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Team:UPO-Sevilla/Biobricks/Parts
From 2010.igem.org
(Difference between revisions)
| Line 260: | Line 260: | ||
<td>Coding sequence</td> | <td>Coding sequence</td> | ||
<td>2010P1; 14K</td> | <td>2010P1; 14K</td> | ||
| - | <td>Green fluorescent protein derived from jellyfish Aequeora victoria wild-type. | + | <td>Green fluorescent protein derived from jellyfish <i>Aequeora victoria</i> wild-type. |
It is used to report the expression behind some promoters.</td> | It is used to report the expression behind some promoters.</td> | ||
</tr> | </tr> | ||
| Line 276: | Line 276: | ||
<td>UPO-16</td> | <td>UPO-16</td> | ||
<td>BBa_C0083</td> | <td>BBa_C0083</td> | ||
| - | <td>aspA</td> | + | <td><i>aspA</i></td> |
<td>Coding sequence</td> | <td>Coding sequence</td> | ||
<td>2010P2; 17A</td> | <td>2010P2; 17A</td> | ||
<td>Coding secuence for Aspartate ammonia-lyase enzyme. AspA aminates fumarate to make | <td>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.</td> | + | aspartate. Aspartate can be used as a bacterial chemotaxis signal for <i>Escherichia coli.</i></td> |
</tr> | </tr> | ||
<tr> | <tr> | ||
| Line 291: | Line 291: | ||
(PoPS) and produces as output the PchA and PchB enzymes that catalyze | (PoPS) and produces as output the PchA and PchB enzymes that catalyze | ||
production of salicylate from the cellular metabolite chorismate. Salicylate | production of salicylate from the cellular metabolite chorismate. Salicylate | ||
| - | can be used as a bacterial chemotaxis signal for Pseudomonas putidas.</td> | + | can be used as a bacterial chemotaxis signal for <i>Pseudomonas putidas.</i></td> |
</tr> | </tr> | ||
</tbody> | </tbody> | ||
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<div class="table"> | <div class="table"> | ||
<table class="tableBio" cellspacing="0" cellpadding="0"> | <table class="tableBio" cellspacing="0" cellpadding="0"> | ||
| - | <caption> | + | <caption>Designed but not used BioBricks</caption> |
<thead> | <thead> | ||
<tr> | <tr> | ||
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<td>UPO-09</td> | <td>UPO-09</td> | ||
<td>BBa_K367004</td> | <td>BBa_K367004</td> | ||
| - | <td>fecI</td> | + | <td><i>fecI</i></td> |
<td>Coding sequence</td> | <td>Coding sequence</td> | ||
<td>finally not made</td> | <td>finally not made</td> | ||
| - | <td>Gene fecI of Escherichia coli, encoding an ECF sigma factor | + | <td>Gene <i>fecI</i> of <i>Escherichia coli</i>, encoding an ECF sigma factor |
used to regulate transcription in response to the FecA-FecR | used to regulate transcription in response to the FecA-FecR | ||
signal transduction pathway in response to ferric citrate</td> | signal transduction pathway in response to ferric citrate</td> | ||
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<td>UPO-10</td> | <td>UPO-10</td> | ||
<td>BBa_K367005</td> | <td>BBa_K367005</td> | ||
| - | <td>fecR</td> | + | <td><i>fecR</i></td> |
<td>Coding sequence</td> | <td>Coding sequence</td> | ||
<td>finally not made</td> | <td>finally not made</td> | ||
| - | <td>Gene fecR from Escherichia coli, encoding a membrane protein involved | + | <td>Gene <i>fecR</i> from <i>Escherichia coli</i>, encoding a membrane protein involved |
in signal transduction of the ferric citrate-dependent Fec system to | in signal transduction of the ferric citrate-dependent Fec system to | ||
stimulate transcription via the ECF sigma factor FecI</td> | stimulate transcription via the ECF sigma factor FecI</td> | ||
Revision as of 14:40, 10 September 2010
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.
| 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. |
| 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. |
| 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 |
| 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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