메뉴 건너뛰기




Volumn 92, Issue 3, 2007, Pages 717-730

A model for protein translation: Polysome self-organization leads to maximum protein synthesis rates

Author keywords

[No Author keywords available]

Indexed keywords

GUANOSINE TRIPHOSPHATE; MESSENGER RNA; TRANSFER RNA;

EID: 33846820156     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.106.087825     Document Type: Article
Times cited : (47)

References (37)
  • 1
    • 85030525102 scopus 로고    scopus 로고
    • Hershey, J. 1987. Protein synthesis. In Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology. F. C. Neidhardt, J. L. Ingraham, K. B. Low, B. Magasanik, M. Schaechter, and H. E. Umbarger, editors. American Society for Microbiology, Washington, DC.
    • Hershey, J. 1987. Protein synthesis. In Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology. F. C. Neidhardt, J. L. Ingraham, K. B. Low, B. Magasanik, M. Schaechter, and H. E. Umbarger, editors. American Society for Microbiology, Washington, DC.
  • 2
    • 0014960630 scopus 로고
    • Visualization of bacterial genes in action
    • Miller, O. L., Jr., B. A. Hamkalo, and C. A. Thomas, Jr. 1970. Visualization of bacterial genes in action. Science. 169:392-395.
    • (1970) Science , vol.169 , pp. 392-395
    • Miller Jr., O.L.1    Hamkalo, B.A.2    Thomas Jr., C.A.3
  • 4
    • 0014245158 scopus 로고
    • Kinetics of biopolymerization on nucleic acid templates
    • MacDonald, C. T., J. H. Gibbs, and A. C. Pipkin. 1968. Kinetics of biopolymerization on nucleic acid templates. Biopolymers. 6:1-5.
    • (1968) Biopolymers , vol.6 , pp. 1-5
    • MacDonald, C.T.1    Gibbs, J.H.2    Pipkin, A.C.3
  • 5
    • 84984085494 scopus 로고
    • Concerning kinetics of polypeptide synthesis on polyribosomes
    • MacDonald, C. T., and J. H. Gibbs. 1969. Concerning kinetics of polypeptide synthesis on polyribosomes. Biopolymers. 7:707-725.
    • (1969) Biopolymers , vol.7 , pp. 707-725
    • MacDonald, C.T.1    Gibbs, J.H.2
  • 6
    • 0019178883 scopus 로고
    • Mathematical modeling of translation of mRNA in eukaryotes; steady-state, time-dependent processes and application to reticulocytes
    • Heinrich, R., and T. A. Rapoport. 1980. Mathematical modeling of translation of mRNA in eukaryotes; steady-state, time-dependent processes and application to reticulocytes. J. Theor. Biol. 86:279-313.
    • (1980) J. Theor. Biol , vol.86 , pp. 279-313
    • Heinrich, R.1    Rapoport, T.A.2
  • 7
    • 0347132484 scopus 로고    scopus 로고
    • Insights into the relation between mRNA and protein expression patterns: I. Theoretical considerations
    • Mehra, A., K. H. Lee, and V. Hatzimanikatis. 2003. Insights into the relation between mRNA and protein expression patterns: I. Theoretical considerations. Biotechnol. Bioeng. 84:822-833.
    • (2003) Biotechnol. Bioeng , vol.84 , pp. 822-833
    • Mehra, A.1    Lee, K.H.2    Hatzimanikatis, V.3
  • 8
    • 33645775569 scopus 로고    scopus 로고
    • An algorithmic framework for genome-wide modeling and analysis of translation networks
    • Mehra, A., and V. Hatzimanikatis. 2006. An algorithmic framework for genome-wide modeling and analysis of translation networks. Biophys. J. 90:1136-1146.
    • (2006) Biophys. J , vol.90 , pp. 1136-1146
    • Mehra, A.1    Hatzimanikatis, V.2
  • 9
    • 0021764898 scopus 로고
    • Translation is a non-uniform process. Effect of tRNA availability on the rate of elongation of nascent polypeptide chains
    • Varenne, S., J. Buc, R. Lloubes, and C. Lazdunski. 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
  • 10
    • 0024962419 scopus 로고
    • Rates of aminoacyl-tRNA selection at 29 sense codons in vivo
    • Curran, J. F., and M. Yarus. 1989. Rates of aminoacyl-tRNA selection at 29 sense codons in vivo. J. Mol. Biol. 209:65-77.
    • (1989) J. Mol. Biol , vol.209 , pp. 65-77
    • Curran, J.F.1    Yarus, M.2
  • 11
    • 0026409389 scopus 로고
    • Absolute in vivo translation rates of individual codons in Escherichia coli: The two glutamic acid codons GAA and GAG are translated with a threefold difference in rate
    • Soerensen, M. A., and S. Pedersen. 1991. Absolute in vivo translation rates of individual codons in Escherichia coli: the two glutamic acid codons GAA and GAG are translated with a threefold difference in rate. J. Mol. Biol. 222:265-280.
    • (1991) J. Mol. Biol , vol.222 , pp. 265-280
    • Soerensen, M.A.1    Pedersen, S.2
  • 12
    • 0014430363 scopus 로고
    • The characterization of separated α- and β-chain polyribosomes in rabbit reticulocytes
    • Kazazian, H. H., Jr., and M. L. Freedman. 1968. The characterization of separated α- and β-chain polyribosomes in rabbit reticulocytes. J. Biol. Chem. 243:6446-6450.
    • (1968) J. Biol. Chem , vol.243 , pp. 6446-6450
    • Kazazian Jr., H.H.1    Freedman, M.L.2
  • 13
    • 0017708060 scopus 로고
    • Nucleotide sequences of ribosome recognition sites in messenger RNAs of vesicular stomatitis virus
    • Rose, J. K. 1977. Nucleotide sequences of ribosome recognition sites in messenger RNAs of vesicular stomatitis virus. Proc. Natl. Acad. Sci. USA. 74:3672-3676.
    • (1977) Proc. Natl. Acad. Sci. USA , vol.74 , pp. 3672-3676
    • Rose, J.K.1
  • 14
    • 0017831045 scopus 로고
    • Post-transcriptional and translational controls of gene expression in eukaryotes
    • Revel, M., and Y. Groner. 1978. Post-transcriptional and translational controls of gene expression in eukaryotes. Annu. Rev. Biochem. 47:1079-1126.
    • (1978) Annu. Rev. Biochem , vol.47 , pp. 1079-1126
    • Revel, M.1    Groner, Y.2
  • 15
    • 14644396660 scopus 로고    scopus 로고
    • Selective charging of tRNA isoacceptors induced by amino-acid starvation
    • 6:151-157
    • Dittmar, K. A., M. A. Sorensen, J. Elf, M. Ehrenberg, and T. Pan. 2005. Selective charging of tRNA isoacceptors induced by amino-acid starvation. EMBO Rep. 6:151-157.
    • (2005) EMBO Rep
    • Dittmar, K.A.1    Sorensen, M.A.2    Elf, J.3    Ehrenberg, M.4    Pan, T.5
  • 16
    • 0022412615 scopus 로고
    • Kinetic studies of Escherichia coli elongation factor Tu-guanosine 5′-triphosphate-aminoacyl-tRNA complexes
    • Louie, A., and F. Jurnak. 1985. Kinetic studies of Escherichia coli elongation factor Tu-guanosine 5′-triphosphate-aminoacyl-tRNA complexes. Biochemistry. 24:6433-6439.
    • (1985) Biochemistry , vol.24 , pp. 6433-6439
    • Louie, A.1    Jurnak, F.2
  • 17
    • 0026521547 scopus 로고
    • Kinetic properties of Escherichia coli ribosomes with altered forms of S12
    • Bilgin, N., F. Claesens, H. Pahverk, and M. Ehrenberg. 1992. Kinetic properties of Escherichia coli ribosomes with altered forms of S12. J. Mol. Biol. 224:1011-1027.
    • (1992) J. Mol. Biol , vol.224 , pp. 1011-1027
    • Bilgin, N.1    Claesens, F.2    Pahverk, H.3    Ehrenberg, M.4
  • 18
    • 0030047916 scopus 로고    scopus 로고
    • Initial binding of the elongation factor Tu·GTP·aminoacyl-tRNA complex preceding codon recognition on the ribosome
    • Rodnina, M. V., T. Pape, R. Fricke, L. Kuhn, and W. Wintermeyer. 1996. Initial binding of the elongation factor Tu·GTP·aminoacyl-tRNA complex preceding codon recognition on the ribosome. J. Biol. Chem. 271:646-652.
    • (1996) J. Biol. Chem , vol.271 , pp. 646-652
    • Rodnina, M.V.1    Pape, T.2    Fricke, R.3    Kuhn, L.4    Wintermeyer, W.5
  • 19
    • 0032535207 scopus 로고    scopus 로고
    • Complete kinetic mechanism of elongation factor Tu-dependent binding of aminoacyl-tRNA to the A site of the E. coli ribosome
    • Pape, T., W. Wintermeyer, and M. V. Rodnina. 1998. Complete kinetic mechanism of elongation factor Tu-dependent binding of aminoacyl-tRNA to the A site of the E. coli ribosome. EMBO J. 17:7490-7497.
    • (1998) EMBO J , vol.17 , pp. 7490-7497
    • Pape, T.1    Wintermeyer, W.2    Rodnina, M.V.3
  • 20
    • 0038433302 scopus 로고    scopus 로고
    • An elongation factor G-induced ribosome rearrangement precedes tRNA-mRNA translocation
    • Savelsbergh, A., V. I. Katunin, D. Mohr, F. Peske, M. V. Rodnina, and W. Wintermeyer. 2003. An elongation factor G-induced ribosome rearrangement precedes tRNA-mRNA translocation. Mol. Cell. 11:1517-1523.
    • (2003) Mol. Cell , vol.11 , pp. 1517-1523
    • Savelsbergh, A.1    Katunin, V.I.2    Mohr, D.3    Peske, F.4    Rodnina, M.V.5    Wintermeyer, W.6
  • 22
    • 0015989446 scopus 로고
    • A linear steady-state treatment of enzymatic chains. General properties, control and effector strength
    • Heinrich, R., and T. A. Rapoport. 1974. A linear steady-state treatment of enzymatic chains. General properties, control and effector strength. Eur. J. Biochem. 42:89-95.
    • (1974) Eur. J. Biochem , vol.42 , pp. 89-95
    • Heinrich, R.1    Rapoport, T.A.2
  • 23
    • 0021847426 scopus 로고
    • Metabolic control and its analysis. Additional relationships between elasticities and control coefficients
    • Fell, D. A., and H. M. Sauro. 1985. Metabolic control and its analysis. Additional relationships between elasticities and control coefficients. Eur. J. Biochem. 148:555-561.
    • (1985) Eur. J. Biochem , vol.148 , pp. 555-561
    • Fell, D.A.1    Sauro, H.M.2
  • 24
    • 0023709196 scopus 로고
    • Metabolic control theory: A structural approach
    • Reder, C. 1988. Metabolic control theory: a structural approach. J. Theor. Biol. 135:175-201.
    • (1988) J. Theor. Biol , vol.135 , pp. 175-201
    • Reder, C.1
  • 25
    • 0027456261 scopus 로고
    • Metabolic channeling and control of the flux
    • Kholodenko, B. N., and H. V. Westerhoff. 1993. Metabolic channeling and control of the flux. FEBS Lett. 320:71-74.
    • (1993) FEBS Lett , vol.320 , pp. 71-74
    • Kholodenko, B.N.1    Westerhoff, H.V.2
  • 28
    • 0345863934 scopus 로고    scopus 로고
    • The CyberCell Database (CCDB): A comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli
    • Sundararaj, S., A. Guo, B. Habibi-Nazhad, M. Rouani, P. Stothard, M. Ellison, and D. S. Wishart. 2004. The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli. Nucleic Acids Res. 32:D293-D295.
    • (2004) Nucleic Acids Res , vol.32
    • Sundararaj, S.1    Guo, A.2    Habibi-Nazhad, B.3    Rouani, M.4    Stothard, P.5    Ellison, M.6    Wishart, D.S.7
  • 29
    • 23244446620 scopus 로고    scopus 로고
    • Quantitative polysome analysis identifies limitations in bacterial cell-free protein synthesis
    • Underwood, K. A., J. R. Swartz, and J. D. Puglisi. 2005. Quantitative polysome analysis identifies limitations in bacterial cell-free protein synthesis. Biotechnol. Bioeng. 91:425-435.
    • (2005) Biotechnol. Bioeng , vol.91 , pp. 425-435
    • Underwood, K.A.1    Swartz, J.R.2    Puglisi, J.D.3
  • 31
    • 0345871250 scopus 로고    scopus 로고
    • Insights into the relation between mRNA and protein expression patterns: II. Experimental observations in Escherichia coli
    • Lee, P. S., L. B. Shaw, L. H. Choe, A. Mehra, V. Hatzimanikatis, and K. H. Lee. 2003. Insights into the relation between mRNA and protein expression patterns: II. Experimental observations in Escherichia coli. Biotechnol. Bioeng. 84:834-841.
    • (2003) Biotechnol. Bioeng , vol.84 , pp. 834-841
    • Lee, P.S.1    Shaw, L.B.2    Choe, L.H.3    Mehra, A.4    Hatzimanikatis, V.5    Lee, K.H.6
  • 32
    • 0030141280 scopus 로고    scopus 로고
    • Analysis and design of metabolic reaction networks via mixed-integer linear optimization
    • Hatzimanikatis, V., C. A. Floudas, and J. E. Bailey. 1996. Analysis and design of metabolic reaction networks via mixed-integer linear optimization. AIChE J. 42:1277-1292.
    • (1996) AIChE J , vol.42 , pp. 1277-1292
    • Hatzimanikatis, V.1    Floudas, C.A.2    Bailey, J.E.3
  • 33
    • 10044224601 scopus 로고    scopus 로고
    • Metabolic control analysis under uncertainty: Framework development and case studies
    • Wang, L., I. Birol, and V. Hatzimanikatis. 2004. Metabolic control analysis under uncertainty: framework development and case studies. Biophys. J. 87:3750-3763.
    • (2004) Biophys. J , vol.87 , pp. 3750-3763
    • Wang, L.1    Birol, I.2    Hatzimanikatis, V.3
  • 34
    • 85030501036 scopus 로고    scopus 로고
    • Reference deleted in proof
    • Reference deleted in proof.
  • 35
    • 85030514738 scopus 로고    scopus 로고
    • Bremer, H., and P. P. Dennis. 1996. Modulation of chemical composition and other parameters of the cell by growth rate. In Escherichia coli and Salmonella typhimurium. F. C. Neidhardt, editor. American Society for Microbiology, Washington, DC.
    • Bremer, H., and P. P. Dennis. 1996. Modulation of chemical composition and other parameters of the cell by growth rate. In Escherichia coli and Salmonella typhimurium. F. C. Neidhardt, editor. American Society for Microbiology, Washington, DC.
  • 36
    • 0030564828 scopus 로고    scopus 로고
    • Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates
    • Dong, H., L. Nilsson, and C. G. Kurland. 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, C.G.3
  • 37
    • 0038620436 scopus 로고    scopus 로고
    • Codon pairs in the genome of Escherichia coli
    • Boycheva, S., G. Chkodrov, and I. Ivanov. 2003. Codon pairs in the genome of Escherichia coli. Bioinformatics. 19:987-998.
    • (2003) Bioinformatics , vol.19 , pp. 987-998
    • Boycheva, S.1    Chkodrov, G.2    Ivanov, I.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.