메뉴 건너뛰기




Volumn 6, Issue 5, 2010, Pages 522-530

Detecting slow-translating regions in E.coli

Author keywords

Codon; Likelihood; Protein; Spatial scan; Translation

Indexed keywords

ESCHERICHIA COLI;

EID: 78651255581     PISSN: 17445485     EISSN: 17445493     Source Type: Journal    
DOI: 10.1504/IJBRA.2010.037990     Document Type: Article
Times cited : (2)

References (28)
  • 1
    • 60849112260 scopus 로고    scopus 로고
    • Studying alternative splicing regulatory networks through partial correlation analysis
    • doi:10.1186/gb-2009-10-1-r3
    • Chen, L. and Zheng, S. (2009) 'Studying alternative splicing regulatory networks through partial correlation analysis', Genome. Biol., Vol. 10, No. R3, doi:10.1186/gb-2009-10-1-r3.
    • (2009) Genome. Biol. , vol.10 , Issue.R3
    • Chen, L.1    Zheng, S.2
  • 2
    • 18144385852 scopus 로고    scopus 로고
    • Clustered bottlenecks in mRNA translation and protein syn
    • thesis
    • Chou, T. and Lakatos, G. (2004) 'Clustered bottlenecks in mRNA translation and protein synthesis', Phys. Rev. Lett., Vol. 93, No. 19, p.198101.
    • (2004) Phys. Rev. Lett. , vol.93 , Issue.19 , pp. 198101
    • Chou, T.1    Lakatos, G.2
  • 3
    • 54849441249 scopus 로고    scopus 로고
    • Rare codons cluster
    • doi:10.1371/journal.pone.0003412
    • Clarke IV, T.F. and Clark, P.L. (2008) 'Rare codons cluster', PLoS ONE, Vol. 3, No. 10, p.e3412, doi:10.1371/journal.pone.0003412.
    • (2008) PLoS ONE , vol.3 , Issue.10
    • Clarke, I.V.T.F.1    Clark, P.L.2
  • 4
    • 46449120581 scopus 로고    scopus 로고
    • Virus attenuation by genome-scale changes in codon pair bias
    • Coleman, J.R., Papamichail, D., Skiena, S., Futcher, B., Wimmer, E. and Mueller, S. (2008) 'Virus attenuation by genome-scale changes in codon pair bias', Science, Vol. 320, No. 5884, pp.1784-1787.
    • (2008) Science , vol.320 , Issue.5884 , pp. 1784-1787
    • Coleman, J.R.1    Papamichail, D.2    Skiena, S.3    Futcher, B.4    Wimmer, E.5    Mueller, S.6
  • 5
    • 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, C.G. (1996) 'Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates', J. Mol. Biol., Vol. 260, No. 5, pp.649-663.
    • (1996) J. Mol. Biol. , vol.260 , Issue.5 , pp. 649-663
    • Dong, H.1    Nilsson, L.2    Kurland, C.G.3
  • 6
    • 34249900723 scopus 로고    scopus 로고
    • Towards a model for protein production rates
    • Dong, J., Schmittmann, B. and Zia, R. (2007) 'Towards a model for protein production rates', J. Stat. Phys., Vol. 128, pp.21-34.
    • (2007) J. Stat. Phys. , vol.128 , pp. 21-34
    • Dong, J.1    Schmittmann, B.2    Zia, R.3
  • 7
    • 34548585028 scopus 로고    scopus 로고
    • Optimizing scaleup yield for protein production: Computationally optimized DNA Assembly (CODA) and translation engineering
    • Hatfield, G.W. and Roth, D.A. (2007) 'Optimizing scaleup yield for protein production: Computationally optimized DNA Assembly (CODA) and translation engineering', Biotechnol. Annu. Rev., Vol. 13, pp.27-42.
    • (2007) Biotechnol. Annu. Rev. , vol.13 , pp. 27-42
    • Hatfield, G.W.1    Roth, D.A.2
  • 8
    • 33845649194 scopus 로고    scopus 로고
    • A spatial scan statistic for survival data
    • Huang, L., Kulldorff, M. and Gregorio, D. (2007) 'A spatial scan statistic for survival data', Biometrics, Vol. 63, No. 1, pp.109-118.
    • (2007) Biometrics , vol.63 , Issue.1 , pp. 109-118
    • Huang, L.1    Kulldorff, M.2    Gregorio, D.3
  • 9
    • 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., Vol. 151, No. 3, pp.389-409.
    • (1981) J. Mol. Biol. , vol.151 , Issue.3 , pp. 389-409
    • Ikemura, T.1
  • 10
    • 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., Vol. 2, No. 1, pp.13-34.
    • (1985) Mol. Biol. Evol. , vol.2 , Issue.1 , pp. 13-34
    • Ikemura, T.1
  • 11
    • 18844362113 scopus 로고    scopus 로고
    • Strategies for efficient production of heterologous proteins in Escherichia coli
    • Jana, S. and Deb, J.K. (2005) 'Strategies for efficient production of heterologous proteins in Escherichia coli', Appl. Microbiol. Biotechnol., Vol. 67, No. 3, pp.289-298.
    • (2005) Appl. Microbiol. Biotechnol. , vol.67 , Issue.3 , pp. 289-298
    • Jana, S.1    Deb, J.K.2
  • 12
    • 0028804911 scopus 로고
    • Effects of rare codon clusters on high-level expression of heterologous proteins in Escherichia coli
    • Kane, J.F. (1995) 'Effects of rare codon clusters on high-level expression of heterologous proteins in Escherichia coli', Curr. Opin. Biotechnol., Vol. 6, No. 5, pp.494-500.
    • (1995) Curr. Opin. Biotechnol. , vol.6 , Issue.5 , pp. 494-500
    • Kane, J.F.1
  • 13
    • 0034888743 scopus 로고    scopus 로고
    • Characterizations of highly expressed genes of four fast-growing bacteria
    • Karlin, S., Mrázek, J., Campbell, A. and Kaiser, D. (2001) 'Characterizations of highly expressed genes of four fast-growing bacteria', J. Bacteriol., Vol. 183, No. 17, pp.5025-5040.
    • (2001) J. Bacteriol. , vol.183 , Issue.17 , pp. 5025-5040
    • Karlin, S.1    Mrázek, J.2    Campbell, A.3    Kaiser, D.4
  • 14
    • 0025763551 scopus 로고
    • Codon bias and gene expression
    • Kurland, C.G. (1991) 'Codon bias and gene expression', FEBS Lett., Vol. 285, No. 2, pp.165-169.
    • (1991) FEBS Lett. , vol.285 , Issue.2 , pp. 165-169
    • Kurland, C.G.1
  • 15
    • 0030805979 scopus 로고    scopus 로고
    • Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli
    • Link, A.J., Robison, K. and Church, G. (1997) 'Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli', Electrophoresis, Vol. 18, pp.1259-1313.
    • (1997) Electrophoresis , vol.18 , pp. 1259-1313
    • Link, A.J.1    Robison, K.2    Church, G.3
  • 16
    • 0348013051 scopus 로고    scopus 로고
    • Hierarchy of sequence-dependent features associated with prokaryotic translation
    • Lithwick, G. and Margalit, H. (2003) 'Hierarchy of sequence-dependent features associated with prokaryotic translation', Genome Res., Vol. 13, No. 12, pp.2665-2673.
    • (2003) Genome Res. , vol.13 , Issue.12 , pp. 2665-2673
    • Lithwick, G.1    Margalit, H.2
  • 17
    • 51649118422 scopus 로고    scopus 로고
    • Folding at the rhythm of the rare codon beat
    • Marin, M. (2008) 'Folding at the rhythm of the rare codon beat', Biotechnol. J., Vol. 3, No. 8, pp.1047-1057.
    • (2008) Biotechnol. J. , vol.3 , Issue.8 , pp. 1047-1057
    • Marin, M.1
  • 18
    • 33745608985 scopus 로고    scopus 로고
    • Integrated analysis of transcriptomic and proteomic data of Desulfovibrio vulgaris: Zero-inflated Poisson regression models to predict abundance of undetected proteins
    • Nie, L., Wu, G., Brockman, F.J. and Zhang, W. (2006) 'Integrated analysis of transcriptomic and proteomic data of Desulfovibrio vulgaris: Zero-inflated Poisson regression models to predict abundance of undetected proteins', Bioinformatics, Vol. 22, No. 13, pp.1641-1647.
    • (2006) Bioinformatics , vol.22 , Issue.13 , pp. 1641-1647
    • Nie, L.1    Wu, G.2    Brockman, F.J.3    Zhang, W.4
  • 19
    • 0031861223 scopus 로고    scopus 로고
    • Genes and proteins of Escherichia coli K-12 (GenProtEC)
    • DOI 10.1093/nar/26.1.54
    • Riley, M. (1998) 'Genes and proteins of Escherichia coli K-12 (GenProtEC)', Nucleic Acids Res., Vol. 6, p.54. (Pubitemid 28295297)
    • (1998) Nucleic Acids Research , vol.26 , Issue.1 , pp. 54
    • Riley, M.1
  • 20
    • 68849083789 scopus 로고    scopus 로고
    • Rare codon content affects the solubility of recombinant proteins in a codon bias-adjusted Escherichia coli strain
    • doi:10.1186/1475-2859-8-41
    • 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., Vol. 8, No. 41, doi:10.1186/1475-2859-8-41.
    • (2009) Microb. Cell Fact. , vol.8 , Issue.41
    • Rosano, G.L.1    Ceccarelli, E.A.2
  • 22
    • 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., Vol. 207, No. 2, pp.365-377.
    • (1989) J. Mol. Biol. , vol.207 , Issue.2 , pp. 365-377
    • Sorensen, M.A.1    Kurland, C.G.2    Pedersen, S.3
  • 23
    • 0030018101 scopus 로고    scopus 로고
    • Ribosome-mediated translational pause and protein domain organization
    • Thanaraj, T.A. and Argos, P. (1996) 'Ribosome-mediated translational pause and protein domain organization', Protein Sci., Vol. 5, No. 8, pp.1594-612.
    • (1996) Protein Sci. , vol.5 , Issue.8 , pp. 1594-1612
    • Thanaraj, T.A.1    Argos, P.2
  • 24
    • 0021764898 scopus 로고
    • Translation is a non-uniform process: Effect oftRNAavailability 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 oftRNAavailability on the rate of elongation of nascent polypeptide chains', J. Mol. Biol., Vol. 180, No. 3, pp.549-576.
    • (1984) J. Mol. Biol. , vol.180 , Issue.3 , pp. 549-576
    • Varenne, S.1    Buc, J.2    Lloubes, R.3    Lazdunski, C.4
  • 26
    • 44349120609 scopus 로고    scopus 로고
    • Analysis of the distribution of functionally relevant rare codons
    • doi: 10.1186/ 1471-2164-
    • Widmann, M., Clairo, M., Dippon, J. and Pleiss, J. (2008) 'Analysis of the distribution of functionally relevant rare codons', BMC Genomics, Vol. 9, No. 207, doi: 10.1186/ 1471-2164-9-207.
    • (2008) BMC Genomics , vol.9 , Issue.207 , pp. 9-207
    • Widmann, M.1    Clairo, M.2    Dippon, J.3    Pleiss, J.4
  • 27
    • 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, Vol. 4, No. 4, p.e5036.
    • (2009) PLoS One , vol.4 , Issue.4
    • Zhang, G.1    Ignatova, Z.2
  • 28
    • 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., Vol. 16, No. 3, pp.274-280.
    • (2009) Nat. Struct. Mol. Biol. , vol.16 , Issue.3 , pp. 274-280
    • Zhang, G.1    Hubalewska, M.2    Ignatova, Z.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.