Team:UANL Mty-Mexico/Contributions/Parts

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Latest revision as of 17:26, 13 February 2012

Team: UANL_Mty-Mexico Team: UANL_Mty-Mexico

Contributions: Parts

Parts

Part name	Description	Favorited
BBa_K566000	OL region from Lambda phage allows biphasic switch (K566002) effective repression: When placed around 2.4 kb apart from OR (included in pRM) and in high [cI] conditions, cI octamerizes and loops the DNA stabilizing cI binding to OR3; such structure represses pRM promoter (K566001).
BBa_K566001	pRM promoter from Lambda phage. It may be positively and negatively regulated according to cI protein concentration. Low [cI] induce it, high [cI] repress it. It needs OL region (K566000) for effective repression. Makes the biphasic switch (K566002) together with OL region.
BBa_K566002	The Biphasic Switch combines positive and negative regulation through a single input. It is turned ON by low lambda cI concentrations and OFF by high cI concentrations.
BBa_K566003	*CFP optimized for E. coli.* Cyan fluorescent protein optimized from part BBa_E0022 with preferential codon usage for improved expression in E. coli. It is a monomeric protein generated on the basis of GFP-like protein from jellyfish Aequorea victoria . It possesses bright fluorescence with exitation/emission maxima at 434 and 477 nm, respectively. It has an extinction coefficient of 26,000 M-1 cm-1.
BBa_K566004	Protein generator of cyan fluorescent protein without transcription terminator. It may be negatively regulated by Mnt repressor (BBa_C0072).
BBa_K566005	pCpcG2 promoter (Green light inducible). Green light inducible pCpcG2 promoter from pJT122 plasmid constructed by Tabor et al. (2010). It is positively regulated by the two component system CcaS/R, which exhibits a maximum response in 535 nm and is inactivated in 650 nm light. Light intensities must be carefully regulated to achieve successful gene expression.
BBa_K566006	penI-pCpcG2-pPenI-mnt. Repression-based potential AND gate. Mnt Repressor is under the control of the PenI repressible promoter. PenI repressor is placed under the control of green light inducible pCpcG2 promoter. pCpcG2 promoter is positively regulated by the two component system CcaS/R, which exhibits a maximum response in 535 nm and is inactivated in 650 nm light.
BBa_K566007	PenI repressor optimized for E. coli (inverted sequence). Optimized PenI repressor with LVA tag from Bacillus licheniformis, with preferential codon usage for improved expression in E. coli. PenI negatively regulates transcription from pPenI promoter (BBa_R0074). The nucleotide sequence was inverted to ease DNA synthesis. .
BBa_K566008	*Mnt repressor optimized for E. coli. Mnt repressor optimized from part BBa_C0072 with preferential codon usage for improved expression in E. coli. It acts on pMnt promoter (BBa_R0073).*
BBa_K566009	pCpcG2 promoter, inverted sequence (Green light inducible). Inverted Green light inducible pCpcG2 promoter, from pJT122 plasmid constructed by Tabor et al. (2010). It is positively regulated by the two component system CcaS/R, which exhibits a maximum response in 535 nm and is inactivated in 650 nm light. Light intensities must be carefully regulated to achieve successful gene expression. The sequence was inverted to ease DNA synthesis.
BBa_K566010	PenI repressor optimized for E. coli (inverted sequence). Optimized PenI repressor with LVA tag from Bacillus licheniformis, with preferential codon usage for improved expression in E. coli. Negatively regulates transcription from pPenI promoter. (BBa_R0074). The nucleotide sequence was inverted to ease DNA synthesis.
BBa_K566011	cI434 repressor from phage 434 optimized for E. coli cI (+LVA). Optimized cI434 repressor with LVA tag from phage 434, with preferential codon usage for improved expression in E. coli.
BBa_K566012	*cI repressor from Lambda phage optimized for E. coli.* Includes LVA tag for faster degradation. It has preferential codons to improve their expression in E. coli.
BBa_K566013	*RFP optimized for E. coli* (+LVA).** Includes LVA tag for faster degradation. Preferential codons usage to improve their expression in E. coli.
BBa_K566015	pRM-RBS-cI434. Composite part for Biphasic switch tests. Include pRM promoter from phage λ pRM promoter from Lambda phage. It may be positively and negatively regulated according to cI protein concentration. Low [cI] turn it ON, high [cI] turn it OFF. It contains three operators named OR1, OR2 and OR3, all cI binding sites. When bound to OR1 and OR2, cI positively regulates pRM; cI binding to OR3 repress pRM. However, due to a low binding affinity to OR3, higher concentrations of the protein are required. A RBS sequence from the Elowitz repressilator that defines the RBS efficiency (BBa_B0034). Also contain the cI434 coding sequence optimized for E. coli, its come from the registered part cI434 repressor protein (BBa_C0052), It binds to the 434 regulatory sequence in λ pRM promoter. The sequence contains a LVA tag for faster degradation.
BBa_K566016	OL-pTetMnt-cI. Induction system for Biphasic Switch. It responds to negative repression from TetR or cI repressor.
BBa_K566017	pRM434-RFP. Red Fluorescent Protein under the control of pRM434 promoter. It was constructed for demonstrating dual state of a biphasic switch.
BBa_K566019	E. coli MxRed. Derived from Dr. Jeff Tabor JT2 E. coli strain, this part is a built-in red-light induction system in E. coli made through chromosome insertion. Avoiding the need of any extra-chromosomal DNA when light-inducing gene expression offering several advantages to the researcher. It is proposed as a photo-chassis that could make useful tools in this field of light induction. Integration include the genes pcyA, ho1, Cph8 and a Mnt working as follows: Genes ho1 and pcyA are responsible for the chromophore synthesis. Cph8 codes for the chimaeric red-light receptor. These three genes are constitutively expressed. Mnt repressor is expressed from pOmpC promoter, and the red light stops its induction. It is therefore used as a NOT-gate to regulate expression from pMnt.
BBa_K566020	Mnt repressor regulated by pOmpC. Mnt repressor optimized from part BBa_C0072 with preferential codon usage for improved expression in E. coli and regulated by pOmpc. It negatively regulates Mnt repressible promoter BBa_R0073.
BBa_K566021	pcyA CDS. Gene in charge of the cromophore synthesis. Along with ho1, in Synechocystis, converts heme into PCB via a two-step oxidation/reduction process.
BBa_K566022	ho1 CDS. ho1, along with pcyA, converts heme into the chromophore phycocyanobillin (PCB).
BBa_K566023	pcyA gene (constitutive expression). pcyA gene transcribed from constitutive promoter. It's in charge of the cromophore synthesis along with ho1 in Synechocystis which converts heme into PCB via a two-step oxidation/reduction process.
BBa_K566024	ho1 gene (constitutive expression). ho1 gene transcribed from constitutive promoter. ho1, along with pcyA, converts heme into the chromophore phycocyanobillin (PCB).
BBa_K566025	Cph8 CDS. The red light-sensing protein Cph8 is expressed in the phosphorylated ground state. It is switched to the unphosphorylated state by 650-nm light and back to the phosphorylated state by 705-nm light. When phosphorylated, Cph8 passes a phosphoryl group to OmpR, which then binds to and activates transcription from PompC. Because it is inactivated by red light, Cph8 can be considered a logical (NOT red) sensor. A genetic inverter or logical NOT gate is used to invert the response of the (NOT red) sensor to that of a red light sensor.
BBa_K566026	Cph8 gene for red-photoreceptor (constitutive expression). Cassette for constitutive expression of Cph8, originally constructed by Dr. Jeff Tabor. This gene codifies for the red light-sensing protein Cph8, which is expressed in the phosphorylated ground state. It is switched to the unphosphorylated state by 650-nm light and back to the phosphorylated state by 705-nm light. When phosphorylated, Cph8 passes a phosphoryl group to OmpR, which then binds to and activates transcription from PompC. Because it is inactivated by red light, Cph8 can be considered a logical (NOT red) sensor. A genetic inverter or logical NOT gate is used to invert the response of the (NOT red) sensor to that of a red light sensor.
BBa_K566027	CcaS. Ccas is a member of cyanobacteriochrome family of proteins. Phycocyanobillin (PCB) binds at a conserved cysteine domain of CcaS and activates signaling activity. CcaS, along with its response regulator CcaR, activates transcription of promoter pCpcG2. Activation shows max response with 535 nm wavelength green light and with 672 nm wavelength red light. When absorbing green light, CcaS autophosphorylates and then carries out phosphotransfer to CcaR. Phosphorylated CcaR (CcaR*) acts as a transcription factor for pCpcG2. This process can be reverted with absorption of red light.
BBa_K566028	CcaR. CcaR is the response regulator of CcaS, which is a member of cyanobacteriochrome family of proteins. Phycocyanobillin (PCB) binds at a conserved cysteine domain of CcaS and activates signaling activity. CcaS, along CcaR, activates transcription of promoter pCpcG2. Activation shows max response with 535 nm wavelength green light and with 672 nm wavelength red light. When absorbing green light, CcaS autophosphorylates and then carries out phosphotransfer to CcaR. Phosphorylated CcaR (CcaR*) acts as a transcription factor for pCpcG2. This process can be reverted with the absorption of red light.
BBa_K566029	CcaR gene (constitutive expression). CcaR is the response regulator of CcaS, which is a member of cyanobacteriochrome family of proteins. Phycocyanobillin (PCB) binds at a conserved cysteine domain of CcaS and activates signaling activity. CcaS, along CcaR, activates transcription of promoter pCpcG2. Activation shows max response with 535 nm wavelength green light and with 672 nm wavelength red light. When absorbing green light, CcaS autophosphorylates and then carries out phosphotransfer to CcaR. Phosphorylated CcaR (CcaR*) acts as a transcription factor for pCpcG2. This process can be reverted with the absorption of red light.
BBa_K566030	CcaS gene (constitutive expression). CcaS gene with constitutive expression. Ccas is a member of cyanobacteriochrome family of proteins. Phycocyanobillin (PCB) binds at a conserved cysteine domain of CcaS and activates signaling activity. CcaS, along with its response regulator CcaR, activates transcription of promoter pCpcG2. Activation shows max response with 535 nm wavelength green light and with 672 nm wavelength red light. When absorbing green light, CcaS autophosphorylates and then carries out phosphotransfer to CcaR. Phosphorylated CcaR (CcaR*) acts as a transcription factor for pCpcG2. This process can be reverted with absorption of red light.
BBa_K566031	E. coli MXGreen. Derived from Dr. Jeff Tabor JT2 E. coli strain, this part is a built-in green-light induction system in E. coli made through chromosome insertion. Avoiding the need of any extra-chromosomal DNA when light-inducing gene expression offering several advantages to the researcher. It is proposed as a photo-chassis that could make useful tools in this field of light induction. Integration was performed for the genes pcyA, ho1, Cph8 and a Mnt working as follows: Genes ho1 and pcyA are responsible for the chromophore synthesis. Cph8 codes for the chimaeric red-light receptor. These three genes are constitutively expressed. Mnt repressor is expressed from pOmpC promoter, which stops being induced in presence of red-light. It is therefore used as a NOT-gate to regulate expression from pMnt.
BBa_K566032	E. coli MXRedGreen.
BBa_K566035	OL region from Lambda (Inverted). Inverted version of the OL region from Lambda phage. The nucleotide sequence was inverted to ease DNA synthesis.
BBa_K566036	pTet/Mnt Hybrid Promoter (Inverted). Inverted version of the Mnt promoter K091105. The nucleotide sequence was inverted to ease DNA synthesis.
BBa_K566037	RBS.3 (Inverted). Inverted version of the RBS.3 (BBa_B0032). It's a middle strenght RBS. The nucleotide sequence was inverted to ease DNA synthesis.
BBa_K566038	cI repressor from Lambda phage optimized for E. coli cI +LVA (Inverted). Inverted version of the cI repressor (K566012). It was optimized for codon usage of E. coli. The nucleotide sequence was inverted to ease DNA synthesis.
BBa_K566039	OL-pTetMnt-cI (Inverted). Inverted version of OL-pTetMnt-cI composite part (BBa_K566016). The nucleotide sequence was inverted to ease DNA synthesis.
BBa_K566040	pRM434-RFP with double terminator. Red Fluorescent Protein under the control of pRM434 promoter (K566017) with a double terminator. It represent the second state for Biphasic switch
BBa_K566042	Second State for Biphasic switch. Biphasic switch proof concept. Composite part of BBa_K566015, BBa_K145015, BBa_B0014 and BBa_K566039. The biphasic switch may be used to control both expression and repression of pRM through a single input, which must control cI protein concentration. Furthermore, if repressor cI434 is placed under pRM's control along with the gene of interest, this switch may be coupled with the modified promoter pRM434 BBa_I12006, which is stimulated by cI but repressed by cI434; hence resulting in a two-state switch controlled through a single input. The expected behavior will be the following: 1) at low concentrations of cI, both promoters will be activated. However, because of cI434 repressing pRM434, only pRM will stay ON eventually leading to the first state. 2) At high concentrations of cI, pRM -and consequently cI434- will be turned OFF, allowing pRM434 to be activated by cI and leading to a second state. pRM promoter from Phage 434 (not to confuse with pRM434 mentioned above) seems to exhibit the same biphasic behavior. This part is intended to prove the behavior shown in figure 1, using fluorescent proteins as reporter genes. It is coupled with the part K566040 , which contains the pRM434 promoter. GFP -transcribed from pRM- represents the first state, while YFP -transcribed from pRM434- represents the second state.

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      <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_K566020" target="_new">BBa_K566020</a></td>
-     <td class="justified"><b>Mnt repressor regulated by pOmpC.</b> Mnt repressor optimized from part <a href="http://partsregistry.org/Part:BBa_C0072" target="_new" >BBa_C0072</a> with preferential codon usage for improved expression in E. coli and regulated by pOmpc. It negatively regulates Mnt repressible promoter (BBa_R0073).</td>
+     <td class="justified"><b>Mnt repressor regulated by pOmpC.</b> Mnt repressor optimized from part <a href="http://partsregistry.org/Part:BBa_C0072" target="_new" >BBa_C0072</a> with preferential codon usage for improved expression in E. coli and regulated by pOmpc. It negatively regulates Mnt repressible promoter <a href="http://partsregistry.org/Part:BBa_R0073" target="_new" >BBa_R0073</a>.</td>
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      <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_K566028" target="_new" >BBa_K566028</a></td>
-     <td class="justified"><b>CcaR.</b> CcaR is the response regulator of CcaS, wich is a member of cyanobacteriochrome family of proteins. Phycocyanobillin (PCB) binds at a conserved cysteine domain of CcaS and activates signaling activity. CcaS, along CcaR, activates transcription of promoter pCpcG2. Activation shows max response with 535 nm wavelength green light and with 672 nm wavelength red light. When absorbing green light, CcaS autophosphorylates and then carries out phosphotransfer to CcaR. Phosphorylated CcaR (CcaR*) acts as a transcription factor for pCpcG2. This process can be reverted with the absorption of red light.</td>
+     <td class="justified"><b>CcaR.</b> CcaR is the response regulator of CcaS, which is a member of cyanobacteriochrome family of proteins. Phycocyanobillin (PCB) binds at a conserved cysteine domain of CcaS and activates signaling activity. CcaS, along CcaR, activates transcription of promoter pCpcG2. Activation shows max response with 535 nm wavelength green light and with 672 nm wavelength red light. When absorbing green light, CcaS autophosphorylates and then carries out phosphotransfer to CcaR. Phosphorylated CcaR (CcaR*) acts as a transcription factor for pCpcG2. This process can be reverted with the absorption of red light.</td>
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      <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_K566029" target="_new" >BBa_K566029</a></td>
-     <td class="justified"><b>CcaR gene (constitutive expression).</b> CcaR is the response regulator of CcaS, wich is a member of cyanobacteriochrome family of proteins. Phycocyanobillin (PCB) binds at a conserved cysteine domain of CcaS and activates signaling activity. CcaS, along CcaR, activates transcription of promoter pCpcG2. Activation shows max response with 535 nm wavelength green light and with 672 nm wavelength red light. When absorbing green light, CcaS autophosphorylates and then carries out phosphotransfer to CcaR. Phosphorylated CcaR (CcaR*) acts as a transcription factor for pCpcG2. This process can be reverted with the absorption of red light.</td>
+     <td class="justified"><b>CcaR gene (constitutive expression).</b> CcaR is the response regulator of CcaS, which is a member of cyanobacteriochrome family of proteins. Phycocyanobillin (PCB) binds at a conserved cysteine domain of CcaS and activates signaling activity. CcaS, along CcaR, activates transcription of promoter pCpcG2. Activation shows max response with 535 nm wavelength green light and with 672 nm wavelength red light. When absorbing green light, CcaS autophosphorylates and then carries out phosphotransfer to CcaR. Phosphorylated CcaR (CcaR*) acts as a transcription factor for pCpcG2. This process can be reverted with the absorption of red light.</td>
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