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Erschienen in: Natural Computing 4/2010

01.12.2010

A synthetic genetic circuit whose signal-response curve is temperature-tunable from band-detection to sigmoidal behaviour

verfasst von: Sangram Bagh, David R. McMillen

Erschienen in: Natural Computing | Ausgabe 4/2010

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Abstract

Programming new cellular functions by using synthetic gene circuits is a key goal in synthetic biology, and an important element of this process is the ability to couple to the information processing systems of the host cell using synthetic systems with various signal-response characteristics. Here, we present a synthetic gene system in Escherichia coli whose signal-response curve may be tuned from band detection (strongest response within a band of input concentrations) to a switch-like sigmoidal response, simply by altering the temperature. This change from a band-detection response to a sigmoidal response has not previously been implemented. The system allows investigation of a range of signal-response behaviours with minimal effort: a single system, once inserted into the cells, provides a range of response curves without any genetic alterations or replacement with other systems. By altering its output, the system may couple to other synthetic or natural genetic circuits, and thus serve as a useful modular component. A mathematical model has also been developed which captures the essential qualitative behaviours of the circuit.

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Literatur
Zurück zum Zitat Adalsteinsson D, McMillen DR, Elston TC (2004) Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks. BMC Bioinf 5:24CrossRef Adalsteinsson D, McMillen DR, Elston TC (2004) Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks. BMC Bioinf 5:24CrossRef
Zurück zum Zitat Anderson JC, Voigt CA, Arkin AP (2007) Environmental signal integration by a modular AND gate. Mol Syst Biol 3:133CrossRef Anderson JC, Voigt CA, Arkin AP (2007) Environmental signal integration by a modular AND gate. Mol Syst Biol 3:133CrossRef
Zurück zum Zitat Andrianantoandro E, Basu S, Karig DK et al. (2006) Synthetic biology: new engineering rules for an emerging discipline. Mol Syst Biol 2: 2006.0028 Andrianantoandro E, Basu S, Karig DK et al. (2006) Synthetic biology: new engineering rules for an emerging discipline. Mol Syst Biol 2: 2006.0028
Zurück zum Zitat Arkin A (2008) Setting the standard in synthetic biology. Nat Biotechnol 26:771–774CrossRef Arkin A (2008) Setting the standard in synthetic biology. Nat Biotechnol 26:771–774CrossRef
Zurück zum Zitat Atkinson MR, Savageau MA, Myers JT et al (2003) Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli. Cell 113:597–607CrossRef Atkinson MR, Savageau MA, Myers JT et al (2003) Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli. Cell 113:597–607CrossRef
Zurück zum Zitat Bagh S, Mazumder M, Velauthapillai T et al (2008) Plasmid-borne prokaryotic gene expression: sources of variability and quantitative system characterization. Phys Rev E 77:021919CrossRef Bagh S, Mazumder M, Velauthapillai T et al (2008) Plasmid-borne prokaryotic gene expression: sources of variability and quantitative system characterization. Phys Rev E 77:021919CrossRef
Zurück zum Zitat Bar-Even A, Paulsson J, Maheshri N et al (2006) Noise in protein expression scales with natural protein abundance. Nat Genet 38:636–643CrossRef Bar-Even A, Paulsson J, Maheshri N et al (2006) Noise in protein expression scales with natural protein abundance. Nat Genet 38:636–643CrossRef
Zurück zum Zitat Bashor CJ, Helman NC, Yan S et al (2008) Using engineered scaffold interactions to reshape MAP kinase pathway signaling dynamics. Science 319:1539–1543CrossRef Bashor CJ, Helman NC, Yan S et al (2008) Using engineered scaffold interactions to reshape MAP kinase pathway signaling dynamics. Science 319:1539–1543CrossRef
Zurück zum Zitat Basu S, Karig D, Weiss R (2003) Engineering signal processing in cells: towards molecular concentration band detection. Nat Comput 2:463–478CrossRefMathSciNet Basu S, Karig D, Weiss R (2003) Engineering signal processing in cells: towards molecular concentration band detection. Nat Comput 2:463–478CrossRefMathSciNet
Zurück zum Zitat Basu S, Gerchman Y, Collins CH et al (2005) A synthetic multicellular system for programmed pattern formation. Nature 434:1130–1134CrossRef Basu S, Gerchman Y, Collins CH et al (2005) A synthetic multicellular system for programmed pattern formation. Nature 434:1130–1134CrossRef
Zurück zum Zitat Benner SA, Sismour M (2005) Synthetic biology. Nat Rev Genet 6:533–543CrossRef Benner SA, Sismour M (2005) Synthetic biology. Nat Rev Genet 6:533–543CrossRef
Zurück zum Zitat Chen M-T, Weiss R (2005) Artificial cell-cell communication in yeast Saccharomyces cerevisiae using signaling elements from Arabidopsis thaliana. Nat Biotechnol 23:1551–1555CrossRef Chen M-T, Weiss R (2005) Artificial cell-cell communication in yeast Saccharomyces cerevisiae using signaling elements from Arabidopsis thaliana. Nat Biotechnol 23:1551–1555CrossRef
Zurück zum Zitat Elowitz MB, Leibler S (2000) A synthetic oscillatory network of transcriptional regulators. Nature 403:335–338CrossRef Elowitz MB, Leibler S (2000) A synthetic oscillatory network of transcriptional regulators. Nature 403:335–338CrossRef
Zurück zum Zitat Feng X-J, Hooshangi S, Chen D et al (2004) Optimizing genetic circuits by global sensitivity analysis. Biophys J 87:2195–2202CrossRef Feng X-J, Hooshangi S, Chen D et al (2004) Optimizing genetic circuits by global sensitivity analysis. Biophys J 87:2195–2202CrossRef
Zurück zum Zitat Friedman BE, Olson JS, Matthews KS (1977) Interaction of lac repressor with inducer. Kinetic and equilibrium measurements. J Mol Biol 111:27–39CrossRef Friedman BE, Olson JS, Matthews KS (1977) Interaction of lac repressor with inducer. Kinetic and equilibrium measurements. J Mol Biol 111:27–39CrossRef
Zurück zum Zitat Gardner T, Cantor CR, Collins JJ (2000) Construction of a genetic toggle switch in Escherichia coli. Nature 403:339–342CrossRef Gardner T, Cantor CR, Collins JJ (2000) Construction of a genetic toggle switch in Escherichia coli. Nature 403:339–342CrossRef
Zurück zum Zitat Gerchman Y, Weiss R (2004) Teaching bacteria a new language. Proc Natl Acad Sci USA 101:2221–2222CrossRef Gerchman Y, Weiss R (2004) Teaching bacteria a new language. Proc Natl Acad Sci USA 101:2221–2222CrossRef
Zurück zum Zitat Gibson MA, Bruck J (2000) Efficient exact stochastic simulation of chemical systems with many species and many channels. J Phys Chem A 104:1876–1889CrossRef Gibson MA, Bruck J (2000) Efficient exact stochastic simulation of chemical systems with many species and many channels. J Phys Chem A 104:1876–1889CrossRef
Zurück zum Zitat Gillespie D (1977) Exact stochastic simulation of coupled chemical reactions. J Phys Chem 81:2340–2361CrossRef Gillespie D (1977) Exact stochastic simulation of coupled chemical reactions. J Phys Chem 81:2340–2361CrossRef
Zurück zum Zitat Guet CC, Elowitz MB, Hsing W et al (2002) Combinatorial synthesis of genetic networks. Science 296:1466–1470CrossRef Guet CC, Elowitz MB, Hsing W et al (2002) Combinatorial synthesis of genetic networks. Science 296:1466–1470CrossRef
Zurück zum Zitat Hasty J, Isaacs F, Dolnik M et al (2001) Designer gene networks: towards fundamental cellular control. Chaos 11:207–220MATHCrossRef Hasty J, Isaacs F, Dolnik M et al (2001) Designer gene networks: towards fundamental cellular control. Chaos 11:207–220MATHCrossRef
Zurück zum Zitat Hasty J, Dolnik M, Rottschafer V et al (2002a) Synthetic gene network for entraining and amplifying cellular oscillations. Phys Rev Lett 88:148101CrossRef Hasty J, Dolnik M, Rottschafer V et al (2002a) Synthetic gene network for entraining and amplifying cellular oscillations. Phys Rev Lett 88:148101CrossRef
Zurück zum Zitat Hasty J, McMillen DR, Collins JJ (2002b) Engineered gene circuits. Nature 420:224–230CrossRef Hasty J, McMillen DR, Collins JJ (2002b) Engineered gene circuits. Nature 420:224–230CrossRef
Zurück zum Zitat Haynes KA, Broderick ML, Brown AD et al (2007) Computing with living hardware. IET Synth Biol 1:44–47CrossRef Haynes KA, Broderick ML, Brown AD et al (2007) Computing with living hardware. IET Synth Biol 1:44–47CrossRef
Zurück zum Zitat Iadevaia S, Mantzaris NV (2006) Genetic network driven control of PHBV copolymer composition. J Biotechnol 122:99–121CrossRef Iadevaia S, Mantzaris NV (2006) Genetic network driven control of PHBV copolymer composition. J Biotechnol 122:99–121CrossRef
Zurück zum Zitat Isaacs FJ, Hasty J, Cantor CR et al (2003) Prediction and measurement of an autoregulatory genetic module. Proc Natl Acad Sci USA 100:7714–7719CrossRef Isaacs FJ, Hasty J, Cantor CR et al (2003) Prediction and measurement of an autoregulatory genetic module. Proc Natl Acad Sci USA 100:7714–7719CrossRef
Zurück zum Zitat Kærn M, Weiss R (2006) Synthetic gene regulatory systems. In: Szallasi Z, Stelling J, Periwal V (eds) System modeling in cellular biology. MIT Press, Cambridge Kærn M, Weiss R (2006) Synthetic gene regulatory systems. In: Szallasi Z, Stelling J, Periwal V (eds) System modeling in cellular biology. MIT Press, Cambridge
Zurück zum Zitat Kærn M, Blake W, Collins JJ (2003) The engineering of gene regulatory networks. Annu Rev Biomed Eng 5:179–206CrossRef Kærn M, Blake W, Collins JJ (2003) The engineering of gene regulatory networks. Annu Rev Biomed Eng 5:179–206CrossRef
Zurück zum Zitat Kærn M, Elston TC, Blake WJ et al (2005) Stochasticity in gene expression: from theories to phenotypes. Nat Rev Genet 6:451–464CrossRef Kærn M, Elston TC, Blake WJ et al (2005) Stochasticity in gene expression: from theories to phenotypes. Nat Rev Genet 6:451–464CrossRef
Zurück zum Zitat Lewis M, Chang G, Horton NC et al (1996) Crystal structure of the lactose operon repressor and its complexes with DNA and inducer. Science 271:1247–1254CrossRef Lewis M, Chang G, Horton NC et al (1996) Crystal structure of the lactose operon repressor and its complexes with DNA and inducer. Science 271:1247–1254CrossRef
Zurück zum Zitat Lieb M (1979) Heat-sensitive lambda repressors retain partial activity during bacteriophage induction. J Virol 32:162–166 Lieb M (1979) Heat-sensitive lambda repressors retain partial activity during bacteriophage induction. J Virol 32:162–166
Zurück zum Zitat Lutz R, Bujard H (1997) Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements. Nucl Acids Res 25:1203–1210CrossRef Lutz R, Bujard H (1997) Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements. Nucl Acids Res 25:1203–1210CrossRef
Zurück zum Zitat Maurer R, Meyer BJ, Ptashne M (1980) Gene regulation at the right operator (OR) of bacteriophage λ. I. OR3 and autogenous negative control by repressor. J Mol Biol 139:147–161CrossRef Maurer R, Meyer BJ, Ptashne M (1980) Gene regulation at the right operator (OR) of bacteriophage λ. I. OR3 and autogenous negative control by repressor. J Mol Biol 139:147–161CrossRef
Zurück zum Zitat Mieschendahl M, Müller-Hill B (1985) F’-coded, temperature-sensitive λ cI857 repressor gene for easy construction and regulation of λ promoter-dependent expression systems. J Bacteriol 164:1366–1369 Mieschendahl M, Müller-Hill B (1985) F’-coded, temperature-sensitive λ cI857 repressor gene for easy construction and regulation of λ promoter-dependent expression systems. J Bacteriol 164:1366–1369
Zurück zum Zitat Paulsson J (2004) Summing up the noise in gene networks. Nature 427:415–418CrossRef Paulsson J (2004) Summing up the noise in gene networks. Nature 427:415–418CrossRef
Zurück zum Zitat Pedraza JM, van Oudenaarden A (2005) Noise propagation in gene networks. Science 307:1965–1969CrossRef Pedraza JM, van Oudenaarden A (2005) Noise propagation in gene networks. Science 307:1965–1969CrossRef
Zurück zum Zitat Ptashne M (1992) A genetic switch: phage λ and higher organisms. Blackwell Science and Cell Press, Cambridge, MA Ptashne M (1992) A genetic switch: phage λ and higher organisms. Blackwell Science and Cell Press, Cambridge, MA
Zurück zum Zitat Ptashne M, Jeffrey A, Johnson AD et al (1980) How the λ repressor and Cro work. Cell 19:1–11CrossRef Ptashne M, Jeffrey A, Johnson AD et al (1980) How the λ repressor and Cro work. Cell 19:1–11CrossRef
Zurück zum Zitat Raser JM, O’Shea EK (2005) Noise in gene expression: origins, consequences, and control. Science 309:2010–2013CrossRef Raser JM, O’Shea EK (2005) Noise in gene expression: origins, consequences, and control. Science 309:2010–2013CrossRef
Zurück zum Zitat Trueba FJ, Koppes LJH (1998) Exponential growth of Escherichia coli B/r during its division cycle is demonstrated by the size distribution in liquid culture. Arch Microbiol 169:491–496CrossRef Trueba FJ, Koppes LJH (1998) Exponential growth of Escherichia coli B/r during its division cycle is demonstrated by the size distribution in liquid culture. Arch Microbiol 169:491–496CrossRef
Zurück zum Zitat Villaverde A, Benito A, Viaplana E et al (1993) Fine regulation of cI857-controlled gene expression in continuous culture of recombinant Escherichia coli by temperature. Appl Environ Microbiol 59:3485–3487 Villaverde A, Benito A, Viaplana E et al (1993) Fine regulation of cI857-controlled gene expression in continuous culture of recombinant Escherichia coli by temperature. Appl Environ Microbiol 59:3485–3487
Zurück zum Zitat Weiss R, Basu S, Hooshangi S et al (2003) Genetic circuit building blocks for cellular computation, communications, and signal processing. Nat Comput 2:47–84CrossRef Weiss R, Basu S, Hooshangi S et al (2003) Genetic circuit building blocks for cellular computation, communications, and signal processing. Nat Comput 2:47–84CrossRef
Zurück zum Zitat Weiss R, Knight TF, Sussman GJ (2004) Genetic process engineering. In: Amos M (ed) Cellular computing. Oxford University Press, Oxford Weiss R, Knight TF, Sussman GJ (2004) Genetic process engineering. In: Amos M (ed) Cellular computing. Oxford University Press, Oxford
Zurück zum Zitat Weiss LE, Badalamenti JP, Weaver LJ et al (2008) Engineering motility as a phenotypic response to LuxI/R-dependent quorum sensing in Escherichia coli. Biotechnol Bioeng 100:1251–1255CrossRef Weiss LE, Badalamenti JP, Weaver LJ et al (2008) Engineering motility as a phenotypic response to LuxI/R-dependent quorum sensing in Escherichia coli. Biotechnol Bioeng 100:1251–1255CrossRef
Zurück zum Zitat You L, Cox RS, Weiss R et al (2004) Programmed population control by cell–cell communication and regulated killing. Nature 428:868–871CrossRef You L, Cox RS, Weiss R et al (2004) Programmed population control by cell–cell communication and regulated killing. Nature 428:868–871CrossRef
Metadaten
Titel
A synthetic genetic circuit whose signal-response curve is temperature-tunable from band-detection to sigmoidal behaviour
verfasst von
Sangram Bagh
David R. McMillen
Publikationsdatum
01.12.2010
Verlag
Springer Netherlands
Erschienen in
Natural Computing / Ausgabe 4/2010
Print ISSN: 1567-7818
Elektronische ISSN: 1572-9796
DOI
https://doi.org/10.1007/s11047-009-9167-3

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