메뉴 건너뛰기




Volumn 109, Issue 42, 2012, Pages 16817-16822

Fine-tuning gene networks using simple sequence repeats

Author keywords

Evolvability; Gene network optimization; Synthetic biology

Indexed keywords

ARTICLE; BACTERIAL GENE; BACTERIAL GENETICS; ESCHERICHIA COLI; FINE TUNING GENE NETWORK; GENE EXPRESSION; GENE MUTATION; GENE SEQUENCE; MOLECULAR GENETICS; MUTAGENESIS; NONHUMAN; PRIORITY JOURNAL; SYNTHETIC BIOLOGY;

EID: 84867631962     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1205693109     Document Type: Article
Times cited : (90)

References (46)
  • 1
    • 15544371346 scopus 로고    scopus 로고
    • Gene regulation at the single-cell level
    • DOI 10.1126/science.1106914
    • Rosenfeld N, Young JW, Alon U, Swain PS, Elowitz MB (2005) Gene regulation at the single-cell level. Science 307:1962-1965. (Pubitemid 40404705)
    • (2005) Science , vol.307 , Issue.5717 , pp. 1962-1965
    • Rosenfeld, N.1    Young, J.W.2    Alon, U.3    Swain, P.S.4    Elowitz, M.B.5
  • 2
    • 34047118521 scopus 로고    scopus 로고
    • Tunability and noise dependence in differentiation dynamics
    • DOI 10.1126/science.1137455
    • Süel GM, Kulkarni RP, Dworkin J, Garcia-Ojalvo J, Elowitz MB (2007) Tunability and noise dependence in differentiation dynamics. Science 315:1716-1719. (Pubitemid 46515626)
    • (2007) Science , vol.315 , Issue.5819 , pp. 1716-1719
    • Suel, G.M.1    Kulkarni, R.P.2    Dworkin, J.3    Garcia-Ojalvo, J.4    Elowitz, M.B.5
  • 3
    • 33845579099 scopus 로고    scopus 로고
    • Fast, cheap and somewhat in control
    • Arkin AP, Fletcher DA (2006) Fast, cheap and somewhat in control. Genome Biol 7:114.
    • (2006) Genome Biol , vol.7 , pp. 114
    • Arkin, A.P.1    Fletcher, D.A.2
  • 4
    • 84863608607 scopus 로고    scopus 로고
    • Scaling up synthetic biology: Do not forget the chassis
    • Danchin A (2012) Scaling up synthetic biology: Do not forget the chassis. FEBS Lett 586:2129-2137.
    • (2012) FEBS Lett , vol.586 , pp. 2129-2137
    • Danchin, A.1
  • 5
    • 71849110893 scopus 로고    scopus 로고
    • Next-generation synthetic gene networks
    • Lu TK, Khalil AS, Collins JJ (2009) Next-generation synthetic gene networks. Nat Biotechnol 27:1139-1150.
    • (2009) Nat Biotechnol , vol.27 , pp. 1139-1150
    • Lu, T.K.1    Khalil, A.S.2    Collins, J.J.3
  • 6
    • 66249088017 scopus 로고    scopus 로고
    • The second wave of synthetic biology: From modules to systems
    • Purnick PE, Weiss R (2009) The second wave of synthetic biology: From modules to systems. Nat Rev Mol Cell Biol 10:410-422.
    • (2009) Nat Rev Mol Cell Biol , vol.10 , pp. 410-422
    • Purnick, P.E.1    Weiss, R.2
  • 7
    • 78650107130 scopus 로고    scopus 로고
    • Prokaryotic gene clusters: A rich toolbox for synthetic biology
    • Fischbach M, Voigt CA (2010) Prokaryotic gene clusters: A rich toolbox for synthetic biology. Biotechnol J 5:1277-1296.
    • (2010) Biotechnol J , vol.5 , pp. 1277-1296
    • Fischbach, M.1    Voigt, C.A.2
  • 8
    • 78650929625 scopus 로고    scopus 로고
    • Tunable signal processing in synthetic MAP kinase cascades
    • O'Shaughnessy EC, Palani S, Collins JJ, Sarkar CA (2011) Tunable signal processing in synthetic MAP kinase cascades. Cell 144:119-131.
    • (2011) Cell , vol.144 , pp. 119-131
    • O'Shaughnessy, E.C.1    Palani, S.2    Collins, J.J.3    Sarkar, C.A.4
  • 9
    • 77952492425 scopus 로고    scopus 로고
    • Tuning and controlling gene expression noise in synthetic gene networks
    • Murphy K, Adams R, Wang X, Balazsi G, Collins J (2010) Tuning and controlling gene expression noise in synthetic gene networks. Nucleic Acids Res 38:2712-2726.
    • (2010) Nucleic Acids Res , vol.38 , pp. 2712-2726
    • Murphy, K.1    Adams, R.2    Wang, X.3    Balazsi, G.4    Collins, J.5
  • 10
    • 77957679279 scopus 로고    scopus 로고
    • Tracking, tuning, and terminating microbial physiology using synthetic riboregulators
    • Callura J, Dwyer D, Isaacs F, Cantor C, Collins J (2010) Tracking, tuning, and terminating microbial physiology using synthetic riboregulators. Proc Natl Acad Sci USA 107:15898-15903.
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 15898-15903
    • Callura, J.1    Dwyer, D.2    Isaacs, F.3    Cantor, C.4    Collins, J.5
  • 11
    • 79952348850 scopus 로고    scopus 로고
    • A synthetic library of RNA control modules for predictable tuning of gene expression in yeast
    • Babiskin AH, Smolke CD (2011) A synthetic library of RNA control modules for predictable tuning of gene expression in yeast. Mol Syst Biol 7:471.
    • (2011) Mol Syst Biol , vol.7 , pp. 471
    • Babiskin, A.H.1    Smolke, C.D.2
  • 12
    • 66149172363 scopus 로고    scopus 로고
    • Diversity-based, model-guided construction of synthetic gene networks with predicted functions
    • Ellis T, Wang X, Collins JJ (2009) Diversity-based, model-guided construction of synthetic gene networks with predicted functions. Nat Biotechnol 27:465-471.
    • (2009) Nat Biotechnol , vol.27 , pp. 465-471
    • Ellis, T.1    Wang, X.2    Collins, J.J.3
  • 13
    • 68949161807 scopus 로고    scopus 로고
    • Programming cells by multiplex genome engineering and accelerated evolution
    • Wang HH, et al. (2009) Programming cells by multiplex genome engineering and accelerated evolution. Nature 460:894-898.
    • (2009) Nature , vol.460 , pp. 894-898
    • Wang, H.H.1
  • 15
    • 77952903892 scopus 로고    scopus 로고
    • Rewiring cells: Synthetic biology as a tool to interrogate the organizational principles of living systems
    • Bashor CJ, Horwitz AA, Peisajovich SG, Lim WA (2010) Rewiring cells: Synthetic biology as a tool to interrogate the organizational principles of living systems. Annu Rev Biophys 39:515-537.
    • (2010) Annu Rev Biophys , vol.39 , pp. 515-537
    • Bashor, C.J.1    Horwitz, A.A.2    Peisajovich, S.G.3    Lim, W.A.4
  • 17
    • 36249017917 scopus 로고    scopus 로고
    • Programming gene expression with combinatorial promoters
    • Cox RS, Surette MG, Elowitz MB (2007) Programming gene expression with combinatorial promoters. Mol Syst Biol 3:145.
    • (2007) Mol Syst Biol , vol.3 , pp. 145
    • Cox, R.S.1    Surette, M.G.2    Elowitz, M.B.3
  • 18
    • 70349964350 scopus 로고    scopus 로고
    • Automated design of synthetic ribosome binding sites to control protein expression
    • Salis HM, Mirsky EA, Voigt CA (2009) Automated design of synthetic ribosome binding sites to control protein expression. Nat Biotechnol 27:946-950.
    • (2009) Nat Biotechnol , vol.27 , pp. 946-950
    • Salis, H.M.1    Mirsky, E.A.2    Voigt, C.A.3
  • 19
  • 20
    • 33747078696 scopus 로고    scopus 로고
    • Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes
    • DOI 10.1038/nbt1226, PII NBT1226
    • Pfleger BF, Pitera DJ, Smolke CD, Keasling JD (2006) Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes. Nat Biotechnol 24:1027-1032. (Pubitemid 44215398)
    • (2006) Nature Biotechnology , vol.24 , Issue.8 , pp. 1027-1032
    • Pfleger, B.F.1    Pitera, D.J.2    Smolke, C.D.3    Keasling, J.D.4
  • 21
    • 84455174703 scopus 로고    scopus 로고
    • Model-driven engineering of RNA devices to quantitatively program gene expression
    • Carothers JM, Goler JA, Juminaga D, Keasling JD (2011) Model-driven engineering of RNA devices to quantitatively program gene expression. Science 334:1716-1719.
    • (2011) Science , vol.334 , pp. 1716-1719
    • Carothers, J.M.1    Goler, J.A.2    Juminaga, D.3    Keasling, J.D.4
  • 23
    • 79961148205 scopus 로고    scopus 로고
    • Tradeoffs and optimality in the evolution of gene regulation
    • Poelwijk FJ, de Vos MGJ, Tans SJ (2011) Tradeoffs and optimality in the evolution of gene regulation. Cell 146:462-470.
    • (2011) Cell , vol.146 , pp. 462-470
    • Poelwijk, F.J.1    De Vos, M.G.J.2    Tans, S.J.3
  • 24
    • 77954811495 scopus 로고    scopus 로고
    • Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction
    • Siegel JB, et al. (2010) Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction. Science 329:309-313.
    • (2010) Science , vol.329 , pp. 309-313
    • Siegel, J.B.1
  • 25
    • 14844364430 scopus 로고    scopus 로고
    • Optimizing genetic circuits by global sensitivity analysis
    • Feng XJ, et al. (2004) Optimizing genetic circuits by global sensitivity analysis. Biophys J 87:2195-2202.
    • (2004) Biophys J , vol.87 , pp. 2195-2202
    • Feng, X.J.1
  • 28
    • 0026544545 scopus 로고
    • The influence of ribosome-binding-site elements on translational efficiency in Bacillus subtilis and Escherichia coli in vivo
    • Vellanoweth RL, Rabinowitz JC (1992) The influence of ribosome-binding-site elements on translational efficiency in Bacillus subtilis and Escherichia coli in vivo. Mol Microbiol 6:1105-1114.
    • (1992) Mol Microbiol , vol.6 , pp. 1105-1114
    • Vellanoweth, R.L.1    Rabinowitz, J.C.2
  • 29
    • 0028584414 scopus 로고
    • Determination of the optimal aligned spacing between the Shine-Dalgarno sequence and the translation initiation codon of Escherichia coli mRNAs
    • Chen H, Bjerknes M, Kumar R, Jay E (1994) Determination of the optimal aligned spacing between the Shine-Dalgarno sequence and the translation initiation codon of Escherichia coli mRNAs. Nucleic Acids Res 22:4953-4957.
    • (1994) Nucleic Acids Res , vol.22 , pp. 4953-4957
    • Chen, H.1    Bjerknes, M.2    Kumar, R.3    Jay, E.4
  • 30
    • 78149432728 scopus 로고    scopus 로고
    • Variable tandem repeats accelerate evolution of coding and regulatory sequences
    • Gemayel R, Vinces MD, Legendre M, Verstrepen KJ (2010) Variable tandem repeats accelerate evolution of coding and regulatory sequences. Annu Rev Genet 44:445-477.
    • (2010) Annu Rev Genet , vol.44 , pp. 445-477
    • Gemayel, R.1    Vinces, M.D.2    Legendre, M.3    Verstrepen, K.J.4
  • 32
    • 62549083590 scopus 로고    scopus 로고
    • Negative autoregulation linearizes the dose-response and suppresses the heterogeneity of gene expression
    • Nevozhay D, Adams RM, Murphy KF, Josic K, Balázsi G (2009) Negative autoregulation linearizes the dose-response and suppresses the heterogeneity of gene expression. Proc Natl Acad Sci USA 106:5123-5128.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 5123-5128
    • Nevozhay, D.1    Adams, R.M.2    Murphy, K.F.3    Josic, K.4    Balázsi, G.5
  • 33
    • 0034688174 scopus 로고    scopus 로고
    • Construction of a genetic toggle switch in Escherichia coli
    • DOI 10.1038/35002131
    • Gardner TS, Cantor CR, Collins JJ (2000) Construction of a genetic toggle switch in Escherichia coli. Nature 403:339-342. (Pubitemid 30062394)
    • (2000) Nature , vol.403 , Issue.6767 , pp. 339-342
    • Gardner, T.S.1    Cantor, C.R.2    Collins, J.J.3
  • 34
    • 77956520011 scopus 로고    scopus 로고
    • Functional roles for noise in genetic circuits
    • Eldar A, Elowitz MB (2010) Functional roles for noise in genetic circuits. Nature 467:167-173.
    • (2010) Nature , vol.467 , pp. 167-173
    • Eldar, A.1    Elowitz, M.B.2
  • 36
    • 40849145522 scopus 로고    scopus 로고
    • Plasmid-borne prokaryotic gene expression: Sources of variability and quantitative system characterization
    • Bagh S, et al. (2008) Plasmid-borne prokaryotic gene expression: Sources of variability and quantitative system characterization. Phys Rev E 77:021919.
    • (2008) Phys Rev e , vol.77 , pp. 021919
    • Bagh, S.1
  • 37
    • 68849127635 scopus 로고    scopus 로고
    • Analysis of genetic toggle switch systems encoded on plasmids
    • Loinger A, Biham O (2009) Analysis of genetic toggle switch systems encoded on plasmids. Phys Rev Lett 103:068104.
    • (2009) Phys Rev Lett , vol.103 , pp. 068104
    • Loinger, A.1    Biham, O.2
  • 38
    • 0345687900 scopus 로고    scopus 로고
    • Slipped-Strand Mispairing Can Function as a Phase Variation Mechanism in Escherichia coli
    • DOI 10.1128/JB.185.23.6990-6994.2003
    • Torres-Cruz J, van der Woude MW (2003) Slipped-strand mispairing can function as a phase variation mechanism in Escherichia coli. J Bacteriol 185:6990-6994. (Pubitemid 37444501)
    • (2003) Journal of Bacteriology , vol.185 , Issue.23 , pp. 6990-6994
    • Torres-Cruz, J.1    Van Der, W.M.W.2
  • 39
    • 0023649836 scopus 로고
    • High frequencies of short frameshifts in poly-CA/TG tandem repeats borne by bacteriophage M13 in Escherichia coli K-12
    • Levinson G, Gutman GA (1987) High frequencies of short frameshifts in poly-CA/TG tandem repeats borne by bacteriophage M13 in Escherichia coli K-12. Nucleic Acids Res 15:5323-5338.
    • (1987) Nucleic Acids Res , vol.15 , pp. 5323-5338
    • Levinson, G.1    Gutman, G.A.2
  • 40
    • 33845648557 scopus 로고    scopus 로고
    • Bacterial contingency loci: The role of simple sequence DNA repeats in bacterial adaptation
    • van Belkum A, Scherer S, van Alphen L, Verbrugh H (2006) Bacterial contingency loci: The role of simple sequence DNA repeats in bacterial adaptation. Annu Rev Genet 40:307-333.
    • (2006) Annu Rev Genet , vol.40 , pp. 307-333
    • Van Belkum, A.1    Scherer, S.2    Van Alphen, L.3    Verbrugh, H.4
  • 41
    • 0029975889 scopus 로고    scopus 로고
    • Repression of lac promoter as a function of distance, phase and quality of an auxiliary lac operator
    • Müller J, Oehler S, Müller-Hill B (1996) Repression of lac promoter as a function of distance, phase and quality of an auxiliary lac operator. J Mol Biol 257:21-29.
    • (1996) J Mol Biol , vol.257 , pp. 21-29
    • Müller, J.1    Oehler, S.2    Müller-Hill, B.3
  • 42
    • 0030068124 scopus 로고    scopus 로고
    • Destabilization of simple repetitive DNA sequences by transcription in yeast
    • Wierdl M, Greene CN, Datta A, Jinks-Robertson S, Petes TD (1996) Destabilization of simple repetitive DNA sequences by transcription in yeast. Genetics 143:713-721. (Pubitemid 26001091)
    • (1996) Genetics , vol.143 , Issue.2 , pp. 713-721
    • Wierdl, M.1    Greene, C.N.2    Datta, A.3    Jinks-Robertson, S.4    Petes, T.D.5
  • 43
    • 0035133535 scopus 로고    scopus 로고
    • An upstream AG determines whether a downstream AG is selected during catalytic step II of splicing
    • DOI 10.1128/MCB.21.5.1509-1514.2001
    • Chua K, Reed R (2001) An upstream AG determines whether a downstream AG is selected during catalytic step II of splicing. Mol Cell Biol 21:1509-1514. (Pubitemid 32156371)
    • (2001) Molecular and Cellular Biology , vol.21 , Issue.5 , pp. 1509-1514
    • Chua, K.1    Reed, R.2
  • 44
    • 0032575051 scopus 로고    scopus 로고
    • A broad-host-range F1p-FRT recombination system for site-specific excision of chromosomally-located DNA sequences: Application for isolation of unmarked Pseudomonas aeruginosa mutants
    • DOI 10.1016/S0378-1119(98)00130-9, PII S0378111998001309
    • Hoang TT, Karkhoff-Schweizer RR, Kutchma AJ, Schweizer HP (1998) A broad-host-range Flp-FRT recombination system for site-specific excision of chromosomally-located DNA sequences: Application for isolation of unmarked Pseudomonas aeruginosa mutants. Gene 212:77-86. (Pubitemid 28269135)
    • (1998) Gene , vol.212 , Issue.1 , pp. 77-86
    • Hoang, T.T.1    Karkhoff-Schweizer, R.R.2    Kutchma, A.J.3    Schweizer, H.P.4
  • 45
    • 31544450286 scopus 로고    scopus 로고
    • Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: The Keio collection
    • 2006.0008
    • Baba T, et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: The Keio collection. Mol Syst Biol 2:2006.0008.
    • (2006) Mol Syst Biol , vol.2
    • Baba, T.1
  • 46
    • 67349270900 scopus 로고    scopus 로고
    • Enzymatic assembly of DNA molecules up to several hundred kilobases
    • Gibson DG, et al. (2009) Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods 6:343-345.
    • (2009) Nat Methods , vol.6 , pp. 343-345
    • Gibson, D.G.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.