Team:UANL Mty-Mexico/Contributions/Parts

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============================================================================================
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*** Acknowledgments ***
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>>>To TU_Delf Team
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Thank you so much to TU_Delft iGEM2010 team for providing us with so many examples of html code and how to apply them.
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If you like some of this code please check it out in their wiki: https://2010.igem.org/Team:TU_Delft#page=Modeling/wiki-tips-tricks
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  <title>Team: UANL_Mty-Mexico</title>
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<META NAME="keywords" CONTENT="UANL,iGEM,Universidad,Autonoma,Nuevo,Leon,Biphasic,switch,Lambda,Genetic,Regulation,Quorum,Sensing,pRM,OL,Green Light,Red Light">
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<META NAME="description" CONTENT="iGEM-UANL is the representative team from Universidad Autonoma de Nuevo León, at Monterrey, México. This team is composed of ten students who spent their summer in the lab, having fun with transformations, constructions and plasmidic DNA extractions. This">
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<META NAME="abstract" CONTENT="Information processing through living things remains a challenge to science. Genetic logic-gates and">
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<META NAME="author" CONTENT="iGEM-UANL">
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             Contributions
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             Contributions: Parts
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     <td class="adjacent">Part name</td>
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    <td class="adjacent">Description</td>
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    <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_K566000">BBa_K566000</a></td>
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    <td class="final"><b>OL region from Lambda phage</b> allows biphasic switch <a href="http://partsregistry.org/Part:BBa_K566002" >(K566002)</a> 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 <a href="http://partsregistry.org/Part:BBa_K566001" >(K566001)</a>.</td>
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    <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_K566001">BBa_K566001</a></td>
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    <td class="final"><b>pRM promoter from Lambda</b> 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 <a href="http://partsregistry.org/Part:BBa_K566000" >(K566000)</a> for effective repression. Makes the biphasic switch <a href="http://partsregistry.org/Part:BBa_K566002" >(K566002)</a> together with OL region. </td>
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    <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_K566002">BBa_K566002</a></td>
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    <td class="final">The <b>Biphasic Switch</b> combines positive and negative regulation through a single input. It is turned ON by low lambda cI concentrations and OFF by high cI concentrations.</td>
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    <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_K566003">BBa_K566003</a></td>
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    <td class="final"> <b>CFP optimized for <i>E. coli</i>.</b> Cyan fluorescent protein optimized from part <a href="http://partsregistry.org/Part:BBa_E0022">BBa_E0022</a> with preferential codon usage for improved expression in <i>E. coli</i>. 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.</td>
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    <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_K566004">BBa_K566004</a></td>
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    <td class="final"><b>Protein generator of cyan fluorescent protein without transcription terminator.</b> It may be negatively regulated by Mnt repressor <a href="http://partsregistry.org/Part:BBa_C0072">(BBa_C0072)</a>.</td>
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    <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_K566005">BBa_K566005</a></td>
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    <td class="final"><b>pCpcG2 promoter (Green light inducible).</b> 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.</td>
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    <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_K566006">BBa_K566006</a></td>
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    <td class="final"> <b>penI-pCpcG2-pPenI-mnt.</b> 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.</td>
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    <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_K566007">BBa_K566007</a></td>
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    <td class="final"><b>PenI repressor optimized for E. coli (inverted sequence).</b> Optimized PenI repressor with LVA tag from Bacillus licheniformis, with preferential codon usage for improved expression in <i>E. coli</i>. PenI negatively regulates transcription from pPenI promoter <a href="http://partsregistry.org/Part:BBa_R0074">(BBa_R0074)</a>.</td>
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    <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_K566008">BBa_K566008</a></td>
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    <td class="final"><b>Mnt repressor optimized for <i>E. coli</i>.<b> Mnt repressor optimized from part BBa_C0072 with preferential codon usage for improved expression in <i>E. coli</i>. It acts on pMnt promoter <a href="http://partsregistry.org/Part:BBa_R0073">(BBa_R0073)</a>.</td>
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    <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_K566009">BBa_K566009</a></td>
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    <td class="final"><b>pCpcG2 promoter, inverted sequence (Green light inducible).</b> 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.</td>
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    <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_K566010">BBa_K566010</a></td>
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    <td class="final"><b>PenI repressor optimized for E. coli (inverted sequence).</b> Optimized PenI repressor with LVA tag from Bacillus licheniformis, with preferential codon usage for improved expression in <i>E. coli</i>. Negatively regulates transcription from pPenI promoter. <a href="http://partsregistry.org/Part:BBa_R0074">(BBa_R0074)</a>. The nucleotide sequence was inverted to ease DNA synthesis.</td>
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    <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_K566011">BBa_K566011</a></td>
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    <td class="final"><b>cI434 repressor from phage 434 optimized for E. coli cI (+LVA).</b> Optimized cI434 repressor with LVA tag from phage 434, with preferential codon usage for improved expression in <i>E. coli</i>.</td>
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    <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_K566012">BBa_K566012</a></td>
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    <td class="final"><b>cI repressor from Lambda phage optimized for <i>E. coli</i>.</b> Includes LVA tag for faster degradation.<br/>
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It has preferential codons to improve their expression in <i>E. coli</i>.</td>
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  </tr> 
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    <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_K566013">BBa_K566013</a></td>
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    <td class="final"><b>RFP optimized for <i>E. coli</i> (+LVA).</b> Includes LVA tag for faster degradation.<br/>
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Preferential codons usage to improve their expression in <i>E. coli</i>.</td>
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  </tr> 
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    <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_K566015">BBa_K566015</a></td>
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    <td class="final"><b>pRM-RBS-cI434.</b> 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. <br/>
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A RBS sequence from the Elowitz repressilator that defines the RBS efficiency <a href="http://partsregistry.org/Part:BBa_B0034">(BBa_B0034)</a>. Also contain the cI434 coding sequence optimized for <i>E. coli</i>, its come from the registered part cI434 repressor protein <a href="http://partsregistry.org/Part:BBa_C0052">(BBa_C0052)</a>, It binds to the 434 regulatory sequence in λ pRM promoter. The sequence contains a LVA tag for faster degradation. </td>
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    <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_K566016" >BBa_K566016</a></td>
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    <td class="final"> <b>OL-pTetMnt-cI.</b> Induction system for Biphasic Switch. <br/>
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It responds to negative repression from TetR or cI repressor. </td>
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  </tr>
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  <tr>
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    <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_K566017" >BBa_K566017</a></td>
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    <td class="final"><b>pRM434-RFP.</b> Red Fluorescent Protein under the control of pRM434 promoter. It was constructed for demonstrating dual state of a biphasic switch. </td>
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    <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_K566019">BBa_K566019</a></td>
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    <td class="final"><b>E. coli MxRed.</b> Derived from Dr. Jeff Tabor JT2 <i>E. coli</i> strain, this part is a built-in red-light induction system in <i>E. coli</i> made through chromosome insertion. Avoiding the need of any extra-chromosomal DNA when light-inducing gene expression offering several advantages to the researcher. <br/>
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It is proposed as a photo-chassis that could make useful tools in this field of light induction. <br/>
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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.
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    <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_K566020">BBa_K566020</a></td>
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    <td class="final"><b>Mnt repressor regulated by pOmpC.</b> </td>
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    <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_K566021">BBa_K566021</a></td>
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    <td class="final"><b>pcyA CDS.</b></td>
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    <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_K566022" >BBa_K566022</a></td>
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    <td class="final"><b>ho1 CDS</b></td>
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  </tr>
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  <tr>
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    <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_K566023" >BBa_K566023</a></td>
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    <td class="final"><b>pcyA gene (constitutive expression).</b> pcyA gene transcribed from constitutive promoter.</td>
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  </tr>
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  <tr>
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    <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_K566024" >BBa_K566024</a></td>
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    <td class="final"><b>ho1 gene (constitutive expression).</b> ho1 gene transcribed from constitutive promoter. ho1, along with pcyA, converts heme into the chromophore phycocyanobillin (PCB). </td>
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    <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_K566025" >BBa_K566025</a></td>
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    <td class="final"><b>Cph8 CDS.</b> 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.</td>
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    <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_K566026" >BBa_K566026</a></td>
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    <td class="final"><b>Cph8 gene for red-photoreceptor (constitutive expression).</b> Cassette for constitutive expression of Cph8, originally constructed by Dr. Jeff Tabor.<br/>
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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. </td>
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    <div class="lateral-button"><a href="https://2011.igem.org/Team:UANL_Mty-Mexico/Project/The_Code">The Code</a></div>
 
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    <div class="lateral-button"><a href="https://2011.igem.org/Team:UANL_Mty-Mexico/Project/Mechanism">Mechanism</a></div>
 
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Revision as of 23:19, 28 September 2011

banner-main iGEM-logo
Team: UANL_Mty-Mexico
Team: UANL_Mty-Mexico {{:Team:UANL_Mty-Mexico/Templates/Banner-template}} {{:Team:UANL_Mty-Mexico/Templates/Menu-template}} Team: UANL_Mty-Mexico
Contributions: Parts
Parts
Part name Description
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).
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.
BBa_K566021 pcyA CDS.
BBa_K566022 ho1 CDS
BBa_K566023 pcyA gene (constitutive expression). pcyA gene transcribed from constitutive promoter.
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.
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Team: UANL_Mty-Mexico

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