Difference between revisions of "Part:BBa K3165046"
| (18 intermediate revisions by 4 users not shown) | |||
| Line 3: | Line 3: | ||
<partinfo>BBa_K3165046 short</partinfo> | <partinfo>BBa_K3165046 short</partinfo> | ||
| − | This part is used to generate i<sup>2</sup>mCherry (Ile) which overcomes the problems in the existing mCherry sequence which undergoes significant truncation in the protein. The single-base mutation at the 48th base causes conversion of the internal start codon into ATC (coding for Ile). | + | This part is used to generate i<sup>2</sup>mCherry (Ile) which overcomes the problems in the existing mCherry <html><a href="https://parts.igem.org/Part:BBa_J18932">(BBa_J18932)</a></html> sequence which undergoes significant truncation in the protein. The single-base mutation at the 48th base causes the conversion of the internal start codon into ATC (coding for Ile). |
<!-- --> | <!-- --> | ||
| Line 11: | Line 11: | ||
===Usage and Biology=== | ===Usage and Biology=== | ||
| − | i<sup>2</sup>mCherry (Ile) is an improved version of mCherry( | + | 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, the 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 | + | 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.<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.<br> | ||
| − | + | 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> | ||
| Line 21: | Line 21: | ||
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> | <html> | ||
| Line 26: | Line 37: | ||
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. | 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> | <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 : | 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 λ</b> for mCherry is <b>585 nm</b> whereas its <b>emisiion λ</b> is <b>602 nm</b>.<br> | ||
| + | Similarly for i<sup>2</sup>mCherry (Ile) the experimental <b>excitation λ</b> was found to be <b>575 nm</b> while the <b>emission λ</b> is found to be <b>617 nm</b>. | ||
| + | |||
<h3> Quantification of Truncation </h3> | <h3> Quantification of Truncation </h3> | ||
| Line 38: | Line 79: | ||
<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> | <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> | </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 ∓ 2.0)%</b> in mCherry(<html><a href="https://parts.igem.org/Part:BBa_J18932">BBa_J18932</a></html>) to <b>(5.03 ∓ 0.5)%</b> in i<sup>2</sup>mCherry (Ile). | ||
<!-- Uncomment this to enable Functional Parameter display | <!-- Uncomment this to enable Functional Parameter display | ||
===Functional Parameters=== | ===Functional Parameters=== | ||
<partinfo>BBa_K3165046 parameters</partinfo> | <partinfo>BBa_K3165046 parameters</partinfo> | ||
<!-- --> | <!-- --> | ||
Latest revision as of 02:05, 22 October 2019
i^2mCherry (Ile) Coding Device (under T7 expression)
This part is used to generate i2mCherry (Ile) which overcomes the problems in the existing mCherry (BBa_J18932) sequence which undergoes significant truncation in the protein. The single-base mutation at the 48th base causes the conversion of the internal start codon into ATC (coding for Ile).
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25INCOMPATIBLE WITH RFC[25]Illegal AgeI site found at 738
- 1000COMPATIBLE WITH RFC[1000]
Usage and Biology
i2mCherry (Ile) is an improved version of mCherry (BBa_J18932), which is widely used as a fluorescent marker. However, the 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.
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.
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.
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 :
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 :
- By analysis of the intensity of the truncated and non-truncated protein bands as seen on the SDS PAGE.
- 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.
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).