Difference between revisions of "Team:ZJU-China/Parts"

    This Part Collection consists of parts from three different systems: oscillation system, light-dependent control system and logical gate system. Parts numbered from K1886000 to K1886002 belong to the oscillation system, in which two quorum sensing auto inducers, AHL and DPD reach their peak value alternately. Parts numbered from K1886003 to K1886006 and K1886017 belong to light-dependent control system, which can output either green or red florescent protein in response to different inputs (green or red light). Parts numbered from K1886010 to K1886013 belong to AND gate system. It can realize the coupling of the output of the two systems mentioned above. The combination of AHL/DPD and green/red light results the production of green/red florescent protein. There is other AND gate circuits that use IPTG/ARA and red/green light as input, in order to test the coupling of light-dependent control system and the AND gate. The range of part number is from K1886000 to K1886017.

Part Number	Part Type	Short Description	Long Description
BBa_K1886000	Device	pluxR->luxS	luxS is controlled by pluxR promoter. luxS is a kind of DPD synthetase, which could produce DPD (4,5-dihydroxy 2,3-pentanedione) under the cooperation of Pfs enzyme. DPD exists widely in Gram-negative bacteria and Gram-positive bacteria as the signaling factor for quorum sensing, in order to complete the information transfer process within different kinds of bacteria.
BBa_K1886001	Device	AHL single-cycled oscillation pluxL-luxR-pluxR-luxI(LAA tag)-pluxL-luxR-pluxR-aiiA(LAA tag)	This circuit is composed of the constitutive promoter -- broken Ptet and membrane protein cph8. Under dark conditions, protein cph8 could transfer its phosphoryl group to intracellular protein ompR (ompR is native protein carried by E.coli), and this process could be inhibited by 650-nm light.
BBa_K1886002	Device	AHL,DPD double-cycled oscillation pluxL-luxR-pluxR-luxI(LAA tag)-pluxL-luxR-pluxR-aiiA(LAA tag)-luxpR-luxS	Two molecules of luxR binds with AHL (catalyzed by luxI), and this compound will promote the activity of pluxR. pluxR controls the expression of gene aiiA , encoding the enzyme which degrades AHLs. And all of these form an AHL single-cycled oscillation.

Part Number	Part Type	Short Description	Long Description
BBa_K1886003	Device	PcpcG2-sfGFP-ccaR	This circuit is composed of the inducible promoter cpcG2 and reporter gene and intracellular protein gene ccaR. ccaR could activate the cpcG2 promoter after being phosphorylated. cpcG2 could be activated by the phosphorylated ccaR protein, and induce the expression of reporter gene sfGFP.
BBa_K1886004	Coding	ccaS	This circuit is composed of the constitutive promoter and photosensitive protein gene ccaS . ccaS protein is membrane protein. After being activated by 520-nm light, it could transfer its phosphoryl group to the intracellular protein ccaR,and this process could be inhibited by 650-nm light.
BBa_K1886005	Device	Constitutive promoter-ho1-pcyA	This circuit is composed of the constitutive promoter, ho1 chromoprotein and pcya chormoprotein. They facilitate Membrane protein ccaS and cph8 to be activated by light of certain wavelength.
BBa_K1886006	Device	broken Ptet-cph8	This circuit is composed of the constitutive promoter -- broken Ptet and membrane protein cph8. Under dark conditions, protein cph8 could transfer its phosphoryl group to intracellular protein ompR (ompR is native protein carried by E.coli), and this process could be inhibited by 650-nm light.

Part Number	Part Type	Short Description	Long Description
BBa_K1886007	Device	AND GATE-input	This is the input part of AND GATE. After being induced by IPTG, plac promoter activates the expression of T7 RNA polymerase which contains two amber mutations (T7 ptag) . After being induced by L-arabinose, pBAD promoter activates the expression of a special tRNA (supD), which is used to identify amber mutation. In the wild-type E.coli, amber mutation will inhibit the translation of T7 RNA polymerase. Therefore, only when the two inputs exist together, T7 RNA polymerase can be expressed, and then T7 promoter can be activated to express the downstream gene.
BBa_K1886008	Device	AND GATE-output-1	This is a report system to test the AND GATE made up of SupD tRNA coding gene and T7 polymerase with two amber mutations. T7 promoter is a very specific promoter which is transcribed only by specific T7 RNA polymerase. Following the PT7 promoter is the reporter gene GFP, Only when the two inputs are given, the GFP gene can be expressed.
BBa_K1886009	Device	AND GATE-output-2	This is a report system to test the AND GATE made up of SupD tRNA coding gene and T7 polymerase with two amber mutations. T7 promoter is a very specific promoter which is transcribed only by specific T7 RNA polymerase. Following the PT7 promoter is the reporter gene RFP, Only when the two inputs are given, the RFP gene can be expressed.
BBa_K1886010	Device	AND GATE-input（AHL+green light)	The circuit to receive input signals is composed of AND GATE, quorum sensing promoter and light-controlled promoter. After being induced by AHL, pLuxR promoter activates the expression of T7 RNA polymerase (T7 ptag) which contains two amber mutations. After being induced by green light, PcpcG2 promoter activates the expression of a special tRNA (supD), which is used to identify amber mutation. In the wild-type E.coli, amber mutation will inhibit the translation of T7 RNA polymerase. Therefore, when AHL and green light exist together, T7 RNA polymerase will be expressed, and then T7 promoter will be activated to express the downstream gene.
BBa_K1886011	Device	AND GATE-input（AHL+red light)	The circuit to receive input signals is composed of AND GATE, quorum sensing promoter and light-controlled promoter. After being induced by AHL, pLuxR promoter activates the expression of T7 RNA polymerase (T7 ptag) which contains two amber mutations. The expression of a special tRNA (supD), which is used to identify amber mutation, is activated by Pλ promoter without the restraint of CL protein. In the wild-type E.coli, amber mutation will inhibit the translation of T7 RNA polymerase, and red light could inhibit the produce of CL protein(for more information, see the part"PompC-NOT Gate"). Therefore, when AHL and red light exist together, T7 RNA polymerase will be expressed, and then T7 promoter will be activated to express the downstream gene.
BBa_K1886012	Device	AND GATE-input（DPD+green light)	The circuit to receive input signals is composed of AND GATE, quorum sensing promoter and light-controlled promoter. After being induced by DPD, plsrA promoter activates the expression of T7 RNA polymerase which contains two amber mutations (T7ptag) . After being induced by green light, PcpcG2 promoter activates the expression of a special tRNA (supD), which is used to identify amber mutation. In the wild-type E.coli, amber mutation will inhibit the translation of T7 RNA polymerase. Therefore, when DPD and green light exist together, T7 RNA polymerase will be expressed, and then T7 promoter will be activated to express the downstream gene.
BBa_K1886013	Device	AND GATE-input（DPD+ red light)	The circuit to receive input signals is composed of AND GATE, quorum sensing promoter and light-controlled promoter. After being induced by DPD, plsrA promoter activates the expression of T7 RNA polymerase which contains two amber mutations(T7ptag) . The expression of a special tRNA (supD), which is used to identify amber mutation, is activated by Pλ promoter without the restraint of CL protein. In the wild-type E.coli, amber mutation will inhibit the translation of T7 RNA polymerase, and red light could inhibit the produce of CL protein(for more information, see the part"PompC-NOT Gate"). Therefore, when DPD and green light exist together, T7 RNA polymerase will be expressed, and then T7 promoter will be activated to express the downstream gene.
BBa_K1886014	Device	AND GATE-input（red light+IPTG）	The circuit to receive input signals is composed of AND GATE, plac promoter and light-controlled promoter. After being induced by IPTG, plac promoter activates the expression of T7 RNA polymerase (T7 ptag) which contains two amber mutations. The expression of a special tRNA (supD), which is used to identify amber mutation, is activated by Pλ promoter without the restraint of CL protein. In the wild-type E.coli, amber mutation will inhibit the translation of T7 RNA polymerase, and red light could inhibit the produce of CL protein(for more information, see the part"PompC-NOT Gate"). Therefore, when IPTG and red light exist together, T7 RNA polymerase will be expressed, and then T7 promoter will be activated to express the downstream gene.
BBa_K1886015	Device	AND GATE-input（green light+IPTG）	The circuit to receive input signals is composed of AND GATE, plac promoter and light-controlled promoter. After being induced by IPTG, plac promoter activates the expression of T7 RNA polymerase (T7 ptag) which contains two amber mutations. After being induced by green light, PcpcG2 promoter activates the expression of a special tRNA (supD), which is used to identify amber mutation. In the wild-type E.coli, amber mutation will inhibit the translation of T7 RNA polymerase. Therefore, when IPTG and green light exist together, T7 RNA polymerase will be expressed, and then T7 promoter will be activated to express the downstream gene.
BBa_K1886016	Device	AND GATE-input（IPTG+ara）	This is the input part of AND GATE. After being induced by L-arabinose, pbad promoter activates the expression of T7 RNA polymerase which contains two amber mutations (T7 ptag) . After being induced by IPTG, plac promoter activates the expression of a special tRNA (supD), which is used to identify amber mutation. In the wild-type E.coli, amber mutation will inhibit the translation of T7 RNA polymerase. Therefore, only when the two inputs exist together, T7 RNA polymerase can be expressed, and then T7 promoter can be activated to express the downstream gene.