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Erschienen in: Natural Computing 1/2016

01.03.2016

Synthetic biology of cell signaling

verfasst von: Jonathan Hansen, Yaakov Benenson

Erschienen in: Natural Computing | Ausgabe 1/2016

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Abstract

Synthetic biology often takes cues from complex natural networks and pathways to create novel biological systems. The design modalities used in synthetic systems generally follow the different classes of gene regulation in cells such as transcriptional, post-transcriptional and post-translational regulation. The latter class is most prominent in cell signaling pathways that operate via multitude of protein–protein interactions. Engineering signaling pathways is a relatively unexplored area. This review discussed the work toward signaling pathway engineering in diverse biological contexts including bacteria, yeast, vertebrate, and plant cells. While creating synthetic signaling cascades is perhaps one of the most challenging tasks in synthetic biology, potential implications can be far-reaching and include new tools for programming cells and tissues, artificial developmental processes, and therapeutic tools.

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Literatur
Zurück zum Zitat Acharya A et al (2002) A heterodimerizing leucine zipper coiled coil system for examining the specificity of a position interactions: amino acids I, V, L, N, A, and K. Biochemistry 41(48):14122–14131CrossRef Acharya A et al (2002) A heterodimerizing leucine zipper coiled coil system for examining the specificity of a position interactions: amino acids I, V, L, N, A, and K. Biochemistry 41(48):14122–14131CrossRef
Zurück zum Zitat Acuto O, Michel F (2003) CD28-mediated co-stimulation: a quantitative support for TCR signalling. Nat Rev Immunol 3(12):939–951CrossRef Acuto O, Michel F (2003) CD28-mediated co-stimulation: a quantitative support for TCR signalling. Nat Rev Immunol 3(12):939–951CrossRef
Zurück zum Zitat Akiba H et al (1999) CD28-independent costimulation of T cells by OX40 ligand and CD70 on activated B cells. J Immunol 162(12):7058–7066 Akiba H et al (1999) CD28-independent costimulation of T cells by OX40 ligand and CD70 on activated B cells. J Immunol 162(12):7058–7066
Zurück zum Zitat Andersson J et al (2004) Differential input by Ste5 scaffold and Msg5 phosphatase route a MAPK cascade to multiple outcomes. EMBO J 23(13):2564–2576CrossRef Andersson J et al (2004) Differential input by Ste5 scaffold and Msg5 phosphatase route a MAPK cascade to multiple outcomes. EMBO J 23(13):2564–2576CrossRef
Zurück zum Zitat Andrews BW, Yi TM, Iglesias PA (2006) Optimal noise filtering in the chemotactic response of Escherichia coli. PLoS Comput Biol 2(11):1407–1418CrossRef Andrews BW, Yi TM, Iglesias PA (2006) Optimal noise filtering in the chemotactic response of Escherichia coli. PLoS Comput Biol 2(11):1407–1418CrossRef
Zurück zum Zitat Antunes MS et al (2006) A synthetic de-greening gene circuit provides a reporting system that is remotely detectable and has a re-set capacity. Plant Biotechnol J 4(6):605–622CrossRefMathSciNet Antunes MS et al (2006) A synthetic de-greening gene circuit provides a reporting system that is remotely detectable and has a re-set capacity. Plant Biotechnol J 4(6):605–622CrossRefMathSciNet
Zurück zum Zitat Antunes MS et al (2009) Engineering key components in a synthetic eukaryotic signal transduction pathway. Mol Syst Biol 5:270CrossRef Antunes MS et al (2009) Engineering key components in a synthetic eukaryotic signal transduction pathway. Mol Syst Biol 5:270CrossRef
Zurück zum Zitat Antunes MS et al (2011) Programmable ligand detection system in plants through a synthetic signal transduction pathway. PLoS ONE 6(1):e16292CrossRef Antunes MS et al (2011) Programmable ligand detection system in plants through a synthetic signal transduction pathway. PLoS ONE 6(1):e16292CrossRef
Zurück zum Zitat Auslaender D et al (2014) A synthetic multifunctional mammalian pH sensor and CO2 transgene-control device. Mol Cell 55(3):397–408CrossRef Auslaender D et al (2014) A synthetic multifunctional mammalian pH sensor and CO2 transgene-control device. Mol Cell 55(3):397–408CrossRef
Zurück zum Zitat Baim SB et al (1991) A chimeric mammalian transactivator based on the lac repressor that is regulated by temperature and isopropyl beta-d-thiogalactopyranoside. Proc Natl Acad Sci USA 88(12):5072–5076CrossRef Baim SB et al (1991) A chimeric mammalian transactivator based on the lac repressor that is regulated by temperature and isopropyl beta-d-thiogalactopyranoside. Proc Natl Acad Sci USA 88(12):5072–5076CrossRef
Zurück zum Zitat Banghart M et al (2004) Light-activated ion channels for remote control of neuronal firing. Nat Neurosci 7(12):1381–1386CrossRef Banghart M et al (2004) Light-activated ion channels for remote control of neuronal firing. Nat Neurosci 7(12):1381–1386CrossRef
Zurück zum Zitat Barrett DM et al (2014) Chimeric antigen receptor therapy for cancer. Annu Rev Med 65(65):333–347CrossRef Barrett DM et al (2014) Chimeric antigen receptor therapy for cancer. Annu Rev Med 65(65):333–347CrossRef
Zurück zum Zitat Bashor CJ et al (2008) Using engineered scaffold interactions to reshape MAP kinase pathway signaling dynamics. Science 319(5869):1539–1543CrossRef Bashor CJ et al (2008) Using engineered scaffold interactions to reshape MAP kinase pathway signaling dynamics. Science 319(5869):1539–1543CrossRef
Zurück zum Zitat Benenson Y (2012a) Biomolecular computing systems: principles, progress and potential. Nat Rev Genet 13(7):455–468CrossRef Benenson Y (2012a) Biomolecular computing systems: principles, progress and potential. Nat Rev Genet 13(7):455–468CrossRef
Zurück zum Zitat Benenson Y (2012b) Synthetic biology with RNA: progress report. Curr Opin Chem Biol 16(3–4):278–284CrossRef Benenson Y (2012b) Synthetic biology with RNA: progress report. Curr Opin Chem Biol 16(3–4):278–284CrossRef
Zurück zum Zitat Busskamp V et al (2012) Optogenetic therapy for retinitis pigmentosa. Gene Ther 19(2):169–175CrossRef Busskamp V et al (2012) Optogenetic therapy for retinitis pigmentosa. Gene Ther 19(2):169–175CrossRef
Zurück zum Zitat Celliere G et al (2011) The plasticity of TGF-beta signaling. BMC Syst Biol 5:184CrossRef Celliere G et al (2011) The plasticity of TGF-beta signaling. BMC Syst Biol 5:184CrossRef
Zurück zum Zitat Chuong AS et al (2014) Noninvasive optical inhibition with a red-shifted microbial rhodopsin. Nat Neurosci 17(8):1123–1129CrossRef Chuong AS et al (2014) Noninvasive optical inhibition with a red-shifted microbial rhodopsin. Nat Neurosci 17(8):1123–1129CrossRef
Zurück zum Zitat Crivici A, Ikura M (1995) Molecular and structural basis of target recognition by calmodulin. Annu Rev Biophys Biomol Struct 24:85–116CrossRef Crivici A, Ikura M (1995) Molecular and structural basis of target recognition by calmodulin. Annu Rev Biophys Biomol Struct 24:85–116CrossRef
Zurück zum Zitat Curran KJ, Pegram HJ, Brentjens RJ (2012) Chimeric antigen receptors for T cell immunotherapy: current understanding and future directions. J Gene Med 14(6):405–415CrossRef Curran KJ, Pegram HJ, Brentjens RJ (2012) Chimeric antigen receptors for T cell immunotherapy: current understanding and future directions. J Gene Med 14(6):405–415CrossRef
Zurück zum Zitat Darrow KN et al (2015) Optogenetic stimulation of the cochlear nucleus using channelrhodopsin-2 evokes activity in the central auditory pathways. Brain Res 1599:44–56CrossRef Darrow KN et al (2015) Optogenetic stimulation of the cochlear nucleus using channelrhodopsin-2 evokes activity in the central auditory pathways. Brain Res 1599:44–56CrossRef
Zurück zum Zitat Deuschle U, Meyer WKH, Thiesen HJ (1995) Tetracycline-reversible silencing of eukaryotic promoters. Mol Cell Biol 15(4):1907–1914CrossRef Deuschle U, Meyer WKH, Thiesen HJ (1995) Tetracycline-reversible silencing of eukaryotic promoters. Mol Cell Biol 15(4):1907–1914CrossRef
Zurück zum Zitat Elowitz MB, Leibler S (2000) A synthetic oscillatory network of transcriptional regulators. Nature 403(6767):335–338CrossRef Elowitz MB, Leibler S (2000) A synthetic oscillatory network of transcriptional regulators. Nature 403(6767):335–338CrossRef
Zurück zum Zitat Fackler OT, Grosse R (2008) Cell motility through plasma membrane blebbing. J Cell Biol 181(6):879–884CrossRef Fackler OT, Grosse R (2008) Cell motility through plasma membrane blebbing. J Cell Biol 181(6):879–884CrossRef
Zurück zum Zitat Falke JJ et al (1997) The two-component signaling pathway of bacterial chemotaxis: a molecular view of signal transduction by receptors, kinases, and adaptation enzymes. Annu Rev Cell Dev Biol 13:457–512CrossRef Falke JJ et al (1997) The two-component signaling pathway of bacterial chemotaxis: a molecular view of signal transduction by receptors, kinases, and adaptation enzymes. Annu Rev Cell Dev Biol 13:457–512CrossRef
Zurück zum Zitat Ferrell JE (1996) Tripping the switch fantastic: how a protein kinase cascade can convert graded inputs into switch-like outputs. Trends Biochem Sci 21(12):460–466CrossRef Ferrell JE (1996) Tripping the switch fantastic: how a protein kinase cascade can convert graded inputs into switch-like outputs. Trends Biochem Sci 21(12):460–466CrossRef
Zurück zum Zitat Furukawa K, Hohmann S (2015) A fungicide-responsive kinase as a tool for synthetic cell fate regulation. Nucleic Acids Res 43(14):7162–7170CrossRef Furukawa K, Hohmann S (2015) A fungicide-responsive kinase as a tool for synthetic cell fate regulation. Nucleic Acids Res 43(14):7162–7170CrossRef
Zurück zum Zitat Fussenegger M et al (2000) Streptogramin-based gene regulation systems for mammalian cells. Nat Biotechnol 18(11):1203–1208CrossRef Fussenegger M et al (2000) Streptogramin-based gene regulation systems for mammalian cells. Nat Biotechnol 18(11):1203–1208CrossRef
Zurück zum Zitat Gambetta GA, Lagarias JC (2001) Genetic engineering of phytochrome biosynthesis in bacteria. Proc Natl Acad Sci USA 98(19):10566–10571CrossRef Gambetta GA, Lagarias JC (2001) Genetic engineering of phytochrome biosynthesis in bacteria. Proc Natl Acad Sci USA 98(19):10566–10571CrossRef
Zurück zum Zitat Ganesh I et al (2013) Engineered fumarate sensing Escherichia coli based on novel chimeric two-component system. J Biotechnol 168(4):560–566CrossRef Ganesh I et al (2013) Engineered fumarate sensing Escherichia coli based on novel chimeric two-component system. J Biotechnol 168(4):560–566CrossRef
Zurück zum Zitat Gardner TS, Cantor CR, Collins JJ (2000) Construction of a genetic toggle switch in Escherichia coli. Nature 403(6767):339–342CrossRef Gardner TS, Cantor CR, Collins JJ (2000) Construction of a genetic toggle switch in Escherichia coli. Nature 403(6767):339–342CrossRef
Zurück zum Zitat Gasser C et al (2014) Engineering of a red-light-activated human cAMP/cGMP-specific phosphodiesterase. Proc Natl Acad Sci USA 111(24):8803–8808CrossRef Gasser C et al (2014) Engineering of a red-light-activated human cAMP/cGMP-specific phosphodiesterase. Proc Natl Acad Sci USA 111(24):8803–8808CrossRef
Zurück zum Zitat Geiger TL, Jyothi MD (2001) Development and application of receptor-modified T lymphocytes for adoptive immunotherapy. Transfus Med Rev 15(1):21–34CrossRef Geiger TL, Jyothi MD (2001) Development and application of receptor-modified T lymphocytes for adoptive immunotherapy. Transfus Med Rev 15(1):21–34CrossRef
Zurück zum Zitat Gilbert W, Mullerhi B (1967) Lac operator in DNA. Proc Natl Acad Sci USA 58(6):2415CrossRef Gilbert W, Mullerhi B (1967) Lac operator in DNA. Proc Natl Acad Sci USA 58(6):2415CrossRef
Zurück zum Zitat Goldbeter A, Koshland DE (1981) An amplified sensitivity arising from covalent modification in biological systems. Proc Natl Acad Sci USA Biol Sci 78(11):6840–6844CrossRefMathSciNet Goldbeter A, Koshland DE (1981) An amplified sensitivity arising from covalent modification in biological systems. Proc Natl Acad Sci USA Biol Sci 78(11):6840–6844CrossRefMathSciNet
Zurück zum Zitat Gossen M, Bujard H (1992) Tight control of gene-expression in mammalian-cells by tetracycline-responsive promoters. Proc Natl Acad Sci USA 89(12):5547–5551CrossRef Gossen M, Bujard H (1992) Tight control of gene-expression in mammalian-cells by tetracycline-responsive promoters. Proc Natl Acad Sci USA 89(12):5547–5551CrossRef
Zurück zum Zitat Gramaglia I et al (1998) Ox-40 ligand: a potent costimulatory molecule for sustaining primary CD4 T cell responses. J Immunol 161(12):6510–6517 Gramaglia I et al (1998) Ox-40 ligand: a potent costimulatory molecule for sustaining primary CD4 T cell responses. J Immunol 161(12):6510–6517
Zurück zum Zitat Hansen J et al (2014) Transplantation of prokaryotic two-component signaling pathways into mammalian cells. Proc Natl Acad Sci USA 111(44):15705–15710CrossRef Hansen J et al (2014) Transplantation of prokaryotic two-component signaling pathways into mammalian cells. Proc Natl Acad Sci USA 111(44):15705–15710CrossRef
Zurück zum Zitat Heinrich R, Neel BG, Rapoport TA (2002) Mathematical models of protein kinase signal transduction. Mol Cell 9(5):957–970CrossRef Heinrich R, Neel BG, Rapoport TA (2002) Mathematical models of protein kinase signal transduction. Mol Cell 9(5):957–970CrossRef
Zurück zum Zitat Hoch JA (2000) Two-component and phosphorelay signal transduction. Curr Opin Microbiol 3(2):165–170CrossRef Hoch JA (2000) Two-component and phosphorelay signal transduction. Curr Opin Microbiol 3(2):165–170CrossRef
Zurück zum Zitat Howell AS et al (2009) Singularity in polarization: rewiring yeast cells to make two buds. Cell 139(4):731–743CrossRefMathSciNet Howell AS et al (2009) Singularity in polarization: rewiring yeast cells to make two buds. Cell 139(4):731–743CrossRefMathSciNet
Zurück zum Zitat Hughes RM et al (2012) Light-mediated control of DNA transcription in yeast. Methods 58(4):385–391CrossRef Hughes RM et al (2012) Light-mediated control of DNA transcription in yeast. Methods 58(4):385–391CrossRef
Zurück zum Zitat Hwang I, Sheen J (2001) Two-component circuitry in Arabidopsis cytokinin signal transduction. Nature 413(6854):383–389CrossRef Hwang I, Sheen J (2001) Two-component circuitry in Arabidopsis cytokinin signal transduction. Nature 413(6854):383–389CrossRef
Zurück zum Zitat Jacob F, Monod J (1961) Genetic regulatory mechanisms in synthesis of proteins. J Mol Biol 3(3):318–356CrossRef Jacob F, Monod J (1961) Genetic regulatory mechanisms in synthesis of proteins. J Mol Biol 3(3):318–356CrossRef
Zurück zum Zitat Johnson LN (2009) The regulation of protein phosphorylation. Biochem Soc Trans 37:627–641CrossRef Johnson LN (2009) The regulation of protein phosphorylation. Biochem Soc Trans 37:627–641CrossRef
Zurück zum Zitat Kapp GT et al (2012) Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair. Proc Natl Acad Sci USA 109(14):5277–5282CrossRef Kapp GT et al (2012) Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair. Proc Natl Acad Sci USA 109(14):5277–5282CrossRef
Zurück zum Zitat Kawahara M, Ueda H, Nagamune T (2010) Engineering cytokine receptors to control cellular functions. Biochem Eng J 48(3):283–294CrossRef Kawahara M, Ueda H, Nagamune T (2010) Engineering cytokine receptors to control cellular functions. Biochem Eng J 48(3):283–294CrossRef
Zurück zum Zitat Kiel C, Yus E, Serrano L (2010) Engineering signal transduction pathways. Cell 140(1):33–47CrossRef Kiel C, Yus E, Serrano L (2010) Engineering signal transduction pathways. Cell 140(1):33–47CrossRef
Zurück zum Zitat Kobayashi H et al (2004) Programmable cells: interfacing natural and engineered gene networks. Proc Natl Acad Sci USA 101(22):8414–8419CrossRef Kobayashi H et al (2004) Programmable cells: interfacing natural and engineered gene networks. Proc Natl Acad Sci USA 101(22):8414–8419CrossRef
Zurück zum Zitat Krell T et al (2010) Bacterial sensor kinases: diversity in the recognition of environmental signals. In: Gottesman S, Harwood CS (eds) Annual Review of Microbiology, vol 64. Annual Reviews, Palo Alto, pp 539–559 Krell T et al (2010) Bacterial sensor kinases: diversity in the recognition of environmental signals. In: Gottesman S, Harwood CS (eds) Annual Review of Microbiology, vol 64. Annual Reviews, Palo Alto, pp 539–559
Zurück zum Zitat Laub MT, Goulian M (2007) Specificity in two-componen signal transduction pathways. Annu Rev Genet 41:121–145CrossRef Laub MT, Goulian M (2007) Specificity in two-componen signal transduction pathways. Annu Rev Genet 41:121–145CrossRef
Zurück zum Zitat Le H et al (2013) Dynamic gene expression for metabolic engineering of mammalian cells in culture. Metab Eng 20:212–220CrossRef Le H et al (2013) Dynamic gene expression for metabolic engineering of mammalian cells in culture. Metab Eng 20:212–220CrossRef
Zurück zum Zitat Lee MJ et al (2012) Sequential application of anticancer drugs enhances cell death by rewiring apoptotic signaling networks. Cell 149(4):780–794CrossRef Lee MJ et al (2012) Sequential application of anticancer drugs enhances cell death by rewiring apoptotic signaling networks. Cell 149(4):780–794CrossRef
Zurück zum Zitat Levskaya A et al (2005) Engineering Escherichia coli to see light: these smart bacteria ‘photograph’ a light pattern as a high-definition chemical image. Nature 438(7067):441–442CrossRef Levskaya A et al (2005) Engineering Escherichia coli to see light: these smart bacteria ‘photograph’ a light pattern as a high-definition chemical image. Nature 438(7067):441–442CrossRef
Zurück zum Zitat Li F et al (2010) Cell culture processes for monoclonal antibody production. Mabs 2(5):466–479CrossRef Li F et al (2010) Cell culture processes for monoclonal antibody production. Mabs 2(5):466–479CrossRef
Zurück zum Zitat Lunt B et al (2010) Inference of direct residue contacts in two-component signaling. In: Simon MI, Crane BR, Crane A (eds) Methods in enzymology: two-component signaling systems, Part C, vol 471. Elsevier, New York, pp 17–41 Lunt B et al (2010) Inference of direct residue contacts in two-component signaling. In: Simon MI, Crane BR, Crane A (eds) Methods in enzymology: two-component signaling systems, Part C, vol 471. Elsevier, New York, pp 17–41
Zurück zum Zitat Mezard M, Mora T (2009) Constraint satisfaction problems and neural networks: a statistical physics perspective. J Physiol Paris 103(1–2):107–113CrossRef Mezard M, Mora T (2009) Constraint satisfaction problems and neural networks: a statistical physics perspective. J Physiol Paris 103(1–2):107–113CrossRef
Zurück zum Zitat Miller MB, Bassler BL (2001) Quorum sensing in bacteria. Annu Rev Microbiol 55:165–199CrossRef Miller MB, Bassler BL (2001) Quorum sensing in bacteria. Annu Rev Microbiol 55:165–199CrossRef
Zurück zum Zitat Mills E, Kevin T (2011) Ca2+-mediated synthetic biosystems offer protein design versatility, signal specificity, and pathway rewiring. Chem Biol 18(12):1611–1619CrossRef Mills E, Kevin T (2011) Ca2+-mediated synthetic biosystems offer protein design versatility, signal specificity, and pathway rewiring. Chem Biol 18(12):1611–1619CrossRef
Zurück zum Zitat Mueller K et al (2014) Orthogonal optogenetic triple-gene control in mammalian cells. ACS Synth Biol 3(11):796–801CrossRef Mueller K et al (2014) Orthogonal optogenetic triple-gene control in mammalian cells. ACS Synth Biol 3(11):796–801CrossRef
Zurück zum Zitat Nagel G et al (2003) Channelrhodopsin-2, a directly light-gated cation-selective membrane channel. Proc Natl Acad Sci USA 100(24):13940–13945CrossRef Nagel G et al (2003) Channelrhodopsin-2, a directly light-gated cation-selective membrane channel. Proc Natl Acad Sci USA 100(24):13940–13945CrossRef
Zurück zum Zitat Novak B, Tyson JJ (2008) Design principles of biochemical oscillators. Nat Rev Mol Cell Biol 9(12):981–991CrossRef Novak B, Tyson JJ (2008) Design principles of biochemical oscillators. Nat Rev Mol Cell Biol 9(12):981–991CrossRef
Zurück zum Zitat O’Shaughnessy EC et al (2011) Tunable signal processing in synthetic MAP kinase cascades. Cell 144(1):119–131CrossRef O’Shaughnessy EC et al (2011) Tunable signal processing in synthetic MAP kinase cascades. Cell 144(1):119–131CrossRef
Zurück zum Zitat Park SH, Zarrinpar A, Lim WA (2003) Rewiring MAP kinase pathways using alternative scaffold assembly mechanisms. Science 299(5609):1061–1064CrossRef Park SH, Zarrinpar A, Lim WA (2003) Rewiring MAP kinase pathways using alternative scaffold assembly mechanisms. Science 299(5609):1061–1064CrossRef
Zurück zum Zitat Pawson T, Warner N (2007) Oncogenic re-wiring of cellular signaling pathways. Oncogene 26(9):1268–1275CrossRef Pawson T, Warner N (2007) Oncogenic re-wiring of cellular signaling pathways. Oncogene 26(9):1268–1275CrossRef
Zurück zum Zitat Procaccini A et al (2011) Dissecting the specificity of protein–protein interaction in bacterial two-component signaling: orphans and crosstalks. PLoS ONE 6(5):e19729CrossRef Procaccini A et al (2011) Dissecting the specificity of protein–protein interaction in bacterial two-component signaling: orphans and crosstalks. PLoS ONE 6(5):e19729CrossRef
Zurück zum Zitat Ptashne M (1967) Specific binding of lambda phage repressor to lambda DNA. Nature 214(5085):232CrossRef Ptashne M (1967) Specific binding of lambda phage repressor to lambda DNA. Nature 214(5085):232CrossRef
Zurück zum Zitat Pule MA et al (2005) A chimeric T cell antigen receptor that augments cytokine release and supports clonal expansion of primary human T cells. Mol Ther 12(5):933–941CrossRef Pule MA et al (2005) A chimeric T cell antigen receptor that augments cytokine release and supports clonal expansion of primary human T cells. Mol Ther 12(5):933–941CrossRef
Zurück zum Zitat Puttick J, Baker EN, Delbaere LTJ (2008) Histidine phosphorylation in biological systems. Biochim Biophys Acta Proteins Proteom 1784(1):100–105CrossRef Puttick J, Baker EN, Delbaere LTJ (2008) Histidine phosphorylation in biological systems. Biochim Biophys Acta Proteins Proteom 1784(1):100–105CrossRef
Zurück zum Zitat Qin L et al (2000) A monomeric histidine kinase derived from EnvZ, an Escherichia coli osmosensor. Mol Microbiol 36(1):24–32CrossRef Qin L et al (2000) A monomeric histidine kinase derived from EnvZ, an Escherichia coli osmosensor. Mol Microbiol 36(1):24–32CrossRef
Zurück zum Zitat Regot S et al (2011) Distributed biological computation with multicellular engineered networks. Nature 469(7329):207–211CrossRef Regot S et al (2011) Distributed biological computation with multicellular engineered networks. Nature 469(7329):207–211CrossRef
Zurück zum Zitat Rinaudo K et al (2007) A universal RNAi-based logic evaluator that operates in mammalian cells. Nat Biotechnol 25(7):795–801CrossRef Rinaudo K et al (2007) A universal RNAi-based logic evaluator that operates in mammalian cells. Nat Biotechnol 25(7):795–801CrossRef
Zurück zum Zitat Rowley JD (1990) The philadelphia-chromosome translocation: a paradigm for understanding leukemia. Cancer 65(10):2178–2184CrossRef Rowley JD (1990) The philadelphia-chromosome translocation: a paradigm for understanding leukemia. Cancer 65(10):2178–2184CrossRef
Zurück zum Zitat Sadelain M, Riviere I, Brentjens R (2003) Targeting tumours with genetically enhanced T lymphocytes. Nat Rev Cancer 3(1):35–45CrossRef Sadelain M, Riviere I, Brentjens R (2003) Targeting tumours with genetically enhanced T lymphocytes. Nat Rev Cancer 3(1):35–45CrossRef
Zurück zum Zitat Shimizu TS, Tu YH, Berg HC (2010) A modular gradient-sensing network for chemotaxis in Escherichia coli revealed by responses to time-varying stimuli. Mol Syst Biol 6(1):382 Shimizu TS, Tu YH, Berg HC (2010) A modular gradient-sensing network for chemotaxis in Escherichia coli revealed by responses to time-varying stimuli. Mol Syst Biol 6(1):382
Zurück zum Zitat Skerker JM et al (2008) Rewiring the specificity of two-component signal transduction systems. Cell 133(6):1043–1054CrossRef Skerker JM et al (2008) Rewiring the specificity of two-component signal transduction systems. Cell 133(6):1043–1054CrossRef
Zurück zum Zitat Tabor JJ et al (2009) A synthetic genetic edge detection program. Cell 137(7):1272–1281CrossRef Tabor JJ et al (2009) A synthetic genetic edge detection program. Cell 137(7):1272–1281CrossRef
Zurück zum Zitat Tay S et al (2010) Single-cell NF-kappa B dynamics reveal digital activation and analogue information processing. Nature 466(7303):267–271CrossRef Tay S et al (2010) Single-cell NF-kappa B dynamics reveal digital activation and analogue information processing. Nature 466(7303):267–271CrossRef
Zurück zum Zitat Thattai M, van Oudenaarden A (2002) Attenuation of noise in ultrasensitive signaling cascades. Biophys J 82(6):2943–2950CrossRef Thattai M, van Oudenaarden A (2002) Attenuation of noise in ultrasensitive signaling cascades. Biophys J 82(6):2943–2950CrossRef
Zurück zum Zitat Tyson JJ, Chen KC, Novak B (2003) Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr Opin Cell Biol 15(2):221–231CrossRef Tyson JJ, Chen KC, Novak B (2003) Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr Opin Cell Biol 15(2):221–231CrossRef
Zurück zum Zitat Tyszkiewicz AB, Muir TW (2008) Activation of protein splicing with light in yeast. Nat Methods 5(4):303–305 Tyszkiewicz AB, Muir TW (2008) Activation of protein splicing with light in yeast. Nat Methods 5(4):303–305
Zurück zum Zitat Wang R, Brattain MG (2007) The maximal size of protein to diffuse through the nuclear pore is larger than 60 kDa. FEBS Lett 581(17):3164–3170CrossRef Wang R, Brattain MG (2007) The maximal size of protein to diffuse through the nuclear pore is larger than 60 kDa. FEBS Lett 581(17):3164–3170CrossRef
Zurück zum Zitat Wang X et al (2014) Optogenetic stimulation of locus ceruleus neurons augments inhibitory transmission to parasympathetic cardiac vagal neurons via activation of brainstem alpha 1 and beta 1 receptors. J Neurosci 34(18):6182–6189CrossRef Wang X et al (2014) Optogenetic stimulation of locus ceruleus neurons augments inhibitory transmission to parasympathetic cardiac vagal neurons via activation of brainstem alpha 1 and beta 1 receptors. J Neurosci 34(18):6182–6189CrossRef
Zurück zum Zitat Weber W et al (2002) Macrolide-based transgene control in mammalian cells and mice. Nat Biotechnol 20(9):901–907CrossRef Weber W et al (2002) Macrolide-based transgene control in mammalian cells and mice. Nat Biotechnol 20(9):901–907CrossRef
Zurück zum Zitat Weigt M et al (2009) Identification of direct residue contacts in protein–protein interaction by message passing. Proc Natl Acad Sci USA 106(1):67–72CrossRef Weigt M et al (2009) Identification of direct residue contacts in protein–protein interaction by message passing. Proc Natl Acad Sci USA 106(1):67–72CrossRef
Zurück zum Zitat Wilkinson MG, Millar JBA (2000) Control of the eukaryotic cell cycle by MAP kinase signaling pathways. Faseb J 14(14):2147–2157CrossRef Wilkinson MG, Millar JBA (2000) Control of the eukaryotic cell cycle by MAP kinase signaling pathways. Faseb J 14(14):2147–2157CrossRef
Zurück zum Zitat Wu CL et al (2003) Phosphorylation of the MAPKKK regulator Ste50p in Saccharomyces cerevisiae: a casein kinase I phosphorylation site is required for proper mating function. Eukaryot Cell 2(5):949–961CrossRef Wu CL et al (2003) Phosphorylation of the MAPKKK regulator Ste50p in Saccharomyces cerevisiae: a casein kinase I phosphorylation site is required for proper mating function. Eukaryot Cell 2(5):949–961CrossRef
Zurück zum Zitat Yamamoto K et al (2005) Functional characterization in vitro of all two-component signal transduction systems from Escherichia coli. J Biol Chem 280(2):1448–1456CrossRef Yamamoto K et al (2005) Functional characterization in vitro of all two-component signal transduction systems from Escherichia coli. J Biol Chem 280(2):1448–1456CrossRef
Zurück zum Zitat Yang X et al (2013) A light-inducible organelle-targeting system for dynamically activating and inactivating signaling in budding yeast. Mol Biol Cell 24(15):2419–2430CrossRef Yang X et al (2013) A light-inducible organelle-targeting system for dynamically activating and inactivating signaling in budding yeast. Mol Biol Cell 24(15):2419–2430CrossRef
Zurück zum Zitat Ye HF et al (2011) A synthetic optogenetic transcription device enhances blood-glucose homeostasis in mice. Science 332(6037):1565–1568CrossRef Ye HF et al (2011) A synthetic optogenetic transcription device enhances blood-glucose homeostasis in mice. Science 332(6037):1565–1568CrossRef
Zurück zum Zitat Yeh BJ et al (2007) Rewiring cellular morphology pathways with synthetic guanine nucleotide exchange factors. Nature 447(7144):596–600CrossRef Yeh BJ et al (2007) Rewiring cellular morphology pathways with synthetic guanine nucleotide exchange factors. Nature 447(7144):596–600CrossRef
Zurück zum Zitat Zhang F et al (2006) Channelrhodopsin-2 and optical control of excitable cells. Nat Methods 3(10):785–792CrossRef Zhang F et al (2006) Channelrhodopsin-2 and optical control of excitable cells. Nat Methods 3(10):785–792CrossRef
Metadaten
Titel
Synthetic biology of cell signaling
verfasst von
Jonathan Hansen
Yaakov Benenson
Publikationsdatum
01.03.2016
Verlag
Springer Netherlands
Erschienen in
Natural Computing / Ausgabe 1/2016
Print ISSN: 1567-7818
Elektronische ISSN: 1572-9796
DOI
https://doi.org/10.1007/s11047-015-9526-1

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