메뉴 건너뛰기




Volumn 7, Issue 7, 2012, Pages 835-845

Synthetic biology challenges long-held hypotheses in translation, codon bias and transcription

Author keywords

Aminoacyl tRNA; Codon bias; Ribosome; Transcription termination; Translation

Indexed keywords

AMINOACYL-TRNA; BEST MODEL; BIOLOGICAL SCIENCE; BIOTECHNOLOGY APPLICATIONS; CLASS II; CODON BIAS; E. COLI; EQUIVALENT CONCENTRATIONS; EXPERIMENTAL APPROACHES; GENETIC CODE; IN-VITRO; IN-VIVO; NUCLEOPHILICITIES; PROTEIN STRUCTURES; RATE LIMITING; RIBOSOME; RNA POLYMERASE; SYNTHETIC BIOLOGY; TESTING HYPOTHESIS; TRANSCRIPTION TERMINATION;

EID: 84863300678     PISSN: 18606768     EISSN: 18607314     Source Type: Journal    
DOI: 10.1002/biot.201200002     Document Type: Review
Times cited : (14)

References (77)
  • 1
    • 84863319226 scopus 로고    scopus 로고
    • Meeting Report: Cold Spring Harbor Asia - Design and Synthesis of Biological Systems. Biotechnol J. DOI: 10.1002/biot.201100490.
    • Na, D., Meeting Report: Cold Spring Harbor Asia - Design and Synthesis of Biological Systems. Biotechnol J. 2012, DOI: 10.1002/biot.201100490.
    • (2012)
    • Na, D.1
  • 2
    • 77957345108 scopus 로고    scopus 로고
    • Update on designing and building minimal cells.
    • Jewett, M. C., Forster, A. C., Update on designing and building minimal cells. Curr Opin Biotechnol. 2010, 21, 697-703.
    • (2010) Curr Opin Biotechnol. , vol.21 , pp. 697-703
    • Jewett, M.C.1    Forster, A.C.2
  • 3
    • 84555189972 scopus 로고    scopus 로고
    • Update on pure translation display with unnatural amino acid incorporation.
    • Watts, R. E., Forster, A. C., Update on pure translation display with unnatural amino acid incorporation. Methods Mol. Biol. 2012, 805, 349-365.
    • (2012) Methods Mol. Biol. , vol.805 , pp. 349-365
    • Watts, R.E.1    Forster, A.C.2
  • 4
    • 84863320394 scopus 로고    scopus 로고
    • The life, the universe and the scientific method. FfAME Press, Gainesville FL,
    • Benner, S. A., The life, the universe and the scientific method. FfAME Press, Gainesville FL, 2009.
    • (2009)
    • Benner, S.A.1
  • 5
    • 33845965687 scopus 로고    scopus 로고
    • Synthetic biology projects in vitro.
    • Forster, A. C., Church, G. M., Synthetic biology projects in vitro. Genome Res. 2007, 17, 1-6.
    • (2007) Genome Res. , vol.17 , pp. 1-6
    • Forster, A.C.1    Church, G.M.2
  • 6
    • 0035477877 scopus 로고    scopus 로고
    • A simplified reconstitution of mRNA-directed peptide synthesis: activity of the epsilon enhancer and an unnatural amino acid.
    • Forster, A. C., Weissbach, H., Blacklow, S. C., A simplified reconstitution of mRNA-directed peptide synthesis: activity of the epsilon enhancer and an unnatural amino acid. Anal Biochem. 2001, 297, 60-70.
    • (2001) Anal Biochem. , vol.297 , pp. 60-70
    • Forster, A.C.1    Weissbach, H.2    Blacklow, S.C.3
  • 7
    • 0000652848 scopus 로고
    • Biosynthetic site-specific incorporation of a non-natural amino acid into a polypeptide.
    • Bain, J. D., Glabe, C. G., Dix, T. A., Chamberlin, A. R. et al., Biosynthetic site-specific incorporation of a non-natural amino acid into a polypeptide. J. Am. Chem. Soc. 1989, 111, 8013-8014.
    • (1989) J. Am. Chem. Soc. , vol.111 , pp. 8013-8014
    • Bain, J.D.1    Glabe, C.G.2    Dix, T.A.3    Chamberlin, A.R.4
  • 8
    • 0024968835 scopus 로고
    • A general method for site-specific incorporation of unnatural amino acids into proteins.
    • Noren, C. J., Anthony-Cahill, S. J., Griffith, M. C., Schultz, P. G., A general method for site-specific incorporation of unnatural amino acids into proteins. Science 1989, 244, 182-188.
    • (1989) Science , vol.244 , pp. 182-188
    • Noren, C.J.1    Anthony-Cahill, S.J.2    Griffith, M.C.3    Schultz, P.G.4
  • 9
    • 0038652110 scopus 로고    scopus 로고
    • Programming peptidomimetic syntheses by translating genetic codes designed de novo.
    • Forster, A. C., Tan, Z., Nalam, M. N. L., Lin, H. et al., Programming peptidomimetic syntheses by translating genetic codes designed de novo. Proc. Natl. Acad. Sci. USA 2003, 100, 6353-6357.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 6353-6357
    • Forster, A.C.1    Tan, Z.2    Nalam, M.N.L.3    Lin, H.4
  • 10
    • 23044489674 scopus 로고    scopus 로고
    • De novo genetic codes and pure translation display.
    • Tan, Z., Blacklow, S. C., Cornish, V. W., Forster, A. C., De novo genetic codes and pure translation display. Methods 2005, 36, 279-290.
    • (2005) Methods , vol.36 , pp. 279-290
    • Tan, Z.1    Blacklow, S.C.2    Cornish, V.W.3    Forster, A.C.4
  • 11
    • 67649888367 scopus 로고    scopus 로고
    • Low modularity of aminoacyl-tRNA substrates in polymerization by the ribosome.
    • Forster, A. C., Low modularity of aminoacyl-tRNA substrates in polymerization by the ribosome. Nucleic Acids Res. 2009, 37, 3747-3755.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 3747-3755
    • Forster, A.C.1
  • 12
    • 71549163430 scopus 로고    scopus 로고
    • Changeability of individual domains of an aminoacyl-tRNA in polymerization by the ribosome.
    • Gao, R., Forster, A. C., Changeability of individual domains of an aminoacyl-tRNA in polymerization by the ribosome. FEBS Lett. 2010, 584, 99-105.
    • (2010) FEBS Lett. , vol.584 , pp. 99-105
    • Gao, R.1    Forster, A.C.2
  • 13
    • 38349062552 scopus 로고    scopus 로고
    • Messenger RNA-programmed incorporation of multiple N-methyl-amino acids into linear and cyclic peptides.
    • Kawakami, T., Murakami, H., Suga, H., Messenger RNA-programmed incorporation of multiple N-methyl-amino acids into linear and cyclic peptides. Chem. Biol. 2008, 15, 32-42.
    • (2008) Chem. Biol. , vol.15 , pp. 32-42
    • Kawakami, T.1    Murakami, H.2    Suga, H.3
  • 14
    • 1942445134 scopus 로고    scopus 로고
    • Transformation of aminoacyl tRNAs for the in vitro selection of "drug-like" molecules.
    • Merryman, C., Green, R., Transformation of aminoacyl tRNAs for the in vitro selection of "drug-like" molecules. Chem. Biol. 2004, 11, 575-582.
    • (2004) Chem. Biol. , vol.11 , pp. 575-582
    • Merryman, C.1    Green, R.2
  • 16
  • 17
    • 84555190565 scopus 로고    scopus 로고
    • Natural product-like macrocyclic N-methyl-peptide inhibitors against a ubiquitin ligase uncovered from a ribosome-expressed de novo library.
    • Yamagishi, Y., Shoji, I., Miyagawa, S., Kawakami, T. et al., Natural product-like macrocyclic N-methyl-peptide inhibitors against a ubiquitin ligase uncovered from a ribosome-expressed de novo library. Chem. Biol. 2011, 18, 1562-1570.
    • (2011) Chem. Biol. , vol.18 , pp. 1562-1570
    • Yamagishi, Y.1    Shoji, I.2    Miyagawa, S.3    Kawakami, T.4
  • 18
    • 84863434152 scopus 로고    scopus 로고
    • In vitro selection of highly modified cyclic peptides that act as tight binding inhibitors. J. Am. Chem. Soc. 2012, DOI: 10.1021/ja301017y.
    • Guillen Schlippe, Y. V., Hartman, M. C., Josephson, K., Szostak, J. W., In vitro selection of highly modified cyclic peptides that act as tight binding inhibitors. J. Am. Chem. Soc. 2012, DOI: 10.1021/ja301017y.
    • Guillen Schlippe, Y.V.1    Hartman, M.C.2    Josephson, K.3    Szostak, J.W.4
  • 19
    • 33846108255 scopus 로고    scopus 로고
    • Towards synthesis of a minimal cell.
    • Forster, A. C., Church, G. M., Towards synthesis of a minimal cell. Mol. Syst. Biol. 2006, 2, 45.
    • (2006) Mol. Syst. Biol. , vol.2 , pp. 45
    • Forster, A.C.1    Church, G.M.2
  • 20
    • 70350491151 scopus 로고    scopus 로고
    • Engineering multigene expression in vitro and in vivo with small terminators for T7 RNA polymerase.
    • Du, L., Gao, R., Forster, A. C., Engineering multigene expression in vitro and in vivo with small terminators for T7 RNA polymerase. Biotechnol. Bioeng. 2009, 104, 1189-1196.
    • (2009) Biotechnol. Bioeng. , vol.104 , pp. 1189-1196
    • Du, L.1    Gao, R.2    Forster, A.C.3
  • 21
    • 84857440093 scopus 로고    scopus 로고
    • Multigene expression in vivo: Supremacy of large versus small terminators for T7 RNA polymerase.
    • Du, L., Villarreal, S., Forster, A. C., Multigene expression in vivo: Supremacy of large versus small terminators for T7 RNA polymerase. Biotechnol. Bioeng. 2012, 109, 1043-1050.
    • (2012) Biotechnol. Bioeng. , vol.109 , pp. 1043-1050
    • Du, L.1    Villarreal, S.2    Forster, A.C.3
  • 22
    • 84863328748 scopus 로고    scopus 로고
    • Multiplexed in vivo His-tagging of enzyme pathways for in vitro single-pot multienzyme catalysis.
    • Wang, H. H., Huang, P.-Y., Xu, G., Haas, W. et al., Multiplexed in vivo His-tagging of enzyme pathways for in vitro single-pot multienzyme catalysis. ACS Synthetic Biology. 2012, 1, 43-52.
    • (2012) ACS Synthetic Biology. , vol.1 , pp. 43-52
    • Wang, H.H.1    Huang, P.-Y.2    Xu, G.3    Haas, W.4
  • 23
    • 58549114677 scopus 로고    scopus 로고
    • Slow peptide bond formation by proline and other N-alkylamino acids in translation.
    • Pavlov, M. Y., Watts, R. E., Tan, Z., Cornish, V. W. et al., Slow peptide bond formation by proline and other N-alkylamino acids in translation. Proc. Natl. Acad. Sci. USA 2009, 106, 50-54.
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 50-54
    • Pavlov, M.Y.1    Watts, R.E.2    Tan, Z.3    Cornish, V.W.4
  • 24
    • 0024962419 scopus 로고
    • Rates of aminoacyl-tRNA selection at 29 sense codons in vivo.
    • Curran, J. F., Yarus, M., Rates of aminoacyl-tRNA selection at 29 sense codons in vivo. J. Mol. Biol. 1989, 209, 65-77.
    • (1989) J. Mol. Biol. , vol.209 , pp. 65-77
    • Curran, J.F.1    Yarus, M.2
  • 26
    • 0035812828 scopus 로고    scopus 로고
    • Uniform binding of aminoacyl-tRNAs to elongation factor Tu by thermodynamic compensation.
    • LaRiviere, F. J., Wolfson, A. D., Uhlenbeck, O. C., Uniform binding of aminoacyl-tRNAs to elongation factor Tu by thermodynamic compensation. Science 2001, 294, 165-168.
    • (2001) Science , vol.294 , pp. 165-168
    • LaRiviere, F.J.1    Wolfson, A.D.2    Uhlenbeck, O.C.3
  • 28
    • 46149104347 scopus 로고    scopus 로고
    • Different aa-tRNAs are selected uniformly on the ribosome.
    • Ledoux, S., Uhlenbeck, O. C., Different aa-tRNAs are selected uniformly on the ribosome. Mol Cell 2008, 31, 114-123.
    • (2008) Mol Cell , vol.31 , pp. 114-123
    • Ledoux, S.1    Uhlenbeck, O.C.2
  • 29
    • 2442697841 scopus 로고    scopus 로고
    • The affinity of elongation factor Tu for an aminoacyl-tRNA is modulated by the esterified amino acid.
    • Dale, T., Sanderson, L. E., Uhlenbeck, O. C., The affinity of elongation factor Tu for an aminoacyl-tRNA is modulated by the esterified amino acid. Biochemistry 2004, 43, 6159-6166.
    • (2004) Biochemistry , vol.43 , pp. 6159-6166
    • Dale, T.1    Sanderson, L.E.2    Uhlenbeck, O.C.3
  • 30
    • 0032535207 scopus 로고    scopus 로고
    • Complete kinetic mechanism of elongation factor Tu-dependent binding of aminoacyl-tRNA to the A site of the E. coli ribosome.
    • Pape, T., Wintermeyer, W., Rodnina, M. V., Complete kinetic mechanism of elongation factor Tu-dependent binding of aminoacyl-tRNA to the A site of the E. coli ribosome. EMBO J. 1998, 17, 7490-7497.
    • (1998) EMBO J. , vol.17 , pp. 7490-7497
    • Pape, T.1    Wintermeyer, W.2    Rodnina, M.V.3
  • 31
    • 0026629246 scopus 로고
    • Cyclosporin A, the cyclophilin class of peptidylprolyl isomerases, and blockade of T cell signal transduction.
    • Walsh, C. T., Zydowsky, L. D., McKeon, F. D., Cyclosporin A, the cyclophilin class of peptidylprolyl isomerases, and blockade of T cell signal transduction. J. Biol. Chem. 1992, 267, 13115-13118.
    • (1992) J. Biol. Chem. , vol.267 , pp. 13115-13118
    • Walsh, C.T.1    Zydowsky, L.D.2    McKeon, F.D.3
  • 32
    • 0026567563 scopus 로고
    • Site-specific incorporation of novel backbone structures into proteins.
    • Ellman, J. A., Mendel, D., Schultz, P. G., Site-specific incorporation of novel backbone structures into proteins. Science 1992, 255, 197-200.
    • (1992) Science , vol.255 , pp. 197-200
    • Ellman, J.A.1    Mendel, D.2    Schultz, P.G.3
  • 33
    • 0027405662 scopus 로고
    • Probing the structure and mechanism of Ras protein with an expanded genetic code.
    • Chung, H. H., Benson, D. R., Schultz, P. G., Probing the structure and mechanism of Ras protein with an expanded genetic code. Science 1993, 259, 806-809.
    • (1993) Science , vol.259 , pp. 806-809
    • Chung, H.H.1    Benson, D.R.2    Schultz, P.G.3
  • 34
    • 5644244186 scopus 로고    scopus 로고
    • Amino acid backbone specificity of the Escherichia coli translation machinery.
    • Tan, Z., Forster, A. C., Blacklow, S. C., Cornish, V. W., Amino acid backbone specificity of the Escherichia coli translation machinery. J. Am. Chem. Soc. 2004, 126, 12752-12753.
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 12752-12753
    • Tan, Z.1    Forster, A.C.2    Blacklow, S.C.3    Cornish, V.W.4
  • 35
    • 35048870262 scopus 로고    scopus 로고
    • Specificity of translation for N-alkyl amino acids.
    • Zhang, B., Tan, Z., Dickson, L. G., Nalam, M. N. L. et al., Specificity of translation for N-alkyl amino acids. J. Am. Chem. Soc. 2007, 129, 11316-11317.
    • (2007) J. Am. Chem. Soc. , vol.129 , pp. 11316-11317
    • Zhang, B.1    Tan, Z.2    Dickson, L.G.3    Nalam, M.N.L.4
  • 36
    • 58049219079 scopus 로고    scopus 로고
    • Ribosomal synthesis of polypeptoids and peptoid-peptide hybrids.
    • Kawakami, T., Murakami, H., Suga, H., Ribosomal synthesis of polypeptoids and peptoid-peptide hybrids. J. Am. Chem. Soc. 2008, 130, 16861-16863.
    • (2008) J. Am. Chem. Soc. , vol.130 , pp. 16861-16863
    • Kawakami, T.1    Murakami, H.2    Suga, H.3
  • 37
    • 44449089912 scopus 로고    scopus 로고
    • The kinetics of ribosomal peptidyl transfer revisited.
    • Johansson, M., Bouakaz, E., Lovmar, M., Ehrenberg, M., The kinetics of ribosomal peptidyl transfer revisited. Mol. Cell 2008, 30, 589-598.
    • (2008) Mol. Cell , vol.30 , pp. 589-598
    • Johansson, M.1    Bouakaz, E.2    Lovmar, M.3    Ehrenberg, M.4
  • 38
    • 79955113244 scopus 로고    scopus 로고
    • Tuning the affinity of aminoacyl-tRNA to elongation factor Tu for optimal decoding.
    • Schrader, J. M., Chapman, S. J., Uhlenbeck, O. C., Tuning the affinity of aminoacyl-tRNA to elongation factor Tu for optimal decoding. Proc. Natl. Acad. Sci. USA. 2011, 108, 5215-5220.
    • (2011) Proc. Natl. Acad. Sci. USA. , vol.108 , pp. 5215-5220
    • Schrader, J.M.1    Chapman, S.J.2    Uhlenbeck, O.C.3
  • 39
    • 77249145819 scopus 로고    scopus 로고
    • Divergent stalling sequences sense and control cellular physiology.
    • Ito, K., Chiba, S., Pogliano, K., Divergent stalling sequences sense and control cellular physiology. Biochem. Biophys. Res. Commun. 2010, 393, 1-5.
    • (2010) Biochem. Biophys. Res. Commun. , vol.393 , pp. 1-5
    • Ito, K.1    Chiba, S.2    Pogliano, K.3
  • 40
    • 33646517888 scopus 로고    scopus 로고
    • Genetically encoded but nonpolypeptide prolyl-tRNA functions in the A site for SecM-mediated ribosomal stall.
    • Muto, H., Nakatogawa, H., Ito, K., Genetically encoded but nonpolypeptide prolyl-tRNA functions in the A site for SecM-mediated ribosomal stall. Mol. Cell. 2006, 22, 545-552.
    • (2006) Mol. Cell. , vol.22 , pp. 545-552
    • Muto, H.1    Nakatogawa, H.2    Ito, K.3
  • 41
    • 46449120581 scopus 로고    scopus 로고
    • Virus attenuation by genome-scale changes in codon pair bias.
    • Coleman, J. R., Papamichail, D., Skiena, S., Futcher, B. et al., Virus attenuation by genome-scale changes in codon pair bias. Science 2008, 320, 1784-1787.
    • (2008) Science , vol.320 , pp. 1784-1787
    • Coleman, J.R.1    Papamichail, D.2    Skiena, S.3    Futcher, B.4
  • 42
    • 0024673103 scopus 로고
    • Nonrandom utilization of codon pairs in Escherichia coli.
    • Gutman, G. A., Hatfield, G. W., Nonrandom utilization of codon pairs in Escherichia coli. Proc. Natl. Acad. Sci. USA. 1989, 86, 3699-3703.
    • (1989) Proc. Natl. Acad. Sci. USA. , vol.86 , pp. 3699-3703
    • Gutman, G.A.1    Hatfield, G.W.2
  • 43
    • 77949404685 scopus 로고    scopus 로고
    • Chemical models of peptide formation in translation.
    • Watts, R. E., Forster, A. C., Chemical models of peptide formation in translation. Biochemistry 2010, 49, 2177-2185.
    • (2010) Biochemistry , vol.49 , pp. 2177-2185
    • Watts, R.E.1    Forster, A.C.2
  • 44
    • 78651083730 scopus 로고    scopus 로고
    • pH-sensitivity of the ribosomal peptidyl transfer reaction dependent on the identity of the A-site aminoacyl-tRNA.
    • Johansson, M., Ieong, K. W., Trobro, S., Strazewski, P. et al., pH-sensitivity of the ribosomal peptidyl transfer reaction dependent on the identity of the A-site aminoacyl-tRNA. Proc. Natl. Acad. Sci. USA. 2011, 108, 79-84.
    • (2011) Proc. Natl. Acad. Sci. USA. , vol.108 , pp. 79-84
    • Johansson, M.1    Ieong, K.W.2    Trobro, S.3    Strazewski, P.4
  • 45
    • 33745071762 scopus 로고    scopus 로고
    • Peptide bond formation does not involve acid-base catalysis by ribosomal residues.
    • Bieling, P., Beringer, M., Adio, S., Rodnina, M. V., Peptide bond formation does not involve acid-base catalysis by ribosomal residues. Nat. Struct. Mol. Biol. 2006, 13, 423-428.
    • (2006) Nat. Struct. Mol. Biol. , vol.13 , pp. 423-428
    • Bieling, P.1    Beringer, M.2    Adio, S.3    Rodnina, M.V.4
  • 46
    • 0019792825 scopus 로고
    • Reasons for the occurrence of the twenty coded protein amino acids.
    • Weber, A. L., Miller, S. L., Reasons for the occurrence of the twenty coded protein amino acids. J. Mol. Evol. 1981, 17, 273-284.
    • (1981) J. Mol. Evol. , vol.17 , pp. 273-284
    • Weber, A.L.1    Miller, S.L.2
  • 47
    • 77649336503 scopus 로고    scopus 로고
    • 2nd, The origin of the biologically coded amino acids.
    • Cleaves, H. J., 2nd, The origin of the biologically coded amino acids. J. Theor. Biol. 2010, 263, 490-498.
    • (2010) J. Theor. Biol. , vol.263 , pp. 490-498
    • Cleaves, H.J.1
  • 48
    • 80054861886 scopus 로고    scopus 로고
    • Systematic chromosomal deletion of bacterial ribosomal protein genes.
    • Shoji, S., Dambacher, C. M., Shajani, Z., Williamson, J. R. et al., Systematic chromosomal deletion of bacterial ribosomal protein genes. J. Mol. Biol. 2011, 413, 751-761.
    • (2011) J. Mol. Biol. , vol.413 , pp. 751-761
    • Shoji, S.1    Dambacher, C.M.2    Shajani, Z.3    Williamson, J.R.4
  • 49
    • 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., 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
  • 50
    • 78650304100 scopus 로고    scopus 로고
    • Synonymous but not the same: the causes and consequences of codon bias.
    • Plotkin, J. B., Kudla, G., Synonymous but not the same: the causes and consequences of codon bias. Nat. Rev. Genet. 2011, 12, 32-42.
    • (2011) Nat. Rev. Genet. , vol.12 , pp. 32-42
    • Plotkin, J.B.1    Kudla, G.2
  • 51
    • 14544277543 scopus 로고    scopus 로고
    • Variation in the strength of selected codon usage bias among bacteria.
    • Sharp, P. M., Bailes, E., Grocock, R. J., Peden, J. F. et al., Variation in the strength of selected codon usage bias among bacteria. Nucleic Acids Res. 2005, 33, 1141-1153.
    • (2005) Nucleic Acids Res. , vol.33 , pp. 1141-1153
    • Sharp, P.M.1    Bailes, E.2    Grocock, R.J.3    Peden, J.F.4
  • 52
    • 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., Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates. J. Mol. Biol. 1996, 260, 649-663.
    • (1996) J. Mol. Biol. , vol.260 , pp. 649-663
    • Dong, H.1    Nilsson, L.2    Kurland, C.G.3
  • 53
    • 0021958933 scopus 로고
    • Codon usage and tRNA content in unicellular and multicellular organisms.
    • Ikemura, T., Codon usage and tRNA content in unicellular and multicellular organisms. Mol. Biol. Evol. 1985, 2, 13-34.
    • (1985) Mol. Biol. Evol. , vol.2 , pp. 13-34
    • Ikemura, T.1
  • 54
    • 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., 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 1999, 238, 143-155.
    • (1999) Gene , vol.238 , pp. 143-155
    • Kanaya, S.1    Yamada, Y.2    Kudo, Y.3    Ikemura, T.4
  • 55
    • 77955955750 scopus 로고    scopus 로고
    • The influence of anticodon-codon interactions and modified bases on codon usage bias in bacteria.
    • Ran, W., Higgs, P. G., The influence of anticodon-codon interactions and modified bases on codon usage bias in bacteria. Mol. Biol. Evol. 2010, 27, 2129-2140.
    • (2010) Mol. Biol. Evol. , vol.27 , pp. 2129-2140
    • Ran, W.1    Higgs, P.G.2
  • 56
    • 17444449538 scopus 로고    scopus 로고
    • Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae.
    • Percudani, R., Pavesi, A., Ottonello, S., Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae. J. Mol. Biol. 1997, 268, 322-330.
    • (1997) J. Mol. Biol. , vol.268 , pp. 322-330
    • Percudani, R.1    Pavesi, A.2    Ottonello, S.3
  • 57
    • 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., tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes. Trends Genet. 2000, 16, 287-289.
    • (2000) Trends Genet. , vol.16 , pp. 287-289
    • Duret, L.1
  • 58
    • 0342614926 scopus 로고    scopus 로고
    • Codon usage tabulated from international DNA sequence databases: status for the year 2000.
    • Nakamura, Y., Gojobori, T., Ikemura, T., Codon usage tabulated from international DNA sequence databases: status for the year 2000. Nucleic Acids Res. 2000, 28, 292.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 292
    • Nakamura, Y.1    Gojobori, T.2    Ikemura, T.3
  • 59
    • 84863310643 scopus 로고    scopus 로고
    • Transfer RNA modification. in: Curtiss III, R., Bock A., Ingrahan J.L., Kaper J.B, et al. (Eds.), Escherichia coli and Salmonella. Cellular and molecular biology. ASM Press, Washington DC
    • Bjork, G. R., Hagervall, T. G., Transfer RNA modification. in: Curtiss III, R., Bock A., Ingrahan J.L., Kaper J.B, et al. (Eds.), Escherichia coli and Salmonella. Cellular and molecular biology. ASM Press, Washington DC 2005.
    • (2005)
    • Bjork, G.R.1    Hagervall, T.G.2
  • 60
    • 70349199628 scopus 로고    scopus 로고
    • Design parameters to control synthetic gene expression in Escherichia coli.
    • e7002
    • Welch, M., Govindarajan, S., Ness, J. E., Villalobos, A. et al., Design parameters to control synthetic gene expression in Escherichia coli. PLoS One 2009, 4, e7002.
    • (2009) PLoS One , vol.4
    • Welch, M.1    Govindarajan, S.2    Ness, J.E.3    Villalobos, A.4
  • 61
    • 64849114915 scopus 로고    scopus 로고
    • Coding-sequence determinants of gene expression in Escherichia coli.
    • Kudla, G., Murray, A. W., Tollervey, D., Plotkin, J. B., Coding-sequence determinants of gene expression in Escherichia coli. Science 2009, 324, 255-258.
    • (2009) Science , vol.324 , pp. 255-258
    • Kudla, G.1    Murray, A.W.2    Tollervey, D.3    Plotkin, J.B.4
  • 62
    • 0038179369 scopus 로고    scopus 로고
    • Selective charging of tRNA isoacceptors explains patterns of codon usage.
    • Elf, J., Nilsson, D., Tenson, T., Ehrenberg, M., Selective charging of tRNA isoacceptors explains patterns of codon usage. Science 2003, 300, 1718-1722.
    • (2003) Science , vol.300 , pp. 1718-1722
    • Elf, J.1    Nilsson, D.2    Tenson, T.3    Ehrenberg, M.4
  • 63
    • 27344446707 scopus 로고    scopus 로고
    • Over expression of a tRNA(Leu) isoacceptor changes charging pattern of leucine tRNAs and reveals new codon reading.
    • Sorensen, M. A., Elf, J., Bouakaz, E., Tenson, T. et al., Over expression of a tRNA(Leu) isoacceptor changes charging pattern of leucine tRNAs and reveals new codon reading. J. Mol. Biol. 2005, 354, 16-24.
    • (2005) J. Mol. Biol. , vol.354 , pp. 16-24
    • Sorensen, M.A.1    Elf, J.2    Bouakaz, E.3    Tenson, T.4
  • 64
    • 84860231100 scopus 로고    scopus 로고
    • The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria.
    • Li, G. W., Oh, E., Weissman, J. S., The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria. Nature 2012, 484, 538-541.
    • (2012) Nature , vol.484 , pp. 538-541
    • Li, G.W.1    Oh, E.2    Weissman, J.S.3
  • 65
    • 0020363515 scopus 로고
    • Preferential codon usage in prokaryotic genes: the optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes.
    • Grosjean, H., Fiers, W., Preferential codon usage in prokaryotic genes: the optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes. Gene 1982, 18, 199-209.
    • (1982) Gene , vol.18 , pp. 199-209
    • Grosjean, H.1    Fiers, W.2
  • 66
    • 47549097539 scopus 로고    scopus 로고
    • Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution.
    • Drummond, D. A., Wilke, C. O., Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell 2008, 134, 341-352.
    • (2008) Cell , vol.134 , pp. 341-352
    • Drummond, D.A.1    Wilke, C.O.2
  • 67
    • 33846786904 scopus 로고    scopus 로고
    • Synonymous codon usage in Escherichia coli: selection for translational accuracy.
    • Stoletzki, N., Eyre-Walker, A., Synonymous codon usage in Escherichia coli: selection for translational accuracy. Mol. Biol. Evol. 2007, 24, 374-381.
    • (2007) Mol. Biol. Evol. , vol.24 , pp. 374-381
    • Stoletzki, N.1    Eyre-Walker, A.2
  • 68
    • 0030806245 scopus 로고    scopus 로고
    • Codon bias in Escherichia coli: the influence of codon context on mutation and selection.
    • Berg, O. G., Silva, P. J., Codon bias in Escherichia coli: the influence of codon context on mutation and selection. Nucleic Acids Res. 1997, 25, 1397-1404.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 1397-1404
    • Berg, O.G.1    Silva, P.J.2
  • 69
    • 84862963791 scopus 로고    scopus 로고
    • Genetic code translation displays a linear trade-off between efficiency and accuracy of tRNA selection.
    • Johansson, M., Zhang, J., Ehrenberg, M., Genetic code translation displays a linear trade-off between efficiency and accuracy of tRNA selection. Proc. Natl. Acad. Sci. USA 2012, 109, 131-136.
    • (2012) Proc. Natl. Acad. Sci. USA , vol.109 , pp. 131-136
    • Johansson, M.1    Zhang, J.2    Ehrenberg, M.3
  • 70
    • 0032504089 scopus 로고    scopus 로고
    • Pausing and termination by bacteriophage T7 RNA polymerase.
    • Lyakhov, D. L., He, B., Zhang, X., Studier, F. W. et al., Pausing and termination by bacteriophage T7 RNA polymerase. J. Mol. Biol. 1998, 280, 201-213.
    • (1998) J. Mol. Biol. , vol.280 , pp. 201-213
    • Lyakhov, D.L.1    He, B.2    Zhang, X.3    Studier, F.W.4
  • 71
    • 0022797369 scopus 로고
    • Single-stranded DNA 'blue' T7 promoter plasmids: a versatile tandem promoter system for cloning and protein engineering.
    • Mead, D. A., Szczesna-Skorupa, E., Kemper, B., Single-stranded DNA 'blue' T7 promoter plasmids: a versatile tandem promoter system for cloning and protein engineering. Protein Eng. 1986, 1, 67-74.
    • (1986) Protein Eng. , vol.1 , pp. 67-74
    • Mead, D.A.1    Szczesna-Skorupa, E.2    Kemper, B.3
  • 72
    • 0029118831 scopus 로고
    • Efficient recovery of infectious vesicular stomatitis virus entirely from cDNA clones.
    • Whelan, S. P., Ball, L. A., Barr, J. N., Wertz, G. T., Efficient recovery of infectious vesicular stomatitis virus entirely from cDNA clones. Proc. Natl. Acad. Sci. USA. 1995, 92, 8388-8392.
    • (1995) Proc. Natl. Acad. Sci. USA. , vol.92 , pp. 8388-8392
    • Whelan, S.P.1    Ball, L.A.2    Barr, J.N.3    Wertz, G.T.4
  • 73
    • 0031591385 scopus 로고    scopus 로고
    • Mutant bacteriophage T7 RNA polymerases with altered termination properties.
    • Lyakhov, D. L., He, B., Zhang, X., Studier, F. W. et al., Mutant bacteriophage T7 RNA polymerases with altered termination properties. J. Mol. Biol. 1997, 269, 28-40.
    • (1997) J. Mol. Biol. , vol.269 , pp. 28-40
    • Lyakhov, D.L.1    He, B.2    Zhang, X.3    Studier, F.W.4
  • 74
    • 0031591384 scopus 로고    scopus 로고
    • Mechanism of inhibition of bacteriophage T7 RNA polymerase by T7 lysozyme.
    • Zhang, X., Studier, F. W., Mechanism of inhibition of bacteriophage T7 RNA polymerase by T7 lysozyme. J. Mol. Biol. 1997, 269, 10-27.
    • (1997) J. Mol. Biol. , vol.269 , pp. 10-27
    • Zhang, X.1    Studier, F.W.2
  • 75
    • 0023042283 scopus 로고
    • Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes.
    • Studier, F. W., Moffatt, B. A., Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. J. Mol. Biol. 1986, 189, 113-130.
    • (1986) J. Mol. Biol. , vol.189 , pp. 113-130
    • Studier, F.W.1    Moffatt, B.A.2
  • 76
    • 0027326224 scopus 로고
    • Termination and slippage by bacteriophage T7 RNA polymerase.
    • Macdonald, L. E., Zhou, Y., McAllister, W. T., Termination and slippage by bacteriophage T7 RNA polymerase. J. Mol. Biol. 1993, 232, 1030-1047.
    • (1993) J. Mol. Biol. , vol.232 , pp. 1030-1047
    • Macdonald, L.E.1    Zhou, Y.2    McAllister, W.T.3
  • 77
    • 0032563099 scopus 로고    scopus 로고
    • Characterization of an unusual, sequence-specific termination signal for T7 RNA polymerase.
    • He, B., Kukarin, A., Temiakov, D., Chin-Bow, S. T. et al., Characterization of an unusual, sequence-specific termination signal for T7 RNA polymerase. J. Biol. Chem. 1998, 273, 18802-18811.
    • (1998) J. Biol. Chem. , vol.273 , pp. 18802-18811
    • He, B.1    Kukarin, A.2    Temiakov, D.3    Chin-Bow, S.T.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.