BioModelsapplication/xmlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000012?filename=BIOMD0000000012.pdfhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000012?filename=BIOMD0000000012-biopax3.owlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000012?filename=BIOMD0000000012-biopax2.owlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000012?filename=BIOMD0000000012.svghttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000012?filename=BIOMD0000000012_url.xmlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000012?filename=BIOMD0000000012_urn.xmlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000012?filename=BIOMD0000000012.mhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000012?filename=BIOMD0000000012.pnghttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000012?filename=BIOMD0000000012.scihttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000012?filename=BIOMD0000000012.xpphttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000012?filename=BIOMD0000000012.vcmlprimaryOK200Nicolas Le NovèreManually curatedL2V3https://www.ebi.ac.uk/biomodels/BIOMD000000001210659856falseBioModelsSBMLModelsElowitz2000 Repressilator2000MODEL6615351360M B Elowitz, S LeiblerM B Elowitz10659856, Networks of interacting biomolecules carry out many essential functions in living cells, but the 'design principles' underlying the functioning of such intracellular networks remain poorly understood, despite intensive efforts including quantitative analysis of relatively simple systems. Here we present a complementary approach to this problem: the design and construction of a synthetic network to implement a particular function. We used three transcriptional repressor systems that are not part of any natural biological clock to build an oscillating network, termed the repressilator, in Escherichia coli. The network periodically induces the synthesis of green fluorescent protein as a readout of its state in individual cells. The resulting oscillations, with typical periods of hours, are slower than the cell-division cycle, so the state of the oscillator has to be transmitted from generation to generation. This artificial clock displays noisy behaviour, possibly because of stochastic fluctuations of its components. Such 'rational network design may lead both to the engineering of new cellular behaviours and to an improved understanding of naturally occurring networks.. 6767, 403. Department of Molecular Biology and Physics, Princeton University, New Jersey 08544, USA. melowitz@princeton.edulenov@ebi.ac.ukEBML-EBIBIOMD0000000012Networks of interacting biomolecules carry out many essential functions in living cells, but the 'design principles' underlying the functioning of such intracellular networks remain poorly understood, despite intensive efforts including quantitative analysis of relatively simple systems. Here we present a complementary approach to this problem: the design and construction of a synthetic network to implement a particular function. We used three transcriptional repressor systems that are not part of any natural biological clock to build an oscillating network, termed the repressilator, in Escherichia coli. The network periodically induces the synthesis of green fluorescent protein as a readout of its state in individual cells. The resulting oscillations, with typical periods of hours, are slower than the cell-division cycle, so the state of the oscillator has to be transmitted from generation to generation. This artificial clock displays noisy behaviour, possibly because of stochastic fluctuations of its components. Such 'rational network design may lead both to the engineering of new cellular behaviours and to an improved understanding of naturally occurring networks.A synthetic oscillatory network of transcriptional regulators.Elowitz M B MB, Leibler S SAlkalescens-Dispar Group, Understanding., Bacterium coli, nucleocytoplasm, artificial sequence, determination, protein complex, synthesize, number, bacterium E3, artificial gene, function, biosynthesis, protein, EAggEC, synthetic DNA, 5330400M04Rik, protein-containing complex, XClock, Enteroaggregative E. coli, presence, Cell, clk, count in organism, protein polypeptide chains, Readability, native protein, polypeptide chain, natural protein, Diffusely Adherent E. coli, Bacillus coli, PIG7, Escherchia coli, chemical analysis, Protein, synthetic, Enteroinvasive Escherichia coli, Enterococcus coli, internal to cell, synthetic genetic interaction (sensu inequality), protein aggregate, multicellular organismal biosynthetic process, protoplasm, bHLHe8, Diffusely Adherent Escherichia coli, single-organism biosynthetic process, Escherichia/Shigella coli, protoplast, Enteroinvasive E. coli, pre-mortem, formation, Engineerings, anabolism, KAT13D, cell-division cycle, synthetic genetic interaction defined by inequality, E coli, proteins, behavioral response to stimulus, mKIAA0334, synthetic constructs, E. coli, synthesis, Eschericia coli, Enteroaggregative Escherichia coli, living, Xclk, SYNTHETIC CONSTRUCT sequences, behavioural response to stimulus, Bacterium coli commune, artificial, assay, quantitative, SIMPLE, behaviour, intracellular, presence or absence in organism, TP53I7, single-organism behaviorextent, 6beta, nucleus of the stria terminalis, artificial sequence, nucleocytoplasm, Public Sectors, interstitial nucleus of stria terminalis, phenol sulfotransferase activity, alpha-Spe, CG30476/Ave, bacterium E3, Phage lambda, alpha-Spc, CG31654, ran, Long Term, 5730420M11Rik, dmTAF[[II]]230, membrane attack complex protein beta2 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protein_coding_transcript, HLA-DR-associated protein II, Enteroinvasive E. coli, DI-2, Engineerings, i59, I-2Dm, INSDC_feature:gene, alpha, inhibitor of granzyme A-activated DNase, nucleus proprius stria terminalis (bed nucleus), AP-2alpha, dRanGAP, bruce, DmelCG4260, I-2PP1, living, Sector, TAF-IBETA, protein synthesis, Taf250, 4-(dimethylamino)-1, syringoma, TAF-Ibeta, CG30476, TAF230, BEST:GH10550, microphthalmia-anophthalmia-coloboma syndrome, transcription, anon-EST:fe2E2, Sectors, DmelCG6303, Effects, AconM, alpha-Spect, number, l(2)jf5, l(2)jf4, 2-Naphthacenecarboxamide, dran, Copyrights, biosynthesis, 5330400M04Rik, protein-containing complex, body system, sulfokinase activity, ara24, CG7826, mRNA decay, fs(3)neo61, clk, CG10422, Sd-RanGAP, Sd-RanGap, Publication, Escherchia coli, MAC, dBRUCE, Gene Products, CG7835, CG42273, system, microphthalmia with colobomatous cyst, synthetic genetic interaction (sensu inequality), Enterprises, dBruce, micrometre, bed nuclei of the stria terminalis, anatomical systems, dTAF[[II]]250, DmelCG4104, Longterm, cell, mac, dopamine sulfotransferase activity, BcDNA:GH08860, cell-division cycle, dre3, messenger RNA, 2pp2a, TPS, Long-Term, Alpha-Adaptin, Public Enterprises, CG10574, HYP, synthesis, dTAF250, Halflife, template RNA, (4S-(4alpha, 2PP2A, mAc, 2-naphtholsulfotransferase activity, dSET, dSet, species, Enterprise, l(3)dre3, terminal complement complex, Alkalescens-Dispar Group, 4-nitrocatechol sulfokinase activity, cellular transcription, microphthalmos bilateral, alpha-Spectrin, Proteins, mAcon, ran10A, Dm-65, function, BG:DS00004.13, EAggEC, synthetic DNA, Cell, dTAF230, mRNA catabolism, near to, read, native protein, I-2PP2A, Public, tps1, chemical analysis, Dm I-2, Long Term Effects, INSDC_feature:mRNA, synthetic, stria terminalis nucleus, TAF[[II]]250/230, CG6303, MENE(2L)-A, alphaSp, Taf[[II]]250, AU020952, microcystic adnexal carcinoma of skin, mating_type_alpha, mRNA, 12aalpha))-, RanGap1, BcDNA:RE67675, DNA-templated, 12a-pentahydroxy-6-methyl-1, Understanding, micron, D630005A10Rik, Longterm Effects, nucleus interstitialis striae terminalis, ME-IV, plan specification, Gene Proteins, Xclk, AP2, Bacterium coli commune, Bam-C, vicinity of, alpha mating type (yeast), DmelCG30476, CG4104, phenol sulfokinase activity, AI266890, quantitative, AA501170, protein translation, A430040A19Rik, IPP2A2, tspst1, BamF, determination, BamC, AP-2, Stp, CG6457, A430032G04Rik, protein, 10, 11, Productivity, 12, Bst, BST, mRNA degradation, Readability, l(3)04276, ranGap, ranGAP, APOLLON, stp, SP116, microcystic adnexal carcinoma, alpha-adaptin, Min, Enterococcus coli, CG4104 PA, AAF30287, DmelCG10422, protein aggregate, Effect, DmelCG42273, multicellular organismal biosynthetic process, alpha-spec, single-organism biosynthetic process, rangap, m-acon, MCOPCB1, CG4260, dtps1, pre-mortem, TAF-I, Public Domains, SD, min, E coli, mRNA breakdown, mAPC, 3'-phosphoadenylyl-sulfate:phenol sulfotransferase activity, behavioral response to stimulus, mKIAA0334, µm, alpha-spectrin, E. coli, Enteroaggregative Escherichia coli, IGAAD, DNA-dependent, Hostacyclin, DmelCG10574, Half Life, Sd, nuclei of stria terminalis, jf5, Long-Term Effects, single-organism behavior, SPH116, phapii, protein anabolism, Coliphage lambda, Papers, CT28175, Dmel_CG7826, StF-IT-1, ham, aryl sulphotransferase activity, um, TAFII-250, Topicycline, TAF250/230, alphaSpec, TAFII250, 4a, cg4260, PST, AVE, bed nucleus of the stria terminalis, nucleus striae terminalis, internal to cell, ST1A1, spectrin, Dmel_CG7835, Domain, Mnb, MNB, MENE (2L)-A, Diffusely Adherent Escherichia coli, 5a, pst, CG4299, AW124434, CG17603, TAF[[II]], M-Acon, organ system, SYNTHETIC CONSTRUCT sequences, Achromycin, SR3-5, bacterial transcription, BRUCE, Bruce, FBgn0010100, artificial, CG9999, mitochondrial adhaerens complex, i2pp2a, Tetracycline Monohydrochloride, footnotes, 4aalpha, alpha-Ada, d230, l(3)alpha-Spec, Enterobacteria phage lambda, Gene, mKIAA1289, dTAFII250, syringomatous carcinoma, Ubiquitin-conjugating BIR domain enzyme apollon, colobomatous orbital cyst, EfW1, presence, l(2)SH2 0460, PHAPII, RanGAP, alpha-ada, method, polypeptide chain, template-activating factor I, intercalate nucleus of stria terminalis, DmelCG1404, dmTAF1, Taf230, method used in an experiment, resistance, klo, alpha-Sp, Enteroinvasive Escherichia coli, bed nucleus striae terminalis, lambda Phage, CG1977, DmelCG9244, TAF250, bHLHe8, protoplasm, 1-naphthol phenol sulfotransferase activity, Taf200, protoplast, formation, nucleus of stria terminalis, ipp2a2, REPR, synthetic genetic interaction defined by inequality, Tetrabid, Taf1p, dbruce, Abstract, st1a3, taf-ibeta, l(2)07054, Long-Term Effect, CG8588, TAF, behaviour, BIR repeat-containing ubiquitin-conjugating enzyme, TP53I7, DYRK1, Bacterium coli, TAF[[II]]250, 3A9, TreS, protein complex, synthesize, malignant, DmelCG1977, igaad, l(3)84Ab, artificial gene, arylsulfotransferase, gsp1, CG1404, count in organism, TC4, tc4, p-nitrophenol sulfotransferase activity, natural protein, Bacillus coli, p230, Protein, I2PP2A, protein biosynthesis, TFIID, TCC, Dyrk1, connected anatomical system, Data Base, l(1)G0075, DmelCG8588, colobomatous microphthalmia, TAF[[II]]230, ARA24, D-alphaAda, hsp60, CC1, 11-dioxo-, FCP-B, l(2)24Ea, stp1, TAF[II]250, synthetic constructs, sample population, Protein Gene Products, dSET/TAF-Ibeta, 2610030F17Rik, DmelCG17603, behavioural response to stimulus, CG9244, l(3)62Bd, concentration, Achromycin V, approaches, BAM, Gsp1, Bam, l(2)SH0460, alfa-Spec, Public., assay, variable, AA407739, 4 Epitetracycline, Spec, Scl, Ran, presence or absence in organism, TAF1synthetic, artificial, synthetic genetic interaction defined by inequality, SYNTHETIC CONSTRUCT sequences, artificial gene, synthetic genetic interaction (sensu inequality), artificial sequence, synthetic DNA, synthetic constructs.falseElowitz2000 - Repressilator Elowitz2000 - Repressilator This model describes the deterministic version of the repressilator system. The authors of this model (see reference) use three transcriptional repressor systems that are not part of any natural biological clock to build an oscillating network that they called the repressilator. The model system was induced in Escherichia coli. In this system, LacI (variable X is the mRNA, variable PX is the protein) inhibits the tetracycline-resistance transposon tetR (Y, PY describe mRNA and protein). Protein tetR inhibits the gene Cl from phage Lambda (Z, PZ: mRNA, protein),and protein Cl inhibits lacI expression. With the appropriate parameter values this system oscillates. This model is described in the article: A synthetic oscillatory network of transcriptional regulators. Elowitz MB, Leibler S. Nature. 2000 Jan; 403(6767):335-338 Abstract: Networks of interacting biomolecules carry out many essential functions in living cells, but the 'design principles' underlying the functioning of such intracellular networks remain poorly understood, despite intensive efforts including quantitative analysis of relatively simple systems. Here we present a complementary approach to this problem: the design and construction of a synthetic network to implement a particular function. We used three transcriptional repressor systems that are not part of any natural biological clock to build an oscillating network, termed the repressilator, in Escherichia coli. The network periodically induces the synthesis of green fluorescent protein as a readout of its state in individual cells. The resulting oscillations, with typical periods of hours, are slower than the cell-division cycle, so the state of the oscillator has to be transmitted from generation to generation. This artificial clock displays noisy behaviour, possibly because of stochastic fluctuations of its components. Such 'rational network design may lead both to the engineering of new cellular behaviours and to an improved understanding of naturally occurring networks. The model is based upon the equations in Box 1 of the paper; however, these equations as printed are dimensionless, and the correct dimensions have been returned to the equations, and the parameters set to reproduce Figure 1C (left). The original model was generated by B.E. Shapiro using Cellerator version 1.0 update 2.1127 using Mathematica 4.2 for Mac OS X (June 4, 2002), November 27, 2002 12:15:32, using (PowerMac,PowerPC, Mac OS X,MacOSX,Darwin). Nicolas Le Novere provided a corrected version generated by SBMLeditor on Sun Aug 20 00:44:05 BST 2006. This removed the EmptySet species. Ran fine on COPASI 4.0 build 18. Bruce Shapiro revised the model with SBMLeditor on 23 October 2006 20:39 PST. This defines default units and correct reactions. The original Cellerator reactions while being mathematically correct did not accurately reflect the intent of the authors. The original notes were mostly removed because they were mostly incorrect in the revised version. Tested with MathSBML 2.6.0. Nicolas Le Novere changed the volume to 1 cubic micrometre, to allow for stochastic simulation. Changed by Lukas Endler to use the average livetime of mRNA instead of its halflife and a corrected value of alpha and alpha0. Moreover, the equations used in this model were clarified, cf. below. The equations given in box 1 of the original publication are rescaled in three respects (lowercase letters denote the rescaled, uppercase letters the unscaled number of molecules per cell): the time is rescaled to the average mRNA lifetime, t_ave: τ = t/t_ave the mRNA concentration is rescaled to the translation efficiency eff: m = M/eff the protein concentration is rescaled to Km: p = P/Km α in the equations should be in units of rescaled proteins per promotor and cell, and β is the ratio of the protein to the mRNA decay rates or the ratio of the mRNA to the protein halflife. In this version of the model α and β are calculated correspondingly to the article, while p and m where just replaced by P/Km resp. M/eff and all equations multiplied by 1/t_ave . Also, to make the equations easier to read, commonly used variables derived from the parameters given in the article by simple rules were introduced. The parameters given in the article were: promotor strength (repressed) ( tps_repr ): 5*10 -4 transcripts/(promotor*s) promotor strength (full) ( tps_active ): 0.5 transcripts/(promotor*s) mRNA half life, τ 1/2,mRNA : 2 min protein half life, τ 1/2,prot : 10 min K M : 40 monomers/cell Hill coefficient n: 2 From these the following constants can be derived: average mRNA lifetime ( t_ave ): τ 1/2,mRNA /ln(2) = 2.89 min mRNA decay rate ( kd_mRNA ): ln(2)/ τ 1/2,mRNA = 0.347 min -1 protein decay rate ( kd_prot ): ln(2)/ τ 1/2,prot transcription rate ( a_tr ): tps_active*60 = 29.97 transcripts/min transcription rate (repressed) ( a0_tr ): tps_repr*60 = 0.03 transcripts/min translation rate ( k_tl ): eff*kd_mRNA = 6.93 proteins/(mRNA*min) α : a_tr*eff*τ 1/2,prot /(ln(2)*K M ) = 216.4 proteins/(promotor*cell*Km) α 0 : a0_tr*eff*τ 1/2,prot /(ln(2)*K M ) = 0.2164 proteins/(promotor*cell*Km) β : k_dp/k_dm = 0.2 Annotation by the Kinetic Simulation Algorithm Ontology (KiSAO): To reproduce the simulations run published by the authors, the model has to be simulated with any of two different approaches. First, one could use a deterministic method ( KISAO_0000035 ) with continuous variables ( KISAO_0000018 ). One sample algorithm to use is the CVODE solver ( KISAO_0000019 ). Second, one could simulate the system using Gillespie's direct method ( KISAO_0000029 ), which is a stochastic method ( KISAO_0000036 ) supporting adaptive timesteps ( KISAO_0000041 ) and using discrete variables ( KISAO_0000016 ). This model is hosted on BioModels Database and identified by: BIOMD0000000012 . To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models . To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information. 2013-07-102009-01-202005-09-13BIOMD000000001210659856CHEBI:33699MODEL6615351360BIOMD0000000012GO:0040029GO:0005623GO:0006402GO:0006412GO:0030163GO:0006351C00046562P03023P04483P03034