
    • Selective differences among translation termination codons
    • Sharp P.M. and Bulmer M. 1988. Selective differences among translation termination codons. Gene 63: 141-145.
    • (1988) Gene , vol.63 , pp. 141-145
    • Sharp, P.M.1    Bulmer, M.2
  • 32
    • 0023762645 scopus 로고
    • Codon usage patterns in Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster and Homo sapiens; a review of the considerable within-species diversity
    • Sharp P.M., Cowe E., Higgins D.G., Shields D.C., Wolfe K.H. and Wright F. 1988. Codon usage patterns in Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster and Homo sapiens; a review of the considerable within-species diversity. Nucleic Acids Res. 16: 8207-8211.
    • (1988) Nucleic Acids Res. , vol.16 , pp. 8207-8211
    • Sharp, P.M.1    Cowe, E.2    Higgins, D.G.3    Shields, D.C.4    Wolfe, K.H.5    Wright, F.6
  • 33
    • 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.- 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
    • 0023652058 scopus 로고
    • Synonymous codon usage in Bacillus subtilis reflects both translational selection and mutational biases
    • Shields D.C. and Sharp P.M. 1987. Synonymous codon usage in Bacillus subtilis reflects both translational selection and mutational biases. Nucleic Acids Res. 19: 8023-40.
    • (1987) Nucleic Acids Res. , vol.19 , pp. 8023-8040
    • Shields, D.C.1    Sharp, P.M.2
  • 35
    • 0036425270 scopus 로고    scopus 로고
    • Synonymous codon usage bias and the expression of human glucocerebrosidase in the methylotrophic yeast, Pichia pastoris
    • Sinclair G. and Choy F.Y. 2004. Synonymous codon usage bias and the expression of human glucocerebrosidase in the methylotrophic yeast, Pichia pastoris. Protein Expr. Purif. 26: 96-105.
    • (2004) Protein Expr. Purif. , vol.26 , pp. 96-105
    • Sinclair, G.1    Choy, F.Y.2
  • 36
    • 0026052097 scopus 로고
    • mRNA leader length and initiation codon context determine alternative AUG selection for the yeast gene MOD5
    • Slusher L.B., Gillman E.C., Martin N.C. and Hopper A.K. 1991. mRNA leader length and initiation codon context determine alternative AUG selection for the yeast gene MOD5. Proc. Natl. Acad. Sci. USA. 88: 9789-9793.
    • (1991) Proc. Natl. Acad. Sci. USA , vol.88 , pp. 9789-9793
    • Slusher, L.B.1    Gillman, E.C.2    Martin, N.C.3    Hopper, A.K.4
  • 37
    • 0035827918 scopus 로고    scopus 로고
    • Cooperative effects by the initiation codon and its flanking regions on translation initiation
    • Stenstrom C.M., Holmgren E. and Isaksson L.A. 2001a. Cooperative effects by the initiation codon and its flanking regions on translation initiation. Gene 273: 259-265.
    • (2001) Gene , vol.273 , pp. 259-265
    • Stenstrom, C.M.1    Holmgren, E.2    Isaksson, L.A.3
  • 38
    • 0035941484 scopus 로고    scopus 로고
    • Codon bias at the 3′-side of the initiation codon is correlated with translation initiation efficiency in Escherichia coli
    • Stenstrom C.M., Jin H., Major L.L., Tate W.P. and Isaksson L.A. 2001b. Codon bias at the 3′-side of the initiation codon is correlated with translation initiation efficiency in Escherichia coli. Gene 263: 273-284.
    • (2001) Gene , vol.263 , pp. 273-284
    • Stenstrom, C.M.1    Jin, H.2    Major, L.L.3    Tate, W.P.4    Isaksson, L.A.5
  • 39
    • 0023109679 scopus 로고
    • Secretion of human insulin by a transformed yeast cell
    • Thim L., Hansen M.T. and Sorensen A.A. 1987. Secretion of human insulin by a transformed yeast cell. FEBS Lett. 212: 307-312.
    • (1987) FEBS Lett. , vol.212 , pp. 307-312
    • Thim, L.1    Hansen, M.T.2    Sorensen, A.A.3
  • 41
    • 0041742381 scopus 로고    scopus 로고
    • Characterisation of mammalian GLUT glucose transporters in a heterologous yeast expression system
    • Wieczorke R., Dlugai S., Krampe S. and Boles E. 2003. Characterisation of mammalian GLUT glucose transporters in a heterologous yeast expression system. Cell Physiol Biochem. 13: 123-134.
    • (2003) Cell Physiol. Biochem. , vol.13 , pp. 123-134
    • Wieczorke, R.1    Dlugai, S.2    Krampe, S.3    Boles, E.4
  • 42
    • 0036423438 scopus 로고    scopus 로고
    • Gene optimization is necessary to express a bivalent anti-human anti-T cell immumotoxin in Pichia pastoris
    • Woo J.H., Liu Y.Y., Mathias A., Stavrou S., Wang Z., Thompson J. and Neville Jr. D.M. 2002. Gene optimization is necessary to express a bivalent anti-human anti-T cell immumotoxin in Pichia pastoris. Protein Expr. Purif. 25: 270-282.
    • (2002) Protein Expr. Purif. , vol.25 , pp. 270-282
    • Woo, J.H.1    Liu, Y.Y.2    Mathias, A.3    Stavrou, S.4    Wang, Z.5    Thompson, J.6    Neville Jr., D.M.7
  • 43
    • 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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.