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Volumn 4, Issue 2, 2015, Pages 107-115

Designing RNA-based genetic control systems for efficient production from engineered metabolic pathways

Author keywords

dynamic control; metabolic engineering; RNA device; simulation; synthetic biology

Indexed keywords

RNA; OXIDOREDUCTASE; STYRENE;

EID: 84924258069     PISSN: None     EISSN: 21615063     Source Type: Journal    
DOI: 10.1021/sb400201u     Document Type: Article
Times cited : (48)

References (39)
  • 1
    • 30344484891 scopus 로고    scopus 로고
    • Internal-sensing machinery directs the activity of the regulatory network in Escherichia coli
    • Martínez-Antonio, A., Janga, S. C., Salgado, H., and Collado-Vides, J. (2006) Internal-sensing machinery directs the activity of the regulatory network in Escherichia coli Trends Microbiol. 14, 22-7
    • (2006) Trends Microbiol. , vol.14 , pp. 22-27
    • Martínez-Antonio, A.1    Janga, S.C.2    Salgado, H.3    Collado-Vides, J.4
  • 3
    • 80053172430 scopus 로고    scopus 로고
    • Engineering microbes for tolerance to next-generation biofuels
    • Dunlop, M. J. (2011) Engineering microbes for tolerance to next-generation biofuels Biotechnol. Biofuels 4, 32
    • (2011) Biotechnol. Biofuels , vol.4 , pp. 32
    • Dunlop, M.J.1
  • 4
    • 0034024497 scopus 로고    scopus 로고
    • Improving lycopene production in Escherichia coli by engineering metabolic control
    • Farmer, W. R. and Liao, J. C. (2000) Improving lycopene production in Escherichia coli by engineering metabolic control Nat. Biotechnol. 18, 533-7
    • (2000) Nat. Biotechnol. , vol.18 , pp. 533-537
    • Farmer, W.R.1    Liao, J.C.2
  • 5
    • 84859633048 scopus 로고    scopus 로고
    • Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids
    • Zhang, F., Carothers, J. M., and Keasling, J. D. (2012) Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids Nat. Biotechnol. 30, 354-9
    • (2012) Nat. Biotechnol. , vol.30 , pp. 354-359
    • Zhang, F.1    Carothers, J.M.2    Keasling, J.D.3
  • 7
    • 84875857527 scopus 로고    scopus 로고
    • Synthetic feedback loop model for increasing microbial biofuel production using a biosensor
    • Harrison, M. E. and Dunlop, M. J. (2012) Synthetic feedback loop model for increasing microbial biofuel production using a biosensor Front. Microbiol. 3, 360
    • (2012) Front. Microbiol. , vol.3 , pp. 360
    • Harrison, M.E.1    Dunlop, M.J.2
  • 8
    • 84924254803 scopus 로고    scopus 로고
    • Programming gene expression by engineering transcript stability control and processing in bacteria
    • in press.
    • Stevens, J. T. and Carothers, J. M. Programming gene expression by engineering transcript stability control and processing in bacteria. Synth. Biol. 2014, in press.
    • (2014) Synth. Biol.
    • Stevens, J.T.1    Carothers, J.M.2
  • 9
    • 0025074907 scopus 로고
    • In vitro selection of RNA molecules that bind specific ligands
    • Ellington, A. D. and Szostak, J. W. (1990) In vitro selection of RNA molecules that bind specific ligands Nature 346, 818-22
    • (1990) Nature , vol.346 , pp. 818-822
    • Ellington, A.D.1    Szostak, J.W.2
  • 10
    • 84455174703 scopus 로고    scopus 로고
    • Model-driven engineering of RNA devices to quantitatively program gene expression
    • Carothers, J. M., Goler, J. A., Juminaga, D., and Keasling, J. D. (2011) Model-driven engineering of RNA devices to quantitatively program gene expression Science 334, 1716-9
    • (2011) Science , vol.334 , pp. 1716-1719
    • Carothers, J.M.1    Goler, J.A.2    Juminaga, D.3    Keasling, J.D.4
  • 11
    • 77952679687 scopus 로고    scopus 로고
    • Genetic control of mammalian T-cell proliferation with synthetic RNA regulatory systems
    • Chen, Y. Y., Jensen, M. C., and Smolke, C. D. (2010) Genetic control of mammalian T-cell proliferation with synthetic RNA regulatory systems Proc. Natl. Acad. Sci. U.S.A. 107, 8531-6
    • (2010) Proc. Natl. Acad. Sci. U.S.A. , vol.107 , pp. 8531-8536
    • Chen, Y.Y.1    Jensen, M.C.2    Smolke, C.D.3
  • 12
    • 84862167101 scopus 로고    scopus 로고
    • High-throughput enzyme evolution in Saccharomyces cerevisiae using a synthetic RNA switch
    • Michener, J. K. and Smolke, C. D. (2012) High-throughput enzyme evolution in Saccharomyces cerevisiae using a synthetic RNA switch Metab. Eng. 14, 306-16
    • (2012) Metab. Eng. , vol.14 , pp. 306-316
    • Michener, J.K.1    Smolke, C.D.2
  • 13
    • 54249113318 scopus 로고    scopus 로고
    • Higher-order cellular information processing with synthetic RNA devices
    • Win, M. N. and Smolke, C. D. (2008) Higher-order cellular information processing with synthetic RNA devices Science 322, 456-60
    • (2008) Science , vol.322 , pp. 456-460
    • Win, M.N.1    Smolke, C.D.2
  • 14
    • 84879164975 scopus 로고    scopus 로고
    • Synthetic RNA devices to expedite the evolution of metabolite-producing microbes
    • Yang, J., Seo, S. W., Jang, S., Shin, S.-I., Lim, C. H., Roh, T.-Y., and Jung, G. Y. (2013) Synthetic RNA devices to expedite the evolution of metabolite-producing microbes Nat. Commun. 4, 1413
    • (2013) Nat. Commun. , vol.4 , pp. 1413
    • Yang, J.1    Seo, S.W.2    Jang, S.3    Shin, S.-I.4    Lim, C.H.5    Roh, T.-Y.6    Jung, G.Y.7
  • 16
    • 34249686497 scopus 로고    scopus 로고
    • Functional expression of prokaryotic and eukaryotic genes in Escherichia coli for conversion of glucose to p-hydroxystyrene
    • Qi, W. W., Vannelli, T., Breinig, S., Ben-Bassat, A., Gatenby, A. A., Haynie, S. L., and Sariaslani, F. S. (2007) Functional expression of prokaryotic and eukaryotic genes in Escherichia coli for conversion of glucose to p-hydroxystyrene Metab. Eng. 9, 268-76
    • (2007) Metab. Eng. , vol.9 , pp. 268-276
    • Qi, W.W.1    Vannelli, T.2    Breinig, S.3    Ben-Bassat, A.4    Gatenby, A.A.5    Haynie, S.L.6    Sariaslani, F.S.7
  • 18
    • 0033156024 scopus 로고    scopus 로고
    • Use and limitations of modular metabolic control analysis in medicine and biotechnology
    • Schuster, S. (1999) Use and limitations of modular metabolic control analysis in medicine and biotechnology Metab. Eng. 1, 232-42
    • (1999) Metab. Eng. , vol.1 , pp. 232-242
    • Schuster, S.1
  • 19
    • 84873739129 scopus 로고    scopus 로고
    • A computational pipeline for identifying kinetic motifs to aid in the design and improvement of synthetic gene circuits
    • Chiang, A. W. T. and Hwang, M.-J. (2013) A computational pipeline for identifying kinetic motifs to aid in the design and improvement of synthetic gene circuits BMC Bioinf. 14 (Suppl 1) S5
    • (2013) BMC Bioinf. , vol.14 , pp. 5
    • Chiang, A.W.T.1    Hwang, M.-J.2
  • 20
    • 79951565301 scopus 로고    scopus 로고
    • Design, construction and characterization of a set of insulated bacterial promoters
    • Davis, J. H., Rubin, A. J., and Sauer, R. T. (2011) Design, construction and characterization of a set of insulated bacterial promoters Nucleic Acids Res. 39, 1131-41
    • (2011) Nucleic Acids Res. , vol.39 , pp. 1131-1141
    • Davis, J.H.1    Rubin, A.J.2    Sauer, R.T.3
  • 21
    • 84897406062 scopus 로고    scopus 로고
    • Predictive combinatorial design of mRNA translation initiation regions for systematic optimization of gene expression levels
    • Seo, S. W., Yang, J.-S., Cho, H.-S., Yang, J., Kim, S. C., Park, J. M., Kim, S., and Jung, G. Y. (2014) Predictive combinatorial design of mRNA translation initiation regions for systematic optimization of gene expression levels Sci. Rep. 4, 4515
    • (2014) Sci. Rep. , vol.4 , pp. 4515
    • Seo, S.W.1    Yang, J.-S.2    Cho, H.-S.3    Yang, J.4    Kim, S.C.5    Park, J.M.6    Kim, S.7    Jung, G.Y.8
  • 22
    • 84873596341 scopus 로고    scopus 로고
    • Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs
    • Na, D., Yoo, S. M., Chung, H., Park, H., Park, J. H., and Lee, S. Y. (2013) Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs Nat. Biotechnol. 31, 170-4
    • (2013) Nat. Biotechnol. , vol.31 , pp. 170-174
    • Na, D.1    Yoo, S.M.2    Chung, H.3    Park, H.4    Park, J.H.5    Lee, S.Y.6
  • 23
    • 0034688173 scopus 로고    scopus 로고
    • A synthetic oscillatory network of transcriptional regulators
    • Elowitz, M. B. and Leibler, S. (2000) A synthetic oscillatory network of transcriptional regulators Nature 403, 335-8
    • (2000) Nature , vol.403 , pp. 335-338
    • Elowitz, M.B.1    Leibler, S.2
  • 24
    • 0018468345 scopus 로고
    • Three methods for selecting values of input variables in the analysis of output from a computer code
    • Mckay, M. D. and Beckman, R. J. (1979) Three methods for selecting values of input variables in the analysis of output from a computer code Technometrics 21, 239-245
    • (1979) Technometrics , vol.21 , pp. 239-245
    • McKay, M.D.1    Beckman, R.J.2
  • 27
    • 84924267695 scopus 로고    scopus 로고
    • Computational Design of RNA Parts, Devices, and Transcripts with Kinetic Folding Algorithms Implemented on Multiprocessor Clusters
    • Springer, New York.
    • Thimmaiah, T., Voje, W. E., and Carothers, J. M. (2014) Computational Design of RNA Parts, Devices, and Transcripts with Kinetic Folding Algorithms Implemented on Multiprocessor Clusters, in Computational Methods in Synthetic Biology, Springer, New York.
    • (2014) Computational Methods in Synthetic Biology
    • Thimmaiah, T.1    Voje, W.E.2    Carothers, J.M.3
  • 28
    • 85006962679 scopus 로고    scopus 로고
    • Kinetic folding design of aptazyme-regulated expression devices (aREDs) as riboswitches for metabolic engineering
    • in press.
    • Sparkman-Yager, D., Correa-Rojas, R. A., and Carothers, J. M. Kinetic folding design of aptazyme-regulated expression devices (aREDs) as riboswitches for metabolic engineering. Methods Enzymol. 2014, in press.
    • (2014) Methods Enzymol.
    • Sparkman-Yager, D.1    Correa-Rojas, R.A.2    Carothers, J.M.3
  • 29
    • 84934439274 scopus 로고    scopus 로고
    • Dual-selection for evolution of in vivo functional aptazymes as riboswitch parts
    • Goler, J. A., Carothers, J. M., and Keasling, J. D. (2014) Dual-selection for evolution of in vivo functional aptazymes as riboswitch parts Methods Mol. Biol. 1111, 221-35
    • (2014) Methods Mol. Biol. , vol.1111 , pp. 221-235
    • Goler, J.A.1    Carothers, J.M.2    Keasling, J.D.3
  • 30
    • 34249079154 scopus 로고    scopus 로고
    • Network motifs: Theory and experimental approaches
    • Alon, U. (2007) Network motifs: theory and experimental approaches Nat. Rev. Genet. 8, 450-61
    • (2007) Nat. Rev. Genet. , vol.8 , pp. 450-461
    • Alon, U.1
  • 31
    • 84874687019 scopus 로고    scopus 로고
    • Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression
    • Qi, L. S., Larson, M. H., Gilbert, L. A., Doudna, J. A., Weissman, J. S., Arkin, A. P., and Lim, W. A. (2013) Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression Cell 152, 1173-83
    • (2013) Cell , vol.152 , pp. 1173-1183
    • Qi, L.S.1    Larson, M.H.2    Gilbert, L.A.3    Doudna, J.A.4    Weissman, J.S.5    Arkin, A.P.6    Lim, W.A.7
  • 32
    • 84881558283 scopus 로고    scopus 로고
    • Design-driven, multi-use research agendas to enable applied synthetic biology for global health
    • Carothers, J. M. (2013) Design-driven, multi-use research agendas to enable applied synthetic biology for global health Syst. Synth. Biol. 7, 79-86
    • (2013) Syst. Synth. Biol. , vol.7 , pp. 79-86
    • Carothers, J.M.1
  • 34
    • 0001811061 scopus 로고
    • ODEPACK, A Systematized Collection of ODE Solvers
    • (Stepleman, R. S. Ed.) North-Holland, Amsterdam, The Netherlands.
    • Hindmarsh, A. (1983) ODEPACK, A Systematized Collection of ODE Solvers, in IMACS Transactions on Scientific Computation (Stepleman, R. S., Ed.) Vol. 1, pp 55-64, North-Holland, Amsterdam, The Netherlands.
    • (1983) IMACS Transactions on Scientific Computation , vol.1 , pp. 55-64
    • Hindmarsh, A.1
  • 37
    • 34250875706 scopus 로고    scopus 로고
    • Initiation of RNA decay in Escherichia coli by 5′ pyrophosphate removal
    • Celesnik, H., Deana, A., and Belasco, J. G. (2007) Initiation of RNA decay in Escherichia coli by 5′ pyrophosphate removal Mol. Cell 27, 79-90
    • (2007) Mol. Cell , vol.27 , pp. 79-90
    • Celesnik, H.1    Deana, A.2    Belasco, J.G.3
  • 39
    • 84875457350 scopus 로고    scopus 로고
    • Bacterial small RNA-based negative regulation: Hfq and its accomplices
    • De Lay, N., Schu, D. J., and Gottesman, S. (2013) Bacterial small RNA-based negative regulation: Hfq and its accomplices J. Biol. Chem. 288, 7996-8003
    • (2013) J. Biol. Chem. , vol.288 , pp. 7996-8003
    • De Lay, N.1    Schu, D.J.2    Gottesman, S.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.