메뉴 건너뛰기




Volumn 15, Issue , 2014, Pages

Properties and determinants of codon decoding time distributions

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; NUCLEOTIDE; TRANSFER RNA; CODON;

EID: 84979850805     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-S6-S13     Document Type: Article
Times cited : (21)

References (53)
  • 2
    • 0023650543 scopus 로고
    • The codon Adaptation Index-a measure of directional synonymous codon usage bias, and its potential applications
    • Sharp PM, Li WH: The codon Adaptation Index-a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 1987, 15(3):1281-1295.
    • (1987) Nucleic Acids Res , vol.15 , Issue.3 , pp. 1281-1295
    • Sharp, P.M.1    Li, W.H.2
  • 3
    • 4644280499 scopus 로고    scopus 로고
    • Solving the riddle of codon usage preferences: a test for translational selection
    • dos Reis M, Savva R, Wernisch L: Solving the riddle of codon usage preferences: a test for translational selection. Nucleic Acids Res 2004, 32(17):5036-5044.
    • (2004) Nucleic Acids Res , vol.32 , Issue.17 , pp. 5036-5044
    • dos Reis, M.1    Savva, R.2    Wernisch, L.3
  • 9
    • 64849114915 scopus 로고    scopus 로고
    • Coding-sequence determinants of gene expression in Escherichia coli
    • Kudla G, Murray AW, Tollervey D, Plotkin JB: Coding-sequence determinants of gene expression in Escherichia coli. Science 2009, 324(5924):255-258.
    • (2009) Science , vol.324 , Issue.5924 , pp. 255-258
    • Kudla, G.1    Murray, A.W.2    Tollervey, D.3    Plotkin, J.B.4
  • 10
    • 84857770146 scopus 로고    scopus 로고
    • Strong association between mRNA folding strength and protein abundance in S. cerevisiae
    • Zur H, Tuller T: Strong association between mRNA folding strength and protein abundance in S. cerevisiae. EMBO reports 2012, 13(3):272-277.
    • (2012) EMBO reports , vol.13 , Issue.3 , pp. 272-277
    • Zur, H.1    Tuller, T.2
  • 11
    • 77649198142 scopus 로고    scopus 로고
    • A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes
    • Gu W, Zhou T, Wilke CO: A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes. PLoS computational biology 2010, 6(2):e1000664.
    • (2010) PLoS computational biology , vol.6 , Issue.2
    • Gu, W.1    Zhou, T.2    Wilke, C.O.3
  • 14
    • 84874722535 scopus 로고    scopus 로고
    • Non-optimal codon usage is a mechanism to achieve circadian clock conditionality
    • Xu Y, Ma P, Shah P, Rokas A, Liu Y, Johnson CH: Non-optimal codon usage is a mechanism to achieve circadian clock conditionality. Nature 2013.
    • (2013) Nature
    • Xu, Y.1    Ma, P.2    Shah, P.3    Rokas, A.4    Liu, Y.5    Johnson, C.H.6
  • 15
    • 84874683740 scopus 로고    scopus 로고
    • Nonoptimal 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: Nonoptimal codon usage affects expression, structure and function of clock protein FRQ. Nature 2013, 495(7439):111-115.
    • (2013) Nature , vol.495 , Issue.7439 , 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
  • 16
    • 62549134121 scopus 로고    scopus 로고
    • Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling
    • Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS: Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 2009, 324(5924):218-223.
    • (2009) Science , vol.324 , Issue.5924 , pp. 218-223
    • Ingolia, N.T.1    Ghaemmaghami, S.2    Newman, J.R.3    Weissman, J.S.4
  • 17
    • 84860231100 scopus 로고    scopus 로고
    • The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria
    • Li GW, Oh E, Weissman JS: The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria. Nature 2012, 484(28):538-541.
    • (2012) Nature , vol.484 , Issue.28 , pp. 538-541
    • Li, G.W.1    Oh, E.2    Weissman, J.S.3
  • 18
    • 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: Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell 2011, 147(4):789-802.
    • (2011) Cell , vol.147 , Issue.4 , pp. 789-802
    • Ingolia, N.T.1    Lareau, L.F.2    Weissman, J.S.3
  • 19
    • 84870527178 scopus 로고    scopus 로고
    • Contributions of mRNA abundance, ribosome loading, and post-or peri-translational effects to temporal repression of C. elegans heterochronic miRNA targets
    • Stadler M, Artiles K, Pak J, Fire A: Contributions of mRNA abundance, ribosome loading, and post-or peri-translational effects to temporal repression of C. elegans heterochronic miRNA targets. Genome research 2012, 22(12):2418-2426.
    • (2012) Genome research , vol.22 , Issue.12 , pp. 2418-2426
    • Stadler, M.1    Artiles, K.2    Pak, J.3    Fire, A.4
  • 20
    • 84856625798 scopus 로고    scopus 로고
    • Highresolution view of the yeast meiotic program revealed by ribosome profiling
    • Brar GA, Yassour M, Friedman N, Regev A, Ingolia NT, Weissman JS: Highresolution view of the yeast meiotic program revealed by ribosome profiling. Science 2012, 335(6068):552-557.
    • (2012) Science , vol.335 , Issue.6068 , pp. 552-557
    • Brar, G.A.1    Yassour, M.2    Friedman, N.3    Regev, A.4    Ingolia, N.T.5    Weissman, J.S.6
  • 21
    • 84859219968 scopus 로고    scopus 로고
    • Balanced codon usage optimizes eukaryotic translational efficiency
    • Qian W, Yang JR, Pearson NM, Maclean C, Zhang J: Balanced codon usage optimizes eukaryotic translational efficiency. PLoS genetics 2012, 8(3): e1002603.
    • (2012) PLoS genetics , vol.8 , Issue.3
    • Qian, W.1    Yang, J.R.2    Pearson, N.M.3    Maclean, C.4    Zhang, J.5
  • 22
    • 84884598021 scopus 로고    scopus 로고
    • Loss of a conserved tRNA anticodon modification perturbs cellular signaling
    • Zinshteyn B, Gilbert WV: Loss of a conserved tRNA anticodon modification perturbs cellular signaling. PLoS genetics 2013, 9(8):e1003675.
    • (2013) PLoS genetics , vol.9 , Issue.8
    • Zinshteyn, B.1    Gilbert, W.V.2
  • 23
    • 84875465945 scopus 로고    scopus 로고
    • Positively charged residues are the major determinants of ribosomal velocity
    • Charneski CA, Hurst LD: Positively charged residues are the major determinants of ribosomal velocity. PLoS biology 2013, 11(3):e1001508.
    • (2013) PLoS biology , vol.11 , Issue.3
    • Charneski, C.A.1    Hurst, L.D.2
  • 25
    • 84941476533 scopus 로고
    • Neue Begründung der Theorie quadratischer Formen von unendlichvielen Veränderlichen
    • Hellinger E: Neue Begründung der Theorie quadratischer Formen von unendlichvielen Veränderlichen. Journal für die reine und angewandte Mathematik 1909, 136:210-271.
    • (1909) Journal für die reine und angewandte Mathematik , vol.136 , pp. 210-271
    • Hellinger, E.1
  • 27
    • 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: 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 1981, 151(3):389-409.
    • (1981) J Mol Biol , vol.151 , Issue.3 , pp. 389-409
    • Ikemura, T.1
  • 28
    • 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(1):13-34.
    • (1985) Mol Biol Evol , vol.2 , Issue.1 , pp. 13-34
    • Ikemura, T.1
  • 29
    • 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 in genetics: TIG 2000, 16(7):287-289.
    • (2000) Trends in genetics: TIG , vol.16 , Issue.7 , pp. 287-289
    • Duret, L.1
  • 30
    • 8744310123 scopus 로고    scopus 로고
    • Codon usage bias from tRNA's point of view: redundancy, specialization, and efficient decoding for translation optimization
    • Rocha EP: Codon usage bias from tRNA's point of view: redundancy, specialization, and efficient decoding for translation optimization. Genome research 2004, 14(11):2279-2286.
    • (2004) Genome research , vol.14 , Issue.11 , pp. 2279-2286
    • Rocha, E.P.1
  • 31
    • 84989342128 scopus 로고    scopus 로고
    • The effect of tRNA levels on decoding times of mRNA codons
    • Dana A, Tuller T: The effect of tRNA levels on decoding times of mRNA codons. Under review 2014.
    • (2014) Under review
    • Dana, A.1    Tuller, T.2
  • 32
    • 56449123499 scopus 로고    scopus 로고
    • Totally asymmetric exclusion process with extended objects: a model for protein synthesis
    • Shaw LB, Zia RK, Lee KH: Totally asymmetric exclusion process with extended objects: a model for protein synthesis. Phys Rev E Stat Nonlin Soft Matter Phys 2003, 68(2 Pt 1):021910.
    • (2003) Phys Rev E Stat Nonlin Soft Matter Phys , vol.68 , Issue.2
    • Shaw, L.B.1    Zia, R.K.2    Lee, K.H.3
  • 35
    • 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(1):143-155.
    • (1999) Gene , vol.238 , Issue.1 , pp. 143-155
    • Kanaya, S.1    Yamada, Y.2    Kudo, Y.3    Ikemura, T.4
  • 36
    • 0021239085 scopus 로고
    • Point mutations close to the AUG initiator codon affect the efficiency of translation of rat preproinsulin in vivo
    • Kozak M: Point mutations close to the AUG initiator codon affect the efficiency of translation of rat preproinsulin in vivo. Nature 1984, 308(5956):241-246.
    • (1984) Nature , vol.308 , Issue.5956 , pp. 241-246
    • Kozak, M.1
  • 38
    • 84880766519 scopus 로고    scopus 로고
    • New Universal Rules of Eukaryotic Translation Initiation Fidelity
    • (Accepted)
    • Zur HTTT: New Universal Rules of Eukaryotic Translation Initiation Fidelity. PLoS Comput Biol 2013, (Accepted).
    • (2013) PLoS Comput Biol
    • Zur, H.T.T.T.1
  • 39
    • 84870717729 scopus 로고    scopus 로고
    • Determinants of translation elongation speed and ribosomal profiling biases in mouse embryonic stem cells
    • Dana A, Tuller T: Determinants of translation elongation speed and ribosomal profiling biases in mouse embryonic stem cells. PLoS computational biology 2012, 8(11):e1002755.
    • (2012) PLoS computational biology , vol.8 , Issue.11
    • Dana, A.1    Tuller, T.2
  • 41
    • 84879345901 scopus 로고    scopus 로고
    • Rate-limiting steps in yeast protein translation
    • Shah P, Ding Y, Niemczyk M, Kudla G, Plotkin JB: Rate-limiting steps in yeast protein translation. Cell 2013, 153(7):1589-1601.
    • (2013) Cell , vol.153 , Issue.7 , pp. 1589-1601
    • Shah, P.1    Ding, Y.2    Niemczyk, M.3    Kudla, G.4    Plotkin, J.B.5
  • 42
    • 84878820561 scopus 로고    scopus 로고
    • rRNA:mRNA pairing alters the length and the symmetry of mRNA-protected fragments in ribosome profiling experiments
    • O'Connor PB, Li GW, Weissman JS, Atkins JF, Baranov PV: rRNA:mRNA pairing alters the length and the symmetry of mRNA-protected fragments in ribosome profiling experiments. Bioinformatics 2013, 29(12):1488-1491.
    • (2013) Bioinformatics , vol.29 , Issue.12 , pp. 1488-1491
    • O'Connor, P.B.1    Li, G.W.2    Weissman, J.S.3    Atkins, J.F.4    Baranov, P.V.5
  • 43
    • 0035106351 scopus 로고    scopus 로고
    • Large-scale analysis of the yeast proteome by multidimensional protein identification technology
    • Washburn MP, Wolters D, Yates JR III: Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nature biotechnology 2001, 19(3):242-247.
    • (2001) Nature biotechnology , vol.19 , Issue.3 , pp. 242-247
    • Washburn, M.P.1    Wolters, D.2    Yates, J.R.3
  • 47
    • 77956024408 scopus 로고    scopus 로고
    • Genome-wide translational profiling by ribosome footprinting
    • Ingolia NT: Genome-wide translational profiling by ribosome footprinting. Methods Enzymol 2010, 470:119-142.
    • (2010) Methods Enzymol , vol.470 , pp. 119-142
    • Ingolia, N.T.1
  • 48
    • 84906235471 scopus 로고    scopus 로고
    • The effect of tRNA levels on decoding times of mRNA codons
    • Dana A, Tuller T: The effect of tRNA levels on decoding times of mRNA codons. Nucleic acids research 2014, 42(14):9171-9181.
    • (2014) Nucleic acids research , vol.42 , Issue.14 , pp. 9171-9181
    • Dana, A.1    Tuller, T.2
  • 49
    • 0036896227 scopus 로고    scopus 로고
    • On choosing and bounding probability metrics
    • Gibbs AL, Su FE: On choosing and bounding probability metrics. International statistical review 2002, 70(3):419-435.
    • (2002) International statistical review , vol.70 , Issue.3 , pp. 419-435
    • Gibbs, A.L.1    Su, F.E.2
  • 52
    • 58149189877 scopus 로고    scopus 로고
    • GtRNAdb: a database of transfer RNA genes detected in genomic sequence
    • Chan PP, Lowe TM: GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res 2009, 37(Database):D93-97.
    • (2009) Nucleic Acids Res , vol.37 , Issue.DATABASE , pp. D93-D97
    • Chan, P.P.1    Lowe, T.M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.