Team:UPO-Sevilla/Biobricks/Parts

From 2010.igem.org

(Difference between revisions)
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                         <td>UPO-04</td>
                         <td>UPO-04</td>
                         <td>BBa_K367000</td>
                         <td>BBa_K367000</td>
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                         <td>prhA</td>
+
                         <td><i>prhA</i></td>
                         <td>Coding sequence</td>
                         <td>Coding sequence</td>
                         <td>Synthesis</td>
                         <td>Synthesis</td>
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                         <td>Ralstonia solanacearum gene prhA, encoding an outer membrane protein
+
                         <td><i>Ralstonia solanacearum</i> gene <i>prhA</i>, encoding an outer membrane protein
                             that senses a signal on plant cell walls and transduces it through the
                             that senses a signal on plant cell walls and transduces it through the
                             bacterial cell envelop to stimulate transcription from several operons.
                             bacterial cell envelop to stimulate transcription from several operons.
-
                             Optimized sequence to be expressed in Escherichia coli.</td>
+
                             Optimized sequence to be expressed in <i>Escherichia coli.</i></td>
                     </tr>
                     </tr>
                     <tr>
                     <tr>
                         <td>UPO-05</td>
                         <td>UPO-05</td>
                         <td>BBa_K367001</td>
                         <td>BBa_K367001</td>
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                         <td>prhR</td>
+
                         <td><i>prhR</i></td>
                         <td>Coding sequence</td>
                         <td>Coding sequence</td>
                         <td>Synthesis</td>
                         <td>Synthesis</td>
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                         <td>Ralstonia solanacearum gene prhR, encoding a membrane signal transduction
+
                         <td><i>Ralstonia solanacearum</i> gene <i>prhR</i>, encoding a membrane signal transduction
                             protein involved in the Prh pathway. The nondiffusible plant cell wall
                             protein involved in the Prh pathway. The nondiffusible plant cell wall
                             signal is transduced by the N-terminal extension of PrhA to the C-terminal
                             signal is transduced by the N-terminal extension of PrhA to the C-terminal
                             part of the transmembrane protein PrhR and then through PrhR across the
                             part of the transmembrane protein PrhR and then through PrhR across the
-
                             cytoplasmic membrane. Optimized sequence to be expressed in Escherichia coli.</td>
+
                             cytoplasmic membrane. Optimized sequence to be expressed <i>in Escherichia coli.</i></td>
                     </tr>
                     </tr>
                     <tr>
                     <tr>
                         <td>UPO-06</td>
                         <td>UPO-06</td>
                         <td>BBa_K367002</td>
                         <td>BBa_K367002</td>
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                         <td>prhI</td>
+
                         <td><i>prhI</i></td>
                         <td>Coding sequence</td>
                         <td>Coding sequence</td>
                         <td>Synthesis</td>
                         <td>Synthesis</td>
-
                         <td>Ralstonia solanacearum gene prhI, encoding an ECF sigma factor responsible
+
                         <td><i>Ralstonia solanacearum</i> gene <i>prhI</i>, encoding an ECF sigma factor responsible
                             for transcription dependent on the Prh signal transduction system. PrhI
                             for transcription dependent on the Prh signal transduction system. PrhI
                             is activated by PrhR and then the sigma factor induces the expression by
                             is activated by PrhR and then the sigma factor induces the expression by
-
                             activating PprhJ promoter. Optimized sequence to be expressed in Escherichia coli.</td>
+
                             activating P<i>prhJ</i> promoter. Optimized sequence to be expressed in <i>Escherichia coli.</i></td>
                     </tr>
                     </tr>
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                         <td>UPO-11</td>
                         <td>UPO-11</td>
                         <td>BBa_K367008</td>
                         <td>BBa_K367008</td>
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                         <td>PprhJ</td>
+
                         <td>P<i>prhJ</i></td>
                         <td>Promoter</td>
                         <td>Promoter</td>
                         <td>Synthesis</td>
                         <td>Synthesis</td>
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                         <td>The PprhJ promoter region, responsive to plant cell contact via signal transduction
+
                         <td>The P<i>prhJ</i> promoter region, responsive to plant cell contact via signal transduction
                             by PrhA and PrhR and activation by ECF sigma factor PrhI. Optimized sequence to be
                             by PrhA and PrhR and activation by ECF sigma factor PrhI. Optimized sequence to be
-
                             expressed in Escherichia coli.</td>
+
                             expressed in <i>Escherichia coli.</i></td>
                     </tr>
                     </tr>
                     <tr>
                     <tr>
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                         <td>UPO-07</td>
                         <td>UPO-07</td>
                         <td>BBa_K367006</td>
                         <td>BBa_K367006</td>
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                         <td>fecA-prhA</td>
+
                         <td><i>fecA-prhA</i></td>
                         <td>Coding sequence</td>
                         <td>Coding sequence</td>
                         <td>Synthesis</td>
                         <td>Synthesis</td>
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                         <td>Artificial coding sequence spanning the first 92 codons of fecA, encoding the signal
+
                         <td>Artificial coding sequence spanning the first 92 codons of <i>fecA</i>, encoding the signal
                             peptide (aa. 1-33), the proposed Ton-box (aa. 54-63), fused to the distal end of
                             peptide (aa. 1-33), the proposed Ton-box (aa. 54-63), fused to the distal end of
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                             the prhA coding sequence at the conserved GSGL motif (aa. 89-92). This hybrid
+
                             the <i>prhA</i> coding sequence at the conserved GSGL motif (aa. 89-92). This hybrid
                             protein allows to sense nondifusible signals and to transduce it by the well known
                             protein allows to sense nondifusible signals and to transduce it by the well known
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                             Fec pathway. Optimized sequence to be expressed in Escherichia coli.</td>
+
                             Fec pathway. Optimized sequence to be expressed in <i>Escherichia coli.</i></td>
                     </tr>
                     </tr>
                     <tr>
                     <tr>
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                         <td>UPO-08</td>
                         <td>UPO-08</td>
                         <td>BBa_K367003</td>
                         <td>BBa_K367003</td>
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                         <td>fecA</td>
+
                         <td><i>fecA</i></td>
                         <td>Coding sequence</td>
                         <td>Coding sequence</td>
                         <td>Made by PCR and SDM</td>
                         <td>Made by PCR and SDM</td>
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                         <td>Gene fecA of Escherichia coli, encoding an outer membrane ferric citrate sensor that
+
                         <td>Gene <i>fecA</i> of <i>Escherichia coli</i>, encoding an outer membrane ferric citrate sensor that
                             initiates signal transduction via FecR and FecI to activate transcription.</td>
                             initiates signal transduction via FecR and FecI to activate transcription.</td>
                     </tr>
                     </tr>
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                         <td>UPO-28</td>
                         <td>UPO-28</td>
                         <td>BBa_K367012</td>
                         <td>BBa_K367012</td>
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                         <td>fecI & fecR</td>
+
                         <td><i>fecI</i> & <i>fecR</i></td>
                         <td>Two overlapping coding sequences</td>
                         <td>Two overlapping coding sequences</td>
                         <td>Made by PCR and SDM</td>
                         <td>Made by PCR and SDM</td>
-
                         <td>fecI and fecR genes of Escherichia coli, encoding an ECF sigma factor and a membrane
+
                         <td><i>fecI</i> and <i>fecR</i> genes of <i>Escherichia coli</i>, encoding an ECF sigma factor and a membrane
                             signal transduction protein respectively, involved in signal transduction of the ferric
                             signal transduction protein respectively, involved in signal transduction of the ferric
                             citrate-dependent Fec system. They have been synthesized in the same Biobrick because
                             citrate-dependent Fec system. They have been synthesized in the same Biobrick because
                             of their 4 bp overlap, not to reduce their expression. FecR protein interacts with the
                             of their 4 bp overlap, not to reduce their expression. FecR protein interacts with the
-
                             outer membrane sensor FecA and activates the sigma factor FecI, which acts over PfecA promoter region.</td>
+
                             outer membrane sensor FecA and activates the sigma factor FecI, which acts over P<i>fecA</i> promoter region.</td>
                     </tr>
                     </tr>
                     <tr>
                     <tr>
                         <td>UPO-12</td>
                         <td>UPO-12</td>
                         <td>BBa_K367009</td>
                         <td>BBa_K367009</td>
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                         <td>PfecA</td>
+
                         <td>P<i>fecA</i></td>
                         <td>Promoter</td>
                         <td>Promoter</td>
                         <td>Made by PCR</td>
                         <td>Made by PCR</td>
-
                         <td>Escherichia coli PfecA promoter region, repressed by Fur under iron excess, and
+
                         <td><i>Escherichia coli</i> P<i>fecA</i> promoter region, repressed by Fur under iron excess, and
                             induced by ferric citrate through the FecA-FecR signal transduction pathway and
                             induced by ferric citrate through the FecA-FecR signal transduction pathway and
                             the FecI ECF sigma factor.</td>
                             the FecI ECF sigma factor.</td>
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                         <td>UPO-17</td>
                         <td>UPO-17</td>
                         <td>BBa_K367010</td>
                         <td>BBa_K367010</td>
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                         <td>gltD</td>
+
                         <td><i>gltD</i></td>
                         <td>Coding sequence</td>
                         <td>Coding sequence</td>
                         <td>Made by PCR and SDM</td>
                         <td>Made by PCR and SDM</td>
-
                         <td>Escherichia coli gltD gene, encoding glutamate synthase beta subunit. Glutamate
+
                         <td><i>Escherichia coli</i> <i>gltD</i> gene, encoding glutamate synthase beta subunit. Glutamate
                             synthetase converts glutamine + 2-oxoglutarate into glutamate. Glutamate is a
                             synthetase converts glutamine + 2-oxoglutarate into glutamate. Glutamate is a
-
                             source of amine groups via transamination, and a chemoattractant for E. coli.</td>
+
                             source of amine groups via transamination, and a chemoattractant for <i>E. coli.</i></td>
                     </tr>
                     </tr>
                     <tr>
                     <tr>
                         <td>UPO-18</td>
                         <td>UPO-18</td>
                         <td>BBa_K367011</td>
                         <td>BBa_K367011</td>
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                         <td>gltB</td>
+
                         <td><i>gltB</i></td>
                         <td>Coding sequence</td>
                         <td>Coding sequence</td>
                         <td>Made by PCR</td>
                         <td>Made by PCR</td>
-
                         <td>Escherichia coli gltB gene, encoding glutamate synthase alpha subunit. Glutamate
+
                         <td><i>Escherichia coli</i> <i>gltB</i> gene, encoding glutamate synthase alpha subunit. Glutamate
                             synthetase converts glutamine + 2-oxoglutarate into glutamate. Glutamate is a
                             synthetase converts glutamine + 2-oxoglutarate into glutamate. Glutamate is a
-
                             source of amine groups via transamination, and a chemoattractant for E. coli.</td>
+
                             source of amine groups via transamination, and a chemoattractant for <i>E. coli.</i></td>
                     </tr>
                     </tr>
                 </tbody>
                 </tbody>

Revision as of 14:33, 10 September 2010

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Parts

In this site you can find all the parts iGEM team UPO-Sevilla had been working on.

BioBricks names give you information about the kind of BioBrick and it is a good way to work with a big quantity of parts (see http://partsregistry.org/Help:BioBrick_Part_Names). But it is hard to write these long names in a microcentrifuge tube! That is why we used a second numerical name for each part. Numerical names are easier to work with in the lab and also to organize the work. You will see this codec next to standard names. This will help you to understand other issues of Bacterial Crowding project, as Circuits and Devices.

New BioBricks
  Part Number iGEM ID Identity Type Origin Description
Prh System UPO-04 BBa_K367000 prhA Coding sequence Synthesis Ralstonia solanacearum gene prhA, encoding an outer membrane protein that senses a signal on plant cell walls and transduces it through the bacterial cell envelop to stimulate transcription from several operons. Optimized sequence to be expressed in Escherichia coli.
UPO-05 BBa_K367001 prhR Coding sequence Synthesis Ralstonia solanacearum gene prhR, encoding a membrane signal transduction protein involved in the Prh pathway. The nondiffusible plant cell wall signal is transduced by the N-terminal extension of PrhA to the C-terminal part of the transmembrane protein PrhR and then through PrhR across the cytoplasmic membrane. Optimized sequence to be expressed in Escherichia coli.
UPO-06 BBa_K367002 prhI Coding sequence Synthesis Ralstonia solanacearum gene prhI, encoding an ECF sigma factor responsible for transcription dependent on the Prh signal transduction system. PrhI is activated by PrhR and then the sigma factor induces the expression by activating PprhJ promoter. Optimized sequence to be expressed in Escherichia coli.
UPO-11 BBa_K367008 PprhJ Promoter Synthesis The PprhJ promoter region, responsive to plant cell contact via signal transduction by PrhA and PrhR and activation by ECF sigma factor PrhI. Optimized sequence to be expressed in Escherichia coli.
Hybrid Protein UPO-07 BBa_K367006 fecA-prhA Coding sequence Synthesis Artificial coding sequence spanning the first 92 codons of fecA, encoding the signal peptide (aa. 1-33), the proposed Ton-box (aa. 54-63), fused to the distal end of the prhA coding sequence at the conserved GSGL motif (aa. 89-92). This hybrid protein allows to sense nondifusible signals and to transduce it by the well known Fec pathway. Optimized sequence to be expressed in Escherichia coli.
Fec System UPO-08 BBa_K367003 fecA Coding sequence Made by PCR and SDM Gene fecA of Escherichia coli, encoding an outer membrane ferric citrate sensor that initiates signal transduction via FecR and FecI to activate transcription.
UPO-28 BBa_K367012 fecI & fecR Two overlapping coding sequences Made by PCR and SDM fecI and fecR genes of Escherichia coli, encoding an ECF sigma factor and a membrane signal transduction protein respectively, involved in signal transduction of the ferric citrate-dependent Fec system. They have been synthesized in the same Biobrick because of their 4 bp overlap, not to reduce their expression. FecR protein interacts with the outer membrane sensor FecA and activates the sigma factor FecI, which acts over PfecA promoter region.
UPO-12 BBa_K367009 PfecA Promoter Made by PCR Escherichia coli PfecA promoter region, repressed by Fur under iron excess, and induced by ferric citrate through the FecA-FecR signal transduction pathway and the FecI ECF sigma factor.
Glutamate Synthetase UPO-17 BBa_K367010 gltD Coding sequence Made by PCR and SDM Escherichia coli gltD gene, encoding glutamate synthase beta subunit. Glutamate synthetase converts glutamine + 2-oxoglutarate into glutamate. Glutamate is a source of amine groups via transamination, and a chemoattractant for E. coli.
UPO-18 BBa_K367011 gltB Coding sequence Made by PCR Escherichia coli gltB gene, encoding glutamate synthase alpha subunit. Glutamate synthetase converts glutamine + 2-oxoglutarate into glutamate. Glutamate is a source of amine groups via transamination, and a chemoattractant for E. coli.
Existing BioBricks
  Part Number iGEM ID Identity Type Origin Description
Expression UPO-01 BBa_J23100 Strong Promoter Promoter Self-annealing primers Constitutive strong promoter. We ordered it like a primer to make our work easier.
UPO-02 BBa_B0030 RBS.1 (strong) Shine-Dalgarno Self-annealing primers Strong RBS based on Ron Weiss thesis.
UPO-03 BBa_B0015 rrnBT1-T7TE Terminator (double) 2010P1; 23L A reliable double transcription terminator.
Reporters UPO-13 BBa_E0040 GFP Coding sequence 2010P1; 14K Green fluorescent protein derived from jellyfish Aequeora victoria wild-type. It is used to report the expression behind some promoters.
UPO-20 BBa_I13522 Ptet-SD-GFP-TT-TT Composite (constitutive protein generator) 2010P2; 8A Constitutive GFP generator. It allows to see bacteria easier and also quantificating their amount.
Chemoattractants Synthesis UPO-16 BBa_C0083 aspA Coding sequence 2010P2; 17A Coding secuence for Aspartate ammonia-lyase enzyme.  AspA aminates fumarate to make aspartate. Aspartate can be used as a bacterial chemotaxis signal for Escherichia coli.
UPO-19 BBa_J45319 SD-pchBA-TT-TT Composite (protein generator) 2010P2;15I PchA & PchB enzyme generator takes as input a transcriptional signal (PoPS) and produces as output the PchA and PchB enzymes that catalyze production of salicylate from the cellular metabolite chorismate. Salicylate can be used as a bacterial chemotaxis signal for Pseudomonas putidas.
Vectors
  Part Number iGEM ID Type Origin
High Copy Vectors UPO-24 pSB1AK3 Plasmid 2010P1; 11A
UPO-25 pSB1AT3 Plasmid 2010P1; 13A
UPO-26 pSB1AC3 Plasmid 2010P1; 9A
UPO-32 pSB1K3 Plasmid 2010P1; 5A
UPO-33 pSB1T3 Plasmid 2010P1; 7A
UPO-34 pSB1C3 Plasmid 2010P1; 3A
UPO-35 pSB1A3 Plasmid 2010P1; 1C
Low Copy Vectors UPO-36 pSB3T5 Plasmid 2010P1; 7C
UPO-37 pSB3C5 Plasmid 2010P1; 3C
UPO-38 pSB4K5 Plasmid 2010P1; 5G
UPO-39 pSB4C5 Plasmid 2010P1; 3E
UPO-40 pSB4A5 Plasmid 2010P1; 1G
New BioBricks
Part Number iGEM ID Identity Type Origin Description
UPO-09 BBa_K367004 fecI Coding sequence finally not made Gene fecI of Escherichia coli, encoding an ECF sigma factor used to regulate transcription in response to the FecA-FecR signal transduction pathway in response to ferric citrate
UPO-10 BBa_K367005 fecR Coding sequence finally not made Gene fecR from Escherichia coli, encoding a membrane protein involved in signal transduction of the ferric citrate-dependent Fec system to stimulate transcription via the ECF sigma factor FecI
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