메뉴 건너뛰기




Volumn 8, Issue , 2012, Pages

Genes adopt non-optimal codon usage to generate cell cycle-dependent oscillations in protein levels

Author keywords

cell cycle; non optimal codons; translation regulation; tRNA expression during cell cycle; wobbling

Indexed keywords

GLUTAMYLPROLYLTRANSFER RNA SYNTHETASE; GLYCYLTHREONYLTRANSFER RNA SYNTHETASE; MESSENGER RNA; TRANSFER RNA; UNCLASSIFIED DRUG; CELL CYCLE PROTEIN; PROTEIN;

EID: 84857715986     PISSN: None     EISSN: 17444292     Source Type: Journal    
DOI: 10.1038/msb.2012.3     Document Type: Article
Times cited : (102)

References (62)
  • 3
  • 6
    • 0034666040 scopus 로고    scopus 로고
    • Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae
    • Coghlan A, Wolfe K (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.2
  • 8
    • 3843068862 scopus 로고    scopus 로고
    • Selective and mutational patterns associated with gene expression in humans: Influences on synonymous composition and intron presence
    • DOI 10.1534/genetics.104.026351
    • Comeron J (2004) Selective and mutational patterns associated with gene expression in humans: influences on synonymous composition and intron presence. Genetics 167: 1293-1304 (Pubitemid 39045637)
    • (2004) Genetics , vol.167 , Issue.3 , pp. 1293-1304
    • Comeron, J.M.1
  • 9
    • 0013936167 scopus 로고
    • Codon-anticodon pairing: The wobble hypothesis
    • Crick FH (1966) Codon-anticodon pairing: the wobble hypothesis. J Mol Biol 19: 548-555
    • (1966) J Mol Biol , vol.19 , pp. 548-555
    • Crick, F.H.1
  • 10
    • 67449152160 scopus 로고    scopus 로고
    • Computational systems biology of the cell cycle
    • Csikász-Nagy A (2009) Computational systems biology of the cell cycle. Brief Bioinform 10: 424-434
    • (2009) Brief Bioinform , vol.10 , pp. 424-434
    • Csikász-Nagy, A.1
  • 11
    • 14644396660 scopus 로고    scopus 로고
    • Selective charging of tRNA isoacceptors induced by amino-acid starvation
    • DOI 10.1038/sj.embor.7400341
    • Dittmar K, Sørensen M, Elf J, Ehrenberg M, Pan T (2005) Selective charging of tRNA isoacceptors induced by amino-acid starvation. EMBO Rep 6: 151-157 (Pubitemid 40309412)
    • (2005) EMBO Reports , vol.6 , Issue.2 , pp. 151-157
    • Dittmar, K.A.1    Sorensen, M.A.2    Elf, J.3    Ehrenberg, M.4    Pan, T.5
  • 12
    • 33846021292 scopus 로고    scopus 로고
    • Tissue-specific differences in human transfer RNA expression
    • Dittmar KA, Goodenbour JM, Pan T (2006) Tissue-specific differences in human transfer RNA expression. PLoS Genet 2: e221
    • (2006) PLoS Genet , vol.2
    • Dittmar, K.A.1    Goodenbour, J.M.2    Pan, T.3
  • 13
    • 30744441602 scopus 로고    scopus 로고
    • A single determinant dominates the rate of yeast protein evolution
    • DOI 10.1093/molbev/msj038
    • Drummond DA, Raval A, Wilke CO (2006) A single determinant dominates the rate of yeast protein evolution. Mol Biol Evol 23: 327-337 (Pubitemid 43100047)
    • (2006) Molecular Biology and Evolution , vol.23 , Issue.2 , pp. 327-337
    • Drummond, D.A.1    Raval, A.2    Wilke, C.O.3
  • 14
    • 47549097539 scopus 로고    scopus 로고
    • Mistranslation-Induced Protein Misfolding as a Dominant Constraint on Coding-Sequence Evolution
    • DOI 10.1016/j.cell.2008.05.042, PII S0092867408007058
    • Drummond DA, Wilke CO (2008) Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell 134: 341-352 (Pubitemid 352010328)
    • (2008) Cell , vol.134 , Issue.2 , pp. 341-352
    • Drummond, D.A.1    Wilke, C.O.2
  • 15
    • 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
    • DOI 10.1016/S0168-9525(00)02041-2, PII S0168952500020412
    • Duret L (2000) tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes. Trends Genet 16: 287-289 (Pubitemid 30389593)
    • (2000) Trends in Genetics , vol.16 , Issue.7 , pp. 287-289
    • Duret, L.1
  • 17
    • 0036849261 scopus 로고    scopus 로고
    • Aminoacyl-tRNA synthetases: Versatile players in the changing theater of translation
    • DOI 10.1017/S1355838202021180
    • Francklyn C, Perona JJ, Puetz J, Hou YM (2002) Aminoacyl-tRNA synthetases: versatile players in the changing theater of translation. RNA 8: 1363-1372 (Pubitemid 35332960)
    • (2002) RNA , vol.8 , Issue.11 , pp. 1363-1372
    • Francklyn, C.1    Perona, J.J.2    Puetz, J.3    Hou, Y.-M.4
  • 18
    • 38649136232 scopus 로고    scopus 로고
    • Methods for kinetic and thermodynamic analysis of aminoacyl-tRNA synthetases
    • DOI 10.1016/j.ymeth.2007.09.007, PII S1046202307001727
    • Francklyn CS, First EA, Perona JJ, Hou YM (2008) Methods for kinetic and thermodynamic analysis of aminoacyl-tRNA synthetases. Methods 44: 100-118 (Pubitemid 351172808)
    • (2008) Methods , vol.44 , Issue.2 , pp. 100-118
    • Francklyn, C.S.1    First, E.A.2    Perona, J.J.3    Hou, Y.-M.4
  • 20
    • 75549089771 scopus 로고    scopus 로고
    • Cyclebase.org: Version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results
    • Gauthier NP, Jensen LJ, Wernersson R, Brunak S, Jensen TS (2010) Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results. Nucleic Acids Res 38: D699-D702
    • (2010) Nucleic Acids Res , vol.38
    • Gauthier, N.P.1    Jensen, L.J.2    Wernersson, R.3    Brunak, S.4    Jensen, T.S.5
  • 22
    • 79954456859 scopus 로고    scopus 로고
    • Determinants of translation efficiency and accuracy
    • Gingold H, Pilpel Y (2011) Determinants of translation efficiency and accuracy. Mol Syst Biol 7: 481
    • (2011) Mol Syst Biol , vol.7 , pp. 481
    • Gingold, H.1    Pilpel, Y.2
  • 23
    • 33845635732 scopus 로고    scopus 로고
    • Diversity of tRNA genes in eukaryotes
    • DOI 10.1093/nar/gkl725
    • Goodenbour JM, Pan T (2006) Diversity of tRNA genes in eukaryotes. Nucleic Acids Res 34: 6137-6146 (Pubitemid 44942735)
    • (2006) Nucleic Acids Research , vol.34 , Issue.21 , pp. 6137-6146
    • Goodenbour, J.M.1    Pan, T.2
  • 24
    • 0020491327 scopus 로고
    • Codon usage in bacteria: Correlation with gene expressivity
    • Gouy M, Gautier C (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, C.2
  • 25
    • 0019519371 scopus 로고
    • Codon catalog usage is a genome strategy modulated for gene expressivity
    • Grantham R, Gautier C, Gouy M, Jacobzone M, Mercier R (1981) Codon catalog usage is a genome strategy modulated for gene expressivity. Nucleic Acids Res 9: r43-r74 (Pubitemid 11128643)
    • (1981) Nucleic Acids Research , vol.9 , Issue.1
    • Grantham, R.1    Gautier, C.2    Gouy, M.3
  • 26
    • 0020363515 scopus 로고
    • Preferential codon usage in prokaryotic genes: The optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes
    • DOI 10.1016/0378-1119(82)90157-3
    • Grosjean H, Fiers W (1982) Preferential codon usage in prokaryotic genes: the optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes. Gene 18: 199-209 (Pubitemid 13232993)
    • (1982) Gene , vol.18 , Issue.3 , pp. 199-209
    • Grosjean, H.1    Fiers, W.2
  • 27
    • 11144357971 scopus 로고    scopus 로고
    • Aminoacyl-tRNAs: Setting the limits of the genetic code
    • DOI 10.1101/gad.1187404
    • Ibba M, Söll D (2004) Aminoacyl-tRNAs: setting the limits of the genetic code. Genes Dev 18: 731-738 (Pubitemid 38480885)
    • (2004) Genes and Development , vol.18 , Issue.7 , pp. 731-738
    • Ibba, M.1    Soll, D.2
  • 28
    • 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 (1981) 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 151: 389-409 (Pubitemid 12252691)
    • (1981) Journal of Molecular Biology , vol.151 , Issue.3 , pp. 389-409
    • Ikemura, T.1
  • 29
    • 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 RNAs
    • DOI 10.1016/0022-2836(82)90250-9
    • 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 RNAs. J Mol Biol 158: 573-597 (Pubitemid 12044688)
    • (1982) Journal of Molecular Biology , vol.158 , Issue.4 , pp. 573-597
    • Ikemura, T.1
  • 30
    • 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 (Pubitemid 15152046)
    • (1985) Molecular Biology and Evolution , vol.2 , Issue.1 , pp. 13-34
    • Ikemura, T.1
  • 31
    • 33749535603 scopus 로고    scopus 로고
    • Co-evolution of transcriptional and post-translational cell-cycle regulation
    • DOI 10.1038/nature05186, PII NATURE05186
    • Jensen L, Jensen T, de Lichtenberg U, Brunak S, Bork P (2006) Co-evolution of transcriptional and post-translational cell-cycle regulation. Nature 443: 594-597 (Pubitemid 44527297)
    • (2006) Nature , vol.443 , Issue.7111 , pp. 594-597
    • Jensen, L.J.1    Jensen, T.S.2    De Lichtenberg, U.3    Brunak, S.4    Bork, P.5
  • 32
    • 0033615965 scopus 로고    scopus 로고
    • Cell cycle-regulated attachment of the ubiquitin-related protein SUMO to the yeast septins
    • Johnson ES, Blobel G (1999) Cell cycle-regulated attachment of the ubiquitin-related protein SUMO to the yeast septins. J Cell Biol 147: 981-994
    • (1999) J Cell Biol , vol.147 , pp. 981-994
    • Johnson, E.S.1    Blobel, G.2
  • 33
    • 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
    • DOI 10.1016/S0378-1119(99)00225-5, PII S0378111999002255
    • Kanaya S, YamadaY, Kudo Y, IkemuraT (1999) 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 238: 143-155 (Pubitemid 29436104)
    • (1999) Gene , vol.238 , Issue.1 , pp. 143-155
    • Kanaya, S.1    Yamada, Y.2    Kudo, Y.3    Ikemura, T.4
  • 35
    • 33646229554 scopus 로고    scopus 로고
    • The action of selection on codon bias in the human genome is related to frequency, complexity, and chronology of amino acids
    • Kotlar D, Lavner Y (2006) The action of selection on codon bias in the human genome is related to frequency, complexity, and chronology of amino acids. BMC Genomics 7: 67
    • (2006) BMC Genomics , vol.7 , pp. 67
    • Kotlar, D.1    Lavner, Y.2
  • 36
    • 64849114915 scopus 로고    scopus 로고
    • Coding-sequence determinants of gene expression in Escherichia coli
    • Kudla G, Murray A, Tollervey D, Plotkin J (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.2    Tollervey, D.3    Plotkin, J.4
  • 37
    • 57149111475 scopus 로고    scopus 로고
    • Translational control of gene expression from transcripts to transcriptomes
    • Lackner D, Bähler J (2008) Translational control of gene expression from transcripts to transcriptomes. Int Rev Cell Mol Biol 271: 199-251
    • (2008) Int Rev Cell Mol Biol , vol.271 , pp. 199-251
    • Lackner, D.1    Bähler, J.2
  • 39
    • 13444291526 scopus 로고    scopus 로고
    • Codon bias as a factor in regulating expression via translation rate in the human genome
    • DOI 10.1016/j.gene.2004.11.035
    • Lavner Y, Kotlar D (2005) Codon bias as a factor in regulating expression via translation rate in the human genome. Gene 345: 127-138 (Pubitemid 40208509)
    • (2005) Gene , vol.345 , Issue.1 SPEC. ISS. , pp. 127-138
    • Lavner, Y.1    Kotlar, D.2
  • 40
    • 0023134450 scopus 로고
    • Translation rate modification by preferential codon usage: Intragenic position effects
    • DOI 10.1016/S0022-5193(87)80251-5
    • Liljenström H, von Heijne G (1987) Translation rate modification by preferential codon usage: intragenic position effects. J Theor Biol 124: 43-55 (Pubitemid 17002611)
    • (1987) Journal of Theoretical Biology , vol.124 , Issue.1 , pp. 43-55
    • Liljenstrom, H.1    Von Heijne, G.2
  • 42
    • 0030854739 scopus 로고    scopus 로고
    • TRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence
    • DOI 10.1093/nar/25.5.955
    • Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25: 955-964 (Pubitemid 27298263)
    • (1997) Nucleic Acids Research , vol.25 , Issue.5 , pp. 955-964
    • Lowe, T.M.1    Eddy, S.R.2
  • 43
  • 45
  • 46
    • 68249130936 scopus 로고    scopus 로고
    • Clustering of codons with rare cognate tRNAs in human genes suggests an extra level of expression regulation
    • Parmley JL, Huynen MA (2009) Clustering of codons with rare cognate tRNAs in human genes suggests an extra level of expression regulation. PLoS Genet 5: e1000548
    • (2009) PLoS Genet , vol.5
    • Parmley, J.L.1    Huynen, M.A.2
  • 47
    • 17444449538 scopus 로고    scopus 로고
    • Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae
    • DOI 10.1006/jmbi.1997.0942
    • Percudani R, Pavesi A, Ottonello S (1997) Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae. J Mol Biol 268: 322-330 (Pubitemid 27208057)
    • (1997) Journal of Molecular Biology , vol.268 , Issue.2 , pp. 322-330
    • Percudani, R.1    Pavesi, A.2    Ottonello, S.3
  • 48
    • 78650304100 scopus 로고    scopus 로고
    • Synonymous but not the same: The causes and consequences of codon bias
    • Plotkin JB, 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
  • 49
    • 23144460836 scopus 로고    scopus 로고
    • The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs
    • DOI 10.1093/nar/gki366
    • Schattner P, Brooks AN, Lowe TM (2005) The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res 33: W686-W689 (Pubitemid 44530010)
    • (2005) Nucleic Acids Research , vol.33 , Issue.WEB. SERV. ISS.
    • Schattner, P.1    Brooks, A.N.2    Lowe, T.M.3
  • 50
    • 0023046874 scopus 로고
    • Codon usage in yeast: Cluster analysis clearly differentiates highly and lowly expressed genes
    • Sharp PM, Tuohy TM, Mosurski KR (1986) Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Res 14: 5125-5143
    • (1986) Nucleic Acids Res , vol.14 , pp. 5125-5143
    • Sharp, P.M.1    Tuohy, T.M.2    Mosurski, K.R.3
  • 51
    • 34250719724 scopus 로고    scopus 로고
    • Generation of a fluorescently labeled endogenous protein library in living human cells
    • DOI 10.1038/nprot.2007.197, PII NPROT.2007.197
    • Sigal A, Danon T, Cohen A, Milo R, Geva-Zatorsky N, Lustig G, Liron Y, Alon U, Perzov N (2007) Generation of a fluorescently labeled endogenous protein library in living human cells. Nat Protoc 2: 1515-1527 (Pubitemid 46952330)
    • (2007) Nature Protocols , vol.2 , Issue.6 , pp. 1515-1527
    • Sigal, A.1    Danon, T.2    Cohen, A.3    Milo, R.4    Geva-Zatorsky, N.5    Lustig, G.6    Liron, Y.7    Alon, U.8    Perzov, N.9
  • 54
    • 60149091189 scopus 로고    scopus 로고
    • Regulation of translation initiation in eukaryotes: Mechanisms and biological targets
    • Sonenberg N, Hinnebusch AG (2009) Regulation of translation initiation in eukaryotes: mechanisms and biological targets. Cell 136: 731-745
    • (2009) Cell , vol.136 , pp. 731-745
    • Sonenberg, N.1    Hinnebusch, A.G.2
  • 58
    • 28544447850 scopus 로고    scopus 로고
    • Nearest-neighbor thermodynamics of deoxyinosine pairs in DNA duplexes
    • Watkins NJ, SantaLucia JJ (2005) Nearest-neighbor thermodynamics of deoxyinosine pairs in DNA duplexes. Nucleic Acids Res 33: 6258-6267
    • (2005) Nucleic Acids Res , vol.33 , pp. 6258-6267
    • Watkins, N.J.1    Santalucia, J.J.2
  • 59
    • 77956694182 scopus 로고    scopus 로고
    • Cell biology, New roles for codon usage
    • Weygand-Durasevic I, Ibba M (2010) Cell biology. New roles for codon usage. Science 329: 1473-1474
    • (2010) Science , vol.329 , pp. 1473-1474
    • Weygand-Durasevic, I.1    Ibba, M.2
  • 60
    • 79958053947 scopus 로고    scopus 로고
    • The yeast rapid tRNA decay pathway primarily monitors the structural integrity of the acceptor and T-stems of mature tRNA
    • Whipple JM, Lane EA, Chernyakov I, D'Silva S, Phizicky EM (2011) The yeast rapid tRNA decay pathway primarily monitors the structural integrity of the acceptor and T-stems of mature tRNA. Genes Dev 25: 1173-1184
    • (2011) Genes Dev , vol.25 , pp. 1173-1184
    • Whipple, J.M.1    Lane, E.A.2    Chernyakov, I.3    D'Silva, S.4    Phizicky, E.M.5
  • 62
    • 4143122090 scopus 로고    scopus 로고
    • Effects of gene expression on molecular evolution in Arabidopsis thaliana and Arabidopsis lyrata
    • DOI 10.1093/molbev/msh191
    • Wright SI, Yau CB, Looseley M, Meyers BC (2004) Effects of gene expression on molecular evolution in Arabidopsis thaliana and Arabidopsis lyrata. Mol Biol Evol 21: 1719-1726 (Pubitemid 39096888)
    • (2004) Molecular Biology and Evolution , vol.21 , Issue.9 , pp. 1719-1726
    • Wright, S.I.1    Yau, C.B.K.2    Looseley, M.3    Meyers, B.C.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.