메뉴 건너뛰기




Volumn 28, Issue 11, 2012, Pages 1438-1445

Large-scale analysis of conserved rare codon clusters suggests an involvement in co-translational molecular recognition events

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

EID: 84861750664     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts149     Document Type: Article
Times cited : (42)

References (59)
  • 2
    • 77949270274 scopus 로고    scopus 로고
    • alpha-Helical nascent polypeptide chains visualized within distinct regions of the ribosomal exit tunnel
    • Bhushan, S. et al. (2010) alpha-Helical nascent polypeptide chains visualized within distinct regions of the ribosomal exit tunnel. Nat. Struct. Mol. Biol., 17, 313-317.
    • (2010) Nat. Struct. Mol. Biol. , vol.17 , pp. 313-317
    • Bhushan, S.1
  • 3
    • 0021921276 scopus 로고
    • Rare codons in E. coli and S. typhimurium signal sequences
    • Burns, D.M. and Beacham, I.R. (1985) Rare codons in E. coli and S. typhimurium signal sequences. FEBS Lett., 189, 318-324.
    • (1985) FEBS Lett. , vol.189 , pp. 318-324
    • Burns, D.M.1    Beacham, I.R.2
  • 4
    • 0242391986 scopus 로고    scopus 로고
    • Codon adaptation index as a measure of dominating codon bias
    • Carbone, A. et al. (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
  • 6
    • 77949456534 scopus 로고    scopus 로고
    • Increased incidence of rare codon clusters at 5' and 3' gene termini: implications for function
    • Clarke, T.F. and Clark, P.L. (2010). Increased incidence of rare codon clusters at 5' and 3' gene termini: implications for function. BMC genomics, 11, 118.
    • (2010) BMC genomics , vol.11 , pp. 118
    • Clarke, T.F.1    Clark, P.L.2
  • 7
    • 0036295371 scopus 로고    scopus 로고
    • Silent mutations affect in vivo protein folding in Escherichia coli
    • Cortazzo, P. et al. (2002) Silent mutations affect in vivo protein folding in Escherichia coli. Biochem. Biophys. Res. Commun., 293, 537-541.
    • (2002) Biochem. Biophys. Res. Commun. , vol.293 , pp. 537-541
    • Cortazzo, P.1
  • 8
    • 79957852647 scopus 로고    scopus 로고
    • The imprint of codons on protein structure
    • Deane, C.M. and Saunders, R. (2011) The imprint of codons on protein structure. Biotechnol. J., 6, 641-649.
    • (2011) Biotechnol. J. , vol.6 , pp. 641-649
    • Deane, C.M.1    Saunders, R.2
  • 9
    • 0342980435 scopus 로고    scopus 로고
    • The PAUSE software for analysis of translational control over protein targeting: application to E. nidulans membrane proteins
    • Dessen, P. and Képès, F. (2000) The PAUSE software for analysis of translational control over protein targeting: application to E. nidulans membrane proteins. Gene, 244, 89-96.
    • (2000) Gene , vol.244 , pp. 89-96
    • Dessen, P.1    Képès, F.2
  • 10
    • 0030564828 scopus 로고    scopus 로고
    • Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates
    • Dong, H. et al. (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
  • 11
    • 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. (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.
    • (2000) Trends Genet , vol.16 , pp. 287-289
    • Duret, L.1
  • 13
    • 75549090603 scopus 로고    scopus 로고
    • The Pfam protein families database
    • Finn, R.D. et al. (2010) The Pfam protein families database. Nucleic Acids Res., 38, D211-D222.
    • (2010) Nucleic Acids Res. , vol.38
    • Finn, R.D.1
  • 14
    • 84857715986 scopus 로고    scopus 로고
    • Genes adopt non-optimal codon usage to generate cell cycle-dependent oscillations in protein levels
    • Frenkel-Morgenstern, M. et al. (2012) Genes adopt non-optimal codon usage to generate cell cycle-dependent oscillations in protein levels. Mol. Syst. Biol., 8, 572.
    • (2012) Mol. Syst. Biol. , vol.8 , pp. 572
    • Frenkel-Morgenstern, M.1
  • 15
    • 0037414435 scopus 로고    scopus 로고
    • Crystal structure of Proteus vulgaris chondroitin sulfate ABC lyase I at 1.9A resolution
    • Huang, W. et al. (2003) Crystal structure of Proteus vulgaris chondroitin sulfate ABC lyase I at 1.9A resolution. J. Mol. Biol., 328, 623-634.
    • (2003) J. Mol. Biol. , vol.328 , pp. 623-634
    • Huang, W.1
  • 16
    • 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
  • 17
    • 79957812064 scopus 로고    scopus 로고
    • Birth, life and death of nascent polypeptide chains
    • Jha, S. and Komar, A.A. (2011) Birth, life and death of nascent polypeptide chains. Biotechnol. J., 6, 623-640.
    • (2011) Biotechnol. J. , vol.6 , pp. 623-640
    • Jha, S.1    Komar, A.A.2
  • 18
    • 0031172424 scopus 로고    scopus 로고
    • Changes of tRNA population during compensatory cell proliferation: differential expression of methionine-tRNA species
    • Kanduc, D. (1997) Changes of tRNA population during compensatory cell proliferation: differential expression of methionine-tRNA species. Arch. Biochem. Biophys., 342, 1-5.
    • (1997) Arch. Biochem. Biophys. , vol.342 , pp. 1-5
    • Kanduc, D.1
  • 19
    • 0030595344 scopus 로고    scopus 로고
    • The "+70 pause": hypothesis of a translational control of membrane protein assembly
    • Képès, F. (1996) The "+70 pause": hypothesis of a translational control of membrane protein assembly. J.Mol.Biol., 262, 77-86.
    • (1996) J. Mol. Biol. , vol.262 , pp. 77-86
    • Képès, F.1
  • 20
    • 0025787343 scopus 로고
    • Ribosomes pause at specific sites during synthesis of membranebound chloroplast reaction center protein D1
    • Kim, J. et al. (1991) Ribosomes pause at specific sites during synthesis of membranebound chloroplast reaction center protein D1. J. Biol. Chem., 266, 14931-14938.
    • (1991) J. Biol. Chem. , vol.266 , pp. 14931-14938
    • Kim, J.1
  • 21
    • 33846504706 scopus 로고    scopus 로고
    • A "silent" polymorphism in the MDR1 gene changes substrate specificity
    • Kimchi-Sarfaty, C. et al. (2007) A "silent" polymorphism in the MDR1 gene changes substrate specificity. Science, 315, 525-528.
    • (2007) Science , vol.315 , pp. 525-528
    • Kimchi-Sarfaty, C.1
  • 22
    • 58149199728 scopus 로고    scopus 로고
    • A pause for thought along the co-translational folding pathway
    • Komar, A.A. (2009). A pause for thought along the co-translational folding pathway. Trends Biochem. Sci., 34, 16-24.
    • (2009) Trends Biochem. Sci. , vol.34 , pp. 16-24
    • Komar, A.A.1
  • 23
    • 0028880533 scopus 로고
    • Kinetics of translation of gamma B crystallin and its circularly permutated variant in an in vitro cell-free system: possible relations to codon distribution and protein folding
    • Komar, A.A. and Jaenicke, R. (1995) Kinetics of translation of gamma B crystallin and its circularly permutated variant in an in vitro cell-free system: possible relations to codon distribution and protein folding. FEBS Lett., 376, 195-198.
    • (1995) FEBS Lett. , vol.376 , pp. 195-198
    • Komar, A.A.1    Jaenicke, R.2
  • 24
    • 0032699491 scopus 로고    scopus 로고
    • Synonymous codon substitutions affect ribosome traffic and protein folding during in vitro translation
    • Komar, A.A. et al. (1999) Synonymous codon substitutions affect ribosome traffic and protein folding during in vitro translation. FEBS Lett., 462, 387-391.
    • (1999) FEBS Lett. , vol.462 , pp. 387-391
    • Komar, A.A.1
  • 25
    • 0026047846 scopus 로고
    • Nonuniform size distribution of nascent globin peptides, evidence for pause localization sites, and a contranslational protein-folding model
    • Krasheninnikov, I.A. et al. (1991) Nonuniform size distribution of nascent globin peptides, evidence for pause localization sites, and a contranslational protein-folding model. J. Protein Chem., 10, 445-453.
    • (1991) J. Protein Chem. , vol.10 , pp. 445-453
    • Krasheninnikov, I.A.1
  • 26
    • 22544486576 scopus 로고    scopus 로고
    • Protein function prediction using local 3D templates
    • Laskowski, R.A. et al. (2005) Protein function prediction using local 3D templates. J. Mol. Biol., 351, 614-626.
    • (2005) J. Mol. Biol. , vol.351 , pp. 614-626
    • Laskowski, R.A.1
  • 27
    • 78651317925 scopus 로고    scopus 로고
    • The European nucleotide archive
    • Leinonen, R. et al. (2011) The European nucleotide archive. Nucleic Acids Res., 39, D28-D31.
    • (2011) Nucleic Acids Res. , vol.39
    • Leinonen, R.1
  • 28
    • 0034695438 scopus 로고    scopus 로고
    • Ribosome traffic in E. coli and regulation of gene expression
    • Lesnik, T. et al. (2000). Ribosome traffic in E. coli and regulation of gene expression. J. Theor. Biol., 202, 175-185.
    • (2000) J. Theor. Biol. , vol.202 , pp. 175-185
    • Lesnik, T.1
  • 29
    • 54249096045 scopus 로고    scopus 로고
    • Electrostatics in the ribosomal tunnel modulate chain elongation rates
    • Lu, J. and Deutsch, C. (2008) Electrostatics in the ribosomal tunnel modulate chain elongation rates. J. Mol. Biol., 384, 73-86.
    • (2008) J. Mol. Biol. , vol.384 , pp. 73-86
    • Lu, J.1    Deutsch, C.2
  • 30
    • 79960976768 scopus 로고    scopus 로고
    • UniProt Knowledgebase: a hub of integrated protein data
    • Magrane, M. and Consortium, U. (2011) UniProt Knowledgebase: a hub of integrated protein data. Database, Vol. 2011, bar009.
    • (2011) Database , vol.2011
    • Magrane, M.1    Consortium, U.2
  • 31
    • 0036908375 scopus 로고    scopus 로고
    • Distribution of rare triplets along mRNA and their relation to protein folding
    • Makhoul, C.H. and Trifonov, E.N. (2002) Distribution of rare triplets along mRNA and their relation to protein folding. J. Biomol. Struct. Dyn., 20, 413-420.
    • (2002) J. Biomol. Struct. Dyn. , vol.20 , pp. 413-420
    • Makhoul, C.H.1    Trifonov, E.N.2
  • 32
    • 0030731696 scopus 로고    scopus 로고
    • Codon usage bias and tRNA abundance in Drosophila
    • Moriyama, E.N. and Powell, J.R. (1997) Codon usage bias and tRNA abundance in Drosophila. J. Mol. Evol., 45, 514-523.
    • (1997) J. Mol. Evol. , vol.45 , pp. 514-523
    • Moriyama, E.N.1    Powell, J.R.2
  • 33
    • 0038025174 scopus 로고    scopus 로고
    • Assembly of the D1 precursor in monomeric photosystem II reaction center precomplexes precedes chlorophyll a-triggered accumulation of reaction center II in barley etioplasts
    • Müller, B. and Eichacker, L.A. (1999) Assembly of the D1 precursor in monomeric photosystem II reaction center precomplexes precedes chlorophyll a-triggered accumulation of reaction center II in barley etioplasts. Plant Cell, 11, 2365-2377.
    • (1999) Plant Cell , vol.11 , pp. 2365-2377
    • Müller, B.1    Eichacker, L.A.2
  • 34
    • 0342614926 scopus 로고    scopus 로고
    • Codon usage tabulated from international DNA sequence databases: status for the year 2000
    • Nakamura, Y. et al. (2000) Codon usage tabulated from international DNA sequence databases: status for the year 2000. Nucleic Acids Res., 28, 292.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 292
    • Nakamura, Y.1
  • 35
    • 0030777303 scopus 로고    scopus 로고
    • CATH-a hierarchic classification of protein domain structures
    • Orengo, C.A. et al. (1997) CATH-a hierarchic classification of protein domain structures. Structure, 5, 1093-1108.
    • (1997) Structure , vol.5 , pp. 1093-1108
    • Orengo, C.A.1
  • 36
    • 68249130936 scopus 로고    scopus 로고
    • Clustering of codons with rare cognate tRNAs in human genes suggests an extra level of expression regulation
    • Parmley, J.L. and Huynen, M.A. (2009) Clustering of codons with rare cognate tRNAs in human genes suggests an extra level of expression regulation. PLoS Genetics, 5, e1000548.
    • (2009) PLoS Genetics , vol.5
    • Parmley, J.L.1    Huynen, M.A.2
  • 37
    • 0023989064 scopus 로고
    • Improved tools for biological sequence comparison
    • Pearson, W.R. and Lipman, D.J. (1988) Improved tools for biological sequence comparison. Proc. Natl Acad. Sci. USA, 85, 2444-2448.
    • (1988) Proc. Natl Acad. Sci. USA , vol.85 , pp. 2444-2448
    • Pearson, W.R.1    Lipman, D.J.2
  • 38
    • 17444449538 scopus 로고    scopus 로고
    • Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae
    • Percudani, R. et al. (1997) Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae. J. Mol. Biol., 268, 322-330.
    • (1997) J. Mol. Biol. , vol.268 , pp. 322-330
    • Percudani, R.1
  • 39
    • 4444356342 scopus 로고    scopus 로고
    • Whole genome analysis reveals a high incidence of non-optimal codons in secretory signal sequences of Escherichia coli
    • Power, P.M. et al. (2004) Whole genome analysis reveals a high incidence of non-optimal codons in secretory signal sequences of Escherichia coli. Biochem. Biophys. Res. Commun., 322, 1038-1044.
    • (2004) Biochem. Biophys. Res. Commun. , vol.322 , pp. 1038-1044
    • Power, P.M.1
  • 40
    • 0023659927 scopus 로고
    • The efficiency of folding of some proteins is increased by controlled rates of translation in vivo
    • Purvis, I.J. et al. (1987) The efficiency of folding of some proteins is increased by controlled rates of translation in vivo. A hypothesis. J. Mol. Biol., 193, 413-417.
    • (1987) A hypothesis. J. Mol. Biol. , vol.193 , pp. 413-417
    • Purvis, I.J.1
  • 41
    • 79953752538 scopus 로고    scopus 로고
    • Molecular mechanism of co-translational protein targeting by the signal recognition particle
    • Saraogi, I. and Shan, S.-O. (2011) Molecular mechanism of co-translational protein targeting by the signal recognition particle. Traffic, 12, 535-542.
    • (2011) Traffic , vol.12 , pp. 535-542
    • Saraogi, I.1    Shan, S.-O.2
  • 42
    • 78049403925 scopus 로고    scopus 로고
    • Synonymous codon usage influences the local protein structure observed
    • Saunders, R. and Deane, C.M. (2010) Synonymous codon usage influences the local protein structure observed. Nucleic Acids Res., 38, 6719-6728.
    • (2010) Nucleic Acids Res. , vol.38 , pp. 6719-6728
    • Saunders, R.1    Deane, C.M.2
  • 44
    • 71549124362 scopus 로고    scopus 로고
    • Structural insight into nascent polypeptide chain-mediated translational stalling
    • Seidelt, B. et al. (2009) Structural insight into nascent polypeptide chain-mediated translational stalling. Science, 326, 1412-1415.
    • (2009) Science , vol.326 , pp. 1412-1415
    • Seidelt, B.1
  • 45
    • 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
  • 46
    • 0022423086 scopus 로고
    • The secondary structure of mRNAs from Escherichia coli: its possible role in increasing the accuracy of translation
    • Shpaer, E.G. (1985) The secondary structure of mRNAs from Escherichia coli: its possible role in increasing the accuracy of translation. Nucleic Acids Res., 13, 275-288.
    • (1985) Nucleic Acids Res. , vol.13 , pp. 275-288
    • Shpaer, E.G.1
  • 47
    • 0024405193 scopus 로고
    • Codon usage determines translation rate in Escherichia coli
    • Sørensen, M.A. et al. (1989) Codon usage determines translation rate in Escherichia coli. J. Mol. Biol., 207, 365-377.
    • (1989) J. Mol. Biol. , vol.207 , pp. 365-377
    • Sørensen, M.A.1
  • 48
    • 0029908504 scopus 로고    scopus 로고
    • Protein secondary structural types are differentially coded on messenger RNA
    • Thanaraj, T.A. and Argos, P. (1996a) Protein secondary structural types are differentially coded on messenger RNA. Protein Sci., 5, 1973-1983.
    • (1996) Protein Sci. , vol.5 , pp. 1973-1983
    • Thanaraj, T.A.1    Argos, P.2
  • 49
    • 0030018101 scopus 로고    scopus 로고
    • Ribosome-mediated translational pause and protein domain organization
    • Thanaraj, T.A. and Argos, P. (1996b) Ribosome-mediated translational pause and protein domain organization. Protein Sci., 5, 1594-1612.
    • (1996) Protein Sci. , vol.5 , pp. 1594-1612
    • Thanaraj, T.A.1    Argos, P.2
  • 50
    • 52949137359 scopus 로고    scopus 로고
    • Synonymous mutations and ribosome stalling can lead to altered folding pathways and distinct minima
    • Tsai, C.-J. et al. (2008) Synonymous mutations and ribosome stalling can lead to altered folding pathways and distinct minima. J. Mol. Biol., 383, 281-291.
    • (2008) J. Mol. Biol. , vol.383 , pp. 281-291
    • Tsai, C.-J.1
  • 51
    • 0034669882 scopus 로고    scopus 로고
    • Why are "natively unfolded" proteins unstructured under physiologic conditions?
    • Uversky, V.N. et al. (2000) Why are "natively unfolded" proteins unstructured under physiologic conditions? Proteins, 41, 415-427.
    • (2000) Proteins , vol.41 , pp. 415-427
    • Uversky, V.N.1
  • 52
    • 0021764898 scopus 로고
    • Translation is a non-uniform process Effect of tRNA availability on the rate of elongation of nascent polypeptide chains
    • Varenne, S. et al. (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
  • 53
    • 13444288174 scopus 로고    scopus 로고
    • E-MSD: an integrated data resource for bioinformatics
    • Velankar, S. et al. (2005) E-MSD: an integrated data resource for bioinformatics. Nucleic Acids Res., 33, D262-D265.
    • (2005) Nucleic Acids Res. , vol.33
    • Velankar, S.1
  • 54
    • 79851503908 scopus 로고    scopus 로고
    • Inserting membrane proteins: the YidC/Oxa1/Alb3 machinery in bacteria, mitochondria, and chloroplasts
    • Wang, P. and Dalbey, R.E. (2011) Inserting membrane proteins: the YidC/Oxa1/Alb3 machinery in bacteria, mitochondria, and chloroplasts. Biochim. Biophys. Acta., 1808, 866-875.
    • (2011) Biochim. Biophys. Acta. , vol.1808 , pp. 866-875
    • Wang, P.1    Dalbey, R.E.2
  • 55
    • 44349120609 scopus 로고    scopus 로고
    • Analysis of the distribution of functionally relevant rare codons
    • Widmann, M. et al. (2008) Analysis of the distribution of functionally relevant rare codons. BMC Genomics, 9, 207.
    • (2008) BMC Genomics , vol.9 , pp. 207
    • Widmann, M.1
  • 56
    • 33847076187 scopus 로고    scopus 로고
    • Experimental confirmation of a key role for nonoptimal codons in protein export
    • Zalucki, Y.M. and Jennings, M.P. (2007) Experimental confirmation of a key role for nonoptimal codons in protein export. Biochem. Biophys. Res. Commun., 355, 143-148.
    • (2007) Biochem. Biophys. Res. Commun. , vol.355 , pp. 143-148
    • Zalucki, Y.M.1    Jennings, M.P.2
  • 57
    • 79957870201 scopus 로고    scopus 로고
    • Coupling between codon usage, translation and protein export in Escherichia coli
    • Zalucki, Y.M. et al. (2011) Coupling between codon usage, translation and protein export in Escherichia coli. Biotechnol. J., 6, 660-667.
    • (2011) Biotechnol. J. , vol.6 , pp. 660-667
    • Zalucki, Y.M.1
  • 58
    • 0029432408 scopus 로고
    • Discontinuous translation and mRNA secondary structure
    • Zama, M. (1995) Discontinuous translation and mRNA secondary structure. Nucleic Acids Symp. Ser., Vol 34, 97-98.
    • (1995) Nucleic Acids Symp. Ser. , vol.34 , pp. 97-98
    • Zama, M.1
  • 59
    • 0033523114 scopus 로고    scopus 로고
    • Co-translational assembly of the D1 protein into photosystem II
    • Zhang, L. et al. (1999) Co-translational assembly of the D1 protein into photosystem II. J. Biol. Chem., 274, 16062-16067.
    • (1999) J. Biol. Chem. , vol.274 , pp. 16062-16067
    • Zhang, L.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.