Difference between revisions of "Team:ETH Zurich/Parts"
| Line 147: | Line 147: | ||
<p><strong>Design notes:</strong> Native signalling peptide removed.</p> | <p><strong>Design notes:</strong> Native signalling peptide removed.</p> | ||
<p><strong>Organism:</strong> <span class="bacterium">Pseudomonas aeruginosa</span></p> | <p><strong>Organism:</strong> <span class="bacterium">Pseudomonas aeruginosa</span></p> | ||
| − | <p><strong> | + | <p><strong>Based on:</strong> <a href="http://parts.igem.org/Part:BBa_K835004">BBa_K835004</a></p> |
<p><strong>Source:</strong> gBlock</p> | <p><strong>Source:</strong> gBlock</p> | ||
<p><strong>Registry:</strong> <a href="http://parts.igem.org/Part:BBa_K2500001">BBa_K2500001</a></p> | <p><strong>Registry:</strong> <a href="http://parts.igem.org/Part:BBa_K2500001">BBa_K2500001</a></p> | ||
| Line 156: | Line 156: | ||
<p><strong>Design notes:</strong>Designed by taking aminoacids 50 to 77 from azurin and adding a start codon (ATG) at the beginning and two stop codons (TAA TAA) at the end.</p> | <p><strong>Design notes:</strong>Designed by taking aminoacids 50 to 77 from azurin and adding a start codon (ATG) at the beginning and two stop codons (TAA TAA) at the end.</p> | ||
<p><strong>Organism:</strong> <span class="bacterium">Pseudomonas aeruginosa</span></p> | <p><strong>Organism:</strong> <span class="bacterium">Pseudomonas aeruginosa</span></p> | ||
| − | <p><strong> | + | <p><strong>Based on:</strong> <a href="http://parts.igem.org/Part:BBa_K2500001">BBa_K2500001</a></p> |
<p><strong>Source:</strong> gBlock</p> | <p><strong>Source:</strong> gBlock</p> | ||
<p><strong>Registry:</strong> <a href="http://parts.igem.org/Part:BBa_K2500002">BBa_K2500002</a></p> | <p><strong>Registry:</strong> <a href="http://parts.igem.org/Part:BBa_K2500002">BBa_K2500002</a></p> | ||
| Line 164: | Line 164: | ||
<summary>BBa_K2500003: p<sub>TlpA</sub></summary> | <summary>BBa_K2500003: p<sub>TlpA</sub></summary> | ||
<p><strong>Organism:</strong> <span class="bacterium">Salmonella typhimurium</span></p> | <p><strong>Organism:</strong> <span class="bacterium">Salmonella typhimurium</span></p> | ||
| − | <p><strong> | + | <p><strong>Based on:</strong> <a href="https://doi.org/10.1038/nchembio.2233">Piraner, Dan I., et al. <cite>Nature chemical biology</cite> 13.1 (2017): 75-80.</a></p> |
<p><strong>Source:</strong> oligonucleotide sequence</p> | <p><strong>Source:</strong> oligonucleotide sequence</p> | ||
<p><strong>Registry:</strong> <a href="http://parts.igem.org/Part:BBa_K2500003">BBa_K2500003</a></p> | <p><strong>Registry:</strong> <a href="http://parts.igem.org/Part:BBa_K2500003">BBa_K2500003</a></p> | ||
| Line 173: | Line 173: | ||
<p><strong>Organism:</strong> <span class="bacterium">Salmonella typhimurium</span></p> | <p><strong>Organism:</strong> <span class="bacterium">Salmonella typhimurium</span></p> | ||
<p><strong>Original sequence:</strong> <a href="https://doi.org/10.1038/nchembio.2233">Piraner, Dan I., et al. <cite>Nature chemical biology</cite> 13.1 (2017): 75-80.</a></p> | <p><strong>Original sequence:</strong> <a href="https://doi.org/10.1038/nchembio.2233">Piraner, Dan I., et al. <cite>Nature chemical biology</cite> 13.1 (2017): 75-80.</a></p> | ||
| − | <p><strong> | + | <p><strong>Based on:</strong> gBlock</p> |
<p><strong>Registry:</strong> <a href="http://parts.igem.org/Part:BBa_K2500004">BBa_K2500004</a></p> | <p><strong>Registry:</strong> <a href="http://parts.igem.org/Part:BBa_K2500004">BBa_K2500004</a></p> | ||
</details> | </details> | ||
| Line 181: | Line 181: | ||
<p><strong>Organism:</strong> <span class="bacterium">Salmonella typhimurium</span></p> | <p><strong>Organism:</strong> <span class="bacterium">Salmonella typhimurium</span></p> | ||
<p><strong>Original sequence:</strong> <a href="https://doi.org/10.1038/nchembio.2233">Piraner, Dan I., et al. <cite>Nature chemical biology</cite> 13.1 (2017): 75-80.</a></p> | <p><strong>Original sequence:</strong> <a href="https://doi.org/10.1038/nchembio.2233">Piraner, Dan I., et al. <cite>Nature chemical biology</cite> 13.1 (2017): 75-80.</a></p> | ||
| − | <p><strong> | + | <p><strong>Based on:</strong> gBlock</p> |
<p><strong>Registry:</strong> <a href="http://parts.igem.org/Part:BBa_K2500005">BBa_K2500005</a></p> | <p><strong>Registry:</strong> <a href="http://parts.igem.org/Part:BBa_K2500005">BBa_K2500005</a></p> | ||
</details> | </details> | ||
| Line 189: | Line 189: | ||
<p><strong>Organism:</strong> phage Phi X 174</p> | <p><strong>Organism:</strong> phage Phi X 174</p> | ||
<p><strong>Original sequence:</strong> provided by dr. Irene Wüthrich from Panke lab at the D-BSSE of ETH Zurich</p> | <p><strong>Original sequence:</strong> provided by dr. Irene Wüthrich from Panke lab at the D-BSSE of ETH Zurich</p> | ||
| − | <p><strong> | + | <p><strong>Based on:</strong> plasmid provided by dr. Irene Wüthrich from Panke lab at the D-BSSE of ETH Zurich</p> |
<p><strong>Registry:</strong> <a href="http://parts.igem.org/Part:BBa_K2500006">BBa_K2500006</a></p> | <p><strong>Registry:</strong> <a href="http://parts.igem.org/Part:BBa_K2500006">BBa_K2500006</a></p> | ||
</details> | </details> | ||
| Line 197: | Line 197: | ||
<p><strong>Design notes:</strong>FIXME FIXME FIXME</p> | <p><strong>Design notes:</strong>FIXME FIXME FIXME</p> | ||
<p><strong>Organism:</strong> <span class="bacterium">Salmonella typhimurium</span></p> | <p><strong>Organism:</strong> <span class="bacterium">Salmonella typhimurium</span></p> | ||
| − | <p><strong> | + | <p><strong>Based on:</strong> <a href="https://doi.org/10.1038/nchembio.2233">Piraner, Dan I., et al. <cite>Nature chemical biology</cite> 13.1 (2017): 75-80.</a></p> |
<p><strong>Source:</strong> gBlock</p> | <p><strong>Source:</strong> gBlock</p> | ||
<p><strong>Registry:</strong> <a href="http://parts.igem.org/Part:BBa_K2500007">BBa_K2500007</a></p> | <p><strong>Registry:</strong> <a href="http://parts.igem.org/Part:BBa_K2500007">BBa_K2500007</a></p> | ||
| Line 204: | Line 204: | ||
<details> | <details> | ||
| − | <summary>BBa_K2500008: p<sub>Const</sub> | + | <summary>BBa_K2500008: p<sub>Const</sub>RBS<sub>eng</sub>_TlpA</summary> |
<p><strong>Design notes:</strong>FIXME FIXME FIXME</p> | <p><strong>Design notes:</strong>FIXME FIXME FIXME</p> | ||
<p><strong>Organism:</strong> <span class="bacterium">Salmonella typhimurium</span></p> | <p><strong>Organism:</strong> <span class="bacterium">Salmonella typhimurium</span></p> | ||
| − | <p><strong> | + | <p><strong>Based on:</strong> <a href="https://doi.org/10.1038/nchembio.2233">Piraner, Dan I., et al. <cite>Nature chemical biology</cite> 13.1 (2017): 75-80.</a></p> |
<p><strong>Source:</strong> gBlock</p> | <p><strong>Source:</strong> gBlock</p> | ||
| − | <p><strong>Registry:</strong> <a href="http://parts.igem.org/Part: | + | <p><strong>Registry:</strong> <a href="http://parts.igem.org/Part:BBa_K2500008">BBa_K2500008</a></p> |
</details> | </details> | ||
<details> | <details> | ||
<summary>BBa_K2500009: RBS<sub>eng</sub>_ProteinE</summary> | <summary>BBa_K2500009: RBS<sub>eng</sub>_ProteinE</summary> | ||
| − | < | + | <p><strong>Design notes:</strong>FIXME FIXME FIXME</p> |
| − | < | + | <p><strong>Organism:</strong> phage Phi X 174</p> |
| − | </ | + | <p><strong>Based on:</strong> provided by dr. Irene Wüthrich from Panke lab at the D-BSSE of ETH Zurich</p> |
| − | <p> | + | <p><strong>Source:</strong> plasmid provided by dr. Irene Wüthrich from Panke lab at the D-BSSE of ETH Zurich</p> |
| − | <p> Registry: <a href="http://parts.igem.org/Part:BBa_K2500009">BBa_K2500009</a></p> | + | <p><strong>Registry:</strong> <a href="http://parts.igem.org/Part:BBa_K2500009">BBa_K2500009</a></p> |
</details> | </details> | ||
<details> | <details> | ||
| − | <summary>BBa_K2500010: AND | + | <summary>BBa_K2500010: AND Gate A</summary> |
| + | <p><strong>Design notes:</strong>In the absence of high concentrations of L-lactate, LldR inhibitor proteins bind to the binding sites O1 and O2 surrounding the p<sub>Lux</sub> promoter leading to the formation of a DNA loop. The p<sub>Lux</sub> promoter is sequestered and inaccessible for transcription. In design A, the distances between the intercalated promoter and the binding sites were taken from <a href="http://parts.igem.org/Part:BBa_K1847007">BBa_K1847007</a>.</p> | ||
<figure class="A"> | <figure class="A"> | ||
<img src="https://static.igem.org/mediawiki/2017/7/72/T--ETH_Zurich--ANDgateA.png" alt="FIXME"> | <img src="https://static.igem.org/mediawiki/2017/7/72/T--ETH_Zurich--ANDgateA.png" alt="FIXME"> | ||
</figure> | </figure> | ||
| − | <p> | + | <p><strong>Based on:</strong> <a href="http://parts.igem.org/Part:BBa_K1847007">BBa_K1847007</a>, <a href="http://parts.igem.org/Part:BBa_R0062">BBa_R0062</a> |
| − | <p> Registry: <a href="http://parts.igem.org/Part:BBa_K2500010">BBa_K2500010</a></p> | + | and <a href="http://parts.igem.org/Part:BBa_C0062">BBa_C0062</a></p> |
| + | <p><strong>Source:</strong> gBlock</p> | ||
| + | <p><strong>Registry:</strong> <a href="http://parts.igem.org/Part:BBa_K2500010">BBa_K2500010</a></p> | ||
</details> | </details> | ||
| − | |||
<details> | <details> | ||
<summary>BBa_K2500011: AND Gate B</summary> | <summary>BBa_K2500011: AND Gate B</summary> | ||
| + | <p><strong>Design notes:</strong>In design B, each binding site was duplicated in order to achieve a potential zipper mechanism and stronger inhibition due to binding more LldR inhibitor proteins.</p> | ||
<figure class="B"> | <figure class="B"> | ||
<img src="https://static.igem.org/mediawiki/2017/6/6a/T--ETH_Zurich--ANDgateB.png" alt="FIXME"> | <img src="https://static.igem.org/mediawiki/2017/6/6a/T--ETH_Zurich--ANDgateB.png" alt="FIXME"> | ||
</figure> | </figure> | ||
| − | <p> | + | <p><strong>Based on:</strong> <a href="http://parts.igem.org/Part:BBa_K1847007">BBa_K1847007</a>, <a href="http://parts.igem.org/Part:BBa_R0062">BBa_R0062</a> |
| − | <p> Registry: <a href="http://parts.igem.org/Part:BBa_K2500011">BBa_K2500011</a></p> | + | and <a href="http://parts.igem.org/Part:BBa_C0062">BBa_C0062</a></p> |
| + | <p><strong>Source:</strong> gBlock</p> | ||
| + | <p><strong>Registry:</strong> <a href="http://parts.igem.org/Part:BBa_K2500011">BBa_K2500011</a></p> | ||
</details> | </details> | ||
<details> | <details> | ||
<summary>BBa_K2500012: AND Gate C</summary> | <summary>BBa_K2500012: AND Gate C</summary> | ||
| + | <p><strong>Design notes:</strong>In design C, an artificial spacer was embedded between the pLux promoter and the O2 binding site in order to influence the looping dynamics.</p> | ||
<figure class="C"> | <figure class="C"> | ||
<img src="https://static.igem.org/mediawiki/2017/c/c2/T--ETH_Zurich--ANDgateC.png" alt="FIXME"> | <img src="https://static.igem.org/mediawiki/2017/c/c2/T--ETH_Zurich--ANDgateC.png" alt="FIXME"> | ||
</figure> | </figure> | ||
| − | <p> | + | <p><strong>Based on:</strong> <a href="http://parts.igem.org/Part:BBa_K1847007">BBa_K1847007</a>, <a href="http://parts.igem.org/Part:BBa_R0062">BBa_R0062</a> |
| − | <p> Registry: <a href="http://parts.igem.org/Part:BBa_K2500012">BBa_K2500012</a></p> | + | and <a href="http://parts.igem.org/Part:BBa_C0062">BBa_C0062</a></p> |
| + | <p><strong>Source:</strong> gBlock</p> | ||
| + | <p><strong>Registry:</strong> <a href="http://parts.igem.org/Part:BBa_K2500012">BBa_K2500012</a></p> | ||
</details> | </details> | ||
| + | |||
| + | <details> | ||
| + | <summary>BBa_K2500013: p<sub>Const</sub>_RBS_LldP/LldR_p<sub>Const</sub>_RBS_LuxR</summary> | ||
| + | <p><strong>Design notes:</strong>FIXME FIXME FIXME</p> | ||
| + | <p><strong>Organism:</strong> <span class="bacterium">FIXME FIXME FIXME</span></p> | ||
| + | <p><strong>Original sequence:</strong> FIXME FIXME FIXME</p> | ||
| + | <p><strong>Source:</strong> FIXME FIXME FIXME</p> | ||
| + | <p><strong>Registry:</strong> <a href="http://parts.igem.org/Part:BBa_K2500013">BBa_K2500013</a></p> | ||
| + | </details> | ||
| + | |||
</div> | </div> | ||
</section> | </section> | ||
Revision as of 09:45, 30 October 2017
Parts
Overview
We submitted in total 14 new BioBricks to the iGEM registry! You can find all parts and their design below.
Basic Parts
| Part | Description | BioBrick |
|---|---|---|
| Bacterioferritin | Heme-deletion mutant of bacterial iron storage protein functioning as an MRI contrast agent | BBa_K2500000 |
| Azurin | Redox protein originating from P. aeruginosa with anti-cancer activity | BBa_K2500001 |
| p28 | Effector domain of azurin | BBa_K2500002 |
| pTlpA | Temperature-responsive promoter optimized for slight activation above 37°C and full activation at 45 °C | BBa_K2500003 |
| TlpA | Temperature-dependent transcriptional repressor of pTlpa | BBa_K2500004 |
| RBS_TlpA | Temperature-dependent transcriptional repressor of pTlpa and synthetic RBS | BBa_K2500005 |
| Protein E | Bacteria-lysing protein encoded by phage Phi X 17 | BBa_K2500006 |
| RBSeng_TlpA | Temperature-dependent transcriptional repressor of pTlpa with engineered RBS | BBa_K2500007 |
| RBSeng_ProteinE | Bacteria-lysing protein encoded by phage Phi X 174 with engineered RBS | BBa_K2500009 |
| AND Gate A | Synthetic promoter responsive to LldR and luxR | BBa_K2500010 |
| Best Basic Part: AND Gate B |
Synthetic promoter responsive to LldR and luxR | BBa_K2500011 |
| AND Gate C | Synthetic promoter responsive to LldR and luxR | BBa_K2500012 |
| pConst_RBS_LldP/ LldR_pConst_RBS_LuxR |
Expression cassette consisting of LuxR and LldP/LldR | BBa_K2500013 |
Composite Parts
| Part | Description | BioBrick |
|---|---|---|
| Best Composite Part: pConstRBSeng_TlpA |
Constitutively expressed temperature-dependent transcriptional repressor of pTlpa with engineered RBS | BBa_K2500008 |
Design
All parts were codon-optimized for expression in E. coli Nissle via Geneious software and modified to remove forbidden restriction sites.
BBa_K2500000: Bacterioferritin
Organism: Escherichia coli Nissle
Original sequence: BBa_K1438001
Source: gBlock
Registry: BBa_K2500000
BBa_K2500001: Azurin
Design notes: Native signalling peptide removed.
Organism: Pseudomonas aeruginosa
Based on: BBa_K835004
Source: gBlock
Registry: BBa_K2500001
BBa_K2500002: p28
Design notes:Designed by taking aminoacids 50 to 77 from azurin and adding a start codon (ATG) at the beginning and two stop codons (TAA TAA) at the end.
Organism: Pseudomonas aeruginosa
Based on: BBa_K2500001
Source: gBlock
Registry: BBa_K2500002
BBa_K2500003: pTlpA
Organism: Salmonella typhimurium
Based on: Piraner, Dan I., et al. Nature chemical biology 13.1 (2017): 75-80.
Source: oligonucleotide sequence
Registry: BBa_K2500003
BBa_K2500004: TlpA
Organism: Salmonella typhimurium
Original sequence: Piraner, Dan I., et al. Nature chemical biology 13.1 (2017): 75-80.
Based on: gBlock
Registry: BBa_K2500004
BBa_K2500005: RBS_TlpA
Organism: Salmonella typhimurium
Original sequence: Piraner, Dan I., et al. Nature chemical biology 13.1 (2017): 75-80.
Based on: gBlock
Registry: BBa_K2500005
BBa_K2500006: Protein E
Organism: phage Phi X 174
Original sequence: provided by dr. Irene Wüthrich from Panke lab at the D-BSSE of ETH Zurich
Based on: plasmid provided by dr. Irene Wüthrich from Panke lab at the D-BSSE of ETH Zurich
Registry: BBa_K2500006
BBa_K2500007: RBSeng_TlpA
Design notes:FIXME FIXME FIXME
Organism: Salmonella typhimurium
Based on: Piraner, Dan I., et al. Nature chemical biology 13.1 (2017): 75-80.
Source: gBlock
Registry: BBa_K2500007
BBa_K2500008: pConstRBSeng_TlpA
Design notes:FIXME FIXME FIXME
Organism: Salmonella typhimurium
Based on: Piraner, Dan I., et al. Nature chemical biology 13.1 (2017): 75-80.
Source: gBlock
Registry: BBa_K2500008
BBa_K2500009: RBSeng_ProteinE
Design notes:FIXME FIXME FIXME
Organism: phage Phi X 174
Based on: provided by dr. Irene Wüthrich from Panke lab at the D-BSSE of ETH Zurich
Source: plasmid provided by dr. Irene Wüthrich from Panke lab at the D-BSSE of ETH Zurich
Registry: BBa_K2500009
BBa_K2500010: AND Gate A
Design notes:In the absence of high concentrations of L-lactate, LldR inhibitor proteins bind to the binding sites O1 and O2 surrounding the pLux promoter leading to the formation of a DNA loop. The pLux promoter is sequestered and inaccessible for transcription. In design A, the distances between the intercalated promoter and the binding sites were taken from BBa_K1847007.
Based on: BBa_K1847007, BBa_R0062 and BBa_C0062
Source: gBlock
Registry: BBa_K2500010
BBa_K2500011: AND Gate B
Design notes:In design B, each binding site was duplicated in order to achieve a potential zipper mechanism and stronger inhibition due to binding more LldR inhibitor proteins.
Based on: BBa_K1847007, BBa_R0062 and BBa_C0062
Source: gBlock
Registry: BBa_K2500011
BBa_K2500012: AND Gate C
Design notes:In design C, an artificial spacer was embedded between the pLux promoter and the O2 binding site in order to influence the looping dynamics.
Based on: BBa_K1847007, BBa_R0062 and BBa_C0062
Source: gBlock
Registry: BBa_K2500012
BBa_K2500013: pConst_RBS_LldP/LldR_pConst_RBS_LuxR
Design notes:FIXME FIXME FIXME
Organism: FIXME FIXME FIXME
Original sequence: FIXME FIXME FIXME
Source: FIXME FIXME FIXME
Registry: BBa_K2500013
