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Volumn 284, Issue 1, 2011, Pages 82-91

Negative feedback and physical limits of genes

Author keywords

Auto repression; Metabolic cost; Output noise; Response time; Trade off

Indexed keywords

GENE EXPRESSION; GENETIC ENGINEERING; GENETICS; METABOLITE;

EID: 79959980480     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2011.06.021     Document Type: Article
Times cited : (10)

References (53)
  • 1
    • 0001422329 scopus 로고
    • Quantitative model for gene regulation by lambda phage repressor
    • Ackers G.K., Johnson A.D., Shea M.A. Quantitative model for gene regulation by lambda phage repressor. Proc. Nat. Acad. Sci. 1982, 79:1129-1133.
    • (1982) Proc. Nat. Acad. Sci. , vol.79 , pp. 1129-1133
    • Ackers, G.K.1    Johnson, A.D.2    Shea, M.A.3
  • 2
    • 0037133671 scopus 로고    scopus 로고
    • Metabolic efficiency and amino acid composition in the proteomes of Escherichia coliand Bacillus subtilis
    • Akashi H., Gojobori T. Metabolic efficiency and amino acid composition in the proteomes of Escherichia coliand Bacillus subtilis. Proc. Nat. Acad. Sci. 2002, 99(6):3695-3700.
    • (2002) Proc. Nat. Acad. Sci. , vol.99 , Issue.6 , pp. 3695-3700
    • Akashi, H.1    Gojobori, T.2
  • 3
    • 79960728465 scopus 로고    scopus 로고
    • An Introduction To System Biology. Design Principles of Biological Circuits. In: Chapman & Hall/CRC Mathematical and Computational Biology Series.
    • Alon, U., 2007a. An Introduction To System Biology. Design Principles of Biological Circuits. In: Chapman & Hall/CRC Mathematical and Computational Biology Series.
    • (2007)
    • Alon, U.1
  • 4
    • 34249079154 scopus 로고    scopus 로고
    • Network motifs: theory and experimental approaches
    • Alon U. Network motifs: theory and experimental approaches. Nat. Rev. Genet. 2007, 8:450-461.
    • (2007) Nat. Rev. Genet. , vol.8 , pp. 450-461
    • Alon, U.1
  • 5
    • 0031879114 scopus 로고    scopus 로고
    • Stochastic kinetic analysis of developmental pathway bifurcation in phage l-infected Escherichia coli cells
    • Arkin A., Ross J., McAdams H.H. Stochastic kinetic analysis of developmental pathway bifurcation in phage l-infected Escherichia coli cells. Genetics 1998, 149:1633-1648.
    • (1998) Genetics , vol.149 , pp. 1633-1648
    • Arkin, A.1    Ross, J.2    McAdams, H.H.3
  • 8
    • 0034212551 scopus 로고    scopus 로고
    • Engineering stability in gene networks by autoregulation
    • Becskei A., Serrano L. Engineering stability in gene networks by autoregulation. Nature 2000, 405:590-593.
    • (2000) Nature , vol.405 , pp. 590-593
    • Becskei, A.1    Serrano, L.2
  • 9
    • 0015680909 scopus 로고
    • Logical reversibility of computation
    • Bennett C.H. Logical reversibility of computation. IBM J. Res. Dev. 1973, 17(6):525-532.
    • (1973) IBM J. Res. Dev. , vol.17 , Issue.6 , pp. 525-532
    • Bennett, C.H.1
  • 10
    • 0010146684 scopus 로고
    • The thermodynamics of computation-a review
    • Bennett C.H. The thermodynamics of computation-a review. Int. J. Theor. Phys. 1982, 21(12):905-940.
    • (1982) Int. J. Theor. Phys. , vol.21 , Issue.12 , pp. 905-940
    • Bennett, C.H.1
  • 13
    • 0037965981 scopus 로고    scopus 로고
    • On schemes of combinatorial transcription logic
    • Buchler N.E., Gerland U., Hwa T. On schemes of combinatorial transcription logic. Proc. Nat. Acad. Sci. 2003, 100(9):5136-5141.
    • (2003) Proc. Nat. Acad. Sci. , vol.100 , Issue.9 , pp. 5136-5141
    • Buchler, N.E.1    Gerland, U.2    Hwa, T.3
  • 14
    • 61449155349 scopus 로고    scopus 로고
    • Models of transcription factor binding: sensitivity of activation functions to model assumptions
    • Chu D., Zabet N.R., Mitavskiy B. Models of transcription factor binding: sensitivity of activation functions to model assumptions. J. Theor. Biol. 2009, 257(3):419-429.
    • (2009) J. Theor. Biol. , vol.257 , Issue.3 , pp. 419-429
    • Chu, D.1    Zabet, N.R.2    Mitavskiy, B.3
  • 15
    • 79953757806 scopus 로고    scopus 로고
    • Optimal parameter settings for information processing in gene regulatory networks
    • Chu D.F., Zabet N.R., Hone A.N.W. Optimal parameter settings for information processing in gene regulatory networks. BioSystems 2011, 104(2-3):99-108.
    • (2011) BioSystems , vol.104 , Issue.2-3 , pp. 99-108
    • Chu, D.F.1    Zabet, N.R.2    Hone, A.N.W.3
  • 16
    • 0037119587 scopus 로고    scopus 로고
    • Stochastic gene expression in a single cell
    • Elowitz M.B., Levine A.J., Siggia E.D., Swain P.S. Stochastic gene expression in a single cell. Science 2002, 297(5584):1183-1186.
    • (2002) Science , vol.297 , Issue.5584 , pp. 1183-1186
    • Elowitz, M.B.1    Levine, A.J.2    Siggia, E.D.3    Swain, P.S.4
  • 18
    • 27244445075 scopus 로고    scopus 로고
    • The linear noise approximation for molecular fluctuations within cells
    • Hayot F., Jayaprakash C. The linear noise approximation for molecular fluctuations within cells. Phys. Biol. 2004, 1:205-210.
    • (2004) Phys. Biol. , vol.1 , pp. 205-210
    • Hayot, F.1    Jayaprakash, C.2
  • 19
    • 14844358192 scopus 로고    scopus 로고
    • Ultrasensitivity and noise propagation in a synthetic transcriptional cascade
    • Hooshangi S., Thiberge S., Weiss R. Ultrasensitivity and noise propagation in a synthetic transcriptional cascade. Proc. Nat. Acad. Sci. 2005, 102(10):3581-3586.
    • (2005) Proc. Nat. Acad. Sci. , vol.102 , Issue.10 , pp. 3581-3586
    • Hooshangi, S.1    Thiberge, S.2    Weiss, R.3
  • 20
    • 38949194331 scopus 로고    scopus 로고
    • Noise propagation and signaling sensitivity in biological networks: a role for positive feedback
    • Hornung G., Barkai N. Noise propagation and signaling sensitivity in biological networks: a role for positive feedback. PLoS Comput. Biol. 2008, 4(1):55-61.
    • (2008) PLoS Comput. Biol. , vol.4 , Issue.1 , pp. 55-61
    • Hornung, G.1    Barkai, N.2
  • 21
    • 15744374885 scopus 로고    scopus 로고
    • Signal processing in single cells
    • Isaacs F.J., Blake W.J., Collins J.J. Signal processing in single cells. Science 2005, 307(5717):1886-1888.
    • (2005) Science , vol.307 , Issue.5717 , pp. 1886-1888
    • Isaacs, F.J.1    Blake, W.J.2    Collins, J.J.3
  • 22
    • 19544379881 scopus 로고    scopus 로고
    • Stochasticity in gene expression: from theories to phenotypes
    • Kaern M., Elston T.C., Blake W.J., Collins J.J. Stochasticity in gene expression: from theories to phenotypes. Nat. Rev. Genet. 2005, 6:451-464.
    • (2005) Nat. Rev. Genet. , vol.6 , pp. 451-464
    • Kaern, M.1    Elston, T.C.2    Blake, W.J.3    Collins, J.J.4
  • 23
    • 58549120549 scopus 로고    scopus 로고
    • Stochasticity in single gene expression with both intrinsic noise and fluctuation in kinetic parameters
    • Lei J. Stochasticity in single gene expression with both intrinsic noise and fluctuation in kinetic parameters. J. Theor. Biol. 2009, 256:485-492.
    • (2009) J. Theor. Biol. , vol.256 , pp. 485-492
    • Lei, J.1
  • 24
    • 0034739013 scopus 로고    scopus 로고
    • Ultimate physical limits to computation
    • Lloyd S. Ultimate physical limits to computation. Nature 2000, 406:1047-1054.
    • (2000) Nature , vol.406 , pp. 1047-1054
    • Lloyd, S.1
  • 25
    • 33646167129 scopus 로고    scopus 로고
    • Plasticity of the cis-regulatory input function of a gene
    • Mayo A.E., Setty Y., Shavit S., Zaslaver A., Alon U. Plasticity of the cis-regulatory input function of a gene. PLOS Biol. 2006, 4(4):e45.
    • (2006) PLOS Biol. , vol.4 , Issue.4
    • Mayo, A.E.1    Setty, Y.2    Shavit, S.3    Zaslaver, A.4    Alon, U.5
  • 26
    • 47649111578 scopus 로고    scopus 로고
    • Exponential sensitivity of noise-driven switching in genetic networks
    • Mehta P., Mukhopadhyay R., Wingreen N.S. Exponential sensitivity of noise-driven switching in genetic networks. Phys. Biol. 2008, 5.
    • (2008) Phys. Biol. , vol.5
    • Mehta, P.1    Mukhopadhyay, R.2    Wingreen, N.S.3
  • 29
    • 0842285841 scopus 로고    scopus 로고
    • Summing up the noise in gene networks
    • Paulsson J. Summing up the noise in gene networks. Nature 2004, 427:415-418.
    • (2004) Nature , vol.427 , pp. 415-418
    • Paulsson, J.1
  • 30
    • 0034608143 scopus 로고    scopus 로고
    • Random signal fluctuations can reduce random fluctuations in regulated components of chemical regulatory networks
    • Paulsson J., Ehrenberg M. Random signal fluctuations can reduce random fluctuations in regulated components of chemical regulatory networks. Phys. Rev. Lett. 2000, 84(23):5447-5450.
    • (2000) Phys. Rev. Lett. , vol.84 , Issue.23 , pp. 5447-5450
    • Paulsson, J.1    Ehrenberg, M.2
  • 31
    • 15544388848 scopus 로고    scopus 로고
    • Noise propagation in gene networks
    • Pedraza J.M., van Oudenaarden A. Noise propagation in gene networks. Science 2005, 307:1965-1969.
    • (2005) Science , vol.307 , pp. 1965-1969
    • Pedraza, J.M.1    van Oudenaarden, A.2
  • 32
    • 0036428761 scopus 로고    scopus 로고
    • Negative autoregulation speeds the response times of transcription networks
    • Rosenfeld N., Elowitz M.B., Alon U. Negative autoregulation speeds the response times of transcription networks. J. Mol. Biol. 2002, 323:785-793.
    • (2002) J. Mol. Biol. , vol.323 , pp. 785-793
    • Rosenfeld, N.1    Elowitz, M.B.2    Alon, U.3
  • 34
    • 0016145568 scopus 로고
    • Comparison of classical and autogenous systems of regulation in inducible operons
    • Savageau M.A. Comparison of classical and autogenous systems of regulation in inducible operons. Nature 1974, 252(5484):546-549.
    • (1974) Nature , vol.252 , Issue.5484 , pp. 546-549
    • Savageau, M.A.1
  • 35
  • 36
    • 43249118966 scopus 로고    scopus 로고
    • Colored extrinsic fluctuations and stochastic gene expression
    • Shahrezaei V., Ollivier J.F., Swain P.S. Colored extrinsic fluctuations and stochastic gene expression. Mol. Syst. Biol. 2008, 4(196).
    • (2008) Mol. Syst. Biol. , vol.4 , Issue.196
    • Shahrezaei, V.1    Ollivier, J.F.2    Swain, P.S.3
  • 37
    • 0036578795 scopus 로고    scopus 로고
    • Network motifs in the transcriptional regulation network of Escherichia coli
    • Shen-Orr S.S., Milo R., Mangan S., Alon U. Network motifs in the transcriptional regulation network of Escherichia coli. Nat. Genet. 2002, 31:64-68.
    • (2002) Nat. Genet. , vol.31 , pp. 64-68
    • Shen-Orr, S.S.1    Milo, R.2    Mangan, S.3    Alon, U.4
  • 38
    • 12244257806 scopus 로고    scopus 로고
    • Noisy signal amplification in ultrasensitive signal transduction
    • Shibata T., Fujimoto K. Noisy signal amplification in ultrasensitive signal transduction. Proc. Nat. Acad. Sci. 2005, 102(2):331-336.
    • (2005) Proc. Nat. Acad. Sci. , vol.102 , Issue.2 , pp. 331-336
    • Shibata, T.1    Fujimoto, K.2
  • 39
    • 0017185026 scopus 로고
    • Non-genetic individuality: chance in the single cell
    • Spudich J.L., Koshland D.E. Non-genetic individuality: chance in the single cell. Nature 1976, 262:467-471.
    • (1976) Nature , vol.262 , pp. 467-471
    • Spudich, J.L.1    Koshland, D.E.2
  • 40
    • 40649083597 scopus 로고    scopus 로고
    • Strong negative self regulation of prokaryotic transcription factors increases the intrinsic noise of protein expression
    • Stekel D.J., Jenkins D.J. Strong negative self regulation of prokaryotic transcription factors increases the intrinsic noise of protein expression. BMC Syst. Biol. 2008, 2(6).
    • (2008) BMC Syst. Biol. , vol.2 , Issue.6
    • Stekel, D.J.1    Jenkins, D.J.2
  • 41
    • 0042360338 scopus 로고    scopus 로고
    • A deoxyribozyme-based molecular automaton
    • Stojanovic M.N., Stefanovic D. A deoxyribozyme-based molecular automaton. Nat. Biotechnol. 2003, 21(9):1069-1074.
    • (2003) Nat. Biotechnol. , vol.21 , Issue.9 , pp. 1069-1074
    • Stojanovic, M.N.1    Stefanovic, D.2
  • 42
    • 0036790975 scopus 로고    scopus 로고
    • Intrinsic and extrinsic contributions to stochasticity in gene expression
    • Swain P.S., Elowitz M.B., Siggia E.D. Intrinsic and extrinsic contributions to stochasticity in gene expression. Proc. Nat. Acad. Sci. 2002, 99(20):12795-12800.
    • (2002) Proc. Nat. Acad. Sci. , vol.99 , Issue.20 , pp. 12795-12800
    • Swain, P.S.1    Elowitz, M.B.2    Siggia, E.D.3
  • 43
    • 36849003440 scopus 로고    scopus 로고
    • Noise-limited frequency signal transmission in gene circuits
    • Tan C., Reza F., You L. Noise-limited frequency signal transmission in gene circuits. Biophys. J. 2007, 93:3753-3761.
    • (2007) Biophys. J. , vol.93 , pp. 3753-3761
    • Tan, C.1    Reza, F.2    You, L.3
  • 44
    • 0035902599 scopus 로고    scopus 로고
    • Intrinsic noise in gene regulatory networks
    • Thattai M., van Oudenaarden A. Intrinsic noise in gene regulatory networks. Proc. Nat. Acad. Sci. 2001, 98(15):8614-8619.
    • (2001) Proc. Nat. Acad. Sci. , vol.98 , Issue.15 , pp. 8614-8619
    • Thattai, M.1    van Oudenaarden, A.2
  • 45
    • 0032077377 scopus 로고    scopus 로고
    • From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli
    • Thieffry D., Huerta A.M., Perez-Rueda E., Collado-Vides J. From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli. BioEssays 1998, 20(5):433-440.
    • (1998) BioEssays , vol.20 , Issue.5 , pp. 433-440
    • Thieffry, D.1    Huerta, A.M.2    Perez-Rueda, E.3    Collado-Vides, J.4
  • 47
    • 77954566837 scopus 로고    scopus 로고
    • A critical quantity for noise attenuation in feedback systems
    • Wang L., Xin J., Nie Q. A critical quantity for noise attenuation in feedback systems. PLoS Comput. Biol. 2010, 6(4):e1000764.
    • (2010) PLoS Comput. Biol. , vol.6 , Issue.4
    • Wang, L.1    Xin, J.2    Nie, Q.3
  • 48
  • 50
    • 79960710673 scopus 로고    scopus 로고
    • Towards modular, scalable and optimal design of transcriptional logic systems. Ph.D. Thesis, School of Computing, University of Kent, UK.
    • Zabet, N.R., 2010. Towards modular, scalable and optimal design of transcriptional logic systems. Ph.D. Thesis, School of Computing, University of Kent, UK.
    • (2010)
    • Zabet, N.R.1
  • 51
    • 77953170555 scopus 로고    scopus 로고
    • Computational limits to binary genes
    • Zabet N.R., Chu D.F. Computational limits to binary genes. J. R. Soc. Interface 2010, 7:945-954.
    • (2010) J. R. Soc. Interface , vol.7 , pp. 945-954
    • Zabet, N.R.1    Chu, D.F.2
  • 53
    • 70450286404 scopus 로고    scopus 로고
    • Physical limits of feedback noise-suppression in biological networks
    • Zhang J., Yuan Z., Zhou T. Physical limits of feedback noise-suppression in biological networks. Phys. Biol. 2009, 6(4):046009.
    • (2009) Phys. Biol. , vol.6 , Issue.4 , pp. 046009
    • Zhang, J.1    Yuan, Z.2    Zhou, T.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.