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Volumn 43, Issue 6, 2015, Pages 3022-3032

Trade-offs between tRNA abundance and mRNA secondary structure support smoothing of translation elongation rate

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; TRANSFER RNA; BACTERIAL RNA; CODON; ESCHERICHIA COLI PROTEIN; FUNGAL RNA; SACCHAROMYCES CEREVISIAE PROTEIN;

EID: 84942284143     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv199     Document Type: Article
Times cited : (92)

References (67)
  • 1
    • 0021731777 scopus 로고
    • Escherichia coli ribosomes translate in vivo with variable rate
    • Pedersen,S. (1984) Escherichia coli ribosomes translate in vivo with variable rate. EMBO J., 3, 2895-2898.
    • (1984) EMBO J. , vol.3 , pp. 2895-2898
    • Pedersen, S.1
  • 2
    • 70349964350 scopus 로고    scopus 로고
    • Automated design of synthetic ribosome binding sites to control protein expression
    • Salis,H.M., Mirsky,E.A. and Voigt,C.A. (2009) Automated design of synthetic ribosome binding sites to control protein expression. Nat. Biotechnol., 27, 946-950.
    • (2009) Nat. Biotechnol. , vol.27 , pp. 946-950
    • Salis, H.M.1    Mirsky, E.A.2    Voigt, C.A.3
  • 3
    • 64849114915 scopus 로고    scopus 로고
    • Coding-sequence determinants of gene expression in Escherichia coli
    • Kudla,G., Murray,A.W., Tollervey,D. and Plotkin,J.B. (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
  • 4
    • 62049083910 scopus 로고    scopus 로고
    • Transient ribosomal attenuation coordinates protein synthesis and co-translational folding
    • Zhang,G., Hubalewska,M. and Ignatova,Z. (2009) Transient ribosomal attenuation coordinates protein synthesis and co-translational folding. Nat. Struct. Mol. Biol., 16, 274-280.
    • (2009) Nat. Struct. Mol. Biol. , vol.16 , pp. 274-280
    • Zhang, G.1    Hubalewska, M.2    Ignatova, Z.3
  • 6
    • 68849083789 scopus 로고    scopus 로고
    • Rare codon content affects the solubility of recombinant proteins in a codon bias-adjusted Escherichia coli strain
    • Rosano,G.L. and Ceccarelli,E.A. (2009) Rare codon content affects the solubility of recombinant proteins in a codon bias-adjusted Escherichia coli strain. Microb. Cell Fact., 8, 41.
    • (2009) Microb. Cell Fact. , vol.8 , pp. 41
    • Rosano, G.L.1    Ceccarelli, E.A.2
  • 7
    • 84884930238 scopus 로고    scopus 로고
    • Translational sensitivity of the Escherichia coli genome to fluctuating tRNA availability
    • Wohlgemuth,S.E., Gorochowski,T.E. and Roubos,J.A. (2013) Translational sensitivity of the Escherichia coli genome to fluctuating tRNA availability. Nucleic Acids Res., 41, 8021-8033.
    • (2013) Nucleic Acids Res. , vol.41 , pp. 8021-8033
    • Wohlgemuth, S.E.1    Gorochowski, T.E.2    Roubos, J.A.3
  • 8
    • 0021764898 scopus 로고
    • Translation is a non-uniform process. Effect of tRNA availability on the rate of elongation of nascent polypeptide chains
    • Varenne,S., Buc,J., Lloubes,R. and Lazdunski,C. (1984) Translation is a non-uniform process. Effect of tRNA availability on the rate of elongation of nascent polypeptide chains. J. Mol. Biol., 180, 549-576.
    • (1984) J. Mol. Biol. , vol.180 , pp. 549-576
    • Varenne, S.1    Buc, J.2    Lloubes, R.3    Lazdunski, C.4
  • 9
    • 0024405193 scopus 로고
    • Codon usage determines translation rate in Escherichia coli
    • Sorensen,M.A., Kurland,C.G. and Pedersen,S. (1989) Codon usage determines translation rate in Escherichia coli. J. Mol. Biol., 207, 365-377.
    • (1989) J. Mol. Biol. , vol.207 , pp. 365-377
    • Sorensen, M.A.1    Kurland, C.G.2    Pedersen, S.3
  • 11
    • 78650304100 scopus 로고    scopus 로고
    • Synonymous but not the same: The causes and consequences of codon bias
    • Plotkin,J.B. and Kudla,G. (2011) Synonymous but not the same: the causes and consequences of codon bias. Nat. Rev. Genet., 12, 32-42.
    • (2011) Nat. Rev. Genet. , vol.12 , pp. 32-42
    • Plotkin, J.B.1    Kudla, G.2
  • 12
    • 80052964856 scopus 로고    scopus 로고
    • Understanding the contribution of synonymous mutations to human disease
    • Sauna,Z.E. and Kimchi-Sarfaty,C. (2011) Understanding the contribution of synonymous mutations to human disease. Nat. Rev. Genet., 12, 683-691.
    • (2011) Nat. Rev. Genet. , vol.12 , pp. 683-691
    • Sauna, Z.E.1    Kimchi-Sarfaty, C.2
  • 13
    • 1442289362 scopus 로고    scopus 로고
    • Enhanced expression of a recombinant malaria candidate vaccine in Escherichia coli by codon optimization
    • Zhou,Z., Schnake,P., Xiao,L. and Lal,A.A. (2004) Enhanced expression of a recombinant malaria candidate vaccine in Escherichia coli by codon optimization. Protein Expr. Purif., 34, 87-94.
    • (2004) Protein Expr. Purif. , vol.34 , pp. 87-94
    • Zhou, Z.1    Schnake, P.2    Xiao, L.3    Lal, A.A.4
  • 16
    • 84964314754 scopus 로고    scopus 로고
    • Measurement of average decoding rates of the 61 sense codons in vivo
    • Gardin,J., Yeasmin,R., Yurovsky,A., Cai,Y., Skiena,S. and Futcher,B. (2014) Measurement of average decoding rates of the 61 sense codons in vivo. Elife, 3, e03735.
    • (2014) Elife , vol.3
    • Gardin, J.1    Yeasmin, R.2    Yurovsky, A.3    Cai, Y.4    Skiena, S.5    Futcher, B.6
  • 18
  • 19
    • 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
  • 20
    • 84906235471 scopus 로고    scopus 로고
    • The effect of tRNA levels on decoding times of mRNA codons
    • Dana,A. and Tuller,T. (2014) The effect of tRNA levels on decoding times of mRNA codons. Nucleic Acids Res., 42, 9171-9181.
    • (2014) Nucleic Acids Res. , vol.42 , pp. 9171-9181
    • Dana, A.1    Tuller, T.2
  • 21
    • 64549100262 scopus 로고    scopus 로고
    • Generic algorithm to predict the speed of translational elongation: Implications for protein biogenesis
    • Zhang,G. and Ignatova,Z. (2009) Generic algorithm to predict the speed of translational elongation: implications for protein biogenesis. PLoS One, 4, e5036.
    • (2009) PLoS One , vol.4
    • Zhang, G.1    Ignatova, Z.2
  • 22
    • 84860231100 scopus 로고    scopus 로고
    • The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria
    • Li,G.-W., Oh,E. and Weissman,J.S. (2012) The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria. Nature, 484, 538-541.
    • (2012) Nature , vol.484 , pp. 538-541
    • Li, G.-W.1    Oh, E.2    Weissman, J.S.3
  • 25
    • 84899821225 scopus 로고    scopus 로고
    • Deciphering the rules by which dynamics of mRNA secondary structure affect translation efficiency in Saccharomyces cerevisiae
    • Mao,Y., Liu,H., Liu,Y. and Shiheng,T. (2014) Deciphering the rules by which dynamics of mRNA secondary structure affect translation efficiency in Saccharomyces cerevisiae. Nucleic Acids Res., 42, 4813-4822.
    • (2014) Nucleic Acids Res. , vol.42 , pp. 4813-4822
    • Mao, Y.1    Liu, H.2    Liu, Y.3    Shiheng, T.4
  • 26
    • 84875465945 scopus 로고    scopus 로고
    • Positively charged residues are the major determinants of ribosomal velocity
    • Charneski,C.A. and Hurst,L.D. (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
  • 27
    • 84893351549 scopus 로고    scopus 로고
    • Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo
    • Rouskin,S., Zubradt,M., Washietl,S., Kellis,M. and Weissman,J.S. (2014) Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo. Nature, 505, 701-705.
    • (2014) Nature , vol.505 , pp. 701-705
    • Rouskin, S.1    Zubradt, M.2    Washietl, S.3    Kellis, M.4    Weissman, J.S.5
  • 28
    • 62549134121 scopus 로고    scopus 로고
    • Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling
    • Ingolia,N.T., Ghaemmaghami,S., Newman,R.S. and Weissman,J.S. (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, R.S.3    Weissman, J.S.4
  • 31
    • 38549144165 scopus 로고    scopus 로고
    • HEG-DB: A database of predicted highly expressed genes in prokaryotic complete genomes under translational selection
    • Puigbò,P., Romeu,A. and Garcia-Vallvé,S. (2008) HEG-DB: a database of predicted highly expressed genes in prokaryotic complete genomes under translational selection. Nucleic Acids Res., 36, D524-D527.
    • (2008) Nucleic Acids Res. , vol.36 , pp. D524-D527
    • Puigbò, P.1    Romeu, A.2    Garcia-Vallvé, S.3
  • 35
    • 58349111875 scopus 로고    scopus 로고
    • AmiGO: Online access to ontology and annotation data
    • Carbon,S., Ireland,A., Mungall,C.J., Shu,S.Q., Marshall,B., Lewis,S. and the AmiGO Hub and the Web Presence Working Group (2009) AmiGO: online access to ontology and annotation data. Bioinformatics, 25, 288-289.
    • (2009) Bioinformatics , vol.25 , pp. 288-289
    • Carbon, S.1    Ireland, A.2    Mungall, C.J.3    Shu, S.Q.4    Marshall, B.5    Lewis, S.6
  • 37
    • 84893427735 scopus 로고    scopus 로고
    • In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features
    • Ding,Y., Tang,Y., Kwok,C.T., Zhang,Y., Bevilacqua,P.C. and Assmann,S.M. (2014) In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features. Nature, 505, 696-700.
    • (2014) Nature , vol.505 , pp. 696-700
    • Ding, Y.1    Tang, Y.2    Kwok, C.T.3    Zhang, Y.4    Bevilacqua, P.C.5    Assmann, S.M.6
  • 38
    • 79551690253 scopus 로고    scopus 로고
    • Folding at the birth of the nascent chain: Coordinating translation with co-translational folding
    • Zhang,G. and Ignatova,Z. (2011) Folding at the birth of the nascent chain: coordinating translation with co-translational folding. Curr. Opin. Struct. Biol., 21, 25-31.
    • (2011) Curr. Opin. Struct. Biol. , vol.21 , pp. 25-31
    • Zhang, G.1    Ignatova, Z.2
  • 39
    • 84925553022 scopus 로고    scopus 로고
    • Local slowdown of translation by nonoptimal codons promotes nascent-chain recognition by SRP in vivo
    • Pechmann,S., Chartron,J.W. and Frydman,J. (2014) Local slowdown of translation by nonoptimal codons promotes nascent-chain recognition by SRP in vivo. Nat. Struct. Mol. Biol., 21, 1100-1105.
    • (2014) Nat. Struct. Mol. Biol. , vol.21 , pp. 1100-1105
    • Pechmann, S.1    Chartron, J.W.2    Frydman, J.3
  • 40
    • 84871436566 scopus 로고    scopus 로고
    • Transfer RNA modifications: Nature's combinatorial chemistry playground
    • Jackman,J.E. and Alfonzo,J.D. (2013) Transfer RNA modifications: nature's combinatorial chemistry playground. Wiley Interdiscip. Rev. RNA, 4, 35-48.
    • (2013) Wiley Interdiscip. Rev. RNA , vol.4 , pp. 35-48
    • Jackman, J.E.1    Alfonzo, J.D.2
  • 41
    • 84899881726 scopus 로고    scopus 로고
    • Transcript level and sequence determinants of protein abundance and noise in Escherichia coli
    • Guimaraes,J.C., Rocha,M. and Arkin,A.P. (2014) Transcript level and sequence determinants of protein abundance and noise in Escherichia coli. Nucleic Acids Res., 42, 4791-4799.
    • (2014) Nucleic Acids Res. , vol.42 , pp. 4791-4799
    • Guimaraes, J.C.1    Rocha, M.2    Arkin, A.P.3
  • 42
    • 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
  • 43
    • 0242391986 scopus 로고    scopus 로고
    • Codon adaptation index as a measure of dominating codon bias
    • Carbone,A., Zinovyev,A. and Képès,F. (2003) Codon adaptation index as a measure of dominating codon bias. Bioinformatics, 19, 2005-2015.
    • (2003) Bioinformatics , vol.19 , pp. 2005-2015
    • Carbone, A.1    Zinovyev, A.2    Képès, F.3
  • 44
    • 84903457409 scopus 로고    scopus 로고
    • The effects of codon context on in vivo translation speed
    • Chevance,F.F.V., Guyon,S.L. and Hughes,K.T. (2014) The effects of codon context on in vivo translation speed. PLoS Genet., 10, e1004392.
    • (2014) PLoS Genet. , vol.10
    • Chevance, F.F.V.1    Guyon, S.L.2    Hughes, K.T.3
  • 47
    • 0034046020 scopus 로고    scopus 로고
    • The SsrASmpB system for protein tagging, directed degradation and ribosome rescue
    • Karzai,A.W., Roche,E.D. and Sauer,R.T. (2000) The SsrASmpB system for protein tagging, directed degradation and ribosome rescue. Nat. Struct. Mol. Biol., 7, 449-455.
    • (2000) Nat. Struct. Mol. Biol. , vol.7 , pp. 449-455
    • Karzai, A.W.1    Roche, E.D.2    Sauer, R.T.3
  • 48
    • 26944431987 scopus 로고    scopus 로고
    • Ribosome rescue: TmRNA tagging activity and capacity in Escherichia coli
    • Moore,S.D. and Sauer,R.T. (2005) Ribosome rescue: tmRNA tagging activity and capacity in Escherichia coli. Mol. Microbiol., 58, 456-466.
    • (2005) Mol. Microbiol. , vol.58 , pp. 456-466
    • Moore, S.D.1    Sauer, R.T.2
  • 49
    • 34548446795 scopus 로고    scopus 로고
    • Halting a cellular production line: Responses to ribosomal pausing during translation
    • Buchan,J.R. and Stansfield,I. (2007) Halting a cellular production line: responses to ribosomal pausing during translation. Biol. Cell, 99, 475-487.
    • (2007) Biol. Cell , vol.99 , pp. 475-487
    • Buchan, J.R.1    Stansfield, I.2
  • 50
    • 84862666301 scopus 로고    scopus 로고
    • A computational framework for the design of optimal protein synthesis
    • Racle,J., Overney,J. and Hatzimanikatis,V. (2012) A computational framework for the design of optimal protein synthesis. Biotechnol. Bioeng., 109, 2127-2133.
    • (2012) Biotechnol. Bioeng. , vol.109 , pp. 2127-2133
    • Racle, J.1    Overney, J.2    Hatzimanikatis, V.3
  • 51
    • 84904268081 scopus 로고    scopus 로고
    • Quantifying the effect of ribosomal density on mRNA stability
    • Edri,S. and Tuller,T. (2014) Quantifying the effect of ribosomal density on mRNA stability. PLoS One, 9, e102308.
    • (2014) PLoS One , vol.9
    • Edri, S.1    Tuller, T.2
  • 52
    • 79952009085 scopus 로고    scopus 로고
    • The functional half-life of an mRNA depends on the ribosome spacing in an early coding region
    • Pedersen,M., Nissen,S., Mitarai,N., Svenningsen,S.L., Sneppen,K. and Pedersen,S. (2011) The functional half-life of an mRNA depends on the ribosome spacing in an early coding region. J. Mol. Biol., 407, 35-44.
    • (2011) J. Mol. Biol. , vol.407 , pp. 35-44
    • Pedersen, M.1    Nissen, S.2    Mitarai, N.3    Svenningsen, S.L.4    Sneppen, K.5    Pedersen, S.6
  • 53
    • 84881488106 scopus 로고    scopus 로고
    • Effect of ribosome shielding on mRNA stability
    • Deneke,C., Lipowsky,R. and Valleriani,A. (2013) Effect of ribosome shielding on mRNA stability. Phys. Biol., 10, 046008.
    • (2013) Phys. Biol. , vol.10
    • Deneke, C.1    Lipowsky, R.2    Valleriani, A.3
  • 54
    • 0033745103 scopus 로고    scopus 로고
    • Nucleotide bias causes a genome wide bias in the amino acid composition of proteins
    • Singer,G.A.C. and Hickey,D.A. (2000) Nucleotide bias causes a genome wide bias in the amino acid composition of proteins. Mol. Biol. Evol., 17, 1581-1588.
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 1581-1588
    • Singer, G.A.C.1    Hickey, D.A.2
  • 55
    • 0033119454 scopus 로고    scopus 로고
    • MRNAs have greater negative folding free energies than shuffled or codon choice randomized sequences
    • Seffens,W. and Digby,D. (1999) mRNAs have greater negative folding free energies than shuffled or codon choice randomized sequences. Nucleic Acids Res., 27, 1578-1584.
    • (1999) Nucleic Acids Res. , vol.27 , pp. 1578-1584
    • Seffens, W.1    Digby, D.2
  • 56
    • 0033572893 scopus 로고    scopus 로고
    • No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution
    • Workman,C. and Krogh,C. (1999) No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution. Nucleic Acids Res., 27, 4816-4822.
    • (1999) Nucleic Acids Res. , vol.27 , pp. 4816-4822
    • Workman, C.1    Krogh, C.2
  • 57
    • 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. and Romano,M.C. (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
  • 59
    • 0031720281 scopus 로고    scopus 로고
    • Codon usages in different gene classes of the Escherichia coli genome
    • Karlin,S., Mrázek,J. and Campbell,A.M. (1998) Codon usages in different gene classes of the Escherichia coli genome. Mol. Microbiol., 29, 1341-1355.
    • (1998) Mol. Microbiol. , vol.29 , pp. 1341-1355
    • Karlin, S.1    Mrázek, J.2    Campbell, A.M.3
  • 62
    • 84905375893 scopus 로고    scopus 로고
    • Codon-by-codon modulation of translational speed and accuracy via mRNA folding
    • Yang,J.-R., Chen,X. and Zhang,J. (2014) Codon-by-codon modulation of translational speed and accuracy via mRNA folding. PLoS Biol., 12, e1001910.
    • (2014) PLoS Biol. , vol.12
    • Yang, J.-R.1    Chen, X.2    Zhang, J.3
  • 64
    • 0030564828 scopus 로고    scopus 로고
    • Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates
    • Dong,H., Nilsson,L. and Kurland,G.C. (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, G.C.3
  • 65
    • 14644396660 scopus 로고    scopus 로고
    • Selective charging of tRNA isoacceptors induced by amino-acid starvation
    • Dittmar,K.A., Sorensen,M.A., Elf,J., Ehrenberg,M. and Pan,T. (2005) Selective charging of tRNA isoacceptors induced by amino-acid starvation. EMBO Rep., 6, 151-157.
    • (2005) EMBO Rep. , vol.6 , pp. 151-157
    • Dittmar, K.A.1    Sorensen, M.A.2    Elf, J.3    Ehrenberg, M.4    Pan, T.5
  • 66
    • 84869047677 scopus 로고    scopus 로고
    • Dynamic changes in translational efficiency are deduced from codon usage of the transcriptome
    • Gingold,H., Dahan,O. and Pilpel,Y. (2012) Dynamic changes in translational efficiency are deduced from codon usage of the transcriptome. Nucleic Acids Res., 40, 10053-10063.
    • (2012) Nucleic Acids Res. , vol.40 , pp. 10053-10063
    • Gingold, H.1    Dahan, O.2    Pilpel, Y.3
  • 67
    • 84924192559 scopus 로고    scopus 로고
    • Emerging roles of tRNA in adaptive translation, signalling dynamics and disease
    • Kirchner,S. and Ignatova,Z. (2015) Emerging roles of tRNA in adaptive translation, signalling dynamics and disease. Nat. Rev. Genet., 16, 98-112.
    • (2015) Nat. Rev. Genet. , vol.16 , pp. 98-112
    • Kirchner, S.1    Ignatova, Z.2


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