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1
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79951997641
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A Modular cloning system for standardized assembly of multigene constructs
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1 Weber, E., Engler, C., Gruetzner, R., Werner, S., Marillonnet, S., A Modular cloning system for standardized assembly of multigene constructs. PLoS One 6 (2011), 38–43.
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Foundations for the design and implementation of synthetic genetic circuits
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2 Slusarczyk, A.L., Lin, A., Weiss, R., Foundations for the design and implementation of synthetic genetic circuits. Nat Rev Genet 13 (2012), 406–420.
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Genetic circuit design automation
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7341-7341 The Cello software package that automates the design of constructs encoding Boolean logic networks in E. coli is described. Cello analyses design space for a desired network and uses existing part characterization and accompanying cell growth data to identify unfavourable designs in silico that are more likely to cause burden and instability when run in vivo.
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3•• Nielsen, A.A.K., Der, B.S., Shin, J., Vaidyanathan, P., Paralanov, V., Strychalski, E.A., Ross, D., Densmore, D., Voigt, C.A., Genetic circuit design automation. Science, 352, 2016 7341-7341 The Cello software package that automates the design of constructs encoding Boolean logic networks in E. coli is described. Cello analyses design space for a desired network and uses existing part characterization and accompanying cell growth data to identify unfavourable designs in silico that are more likely to cause burden and instability when run in vivo.
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Science
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Nielsen, A.A.K.1
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84890178034
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Advances in genetic circuit design: novel biochemistries, deep part mining, and precision gene expression
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4 Nielsen, A.A., Segall-Shapiro, T.H., Voigt, C.A., Advances in genetic circuit design: novel biochemistries, deep part mining, and precision gene expression. Curr Opin Chem Biol 17 (2013), 878–892.
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Nielsen, A.A.1
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5
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84880772006
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Effects of genetic variation on the E. coli host–circuit interface
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How host cell variation impacts a synthetic construct was assessed by analysing the behaviour of a simple construct expressing three fluorescent proteins in a large panel of different E. coli strains. In different genetic backgrounds host metabolism and growth characteristics change significantly leading to altered construct performance. This work underlines the importance of choosing the appropriate host cell for construct function and for characterization.
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5•• Cardinale, S., Joachimiak, M.P., Arkin, A.P., Effects of genetic variation on the E. coli host–circuit interface. Cell Rep 4 (2013), 231–237 How host cell variation impacts a synthetic construct was assessed by analysing the behaviour of a simple construct expressing three fluorescent proteins in a large panel of different E. coli strains. In different genetic backgrounds host metabolism and growth characteristics change significantly leading to altered construct performance. This work underlines the importance of choosing the appropriate host cell for construct function and for characterization.
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Cell Rep
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Cardinale, S.1
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84861865655
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Rewritable digital data storage in live cells via engineered control of recombination directionality
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6 Bonnet, J., Subsoontorn, P., Endy, D., Rewritable digital data storage in live cells via engineered control of recombination directionality. Proc Natl Acad Sci 109 (2012), 8884–8889.
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Bonnet, J.1
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Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca
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7 Temme, K., Zhao, D., Voigt, Ca., Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca. Proc Natl Acad Sci 109 (2012), 7085–7090.
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Temme, K.1
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84887870749
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Refactoring the silent spectinabilin gene cluster using a plug-and-play scaffold
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8 Shao, Z., Rao, G., Li, C., Abil, Z., Luo, Y., Zhao, H., Refactoring the silent spectinabilin gene cluster using a plug-and-play scaffold. ACS Synth Biol 2 (2013), 662–669.
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Shao, Z.1
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9
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84925014516
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Proteome reallocation in Escherichia coli with increasing specific growth rate
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9 Peebo, K., Valgepea, K., Maser, A., Nahku, R., Adamberg, K., Vilu, R., Proteome reallocation in Escherichia coli with increasing specific growth rate. Mol BioSyst 11 (2015), 1184–1193.
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Peebo, K.1
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10
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84902184652
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Visual account of protein investment in cellular functions
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10 Liebermeister, W., Noor, E., Flamholz, A., Davidi, D., Bernhardt, J., Milo, R., Visual account of protein investment in cellular functions. Proc Natl Acad Sci U S A 111 (2014), 8488–8493.
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Liebermeister, W.1
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11
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84952705872
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11 Lynch, M., Marinov, G.K., The bioenergetic costs of a gene. Proc Natl Acad Sci, 112, 2015, 201514974.
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Lynch, M.1
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84959319814
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Dealing with the genetic load in bacterial synthetic biology circuits: convergences with the Ohm's law
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12 Carbonell-Ballestero, M., Garcia-Ramallo, E., Montañez, R., Rodriguez-Caso, C., Macía, J., Dealing with the genetic load in bacterial synthetic biology circuits: convergences with the Ohm's law. Nucleic Acids Res, 44, 2015 gkv1280.
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Carbonell-Ballestero, M.1
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13
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77953115788
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Cost of unneeded proteins in E. coli is reduced after several generations in exponential growth
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13 Shachrai, I., Zaslaver, A., Alon, U., Dekel, E., Cost of unneeded proteins in E. coli is reduced after several generations in exponential growth. Mol Cell 38 (2010), 758–767.
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Shachrai, I.1
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14 Scott, M., Mateescu, E.M., Zhang, Z., Hwa, T., Interdependence of cell growth and gene expression: origins and consequences. Science 330 (2010), 1099–1102.
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Scott, M.1
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15
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84938509078
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Isocost lines describe the cellular economy of genetic circuits
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The competition for gene expression resources between two constructs present in the same E. coli cells was experimentally and mathematically analyzed. Both the host cell ribosomes and RNA polymerases were revealed to be limited resources that determined the performances of the synthetic constructs when running together in a cell.
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15• Gyorgy, A., Jiménez, J.I., Yazbek, J., Huang, H-H., Chung, H., Weiss, R., Del Vecchio, D., Isocost lines describe the cellular economy of genetic circuits. Biophys. J 109 (2015), 639–646 The competition for gene expression resources between two constructs present in the same E. coli cells was experimentally and mathematically analyzed. Both the host cell ribosomes and RNA polymerases were revealed to be limited resources that determined the performances of the synthetic constructs when running together in a cell.
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Gyorgy, A.1
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16
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84896901420
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Using synthetic biological parts and microbioreactors to explore the protein expression characteristics of Escherichia coli
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16 Gorochowski, T.E., van den Berg, E., Kerkman, R., Roubos, J.a., Bovenberg, R.a.L., Using synthetic biological parts and microbioreactors to explore the protein expression characteristics of Escherichia coli. ACS Synth Biol 3 (2014), 129–139.
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Gorochowski, T.E.1
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17
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17 Cookson, N.a., Mather, W.H., Danino, T., Mondragón-Palomino, O., Williams, R.J., Tsimring, L.S., Hasty, J., Queueing up for enzymatic processing: correlated signaling through coupled degradation. Mol Syst Biol, 7, 2011, 561.
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18
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84945905016
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Inflating bacterial cells by increased protein synthesis
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18 Basan, M., Zhu, M., Dai, X., Warren, M., Sévin, D., Wang, Y., Hwa, T., Inflating bacterial cells by increased protein synthesis. Mol Syst Biol, 11, 2015 836-836.
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19 Dennis, P.P., Bremer, H., Macromolecular composition during steady-state growth of Escherichia coli B-r. J Bacteriol 119 (1974), 270–281.
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20
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84884611067
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Visualization of evolutionary stability dynamics and competitive fitness of Escherichia coli engineered with randomized multigene circuits
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Fluorescent protein production from a diverse library of genetic contructs expressing CFP, RFP and YFP was measured over 200 generations of growth in E. coli to examine what features lead to mutation and thus genetic instability. Constructs with fewer genes, low expression levels and less repetitive DNA exhibited higher evolutionary stability.
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20• Sleight, S.C., Sauro, H.M., Visualization of evolutionary stability dynamics and competitive fitness of Escherichia coli engineered with randomized multigene circuits. ACS Synth Biol 2 (2013), 519–528 Fluorescent protein production from a diverse library of genetic contructs expressing CFP, RFP and YFP was measured over 200 generations of growth in E. coli to examine what features lead to mutation and thus genetic instability. Constructs with fewer genes, low expression levels and less repetitive DNA exhibited higher evolutionary stability.
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ACS Synth Biol
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Sleight, S.C.1
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21 Schaerli, Y., Munteanu, A., Gili, M., Cotterell, J., Sharpe, J., Isalan, M., A unified design space of synthetic stripe-forming networks. Nat Commun, 5, 2014, 4905.
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22 Klumpp, S., Zhang, Z., Hwa, T., Growth rate-dependent global effects on gene expression in bacteria. Cell 139 (2009), 1366–1375.
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84869451704
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Genetic circuit performance under conditions relevant for industrial bioreactors
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To assess engineered bacteria performance in industrial environments, constructs encoding AND and NOR logic gate gene circuits were grown and tested in different growth media and a variety of E. coli strains. The NOR gate showed robust behavior across tests, but the AND gate varied significantly in its performance, and failed to exhibit one of its key output states when grown in an industrial bioreactor.
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23• Moser, F., Broers, N.J., Hartmans, S., Tamsir, A., Kerkman, R., Roubos, J.a., Bovenberg, R., Voigt, C.a., Genetic circuit performance under conditions relevant for industrial bioreactors. ACS Synth Biol 1 (2012), 555–564 To assess engineered bacteria performance in industrial environments, constructs encoding AND and NOR logic gate gene circuits were grown and tested in different growth media and a variety of E. coli strains. The NOR gate showed robust behavior across tests, but the AND gate varied significantly in its performance, and failed to exhibit one of its key output states when grown in an industrial bioreactor.
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24
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84905376865
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A resource allocator for transcription based on a highly fragmented T7 RNA polymerase
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24 Segall-Shapiro, T.H., Meyer, A.J., Ellington, A.D., Sontag, E.D., Voigt, C.a., A resource allocator for transcription based on a highly fragmented T7 RNA polymerase. Mol Syst Biol, 10, 2014, 742.
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25
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84942133361
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Using promoter libraries to reduce metabolic burden due to plasmid-encoded proteins in recombinant Escherichia coli
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25 Pasini, M., Fernández-Castané, A., Jaramillo, A., de Mas, C., Caminal, G., Ferrer, P., Using promoter libraries to reduce metabolic burden due to plasmid-encoded proteins in recombinant Escherichia coli. N Biotechnol 33 (2016), 78–90.
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26 Lou, C., Stanton, B., Chen, Y., Munsky, B., Voigt, C.A., Ribozyme-based insulator parts buffer synthetic circuits from genetic context. Nat Biotechnol 30 (2012), 1137–1142.
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84928927536
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Quantifying cellular capacity identifies gene expression designs with reduced burden
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By expressing unregulated GFP production from the chromosome of engineered E. coli and measuring dynamic changes in fluorescence output when constructs were introduced and expressed, the capacity of the host cell for gene expression could be calculated and simulated with an accompanying model. This method revealed that constructs could be optimized for more efficient use of host resources by lowering their use of free ribosomes.
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27•• Ceroni, F., Algar, R., Stan, G., Ellis, T., Quantifying cellular capacity identifies gene expression designs with reduced burden. Nat Methods 12 (2015), 415–418 By expressing unregulated GFP production from the chromosome of engineered E. coli and measuring dynamic changes in fluorescence output when constructs were introduced and expressed, the capacity of the host cell for gene expression could be calculated and simulated with an accompanying model. This method revealed that constructs could be optimized for more efficient use of host resources by lowering their use of free ribosomes.
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Nat Methods
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Ceroni, F.1
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Linear DNA for rapid prototyping of synthetic biological circuits in an escherichia coli based TX-TL cell-free system
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28 Sun, Z.Z., Yeung, E., Hayes, C.A., Noireaux, V., Murray, R.M., Linear DNA for rapid prototyping of synthetic biological circuits in an escherichia coli based TX-TL cell-free system. ACS Synth Biol 3 (2014), 387–397.
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29
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Rapidly characterizing the fast dynamics of RNA genetic circuitry with cell-free transcription–translation (TX–TL) systems
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29 Takahashi, M.K., Chappell, J., Hayes, C.A., Sun, Z.Z., Kim, J., Singhal, V., Spring, K.J., Al-Khabouri, S., Fall, C.P., Noireaux, V., et al. Rapidly characterizing the fast dynamics of RNA genetic circuitry with cell-free transcription–translation (TX–TL) systems. ACS Synth Biol 4 (2015), 503–515.
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30
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An E. coli cell-free system was shown to be an effective a simplified expression platform to characterize synthetic constructs and mathematically investigate and quantify the effects of load and burden. As in vivo, the cell-free system exhibits expression limitation due to finite polymerase and ribosomes resources, with the latter showing the most impact.
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30• Siegal-gaskins, D., Tuza, Z.A., Kim, J., Noireaux, V., Murray, R.M., Gene circuit performance characterization and resource usage in a cell-free breadboard. ACS Synth Biol 3 (2014), 416–425 An E. coli cell-free system was shown to be an effective a simplified expression platform to characterize synthetic constructs and mathematically investigate and quantify the effects of load and burden. As in vivo, the cell-free system exhibits expression limitation due to finite polymerase and ribosomes resources, with the latter showing the most impact.
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31
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Tunable protein degradation in bacteria
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Lon protease from M. florum was expressed in E. coli and L. lactis to specifically target and degrade only the proteins expressed with a corresponding recognition tag. By removing the need to use E. coli's own native proteases to turn over heterologous proteins from synthetic constructs, this orthogonal protease was shown to reduce the load on the host.
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31•• Cameron, D.E., Collins, J.J., Tunable protein degradation in bacteria. Nat Biotechnol 32 (2014), 1276–1281 Lon protease from M. florum was expressed in E. coli and L. lactis to specifically target and degrade only the proteins expressed with a corresponding recognition tag. By removing the need to use E. coli's own native proteases to turn over heterologous proteins from synthetic constructs, this orthogonal protease was shown to reduce the load on the host.
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32 Dürrschmid, K., Reischer, H., Schmidt-Heck, W., Hrebicek, T., Guthke, R., Rizzi, A., Bayer, K., Monitoring of transcriptome and proteome profiles to investigate the cellular response of E. coli towards recombinant protein expression under defined chemostat conditions. J Biotechnol 135 (2008), 34–44.
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When a toxic molecule is produced in E. coli intracellular stress response genes are often activated. Microarray experiments were used here to identify promoters responding to the accumulation of the toxic intermediate metabolite farnesyl pyrophosphate (FPP) in the isoprenoid biosynthetic pathway. The identified promoters were then used to control production and conversion of FPP, helping to automatically optimise the final product titre.
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34•• Dahl, R.H., Zhang, F., Alonso-Gutierrez, J., Baidoo, E., Batth, T.S., Redding-Johanson, A.M., Petzold, C.J., Mukhopadhyay, A., Lee, T.S., Adams, P.D., et al. Engineering dynamic pathway regulation using stress-response promoters. Nat Biotechnol 31 (2013), 1039–1046 When a toxic molecule is produced in E. coli intracellular stress response genes are often activated. Microarray experiments were used here to identify promoters responding to the accumulation of the toxic intermediate metabolite farnesyl pyrophosphate (FPP) in the isoprenoid biosynthetic pathway. The identified promoters were then used to control production and conversion of FPP, helping to automatically optimise the final product titre.
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Dahl, R.H.1
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37 Bassalo, M.C., Garst, A.D., Halweg-Edwards, A.L., Grau, W.C., Domaille, D.W., Mutalik, V.K., Arkin, A.P., Gill, R.T., Rapid and efficient one-step metabolic pathway integration in E. coli. ACS Synth Biol 5 (2016), 561–568.
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