Difference between revisions of "Team:ETH Zurich/Parts"

Line 172: Line 172:
 
<summary>BBa_K2500004: TlpA</summary>
 
<summary>BBa_K2500004: TlpA</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>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>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>Based on:</strong> gBlock</p>
+
<p><strong>Source:</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>Design notes:</strong>FIXME FIXME FIXME RBS info</p>
 
<p><strong>Design notes:</strong>FIXME FIXME FIXME RBS info</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>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>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>Based on:</strong> gBlock</p>
+
<p><strong>Source:</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:
 
<summary>BBa_K2500006: Protein E</summary>
 
<summary>BBa_K2500006: Protein E</summary>
 
<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>Based on:</strong> provided by dr. Irene Wüthrich from Panke lab at the D-BSSE of ETH Zurich</p>
−
<p><strong>Based on:</strong> plasmid provided by dr. Irene Wüthrich from Panke lab at the D-BSSE of ETH Zurich</p>
+
<p><strong>Source:</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 199: Line 199:
 
<p><strong>Organism:</strong> <span class="bacterium">Salmonella typhimurium</span></p>
 
<p><strong>Organism:</strong> <span class="bacterium">Salmonella typhimurium</span></p>
 
<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>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> FIXME RedLibs + 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>
 
</details>
 
</details>
Line 209: Line 209:
 
<p><strong>Organism:</strong> <span class="bacterium">Salmonella typhimurium</span></p>
 
<p><strong>Organism:</strong> <span class="bacterium">Salmonella typhimurium</span></p>
 
<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>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>FIXME RedLibs + gBlock</p>
 
<p><strong>Registry:</strong> <a href="http://parts.igem.org/Part:BBa_K2500008">BBa_K2500008</a></p>
 
<p><strong>Registry:</strong> <a href="http://parts.igem.org/Part:BBa_K2500008">BBa_K2500008</a></p>
 
</details>
 
</details>
Line 218: Line 218:
 
<p><strong>Organism:</strong> phage Phi X 174</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><strong>Based on:</strong> provided by dr. Irene Wüthrich from Panke lab at the D-BSSE of ETH Zurich</p>
−
<p><strong>Source:</strong> plasmid provided by dr. Irene Wüthrich from Panke lab at the D-BSSE of ETH Zurich</p>
+
<p><strong>Source:</strong> FIXME RedLibs + 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_K2500009">BBa_K2500009</a></p>
 
<p><strong>Registry:</strong> <a href="http://parts.igem.org/Part:BBa_K2500009">BBa_K2500009</a></p>
 
</details>
 
</details>

Revision as of 10:01, 30 October 2017

Parts

FIXME

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

Based on: 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

Based on: Piraner, Dan I., et al. Nature chemical biology 13.1 (2017): 75-80.

Source: gBlock

Registry: BBa_K2500004

BBa_K2500005: RBS_TlpA

Design notes:FIXME FIXME FIXME RBS info

Organism: Salmonella typhimurium

Based on: Piraner, Dan I., et al. Nature chemical biology 13.1 (2017): 75-80.

Source: gBlock

Registry: BBa_K2500005

BBa_K2500006: Protein E

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_K2500006

BBa_K2500007: RBSeng_TlpA

Design notes:FIXME FIXME FIXME RBS info

Organism: Salmonella typhimurium

Based on: Piraner, Dan I., et al. Nature chemical biology 13.1 (2017): 75-80.

Source: FIXME RedLibs + gBlock

Registry: BBa_K2500007

BBa_K2500008: pConst_RBSeng_TlpA

Design notes:FIXME FIXME FIXME RBS info

Organism: Salmonella typhimurium

Based on: Piraner, Dan I., et al. Nature chemical biology 13.1 (2017): 75-80.

Source:FIXME RedLibs + gBlock

Registry: BBa_K2500008

BBa_K2500009: RBSeng_ProteinE

Design notes:FIXME FIXME FIXME RBS info

Organism: phage Phi X 174

Based on: provided by dr. Irene Wüthrich from Panke lab at the D-BSSE of ETH Zurich

Source: FIXME RedLibs + 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.

FIXME

Organism: FIXME FIXME FIXME

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.

FIXME

Organism: FIXME FIXME FIXME

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.

FIXME

Organism: FIXME FIXME FIXME

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

Based on: BBa_K1847007, BBa_R0062 and BBa_C0062

Source: FIXME

Registry: BBa_K2500013