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Volumn 33, Issue 1, 2014, Pages 21-34

Translation elongation can control translation initiation on eukaryotic mRNAs

Author keywords

Codon usage; Ribosome speed; Translation; Translation elongation; Translational control

Indexed keywords

MESSENGER RNA;

EID: 84894646451     PISSN: 02614189     EISSN: 14602075     Source Type: Journal    
DOI: 10.1002/embj.201385651     Document Type: Article
Times cited : (152)

References (56)
  • 1
    • 84861843696 scopus 로고    scopus 로고
    • A mechanistic overview of translation initiation in eukaryotes
    • Aitken CE, Lorsch JR (2012) A mechanistic overview of translation initiation in eukaryotes. Nat Struct Mol Biol 19: 568 - 576
    • (2012) Nat Struct Mol Biol , vol.19 , pp. 568-576
    • Aitken, C.E.1    Lorsch, J.R.2
  • 3
    • 0032579440 scopus 로고    scopus 로고
    • Designer deletion strains derived from Saccharomyces cerevisiae S288C: A useful set of strains and plasmids for PCR-mediated gene disruption and other applications
    • Brachmann CB, Davies A, Cost GJ, Caputo E, Li J, Hieter P, Boeke JD (1998) Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR-mediated gene disruption and other applications. Yeast 14: 115 - 132
    • (1998) Yeast , vol.14 , pp. 115-132
    • Brachmann, C.B.1    Davies, A.2    Cost, G.J.3    Caputo, E.4    Li, J.5    Hieter, P.6    Boeke, J.D.7
  • 4
    • 0036438894 scopus 로고    scopus 로고
    • Regulation of peptide-chain elongation in mammalian cells
    • Browne GJ, Proud CG (2002) Regulation of peptide-chain elongation in mammalian cells. Eur J Biochem 269: 5360 - 5368
    • (2002) Eur J Biochem , vol.269 , pp. 5360-5368
    • Browne, G.J.1    Proud, C.G.2
  • 5
    • 0037274714 scopus 로고    scopus 로고
    • In vivo Introduction of Unpreferred Synonymous Codons into the Drosophila Adh Gene Results in Reduced Levels of ADH Protein
    • Carlini DB, Stephan W (2003) In vivo Introduction of Unpreferred Synonymous Codons Into the Drosophila Adh Gene Results in Reduced Levels of ADH Protein. Genetics 163: 239 - 243
    • (2003) Genetics , vol.163 , pp. 239-243
    • Carlini, D.B.1    Stephan, W.2
  • 6
    • 84864828979 scopus 로고    scopus 로고
    • Reprogramming of tRNA modifications controls the oxidative stress response by codon-biased translation of proteins
    • Chan CTY, Pang YLJ, Deng W, Babu IR, Dyavaiah M, Begley TJ, Dedon PC (2012) Reprogramming of tRNA modifications controls the oxidative stress response by codon-biased translation of proteins. Nat Commun 3: 937
    • (2012) Nat Commun , vol.3 , pp. 937
    • Chan, C.T.Y.1    Pang, Y.L.J.2    Deng, W.3    Babu, I.R.4    Dyavaiah, M.5    Begley, T.J.6    Dedon, P.C.7
  • 7
    • 84875465945 scopus 로고    scopus 로고
    • Positively charged residues are the major determinants of ribosomal velocity
    • Charneski CA, Hurst LD (2013) Positively charged residues are the major determinants of ribosomal velocity. PLoS Biol 11: e1001508
    • (2013) PLoS Biol , vol.11
    • Charneski, C.A.1    Hurst, L.D.2
  • 8
    • 80055071250 scopus 로고    scopus 로고
    • The role of tRNA and ribosome competition in coupling the expression of different mRNAs in Saccharomyces cerevisiae
    • Chu D, Barnes DJ, von der Haar T (2011) The role of tRNA and ribosome competition in coupling the expression of different mRNAs in Saccharomyces cerevisiae. Nucleic Acids Res 39: 6705 - 6714
    • (2011) Nucleic Acids Res , vol.39 , pp. 6705-6714
    • Chu, D.1    Barnes, D.J.2    Von Der-Haar, T.3
  • 9
    • 84869074692 scopus 로고    scopus 로고
    • The architecture of eukaryotic translation
    • Chu D, von der Haar T (2012) The architecture of eukaryotic translation. Nucleic Acids Res 40: 10098 - 10106
    • (2012) Nucleic Acids Res , vol.40 , pp. 10098-10106
    • Chu, D.1    Von Der-Haar, T.2
  • 10
    • 84856117068 scopus 로고    scopus 로고
    • A novel and versatile computational tool to model translation
    • Chu D, Zabet N, von der Haar T (2012) A novel and versatile computational tool to model translation. Bioinformatics 28: 292 - 293
    • (2012) Bioinformatics , vol.28 , pp. 292-293
    • Chu, D.1    Zabet, N.2    Von Der-Haar, T.3
  • 11
    • 84873510362 scopus 로고    scopus 로고
    • Ribosome traffic on mRNAs maps to gene ontology: Genome-wide quantification of translation initiation rates and polysome size regulation
    • Ciandrini L, Stansfield I, Romano MC (2013) Ribosome traffic on mRNAs maps to gene ontology: genome-wide quantification of translation initiation rates and polysome size regulation. PLoS Comput Biol 9: e1002866
    • (2013) PLoS Comput Biol , vol.9
    • Ciandrini, L.1    Stansfield, I.2    Romano, M.C.3
  • 12
    • 84870717729 scopus 로고    scopus 로고
    • Determinants of translation elongation speed and ribosomal profiling biases in mouse embryonic stem cells
    • Dana A, Tuller T (2012) Determinants of translation elongation speed and ribosomal profiling biases in mouse embryonic stem cells. PLoS Comput Biol 8: e1002755
    • (2012) PLoS Comput Biol , vol.8
    • Dana, A.1    Tuller, T.2
  • 14
    • 34948856961 scopus 로고    scopus 로고
    • Ribosome kinetics and aa-tRNA competition determine rate and fidelity of peptide synthesis
    • Fluitt A, Pienaar E, Viljoen H (2007) Ribosome kinetics and aa-tRNA competition determine rate and fidelity of peptide synthesis. Comput Biol Chem 31: 335 - 346
    • (2007) Comput Biol Chem , vol.31 , pp. 335-346
    • Fluitt, A.1    Pienaar, E.2    Viljoen, H.3
  • 17
    • 0028327578 scopus 로고
    • Requirements for intercistronic distance and level of eukaryotic initiation factor 2 activity in reinitiation on GCN4 mRNA vary with the downstream cistron
    • Grant CM, Miller PF, Hinnebusch AG (1994) Requirements for intercistronic distance and level of eukaryotic initiation factor 2 activity in reinitiation on GCN4 mRNA vary with the downstream cistron. Mol Cell Proteomics 14: 2616 - 2628
    • (1994) Mol Cell Proteomics , vol.14 , pp. 2616-2628
    • Grant, C.M.1    Miller, P.F.2    Hinnebusch, A.G.3
  • 18
    • 42449124168 scopus 로고    scopus 로고
    • Optimized protein extraction for quantitative proteomics of yeasts
    • von der Haar T (2007) Optimized protein extraction for quantitative proteomics of yeasts. PLoS ONE 2: e1078
    • (2007) PLoS ONE , vol.2
    • Von Der-Haar, T.1
  • 19
    • 57149143976 scopus 로고    scopus 로고
    • A quantitative estimation of the global translational activity in logarithmically growing yeast cells
    • von der Haar T (2008) A quantitative estimation of the global translational activity in logarithmically growing yeast cells. BMC Syst Biol 2: 87
    • (2008) BMC Syst Biol , vol.2 , pp. 87
    • Von Der-Haar, T.1
  • 20
    • 77749268307 scopus 로고    scopus 로고
    • Experimentally increased codon bias in the Drosophila Adh gene leads to an increase in larval, but not adult, alcohol dehydrogenase activity
    • Hense W, Anderson N, Hutter S, Stephan W, Parsch J, Carlini DB (2010) Experimentally increased codon bias in the Drosophila Adh gene leads to an increase in larval, but not adult, alcohol dehydrogenase activity. Genetics 184: 547 - 555
    • (2010) Genetics , vol.184 , pp. 547-555
    • Hense, W.1    Anderson, N.2    Hutter, S.3    Stephan, W.4    Parsch, J.5    Carlini, D.B.6
  • 22
    • 33646089874 scopus 로고    scopus 로고
    • Codon optimization, expression, and characterization of an internalizing anti-ErbB2 single-chain antibody in Pichia pastoris
    • Hu S, Li L, Qiao J, Guo Y, Cheng L, Liu J (2006) Codon optimization, expression, and characterization of an internalizing anti-ErbB2 single-chain antibody in Pichia pastoris. Protein Expr Purif 47: 249 - 257
    • (2006) Protein Expr Purif , vol.47 , pp. 249-257
    • Hu, S.1    Li, L.2    Qiao, J.3    Guo, Y.4    Cheng, L.5    Liu, J.6
  • 23
    • 0019949369 scopus 로고
    • Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer R
    • Ikemura T (1982) Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer R. J Mol Biol 158: 573 - 597
    • (1982) J Mol Biol , vol.158 , pp. 573-597
    • Ikemura, T.1
  • 24
    • 62549134121 scopus 로고    scopus 로고
    • Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling
    • Ingolia NT, Ghaemmaghami S, Newman JRS, Weissman JS (2009) Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324: 218 - 223
    • (2009) Science , vol.324 , pp. 218-223
    • Ingolia, N.T.1    Ghaemmaghami, S.2    Newman, J.R.S.3    Weissman, J.S.4
  • 25
    • 81055155799 scopus 로고    scopus 로고
    • Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes
    • Ingolia NT, Lareau LF, Weissman JS (2011) Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell 147: 789 - 802
    • (2011) Cell , vol.147 , pp. 789-802
    • Ingolia, N.T.1    Lareau, L.F.2    Weissman, J.S.3
  • 26
    • 84857450275 scopus 로고    scopus 로고
    • Xylitol production is increased by expression of codon-optimized Neurospora crassa xylose reductase gene in Candida tropicalis
    • Jeon WY, Yoon BH, Ko BS, Shim WY, Kim JH (2012) Xylitol production is increased by expression of codon-optimized Neurospora crassa xylose reductase gene in Candida tropicalis. Bioprocess Biosyst Eng 35: 191 - 198
    • (2012) Bioprocess Biosyst Eng , vol.35 , pp. 191-198
    • Jeon, W.Y.1    Yoon, B.H.2    Ko, B.S.3    Shim, W.Y.4    Kim, J.H.5
  • 27
  • 28
    • 0025789743 scopus 로고
    • Evaluation of foreign gene codon optimization in yeast: Expression of a mouse IG kappa chain
    • Kotula L, Curtis PJ (1991) Evaluation of foreign gene codon optimization in yeast: expression of a mouse IG kappa chain. Biotechnology 9: 1386 - 1389
    • (1991) Biotechnology , vol.9 , pp. 1386-1389
    • Kotula, L.1    Curtis, P.J.2
  • 29
    • 64849114915 scopus 로고    scopus 로고
    • Coding-sequence determinants of gene expression in Escherichia coli
    • Kudla G, Murray AW, Tollervey D, Plotkin JB (2009) Coding-sequence determinants of gene expression in Escherichia coli. Science 324: 255 - 258
    • (2009) Science , vol.324 , pp. 255-258
    • Kudla, G.1    Murray, A.W.2    Tollervey, D.3    Plotkin, J.B.4
  • 31
    • 84873467908 scopus 로고    scopus 로고
    • Cotranslational response to proteotoxic stress by elongation pausing of ribosomes
    • Liu B, Han Y, Qian S-B (2013) Cotranslational response to proteotoxic stress by elongation pausing of ribosomes. Mol Cell 49: 453 - 463
    • (2013) Mol Cell , vol.49 , pp. 453-463
    • Liu, B.1    Han, Y.2    Qian, S.-B.3
  • 33
    • 0031768680 scopus 로고    scopus 로고
    • Posttranscriptional control of gene expression in yeast
    • McCarthy JEG (1998) Posttranscriptional control of gene expression in yeast. Microbiol Mol Biol Rev 62: 1492 - 1553
    • (1998) Microbiol Mol Biol Rev , vol.62 , pp. 1492-1553
    • McCarthy, J.E.G.1
  • 34
    • 77956553901 scopus 로고    scopus 로고
    • Decoding accuracy in eRF1 mutants and its correlation with pleiotropic quantitative traits in yeast
    • Merritt GH, Naemi WR, Mugnier P, Webb HM, Tuite MF, von der Haar T (2010) Decoding accuracy in eRF1 mutants and its correlation with pleiotropic quantitative traits in yeast. Nucleic Acids Res 38: 5479 - 5492
    • (2010) Nucleic Acids Res , vol.38 , pp. 5479-5492
    • Merritt, G.H.1    Naemi, W.R.2    Mugnier, P.3    Webb, H.M.4    Tuite, M.F.5    Von Der-Haar, T.6
  • 35
    • 77957947581 scopus 로고    scopus 로고
    • Secretory expression and purification of a soluble NADH cytochrome b5 reductase enzyme from Mucor racemosus in Pichia pastoris based on codon usage adaptation
    • Mirzaei SA, Tabatabaei Yazdi M, Sepehrizadeh Z (2010) Secretory expression and purification of a soluble NADH cytochrome b5 reductase enzyme from Mucor racemosus in Pichia pastoris based on codon usage adaptation. Biotechnol Lett 32: 1705 - 1711
    • (2010) Biotechnol Lett , vol.32 , pp. 1705-1711
    • Mirzaei, S.A.1    Tabatabaei Yazdi, M.2    Sepehrizadeh, Z.3
  • 36
    • 33746649199 scopus 로고    scopus 로고
    • In vivo robustness analysis of cell division cycle genes in Saccharomyces cerevisiae
    • Moriya H, Shimizu-Yoshida Y, Kitano H (2006) In vivo robustness analysis of cell division cycle genes in Saccharomyces cerevisiae. PLoS Genet 2: e111
    • (2006) PLoS Genet , vol.2
    • Moriya, H.1    Shimizu-Yoshida, Y.2    Kitano, H.3
  • 37
    • 3242676308 scopus 로고    scopus 로고
    • Codon optimization of the human papillomavirus 11 (HPV 11) L1 gene leads to increased gene expression and formation of virus-like particles in mammalian epithelial cells
    • Mossadegh N, Gissmann L, Müller M, Zentgraf H, Alonso A, Tomakidi P (2004) Codon optimization of the human papillomavirus 11 (HPV 11) L1 gene leads to increased gene expression and formation of virus-like particles in mammalian epithelial cells. Virology 326: 57 - 66
    • (2004) Virology , vol.326 , pp. 57-66
    • Mossadegh, N.1    Gissmann, L.2    Müller, M.3    Zentgraf, H.4    Alonso, A.5    Tomakidi, P.6
  • 38
    • 0033516966 scopus 로고    scopus 로고
    • Codon optimization effect on translational efficiency of DNA vaccine in mammalian cells: Analysis of plasmid DNA encoding a CTL epitope derived from microorganisms
    • Nagata T, Uchijima M, Yoshida A, Kawashima M, Koide Y (1999) Codon optimization effect on translational efficiency of DNA vaccine in mammalian cells: analysis of plasmid DNA encoding a CTL epitope derived from microorganisms. Biochem Biophys Res Commun 261: 445 - 451
    • (1999) Biochem Biophys Res Commun , vol.261 , pp. 445-451
    • Nagata, T.1    Uchijima, M.2    Yoshida, A.3    Kawashima, M.4    Koide, Y.5
  • 39
    • 34547657193 scopus 로고    scopus 로고
    • Positive selection for unpreferred codon usage in eukaryotic genomes
    • Neafsey DE, Galagan JE (2007) Positive selection for unpreferred codon usage in eukaryotic genomes. BMC Evol Biol 7: 119
    • (2007) BMC Evol Biol , vol.7 , pp. 119
    • Neafsey, D.E.1    Galagan, J.E.2
  • 40
  • 41
    • 0036314780 scopus 로고    scopus 로고
    • Cellular stresses profoundly inhibit protein synthesis and modulate the states of phosphorylation of multiple translation factors
    • Patel J, McLeod LE, Vries RGJ, Flynn A, Wang X, Proud CG (2002) Cellular stresses profoundly inhibit protein synthesis and modulate the states of phosphorylation of multiple translation factors. Eur J Biochem 269: 3076 - 3085
    • (2002) Eur J Biochem , vol.269 , pp. 3076-3085
    • Patel, J.1    McLeod, L.E.2    Vries, R.G.J.3    Flynn, A.4    Wang, X.5    Proud, C.G.6
  • 43
    • 0030861159 scopus 로고    scopus 로고
    • Evolution of codon usage bias in Drosophila
    • Powell JR, Moriyama EN (1997) Evolution of codon usage bias in Drosophila. Proc Natl Acad Sci USA 94: 7784 - 7790
    • (1997) Proc Natl Acad Sci USA , vol.94 , pp. 7784-7790
    • Powell, J.R.1    Moriyama, E.N.2
  • 45
    • 0028360029 scopus 로고
    • Stepwise removal of the C-terminal 12 amino acids of firefly luciferase results in graded loss of activity
    • Sala-Newby GB, Campbell AK (1994) Stepwise removal of the C-terminal 12 amino acids of firefly luciferase results in graded loss of activity. Biochim Biophys Acta 1206: 155 - 160
    • (1994) Biochim Biophys Acta , vol.1206 , pp. 155-160
    • Sala-Newby, G.B.1    Campbell, A.K.2
  • 46
    • 17444384877 scopus 로고    scopus 로고
    • Discrimination between defects in elongation fidelity and termination efficiency provides mechanistic insights into translational readthrough
    • Salas-Marco J, Bedwell DM (2005) Discrimination between defects in elongation fidelity and termination efficiency provides mechanistic insights into translational readthrough. J Mol Biol 348: 801 - 815
    • (2005) J Mol Biol , vol.348 , pp. 801-815
    • Salas-Marco, J.1    Bedwell, D.M.2
  • 48
    • 0024669291 scopus 로고
    • A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae
    • Sikorski RS, Hieter P (1989) A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 000: 19 - 27
    • (1989) Genetics , pp. 19-27
    • Sikorski, R.S.1    Hieter, P.2
  • 49
    • 0036425270 scopus 로고    scopus 로고
    • Synonymous codon usage bias and the expression of human glucocerebrosidase in the methylotrophic yeast, Pichia pastoris
    • Sinclair G, Choy FYM (2002) Synonymous codon usage bias and the expression of human glucocerebrosidase in the methylotrophic yeast, Pichia pastoris. Protein Expr Purif 26: 96 - 105
    • (2002) Protein Expr Purif , vol.26 , pp. 96-105
    • Sinclair, G.1    Choy, F.Y.M.2
  • 50
    • 0037473220 scopus 로고    scopus 로고
    • Codon optimization of Caenorhabditis elegans GluCl ion channel genes for mammalian cells dramatically improves expression levels
    • Slimko EM, Lester HA (2003) Codon optimization of Caenorhabditis elegans GluCl ion channel genes for mammalian cells dramatically improves expression levels. J Neurosci Methods 124: 75 - 81
    • (2003) J Neurosci Methods , vol.124 , pp. 75-81
    • Slimko, E.M.1    Lester, H.A.2
  • 51
    • 81755184408 scopus 로고    scopus 로고
    • Wobble base-pairing slows in vivo translation elongation in metazoans
    • Stadler M, Fire A (2011) Wobble base-pairing slows in vivo translation elongation in metazoans. RNA 17: 2063 - 2073
    • (2011) RNA , vol.17 , pp. 2063-2073
    • Stadler, M.1    Fire, A.2
  • 52
  • 53
    • 0024117032 scopus 로고
    • Ribosome pausing and stacking during translation of a eukaryotic mRNA
    • Wolin SL, Walter P (1988) Ribosome pausing and stacking during translation of a eukaryotic mRNA. EMBO J 7: 3559 - 3569
    • (1988) EMBO J , vol.7 , pp. 3559-3569
    • Wolin, S.L.1    Walter, P.2
  • 54
    • 0042324336 scopus 로고    scopus 로고
    • Effect of codon optimization on expression levels of a functionally folded Malaria vaccine candidate in prokaryotic and eukaryotic expression systems
    • Yadava A, Ockenhouse CF (2003) Effect of codon optimization on expression levels of a functionally folded Malaria vaccine candidate in prokaryotic and eukaryotic expression systems. Infect Immun 71: 4961 - 4969
    • (2003) Infect Immun , vol.71 , pp. 4961-4969
    • Yadava, A.1    Ockenhouse, C.F.2
  • 55
    • 84874683740 scopus 로고    scopus 로고
    • Non-optimal codon usage affects expression, structure and function of clock protein FRQ
    • Zhou M, Guo J, Cha J, Chae M, Chen S, Barral JM, Sachs MS, Liu Y (2013) Non-optimal codon usage affects expression, structure and function of clock protein FRQ. Nature 495: 111 - 115
    • (2013) Nature , vol.495 , pp. 111-115
    • Zhou, M.1    Guo, J.2    Cha, J.3    Chae, M.4    Chen, S.5    Barral, J.M.6    Sachs, M.S.7    Liu, Y.8
  • 56
    • 51049096159 scopus 로고    scopus 로고
    • Effects of codon distributions and tRNA competition on protein translation
    • Zouridis H, Hatzimanikatis V (2008) Effects of codon distributions and tRNA competition on protein translation. Biophys J 95: 1018 - 1033
    • (2008) Biophys J , vol.95 , pp. 1018-1033
    • Zouridis, H.1    Hatzimanikatis, V.2


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