Difference between revisions of "Part:BBa K3165013"

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<partinfo>BBa_K3165013 short</partinfo>
 
<partinfo>BBa_K3165013 short</partinfo>
  
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An improved alternative of mCherry (BBa_J18932) designed to minimise the amount of truncated protein by modifying the internal start codon of the existing sequence.
+
An improved alternative of mCherry <html><a href="https://parts.igem.org/Part:BBa_J18932">(BBa_J18932)</a></html> designed to minimise the amount of truncated protein by modifying the internal start codon of the existing sequence.
  
  
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<h2> Biology </h2>
 
<h2> Biology </h2>
  
−
i<sup>2</sup>mCherry (Ile) is an improved version of mCherry<html><a href="https://parts.igem.org/Part:BBa_J19832">(BBa_J19832)</a></html>, which is widely used as a fluorescent marker. However, N-terminal fusion of proteins with mCherry is not suited for studying various signal peptides due to the significant truncation that arises due to the presence of an RBS like sequence upstream of the ninth amino acid, Met which happens to be coded by the start codon (ATG). The RBS like sequence along with the start codon causes the transcription to begin at an internal site, resulting in significant truncation during protein expression.<br>
+
i<sup>2</sup>mCherry (Ile) is an improved version of mCherry <html><a href="https://parts.igem.org/Part:BBa_J18932">(BBa_J18932)</a></html>, which is widely used as a fluorescent marker. However, N-terminal fusion of proteins with mCherry is not suited for studying various signal peptides due to the significant truncation that arises due to the presence of an RBS like sequence upstream of the ninth amino acid, Met which happens to be coded by the start codon (ATG). The RBS like sequence along with the start codon causes the transcription to begin at an internal site, resulting in significant truncation during protein expression.<br>
−
The 2018 IIsc-Bangalore team attempted to reduce the truncation of the mCherry sequence by modifying the internal RBS like sequence and decreasing its ability to pair with the ribosome. Their improved part imCherry<html><a href="https://parts.igem.org/Part:BBa_K2609006">(BBa_K2609006)</a></html> reported a considerable decrease in the truncation but they couldn't get rid of the truncated product entirely. <br>
+
The 2018 IIsc-Bangalore team attempted to reduce the truncation of the mCherry sequence by modifying the internal RBS like sequence and decreasing its ability to pair with the ribosome. Their improved part imCherry <html><a href="https://parts.igem.org/Part:BBa_K2609006">(BBa_K2609006)</a></html> reported a considerable decrease in the truncation but they couldn't get rid of the truncated product entirely. <br>
 
In order to completely shut down the truncation caused by mCherry, we modified the internal start codon (ATG) via a single base mutation at then 48th nucleotide to convert ATG to ATC (coding for Ile). In the absence of a start codon, no transcription is expected, thus eliminating the chances of any truncated products.
 
In order to completely shut down the truncation caused by mCherry, we modified the internal start codon (ATG) via a single base mutation at then 48th nucleotide to convert ATG to ATC (coding for Ile). In the absence of a start codon, no transcription is expected, thus eliminating the chances of any truncated products.
  
 
<h2> Usage </h2>
 
<h2> Usage </h2>
  
−
i<sup>2</sup>mCherry(Ile) was developed to overcome the shortcomings of the existing mCherry <a href="https://parts.igem.org/Part:BBa_J19832">(BBa_J19832)</a></html> BioBrick which is not suitable for protein fusion studies due to the truncation faced at the N-terminal. As a consequence of reduced truncation, i<sup>2</sup>mCherry can be used for studying signal peptides and other N-terminal protein fusion components.
+
i<sup>2</sup>mCherry(Ile) was developed to overcome the shortcomings of the existing mCherry <html> <a href="https://parts.igem.org/Part:BBa_J18932">(BBa_J18932)</a></html> BioBrick which is not suitable for protein fusion studies due to the truncation faced at the N-terminal. As a consequence of reduced truncation, i<sup>2</sup>mCherry can be used for studying signal peptides and other N-terminal protein fusion components.
  
 
<h2> Characterization </h2>
 
<h2> Characterization </h2>
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The protein was expressed under the T7 promoter in <i>Escherichia coli</i> (BL21DE3) with 6xHistag at the N-terminal. The transformed bacteria were incubated at 37<sup>o</sup>C for over 4 hours. The cells were lysed by sonication and the lysate was collected via centrifugation. The lysate was run on an SDS PAGE which showed two bands. The size of the protein of interest along with the 6xHistag is around 27 kDa. The upper band corresponds to the non-truncated protein while the lower band represents the truncated product.  
 
The protein was expressed under the T7 promoter in <i>Escherichia coli</i> (BL21DE3) with 6xHistag at the N-terminal. The transformed bacteria were incubated at 37<sup>o</sup>C for over 4 hours. The cells were lysed by sonication and the lysate was collected via centrifugation. The lysate was run on an SDS PAGE which showed two bands. The size of the protein of interest along with the 6xHistag is around 27 kDa. The upper band corresponds to the non-truncated protein while the lower band represents the truncated product.  
  
 +
<html>
 +
<center>
 +
<figure>
 +
                    <img style="width:40%;" src="https://static.igem.org/mediawiki/parts/f/f2/T--IISc-Bangalore--i2mCherry_%28Ile%29_SDS.png">
 +
                    <figcaption><i><b>Fig(1) : SDS PAGE for mCherry and i<sup>2</sup>mCherry (Ile)</b></i></figcaption>
 +
                  </figure>
 +
</center>
 +
</html>
 +
 +
From the SDS PAGE, we clearly observe two bands when using mCherry, while i<sup>2</sup>mCherry (Ile) gave one very large spot on the polyacrylamide gel with a trailing smear kind of band. The observed dark band is seen at the desired size (roughly around 27 kDa) confirming that the bands correspond to our protein of interest.
 +
 +
<html>
 +
<h3> Purification using Ni-NTA with <a href="https://parts.igem.org/Part:BBa_K3165046">BBa_K3165046</a></h3></html>
 +
 +
The cell lysate thus obtained was purified using Ni-NTA beads as only the non-truncated protein having 6xHistag can bind to the beads. Ideally, the supernatant after binding should have the truncated protein while the eluted fraction should contain the non-truncated protein. This idealisation does not hold true as the binding of Ni-NTA is not perfect.
 +
 +
<html>
 +
<center>
 +
<figure>
 +
                    <img style="width:70%;" src="https://static.igem.org/mediawiki/parts/5/59/T--IISc-Bangalore--i2mCherry_%28Ile%29_Ni-NTA.png">
 +
                    <figcaption><i><b>Fig (2) : SDS PAGE for Ni-NTA Purification of i<sup>2</sup>mCherry (Ile)</b></i></figcaption>
 +
                  </figure>
 +
</center>
 +
</html>
 +
 +
 +
<h3> Fluorescence Analysis </h3>
 +
 +
Wavelengths scans of the protein lysate were performed to obtain the excitation and emission spectra of the fluorescent protein. The fluorescence data obtained were corrected for the blank (untransformed BL21DE3 protein lysate) and the data so obtained is presented below :
 +
<html>
 +
<center>
 +
<figure>
 +
                    <img style="width:100%;" src="https://static.igem.org/mediawiki/parts/6/6f/T--IISc-Bangalore--mCherry_Spectra.png">
 +
                    <figcaption><i><b>Fig(1) : Excitation and Emission Spectra of mCherry</b></i></figcaption>
 +
                  </figure>
 +
</center>
 +
</html>
 +
 +
<html>
 +
<center>
 +
<figure>
 +
                    <img style="width:100%;" src="https://static.igem.org/mediawiki/parts/0/0f/T--IISc-Bangalore--i2mCherry_%28Ile%29_Spectra.png">
 +
                    <figcaption><i><b>Fig(2) : Excitation and Emission Spectra of i<sup>2</sup>mCherry (Ile)</b></i></figcaption>
 +
                  </figure>
 +
</center>
 +
</html>
 +
<br>
 +
From the fluorescence data, we found out that the <b>excitation &lambda;</b> for mCherry is <b>585 nm</b> whereas its <b>emisiion &lambda;</b> is <b>602 nm</b>.<br>
 +
Similarly for i<sup>2</sup>mCherry (Ile) the experimental <b>excitation &lambda;</b> was found to be <b>575 nm</b> while the <b>emission &lambda;</b> is found to be <b>617 nm</b>.
 +
 +
<h3> Quantification of Truncation </h3>
 +
 +
The truncation of i<sup>2</sup>mCherry was quantified by the two following ways :<br><br>
 +
<ol>
 +
<li>By analysis of the intensity of the truncated and non-truncated protein bands as seen on the SDS PAGE.</li><br>
 +
<li>By combining the data of fluorescence and the gel intensity data of the Ni-NTA purification products (supernatant, wash and elution). Assuming the fluorescence of the truncated and non-truncated parts to be similar, we divide the fluorescence of each sample into two parts: one due to the truncated product and the other due to the non-truncated protein. The sum of the fluorescence of the two fractions was then used as a measure to estimate their concentration to determine truncation.</li>
 +
</ol>
 +
<html>
 +
<center>
 +
<figure>
 +
                    <img style="width:70%;" src="https://static.igem.org/mediawiki/parts/6/63/T--IISc-Bangalore--iletable.png">
 +
                   
 +
                  </figure>
 +
</center>
 +
</html>
 +
<html>
 +
<center>
 +
<figure>
 +
                    <img style="width:70%;" src="https://static.igem.org/mediawiki/parts/e/ea/T--IISc-Bangalore--ilescatter.png">
 +
                    <figcaption><i><b>Fig(3) : Scatter Plot for the percentage truncation of mCherry and i<sup>2</sup>mCherry (Ile)</b></i></figcaption>
 +
                  </figure>
 +
</center>
 +
</html>
 +
 +
It is evident from the data that some amount of truncated protein was still produced irrespective of the presence or absence of the internal start codon. The presence of the RBS like sequence in the gene might be the reason behind the continued production of the truncated product.
 +
 +
<h3> Truncation Reduction </h3>
 +
 +
The Truncation was reduced from <b>(48.5 &#8723; 2.0)%</b> in mCherry(<html><a href="https://parts.igem.org/Part:BBa_J18932">BBa_J18932</a></html>) to <b>(5.03 &#8723; 0.5)%</b> in i<sup>2</sup>mCherry (Ile).
 +
<br>
 
<h3> References : </h3>
 
<h3> References : </h3>
  

Latest revision as of 18:13, 13 November 2019


i^2mCherry (Ile)

An improved alternative of mCherry (BBa_J18932) designed to minimise the amount of truncated protein by modifying the internal start codon of the existing sequence.


Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal AgeI site found at 679
  • 1000
    COMPATIBLE WITH RFC[1000]

Usage and Biology

Biology

i2mCherry (Ile) is an improved version of mCherry (BBa_J18932), which is widely used as a fluorescent marker. However, N-terminal fusion of proteins with mCherry is not suited for studying various signal peptides due to the significant truncation that arises due to the presence of an RBS like sequence upstream of the ninth amino acid, Met which happens to be coded by the start codon (ATG). The RBS like sequence along with the start codon causes the transcription to begin at an internal site, resulting in significant truncation during protein expression.
The 2018 IIsc-Bangalore team attempted to reduce the truncation of the mCherry sequence by modifying the internal RBS like sequence and decreasing its ability to pair with the ribosome. Their improved part imCherry (BBa_K2609006) reported a considerable decrease in the truncation but they couldn't get rid of the truncated product entirely.
In order to completely shut down the truncation caused by mCherry, we modified the internal start codon (ATG) via a single base mutation at then 48th nucleotide to convert ATG to ATC (coding for Ile). In the absence of a start codon, no transcription is expected, thus eliminating the chances of any truncated products.

Usage

i2mCherry(Ile) was developed to overcome the shortcomings of the existing mCherry (BBa_J18932) BioBrick which is not suitable for protein fusion studies due to the truncation faced at the N-terminal. As a consequence of reduced truncation, i2mCherry can be used for studying signal peptides and other N-terminal protein fusion components.

Characterization

Expression with BBa_K3165046

The protein was expressed under the T7 promoter in Escherichia coli (BL21DE3) with 6xHistag at the N-terminal. The transformed bacteria were incubated at 37oC for over 4 hours. The cells were lysed by sonication and the lysate was collected via centrifugation. The lysate was run on an SDS PAGE which showed two bands. The size of the protein of interest along with the 6xHistag is around 27 kDa. The upper band corresponds to the non-truncated protein while the lower band represents the truncated product.

Fig(1) : SDS PAGE for mCherry and i2mCherry (Ile)

From the SDS PAGE, we clearly observe two bands when using mCherry, while i2mCherry (Ile) gave one very large spot on the polyacrylamide gel with a trailing smear kind of band. The observed dark band is seen at the desired size (roughly around 27 kDa) confirming that the bands correspond to our protein of interest.

Purification using Ni-NTA with BBa_K3165046

The cell lysate thus obtained was purified using Ni-NTA beads as only the non-truncated protein having 6xHistag can bind to the beads. Ideally, the supernatant after binding should have the truncated protein while the eluted fraction should contain the non-truncated protein. This idealisation does not hold true as the binding of Ni-NTA is not perfect.

Fig (2) : SDS PAGE for Ni-NTA Purification of i2mCherry (Ile)


Fluorescence Analysis

Wavelengths scans of the protein lysate were performed to obtain the excitation and emission spectra of the fluorescent protein. The fluorescence data obtained were corrected for the blank (untransformed BL21DE3 protein lysate) and the data so obtained is presented below :

Fig(1) : Excitation and Emission Spectra of mCherry

Fig(2) : Excitation and Emission Spectra of i2mCherry (Ile)

From the fluorescence data, we found out that the excitation λ for mCherry is 585 nm whereas its emisiion λ is 602 nm.
Similarly for i2mCherry (Ile) the experimental excitation λ was found to be 575 nm while the emission λ is found to be 617 nm.

Quantification of Truncation

The truncation of i2mCherry was quantified by the two following ways :

  1. By analysis of the intensity of the truncated and non-truncated protein bands as seen on the SDS PAGE.

  2. By combining the data of fluorescence and the gel intensity data of the Ni-NTA purification products (supernatant, wash and elution). Assuming the fluorescence of the truncated and non-truncated parts to be similar, we divide the fluorescence of each sample into two parts: one due to the truncated product and the other due to the non-truncated protein. The sum of the fluorescence of the two fractions was then used as a measure to estimate their concentration to determine truncation.

Fig(3) : Scatter Plot for the percentage truncation of mCherry and i2mCherry (Ile)

It is evident from the data that some amount of truncated protein was still produced irrespective of the presence or absence of the internal start codon. The presence of the RBS like sequence in the gene might be the reason behind the continued production of the truncated product.

Truncation Reduction

The Truncation was reduced from (48.5 ∓ 2.0)% in mCherry(BBa_J18932) to (5.03 ∓ 0.5)% in i2mCherry (Ile).

References :

(1) https://parts.igem.org/wiki/index.php?title=Part:BBa_K2609006