Difference between revisions of "Template:Heidelberg/best basic"

 
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   {{Heidelberg/partspanelleft|{{#tag:html|<a href="http://parts.igem.org/Part:BBa_K2398000">BBa_K2398000</a>}}|We present as best basic part the codon-optimized version of the cytochrome c protein that is able to convert silicon educts to organosilicon products.|https://static.igem.org/mediawiki/2017/1/1d/T--Heidelberg--CytochromeCRMA.png|}}
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      <h4><a href="http://parts.igem.org/Part:BBa_K2398000" style="color: #9d1c20 !important">BBa_K2398000</a></h4>
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            We present as best basic part the codon-optimized version of the cytochrome c protein derived from <i><a href="http://www.rcsb.org/pdb/explore.do?structureId=3cp5" style="color: #9d1c20 !important">Rhodotermus marinus</a></i> that is able to convert silicon educts to organosilicon products.
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            <img src="https://static.igem.org/mediawiki/2017/1/1d/T--Heidelberg--CytochromeCRMA.png" class="img-responsive" alt="Circularization Construct">
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This cytochrome c variant provides an easy to use tool that is accessible to everyone in the synthetic biology community and allows the user to harness the vast potential of organosilicons.
 
This cytochrome c variant provides an easy to use tool that is accessible to everyone in the synthetic biology community and allows the user to harness the vast potential of organosilicons.
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This basic part exhibits a strong tendency to form silicon-carbon bonds and is, therefore, a valuable addition to perform controlled organic chemistry in microorganisms.
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This basic part exhibits a strong tendency to form silicon-carbon bonds and is a valuable addition to perform controlled organic chemistry in microorganisms.
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A triple mutant of this part has already been applied in the successful synthesis of organosilicons as a proof-of-concept.
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A triple mutant [Arnold et al., 2016] of this part has already been applied in the successful synthesis of organosilicons as a proof-of-concept.<br><br>
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As a next step, this part can be implemented in the directed evolution approach of phage-assisted continuous evolution (PACE) or in the phage-related discontinuous evolution (PREDCEL) approach to improve organosilicon synthesis by cytochrome engineering.
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As a next step, this part can be implemented in the directed evolution approach of phage-assisted continuous evolution ({{#tag:html|<a href="https://2017.igem.org/Team:Heidelberg/Pace" style="color: #9d1c20 !important">PACE</a>}}) or in the phage-related discontinuous evolution ({{#tag:html|<a href="https://2017.igem.org/Team:Heidelberg/Predcel" style="color: #9d1c20 !important">PREDCEL</a>}}) approach to improve organosilicon synthesis by cytochrome engineering.
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For the characterization of this part, we conducted experiments for the production of organosilicons and therefore used a previously described triple mutant, already engineered by [Arnold et al., 2016]. According to the {{#tag:html|<a href="https://2017.igem.org/Team:Heidelberg/Experiments" style="color: #9d1c20 !important">protocol</a>}}, we obtained the matured cytochrome c and performed conversion experiments analyzed via GC-MS method.<br><br> The following figures show the results obtained with the previously engineered enzyme. First, we tested the enzyme on the conversion of the compound (1) with (3) to the final product of (5) (Fig. 1). The gas chromatogram shows one product peak which emerges at 9.2 min retention time. Analysis of the gas chromatogram indicates a conversion rate of >99% on the basis of the non-existence of the respective educt peak. As we performed GC-MS analysis, mass spectrometry data were also available which can be seen in Fig. 3 for the product peak that emerges at 9.2 minutes. It shows the fission of this product and can clearly be identified as our desired product (5). Furthermore, we performed experiments on the compound (1) which differs from compound (2) in its amino functional group. The product is eluted after 11.7 minutes retention time (Fig. 4) and also confirmed as the right product via mass spectrometry in Fig. 5. Worth mentioning, there is still educt (1) present which emerges at 6.9 minutes retention time, indicating incomplete conversion. Calculations showed a conversion rate of 47.5% for the product (4).As these results only show activity for a previously engineered cytochrome c, we are convinced that our part is still functional despite not as effective as the mutant. This part as our best basic part is intended as a platform for future teams to evolve their own cytochrome c for their specific target molecule.
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{{Heidelberg/templateus/Imagesection|https://static.igem.org/mediawiki/2017/f/fd/T--Heidelberg--Compounds.png|Figure 1:|Compounds used in the project of organosilicons and its respective products.|style = float:none}}
  
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{{Heidelberg/templateus/Imagesection|https://static.igem.org/mediawiki/parts/9/92/T--Heidelberg--GCAnilineCompound.png|Figure 1:|Gas chromatogram for the reaction of educt (1) and (5) to the product (3). 11.7 minutes retention time, indicates product formation. Unconverted educts converge 6.9 and 7.2, 7.4 minutes|}}
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{{Heidelberg/templateus/Imagesection|https://static.igem.org/mediawiki/parts/9/92/T--Heidelberg--GCAnilineCompound.png|Figure 2:|Gas chromatogram for the reaction of educt (1) and (3) to the product (5). 11.7 minutes retention time indicates product formation. Unconverted educts converge 6.9 and 7.2 (7.4) minutes.|style = float:none}}
  
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{{Heidelberg/templateus/Imagesection|https://static.igem.org/mediawiki/parts/1/16/T--Heidelberg--MSAnilineCompound.png|Figure 2:|Mass chromatogram shows the breakdown of the product (3) <i>ethyl 2-((4-aminophenyl)dimethylsilyl)propanoate</i>. The product itself corresponds to a mass of 251 dalton|}}
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{{Heidelberg/templateus/Imagesection|https://static.igem.org/mediawiki/parts/1/16/T--Heidelberg--MSAnilineCompound.png|Figure 3:|Mass chromatogram shows the breakdown of the product (5). The product itself corresponds to a mass of 251 daltons.|style = float:none}}
  
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{{Heidelberg/templateus/Imagesection|https://static.igem.org/mediawiki/parts/e/ef/T--Heidelberg--GCNonAninlineCompound.png|Figure 3:|Gas chromatogram for the reaction of educt (2) and (5) to the product (4). 9.2 minutes retention time indicates product formation.|}}
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{{Heidelberg/templateus/Imagesection|https://static.igem.org/mediawiki/parts/e/ef/T--Heidelberg--GCNonAninlineCompound.png|Figure 4:|Gas chromatogram for the reaction of educt (2) and (3) to the product (4). 9.2 minutes retention time indicates product formation.|style = float:none}}
  
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{{Heidelberg/templateus/Imagesection|https://static.igem.org/mediawiki/parts/2/2b/T--Heidelberg--MSNonAnilineCompound.png|Figure 4:|Mass chromatogram shows the breakdown of the product (4) <i>ethyl 2-(dimethyl(phenyl)silyl)propanoate</i>. The product itself corresponds to a mass of 236 dalton|}}
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{{Heidelberg/templateus/Imagesection|https://static.igem.org/mediawiki/parts/2/2b/T--Heidelberg--MSNonAnilineCompound.png|Figure 5:|Mass chromatogram shows the breakdown of the product (4). The product itself corresponds to a mass of 236 daltons.|style = float:none}}  
 
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Latest revision as of 03:38, 2 November 2017

BBa_K2398000

We present as best basic part the codon-optimized version of the cytochrome c protein derived from Rhodotermus marinus that is able to convert silicon educts to organosilicon products.
Circularization Construct
This cytochrome c variant provides an easy to use tool that is accessible to everyone in the synthetic biology community and allows the user to harness the vast potential of organosilicons. This basic part exhibits a strong tendency to form silicon-carbon bonds and is a valuable addition to perform controlled organic chemistry in microorganisms. A triple mutant [Arnold et al., 2016] of this part has already been applied in the successful synthesis of organosilicons as a proof-of-concept.

As a next step, this part can be implemented in the directed evolution approach of phage-assisted continuous evolution (PACE) or in the phage-related discontinuous evolution (PREDCEL) approach to improve organosilicon synthesis by cytochrome engineering. For the characterization of this part, we conducted experiments for the production of organosilicons and therefore used a previously described triple mutant, already engineered by [Arnold et al., 2016]. According to the protocol, we obtained the matured cytochrome c and performed conversion experiments analyzed via GC-MS method.

The following figures show the results obtained with the previously engineered enzyme. First, we tested the enzyme on the conversion of the compound (1) with (3) to the final product of (5) (Fig. 1). The gas chromatogram shows one product peak which emerges at 9.2 min retention time. Analysis of the gas chromatogram indicates a conversion rate of >99% on the basis of the non-existence of the respective educt peak. As we performed GC-MS analysis, mass spectrometry data were also available which can be seen in Fig. 3 for the product peak that emerges at 9.2 minutes. It shows the fission of this product and can clearly be identified as our desired product (5). Furthermore, we performed experiments on the compound (1) which differs from compound (2) in its amino functional group. The product is eluted after 11.7 minutes retention time (Fig. 4) and also confirmed as the right product via mass spectrometry in Fig. 5. Worth mentioning, there is still educt (1) present which emerges at 6.9 minutes retention time, indicating incomplete conversion. Calculations showed a conversion rate of 47.5% for the product (4).As these results only show activity for a previously engineered cytochrome c, we are convinced that our part is still functional despite not as effective as the mutant. This part as our best basic part is intended as a platform for future teams to evolve their own cytochrome c for their specific target molecule.
Figure 1:
Compounds used in the project of organosilicons and its respective products.
Figure 2:
Gas chromatogram for the reaction of educt (1) and (3) to the product (5). 11.7 minutes retention time indicates product formation. Unconverted educts converge 6.9 and 7.2 (7.4) minutes.
Figure 3:
Mass chromatogram shows the breakdown of the product (5). The product itself corresponds to a mass of 251 daltons.
Figure 4:
Gas chromatogram for the reaction of educt (2) and (3) to the product (4). 9.2 minutes retention time indicates product formation.
Figure 5:
Mass chromatogram shows the breakdown of the product (4). The product itself corresponds to a mass of 236 daltons.