Difference between revisions of "Team:ShanghaitechChina/Description"

Revision as of 08:20, 19 October 2016

igem2016:ShanghaiTech

Improve the characterization

>Contribution:

Biobrick: BBa_K1583003
Group: ShanghaitechChina

Author: Lechen Qian, Shijie Gu

Summary: We created new way to characterize this biobrick by utilizing Ni-NTA-Metal-Histag coordination chemistry and fluorescence emission traits of Quantum Dots (QDs) in our project. We demonstrated the validity of the approach for measurement of biofilm composed by CsgA-His density of E. coli curli system and think highly of this characterization for its general application in other biofilm systems.Also, we harness TEM to help us scrutinize the binding effect in microsopic world.

>Improvement

Quantum dots binding test

In order to test the effect of binding between CsgA-Histag mutant and inorganic nanoparticles, we apply same amount of suspended QDs solution into M63 medium which has cultured biofilm for 72h. After 1h incubation, we used PBS to mildly wash the well, and the result was consistent with our anticipation: On the left, CsgA-Histag mutant were induced and thus secreted biofilm, and firmly attached with QDS and thus show bright fluorescence. Therefore, we ensure the stable coordinate bonds between CsgA-Histag mutant and QDs can manage to prevent QDs from being taken away by liquid flow. The picture was snapped by ChemiDoc MP,BioRad, false colored.

**Fig. 1**：Binding test between CsgA-his and Quantum dots. The image was snaped by ChemiDoc MP,BioRad, false colored.

Comparison test of Quantum dots Binding between CsgA-his and CsgA

In order to prove the effect of binding between CsgA-Histag mutant and inorganic nanoparticles is distinct, we apply same amount of suspended CdSeS/ZnS QDs solution followed by the same procedure mentioned above. After 1h incubation, we used PBS washing 2 times. The picture verify out postulation: On the left, CsgA-Histag mutant were induced and its biofilm bind with QDS. CsgA biofilm cannot bind with QDs thus its red fluorescence is a lot weaker.

CdS nanorods Templating

As for biofilm characterization, transmission electron microscopy is frequently to be used to visualize the nanofiber network. However, we found it really difficult to find out whether biofilm is well self-assemble extracellularly due to its thin and inconspicuous attributes against the background. Amazingly, after incubation with CdS nanorods , the biofilm areas are densely templated by CdS nanorods and we can easily confirm the expression of biofilm.

**Fig. 3**：Representative TEM images of biotemplated CdS nanorods on CsgA-His. After applied inducer, CsgA-His mutant constructed and expressed to form biofilm composed by CsgA-His subunits. Incubation with nanorods for 1h, nanomaterials are densely attached to biofilm.

Details see ShanghaitechChina team's protocol

Optimize the codon

>Contribution:

Biobrick: BBa_K2132005
Group: ShanghaitechChina

Author: Yifan Chen

Summary: We optimized [FeFe] Hydrogenases originally from the bacterium Clostridium acetobutylicum (Original coding sequence: hydA, BBa_K535002. Optimized coding sequence: hydA with SpyTag and Histag BBa_K2132005) to accept electrons and therefor enable catalytic production of hydrogen in our project. The optimized coding sequence would produce more protein, theoretically. And optimization also improved the activity of [FeFe] Hydrogenases according to the experiment that we did.

>Improvement

Codon usage bias adjustment

We analysed the Codon Adaptation Index (CAI) of the optimized coding sequence and the original one. And the distribution of codon usage frequency along the length of the gene sequence is increased from 0.33 to 0.97. A CAI of 1.0 is considered to be perfect in the desired expression organism, and a CAI of > 0.8 is regarded as good, in terms of high gene expression level.

**Fig. 4**：The distribution of codon usage frequency along the length of the gene sequence.

We also compared the Frequency of Optimal Codons (FOP). The value of 100 is set for the codon with the highest usage frequency for a given amino acid in the desired expression organism. As we can see, the percentage of 91-100 increased largely, from 36 to 86, after the optimization.

**Fig. 5**：The percentage distribution of codons in computed codon quality groups.

Remove repeat sequences

	Max Direct Repeat	Max Inverted Repeat	Max Dyad Repeat
After Optimization	Size:15 Distance:3 Frequency:2	None	None
Size:16 Distance:231 Frequency:2	None	Size: 13 Tm: 34.6 Start Positions: 680, 1357

>Conclusion

A wide variety of factors regulate and influence gene expression levels, and after taking into consideration as many of them as possible, OptimumGene™ produced the single gene that can reach the highest possible level of expression.

In this case, the native gene employs tandem rare codons that can reduce the efficiency of translation or even disengage the translational machinery. We changed the codon usage bias in E. coli by upgrading the CAI from 0.33 to 0.97 . GC content and unfavorable peaks have been optimized to prolong the half-life of the mRNA. The Stem-Loop structures, which impact ribosomal binding and stability of mRNA, were broken. In addition, the optimization process has screened and successfully modified those negative cis-acting sites as listed in the Parts Collection.

**Fig. 6**：The protein alignment of new and old protein.

@@ Line 88: / Line 88: @@
 </ul></h4>
 <h3>>Improvement</h3>
-<h4>Hydrogenases expression and enzyme activity assay</h4>
+<h4>Codon usage bias adjustment</h4>
+<p>We analysed the Codon Adaptation Index (CAI) of the optimized coding sequence and the original one. And the distribution of codon usage frequency along the length of the gene sequence is increased from 0.33 to 0.97. A CAI of 1.0 is considered to be perfect in the desired expression organism, and a CAI of > 0.8 is regarded as good, in terms of high gene expression level.</p>
+<figure align="center">
+<img src="https://static.igem.org/mediawiki/2016/a/ab/SHTU_D1.png" width="40%">
+<figcaption>
+<b>Fig. 4</b>：The distribution of codon usage frequency along the length of the gene sequence.
+</figcaption>
+</figure>
+<p>We also compared the Frequency of Optimal Codons (FOP). The value of 100 is set for the codon with the highest usage frequency for a given amino acid in the desired expression organism. As we can see, the percentage of 91-100 increased largely, from 36 to 86, after the optimization.</p>
+<figure align="center">
+<img src="https://static.igem.org/mediawiki/2016/1/1c/SHTU_D2.png" width="40%">
+<figcaption>
+<b>Fig. 5</b>：The percentage distribution of codons in computed codon quality groups.
+</figcaption>
+</figure>
+<h4>Remove repeat sequences</h4>
+ <div class="col-lg-12">
+<table align="center" border="0" cellpadding="0" cellspacing="0" class="table table-hover">
+	<thead>
+		<tr>
+			<th><strong> </strong></th>
+			<th><strong>Max Direct Repeat</strong></th>
+			<th><strong>Max Inverted Repeat</strong></th>
+			<th><strong>Max Dyad Repeat</strong></th>
+		</tr>
+	</thead>
+<tbody>
+		<tr>
+			<td>After Optimization</a></td>
+			<td>Size:15 Distance:3 Frequency:2</td>
+			<td>None</td>
+			<td>None</td>
+		</tr>
+		<tr>
+			<td>Size:16 Distance:231 Frequency:2</td>
+			<td>None</td>
+			<td>Size: 13 Tm: 34.6 Start Positions: 680, 1357</td>
+		</tr>
+ 			</tbody>
+</table>
+       </div>
+<h3>>Conclusion</h3>
+<p>A wide variety of factors regulate and influence gene expression levels, and after taking into consideration as many of them as possible, OptimumGene™ produced the single gene that can reach the highest possible level of expression.</p>
+<p>In this case, the native gene employs tandem rare codons that can reduce the efficiency of translation or even disengage the translational machinery. We changed the codon usage bias in <em>E. coli</em> by upgrading the CAI from 0.33 to 0.97 . GC content and unfavorable peaks have been optimized to prolong the half-life of the mRNA. The Stem-Loop structures, which impact ribosomal binding and stability of mRNA, were broken. In addition, the optimization process has screened and successfully modified those negative cis-acting sites as listed in the <a href="https://2016.igem.org/Team:ShanghaitechChina/Parts#p3">Parts Collection</a>.</p>
+<figure align="center">
+<img src="https://static.igem.org/mediawiki/2016/e/ea/SHTU_D3.png" width="40%">
+<figcaption>
+<b>Fig. 6</b>：The protein alignment of new and old protein.
+</figcaption>
+</figure>