메뉴 건너뛰기




Volumn 3, Issue 6, 2014, Pages 416-425

Gene circuit performance characterization and resource usage in a cell-free "breadboard"

Author keywords

biological circuit prototyping; cell free systems; crosstalk; in vitro synthetic biology; RNA aptamer

Indexed keywords

DNA; MESSENGER RNA; NUCLEOSIDE TRIPHOSPHATE; RNA POLYMERASE; APTAMER; DNA DIRECTED RNA POLYMERASE; SYNTHETIC DNA;

EID: 84903211692     PISSN: None     EISSN: 21615063     Source Type: Journal    
DOI: 10.1021/sb400203p     Document Type: Article
Times cited : (142)

References (47)
  • 1
    • 84864258391 scopus 로고    scopus 로고
    • Synthetic biology: An emerging engineering discipline
    • Cheng, A. A. and Lu, T. K. (2012) Synthetic biology: An emerging engineering discipline Annu. Rev. Biomed. Eng. 14, 155-178
    • (2012) Annu. Rev. Biomed. Eng. , vol.14 , pp. 155-178
    • Cheng, A.A.1    Lu, T.K.2
  • 2
    • 84863322344 scopus 로고    scopus 로고
    • Contextualizing context for synthetic biology - Identifying causes of failure of synthetic biological systems
    • Cardinale, S. and Arkin, A. P. (2012) Contextualizing context for synthetic biology - Identifying causes of failure of synthetic biological systems Biotechnol. J. 7, 856-866
    • (2012) Biotechnol. J. , vol.7 , pp. 856-866
    • Cardinale, S.1    Arkin, A.P.2
  • 3
    • 84869462746 scopus 로고    scopus 로고
    • Insulating gene circuits from context by RNA processing
    • Bashor, C. J. and Collins, J. J. (2012) Insulating gene circuits from context by RNA processing Nat. Biotechnol. 30, 1061-1062
    • (2012) Nat. Biotechnol. , vol.30 , pp. 1061-1062
    • Bashor, C.J.1    Collins, J.J.2
  • 4
    • 84880772006 scopus 로고    scopus 로고
    • Effects of genetic variation on the E coli host-circuit interface
    • Cardinale, S., Joachimiak, M. P., and Arkin, A. P. (2013) Effects of genetic variation on the E. coli host-circuit interface Cell Rep. 4, 231-237
    • (2013) Cell Rep. , vol.4 , pp. 231-237
    • Cardinale, S.1    Joachimiak, M.P.2    Arkin, A.P.3
  • 5
    • 77955591445 scopus 로고    scopus 로고
    • Oscillations by minimal bacterial suicide circuits reveal hidden facets of host-circuit physiology
    • Marguet, P., Tanouchi, Y., Spitz, E., Smith, C., and You, L. (2010) Oscillations by minimal bacterial suicide circuits reveal hidden facets of host-circuit physiology PLoS ONE 5, e11909
    • (2010) PLoS ONE , vol.5 , pp. 11909
    • Marguet, P.1    Tanouchi, Y.2    Spitz, E.3    Smith, C.4    You, L.5
  • 6
    • 70350324632 scopus 로고    scopus 로고
    • Emergent bistability by a growth-modulating positive feedback circuit
    • Tan, C., Marguet, P., and You, L. (2009) Emergent bistability by a growth-modulating positive feedback circuit Nat. Chem. Biol. 5, 842-848
    • (2009) Nat. Chem. Biol. , vol.5 , pp. 842-848
    • Tan, C.1    Marguet, P.2    You, L.3
  • 7
    • 78649788244 scopus 로고    scopus 로고
    • Efficient cell-free expression with the endogenous E coli RNA polymerase and sigma factor 70
    • Shin, J. and Noireaux, V. (2010) Efficient cell-free expression with the endogenous E. coli RNA polymerase and sigma factor 70 J. Biol. Eng. 4, 8
    • (2010) J. Biol. Eng. , vol.4 , pp. 8
    • Shin, J.1    Noireaux, V.2
  • 8
    • 84863610029 scopus 로고    scopus 로고
    • An E coli cell-free expression toolbox: Application to synthetic gene circuits and artificial cells
    • Shin, J. and Noireaux, V. (2012) An E. coli cell-free expression toolbox: Application to synthetic gene circuits and artificial cells ACS Synth. Biol. 1 (1) 29-41
    • (2012) ACS Synth. Biol. , vol.1 , Issue.1 , pp. 29-41
    • Shin, J.1    Noireaux, V.2
  • 9
    • 84899918637 scopus 로고    scopus 로고
    • Linear DNA for rapid prototyping of synthetic biological circuits in an Escherichia coli based TX-TL cell-free system
    • 10.1021/sb400131a
    • Sun, Z. Z., Yeung, E., Hayes, C. A., Noireaux, V., and Murray, R. M. (2013) Linear DNA for rapid prototyping of synthetic biological circuits in an Escherichia coli based TX-TL cell-free system ACS Synth. Biol. 10.1021/sb400131a
    • (2013) ACS Synth. Biol.
    • Sun, Z.Z.1    Yeung, E.2    Hayes, C.A.3    Noireaux, V.4    Murray, R.M.5
  • 10
    • 84902337814 scopus 로고    scopus 로고
    • An in silico modeling toolbox for rapid prototyping of circuits in a biomolecular "breadboard" system
    • Florence, Italy.
    • Tuza, Z., Singhal, V., Kim, J., and Murray, R. M. An in silico modeling toolbox for rapid prototyping of circuits in a biomolecular " breadboard" system. 52nd IEEE Conference on Decision and Control (CDC). Florence, Italy, 2013.
    • (2013) 52nd IEEE Conference on Decision and Control (CDC)
    • Tuza, Z.1    Singhal, V.2    Kim, J.3    Murray, R.M.4
  • 11
    • 83255164998 scopus 로고    scopus 로고
    • Cell-free synthetic biology: Thinking outside the cell
    • Hodgman, C. E. and Jewett, M. C. (2012) Cell-free synthetic biology: Thinking outside the cell Metab. Eng. 14, 261-269
    • (2012) Metab. Eng. , vol.14 , pp. 261-269
    • Hodgman, C.E.1    Jewett, M.C.2
  • 12
    • 84876382897 scopus 로고    scopus 로고
    • Validation of an entirely in vitro approach for rapid prototyping of DNA regulatory elements for synthetic biology
    • Chappell, J., Jensen, K., and Freemont, P. S. (2013) Validation of an entirely in vitro approach for rapid prototyping of DNA regulatory elements for synthetic biology Nucleic Acids Res. 41, 3471-3481
    • (2013) Nucleic Acids Res. , vol.41 , pp. 3471-3481
    • Chappell, J.1    Jensen, K.2    Freemont, P.S.3
  • 14
    • 79251480753 scopus 로고    scopus 로고
    • Coarse-grained dynamics of protein synthesis in a cell-free system
    • Karzbrun, E., Shin, J., Bar-Ziv, R., and Noireaux, V. (2011) Coarse-grained dynamics of protein synthesis in a cell-free system Phys. Rev. Lett. 106, 048104
    • (2011) Phys. Rev. Lett. , vol.106 , pp. 048104
    • Karzbrun, E.1    Shin, J.2    Bar-Ziv, R.3    Noireaux, V.4
  • 16
    • 84988041776 scopus 로고    scopus 로고
    • Modeling the effects of compositional context on promoter activity in an E coli extract based transcription-translation system
    • submitted
    • Yeung, E., Ng, A., Kim, J., Sun, Z. Z., and Murray, R. M. (2014) Modeling the effects of compositional context on promoter activity in an E. coli extract based transcription-translation system. 53rd IEEE Conference on Decision and Control (CDC), submitted.
    • (2014) 53rd IEEE Conference on Decision and Control (CDC)
    • Yeung, E.1    Ng, A.2    Kim, J.3    Sun, Z.Z.4    Murray, R.M.5
  • 17
    • 84896951733 scopus 로고    scopus 로고
    • The Spinach RNA aptamer as a characterization tool for synthetic biology
    • Pothoulakis, G., Ceroni, F., Reeve, B., and Ellis, T. (2013) The Spinach RNA aptamer as a characterization tool for synthetic biology ACS Synth. Biol. 3 (3) 182-187
    • (2013) ACS Synth. Biol. , vol.3 , Issue.3 , pp. 182-187
    • Pothoulakis, G.1    Ceroni, F.2    Reeve, B.3    Ellis, T.4
  • 19
    • 84860443532 scopus 로고    scopus 로고
    • Experiment and mathematical modeling of gene expression dynamics in a cell-free system
    • Stögbauer, T., Windhager, L., Zimmer, R., and Rädler, J. O. (2012) Experiment and mathematical modeling of gene expression dynamics in a cell-free system Integr. Biol. 4, 494-501
    • (2012) Integr. Biol. , vol.4 , pp. 494-501
    • Stögbauer, T.1    Windhager, L.2    Zimmer, R.3    Rädler, J.O.4
  • 20
    • 4344670572 scopus 로고    scopus 로고
    • Substrate replenishment extends protein synthesis with an in vitro translation system designed to mimic the cytoplasm
    • DOI 10.1002/bit.20139
    • Jewett, M. C. and Swartz, J. R. (2004) Substrate replenishment extends protein synthesis with an in vitro translation system designed to mimic the cytoplasm Biotechnol. Bioeng. 87, 465-472 (Pubitemid 39150047)
    • (2004) Biotechnology and Bioengineering , vol.87 , Issue.4 , pp. 465-472
    • Jewett, M.C.1    Swartz, J.R.2
  • 21
    • 0033404584 scopus 로고    scopus 로고
    • Prolonging cell-free protein synthesis with a novel ATP regeneration system
    • DOI 10.1002/(SICI)1097-0290(1999)66:3<180::AID-BIT6>3.0.CO;2-S
    • Kim, D. M. and Swartz, J. R. (1999) Prolonging cell-free protein synthesis with a novel ATP regeneration system Biotechnol. Bioeng. 66, 180-188 (Pubitemid 30010342)
    • (1999) Biotechnology and Bioengineering , vol.66 , Issue.3 , pp. 180-188
    • Kim, D.-M.1    Swartz, J.R.2
  • 22
    • 84882666602 scopus 로고    scopus 로고
    • Real-time mRNA measurement during an in vitro transcription and translation reaction using binary probes
    • Niederholtmeyer, H., Xu, L., and Maerkl, S. J. (2013) Real-time mRNA measurement during an in vitro transcription and translation reaction using binary probes ACS Synth. Biol. 2, 411-417
    • (2013) ACS Synth. Biol. , vol.2 , pp. 411-417
    • Niederholtmeyer, H.1    Xu, L.2    Maerkl, S.J.3
  • 23
    • 84886838580 scopus 로고    scopus 로고
    • Protocols for implementing an Escherichia coli based TX-TL cell-free expression system for synthetic biology
    • Sun, Z. Z., Hayes, C. A., Shin, J., Caschera, F., Murray, R. M., and Noireaux, V. (2013) Protocols for implementing an Escherichia coli based TX-TL cell-free expression system for synthetic biology J. Vis. Exp. 79, e50762
    • (2013) J. Vis. Exp. , vol.79 , pp. 50762
    • Sun, Z.Z.1    Hayes, C.A.2    Shin, J.3    Caschera, F.4    Murray, R.M.5    Noireaux, V.6
  • 25
    • 84883495741 scopus 로고    scopus 로고
    • Biomolecular resource utilization in elementary cell-free gene circuits
    • Washington, DC
    • Siegal-Gaskins, D., Noireaux, V., and Murray, R. M. Biomolecular resource utilization in elementary cell-free gene circuits. American Control Conference (ACC), Washington, DC, 2013; pp 1531-1536.
    • (2013) American Control Conference (ACC) , pp. 1531-1536
    • Siegal-Gaskins, D.1    Noireaux, V.2    Murray, R.M.3
  • 27
    • 78449268845 scopus 로고    scopus 로고
    • Interdependence of cell growth and gene expression: Origins and consequences
    • Scott, M., Gunderson, C. W., Mateescu, E. M., Zhang, Z., and Hwa, T. (2010) Interdependence of cell growth and gene expression: origins and consequences Science 330, 1099-1102
    • (2010) Science , vol.330 , pp. 1099-1102
    • Scott, M.1    Gunderson, C.W.2    Mateescu, E.M.3    Zhang, Z.4    Hwa, T.5
  • 30
    • 80055071250 scopus 로고    scopus 로고
    • The role of tRNA and ribosome competition in coupling the expression of different mRNAs in Saccharomyces cerevisiae
    • Chu, D., Barnes, D. J., and von der Haar, T. (2011) The role of tRNA and ribosome competition in coupling the expression of different mRNAs in Saccharomyces cerevisiae Nucleic Acids Res. 39, 6705-6714
    • (2011) Nucleic Acids Res. , vol.39 , pp. 6705-6714
    • Chu, D.1    Barnes, D.J.2    Von Der Haar, T.3
  • 31
    • 84855481443 scopus 로고    scopus 로고
    • Competition for catalytic resources alters biological network dynamics
    • Rondelez, Y. (2012) Competition for catalytic resources alters biological network dynamics Phys. Rev. Lett. 108, 018102
    • (2012) Phys. Rev. Lett. , vol.108 , pp. 018102
    • Rondelez, Y.1
  • 32
    • 0027250549 scopus 로고
    • Synthesis of proteins in Escherichia coli is limited by the concentration of free ribosomes. Expression from reporter genes does not always reflect functional mRNA levels
    • DOI 10.1006/jmbi.1993.1319
    • Vind, J., Sørensen, M. A., Rasmussen, M. D., and Pedersen, S. (1993) Synthesis of proteins in Escherichia coli is limited by the concentration of free ribosomes. Expression from reporter genes does not always reflect functional mRNA levels J. Mol. Biol. 231, 678-688 (Pubitemid 23211307)
    • (1993) Journal of Molecular Biology , vol.231 , Issue.3 , pp. 678-688
    • Vind, J.1    Sorensen, M.A.2    Rasmussen, M.D.3    Pedersen, S.4
  • 33
    • 49349113285 scopus 로고    scopus 로고
    • Ribosome collisions and translation efficiency: Optimization by codon usage and mRNA destabilization
    • Mitarai, N., Sneppen, K., and Pedersen, S. (2008) Ribosome collisions and translation efficiency: Optimization by codon usage and mRNA destabilization J. Mol. Biol. 382, 236-245
    • (2008) J. Mol. Biol. , vol.382 , pp. 236-245
    • Mitarai, N.1    Sneppen, K.2    Pedersen, S.3
  • 34
    • 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
    • Sørensen, M. A. and Pedersen, S. (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 (Pubitemid 121004006)
    • (1991) Journal of Molecular Biology , vol.222 , Issue.2 , pp. 265-280
    • Sorensen, M.A.1    Pedersen, S.2
  • 35
    • 27644482393 scopus 로고    scopus 로고
    • Lost in translation: The influence of ribosomes on bacterial mRNA decay
    • DOI 10.1101/gad.1348805
    • Deana, A. and Belasco, J. G. (2005) Lost in translation: the influence of ribosomes on bacterial mRNA decay Genes Dev. 19, 2526-2533 (Pubitemid 41565972)
    • (2005) Genes and Development , vol.19 , Issue.21 , pp. 2526-2533
    • Deana, A.1    Belasco, J.G.2
  • 36
    • 79952009085 scopus 로고    scopus 로고
    • The functional half-life of an mRNA depends on the ribosome spacing in an early coding region
    • Pedersen, M., Nissen, S., Mitarai, N., Lo Svenningsen, S., Sneppen, K., and Pedersen, S. (2011) The functional half-life of an mRNA depends on the ribosome spacing in an early coding region J. Mol. Biol. 407, 35-44
    • (2011) J. Mol. Biol. , vol.407 , pp. 35-44
    • Pedersen, M.1    Nissen, S.2    Mitarai, N.3    Lo Svenningsen, S.4    Sneppen, K.5    Pedersen, S.6
  • 37
    • 84894515074 scopus 로고    scopus 로고
    • Statistical mechanical model of coupled transcription from multiple promoters due to transcription factor titration
    • Rydenfelt, M., Cox, R. S., Garcia, H., and Phillips, R. (2014) Statistical mechanical model of coupled transcription from multiple promoters due to transcription factor titration Phys. Rev. E 89, 012702
    • (2014) Phys. Rev. e , vol.89 , pp. 012702
    • Rydenfelt, M.1    Cox, R.S.2    Garcia, H.3    Phillips, R.4
  • 38
    • 3042741121 scopus 로고    scopus 로고
    • Engineered riboregulators enable post-transcriptional control of gene expression
    • DOI 10.1038/nbt986
    • Isaacs, F. J., Dwyer, D. J., Ding, C., Pervouchine, D. D., Cantor, C. R., and Collins, J. J. (2004) Engineered riboregulators enable post-transcriptional control of gene expression Nat. Biotechnol. 22, 841-847 (Pubitemid 38886602)
    • (2004) Nature Biotechnology , vol.22 , Issue.7 , pp. 841-847
    • Isaacs, F.J.1    Dwyer, D.J.2    Ding, C.3    Pervouchine, D.D.4    Cantor, C.R.5    Collins, J.J.6
  • 39
    • 79957700542 scopus 로고    scopus 로고
    • Versatile RNA-sensing transcriptional regulators for engineering genetic networks
    • Lucks, J. B., Qi, L., Mutalik, V. K., Wang, D., and Arkin, A. P. (2011) Versatile RNA-sensing transcriptional regulators for engineering genetic networks Proc. Natl. Acad. Sci. U.S.A. 108, 8617-8622
    • (2011) Proc. Natl. Acad. Sci. U.S.A. , vol.108 , pp. 8617-8622
    • Lucks, J.B.1    Qi, L.2    Mutalik, V.K.3    Wang, D.4    Arkin, A.P.5
  • 40
    • 84866559567 scopus 로고    scopus 로고
    • De novo automated design of small RNA circuits for engineering synthetic riboregulation in living cells
    • Rodrigo, G., Landrain, T. E., and Jaramillo, A. (2012) De novo automated design of small RNA circuits for engineering synthetic riboregulation in living cells Proc. Natl. Acad. Sci. U.S.A. 109, 15271-15276
    • (2012) Proc. Natl. Acad. Sci. U.S.A. , vol.109 , pp. 15271-15276
    • Rodrigo, G.1    Landrain, T.E.2    Jaramillo, A.3
  • 41
    • 84903218451 scopus 로고    scopus 로고
    • Modelling the burden caused by gene expression: An in silico investigation into the interactions between synthetic gene circuits and their chassis cell
    • arXiv:1309.7798
    • Algar, R., Ellis, T., and Stan, G.-B. (2013) Modelling the burden caused by gene expression: An in silico investigation into the interactions between synthetic gene circuits and their chassis cell arXiv arXiv:1309.7798
    • (2013) ArXiv
    • Algar, R.1    Ellis, T.2    Stan, G.-B.3
  • 42
    • 84869078490 scopus 로고    scopus 로고
    • Iterative plug-and-play methodology for constructing and modifying synthetic gene networks
    • Litcofsky, K. D., Afeyan, R. B., Krom, R. J., Khalil, A. S., and Collins, J. J. (2012) Iterative plug-and-play methodology for constructing and modifying synthetic gene networks Nat. Methods 9, 1077-1080
    • (2012) Nat. Methods , vol.9 , pp. 1077-1080
    • Litcofsky, K.D.1    Afeyan, R.B.2    Krom, R.J.3    Khalil, A.S.4    Collins, J.J.5
  • 43
    • 84884658678 scopus 로고    scopus 로고
    • Randomized BioBrick assembly: A novel DNA assembly method for randomizing and optimizing genetic circuits and metabolic pathways
    • Sleight, S. C. and Sauro, H. M. (2013) Randomized BioBrick assembly: A novel DNA assembly method for randomizing and optimizing genetic circuits and metabolic pathways ACS Synth. Biol. 2 (9) 506-518
    • (2013) ACS Synth. Biol. , vol.2 , Issue.9 , pp. 506-518
    • Sleight, S.C.1    Sauro, H.M.2
  • 45
    • 77956335113 scopus 로고    scopus 로고
    • Protein synthesis in a device with nanoporous membranes and microchannels
    • Mei, Q., Khnouf, R., Simon, A., and Fan, Z. H. (2010) Protein synthesis in a device with nanoporous membranes and microchannels Lab Chip 10, 2541-2545
    • (2010) Lab Chip , vol.10 , pp. 2541-2545
    • Mei, Q.1    Khnouf, R.2    Simon, A.3    Fan, Z.H.4
  • 47
    • 84871321022 scopus 로고    scopus 로고
    • RNase E: At the interface of bacterial RNA processing and decay
    • Mackie, G. A. (2013) RNase E: At the interface of bacterial RNA processing and decay Nat. Rev. Microbiol. 11, 45-57
    • (2013) Nat. Rev. Microbiol. , vol.11 , pp. 45
    • MacKie, G.A.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.