Difference between revisions of "Part:BBa K1934040"

 
 
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<partinfo>BBa_K1934040 short</partinfo>
 
<partinfo>BBa_K1934040 short</partinfo>
  
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This part is composed of the RFP coding sequence under the control of the pTAC promoter and a  
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This part is composed of the RFP coding sequence under the control of the pTAC promoter, a strong RBS and a bidirectional terminator.  
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strong RBS.
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<!-- Add more about the biology of this part here
 
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<partinfo>BBa_K1934040 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K1934040 SequenceAndFeatures</partinfo>
  
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=='''Characterization'''==
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<html>
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<h3 id="CBD">Description</h3>
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<p>pTAC promoter was taken from part <a href="https://parts.igem.org/Part:BBa_K864400">BBa_K864400</a>. This promoter is a hybrid of two operons: the trp and lac operons. This promoter is  inducible by IPTG and  commonly used in <i>Escherichia coli</i> for overproduction of proteins. <i>E. coli</i> NM522 strain that we used in our lab constitutively produces the LacIq protein, a strong pTAC promoter repressor. However, in absence of IPTG, we observed a strong leakage when plating our <a href="https://parts.igem.org/Part:BBa_K1934000">BBa_K1934000</a> transformants. Therefore, we decided to put a RFP reporter ORF under control of the pTAC promoter to characterize the promoter-driven transcriptional noise.
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</p>
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<h3 id="CBD">Expression of the pTAC-RFP fusion in presence of increasing amount of the inductor IPTG</h3>
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<h5 id="CBD">Experimental design</h5>
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The RFP coding sequence (<a href="https://parts.igem.org/Part:BBa_E1010">BBa_E1010</a>) was placed <i>in silico</i> under the control of the pTAC promoter (<a href="https://parts.igem.org/Part:BBa_K864400">BBa_K864400</a>), a strong RBS (<a href="https://parts.igem.org/Part:BBa_B0030">BBa_B0030</a>) and a bidirectional terminator (<a href="https://parts.igem.org/Part:BBa_B0011">BBa_B0011</a>). IDT performed the DNA synthesis and delivered the part as gBlock. The construct was cloned by conventional ligation into pSB1C3 plasmid and then transformed into <i>E. coli</i> NM522 strain.
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In order to study the efficiency of the pTAC promoter for the overproduction of proteins, recombinant clones were grown overnight in LB at 37°C in duplicate in three different induction conditions (IPTG concentrations): 0 mmol.L<sup>-1</sup>, 1 mmol.L<sup>-1</sup> and 5 mmol.L<sup>-1</sup>. OD<sub>600</sub> of each culture was measured every hour over six hours.
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<i>E. coli</i> NM522 strain was grown overnight in LB at 37°C in the same three induction conditions as control.
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<h5 id="CBD">Results</h5>
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<ul style="list-style-type:circle">
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  <li><b>Noise of the pTAC: fluorescence in absence of IPTG</b></li>
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</ul>
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<p>We studied the noise of the promoter by comparing the normalized fluorescence between the construction and the NM522 strain without any induction of IPTG.</p>
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<figure><p style="text-align:center;"><img src="https://static.igem.org/mediawiki/2016/f/fc/INSA-Lyon_RFP-NM522.jpg" width = "800"/><figcaption><b>Figure 1. Fluorescence/OD<sub>600</sub> comparison between NM522 with or without the plasmid (RFP). </b> Fluorescence of each sample was measured every hour over six hours with ChemiDoc Imaging system and was normalized by dividing by the OD<sub>600</sub>. After one hour, a significant expression difference was noticed; NM522 strain with plasmid revealed a higher protein expression. </figcaption></figure>
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<p>An ANOVA was made to see if there was a time effect between the two populations. We obtained a p-value of 0.61, suggesting that time had no effect on pTAC-RFP expression in absence of IPTG (α<0.05). Given this result, we gathered data to analyze if there was a significant difference between the two strains.
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A Student test was performed with the variance not equal. The p-value of 5.44*10<sup>-4</sup> indicated that the strain carrying pTAC-RFP transcriptional fusion displayed a higher fluorescence than the control strain.</p>
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<ul style="list-style-type:circle">
 +
  <li><b>pTAC induction by increasing concentration of IPTG</b></li>
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</ul>
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<p>Then we studied the induction of the promoter by comparing the normalized fluorescence of the construction under the induction of [IPTG] = 0 and 1 mmol.L<sup>-1</sup>.</p>
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 +
<figure><p style="text-align:center;"><img src="https://static.igem.org/mediawiki/2016/b/bd/INSA-Lyon_0vs1.jpg" width = "800"/><figcaption><b>Figure 2. Fluorescence/OD<sub>600</sub> comparison between NM522 strains with plasmid (RFP) and with IPTG induction of 0 or 1 mmol.L<sup>-1</sup>. </b> Fluorescence of each sample was measured every hour over six hours with ChemiDoc Imaging system and was normalized by dividing by the OD<sub>600</sub>. After one hour, a significant expression difference was noticed; IPTG induction enables a higher protein expression rate. </figcaption></figure>
 +
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<p>An ANOVA test was made to see if there was a time effect between the two populations. A p-value of 0.21 indicated that time had no effect on the fluorescence induction (α<0.05). Data was therefore gathered in order to compare the strain fluorescence with 1 mmol.L<sup>-1</sup> IPTG and no IPTG.
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We realized a Student test with the variance not equal and obtained a p-value of 8.57*10<sup>-3</sup>, showing a difference of fluorescence due to the presence of IPTG in the medium.</p>
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<p>Finally, we compared the expression of the pTAC-RFP transcriptional fusion in 2 concentrations of IPTG: 1 and 5 mmol.L<sup>-1</sup>.</p>
 +
 +
<figure><p style="text-align:center;"><img src="https://static.igem.org/mediawiki/2016/6/64/INSA-Lyon_1vs5.jpg" width = "800"/><figcaption><b>Figure 3. Fluorescence/OD<sub>600</sub> comparison between NM522 strains with plasmid (RFP) and with IPTG induction of 1 or 5 mmol.L<sup>-1</sup> </b> Fluorescence of each sample was measured every hour over six hours with ChemiDoc Imaging system and was normalized by dividing by the OD<sub>600</sub>. Even after six hours of incubation, no significant expression difference was observed, protein expression rate was not correlated with the concentration of IPTG. </figcaption></figure>
 +
 +
<p>An ANOVA was made to see if there was a time effect between the two populations. A p-value of 0.06 indicated that time had no effect (α<0.05). From there, we could gather the data to analyze if there was a significant difference between the two concentrations of IPTG.</p>
 +
<p>We realized a Student test with the variance not equal and obtained a p-value of 0.61, indicating that no significant difference of fluorescence was observed with the rise of IPTG concentration.</p>
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<h3 id="CBD">Conclusion</h3>
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<p>In the case of RFP, the pTAC promoter seemed to not enable a gene tune because statistics showed that there was a significant noise, even in the absence of IPTG.</p>
  
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</html>
 
<!-- Uncomment this to enable Functional Parameter display  
 
<!-- Uncomment this to enable Functional Parameter display  
 
===Functional Parameters===
 
===Functional Parameters===
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<partinfo>BBa_K1934040 parameters</partinfo>
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<partinfo>BBa_K1934060 parameters</partinfo>
 
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Latest revision as of 19:36, 25 October 2016

RFP under the control of pTAC promoter

This part is composed of the RFP coding sequence under the control of the pTAC promoter, a strong RBS and a bidirectional terminator.

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 637
    Illegal AgeI site found at 749
  • 1000
    COMPATIBLE WITH RFC[1000]

Characterization

Description

pTAC promoter was taken from part BBa_K864400. This promoter is a hybrid of two operons: the trp and lac operons. This promoter is inducible by IPTG and commonly used in Escherichia coli for overproduction of proteins. E. coli NM522 strain that we used in our lab constitutively produces the LacIq protein, a strong pTAC promoter repressor. However, in absence of IPTG, we observed a strong leakage when plating our BBa_K1934000 transformants. Therefore, we decided to put a RFP reporter ORF under control of the pTAC promoter to characterize the promoter-driven transcriptional noise.

Expression of the pTAC-RFP fusion in presence of increasing amount of the inductor IPTG

Experimental design
The RFP coding sequence (BBa_E1010) was placed in silico under the control of the pTAC promoter (BBa_K864400), a strong RBS (BBa_B0030) and a bidirectional terminator (BBa_B0011). IDT performed the DNA synthesis and delivered the part as gBlock. The construct was cloned by conventional ligation into pSB1C3 plasmid and then transformed into E. coli NM522 strain. In order to study the efficiency of the pTAC promoter for the overproduction of proteins, recombinant clones were grown overnight in LB at 37°C in duplicate in three different induction conditions (IPTG concentrations): 0 mmol.L-1, 1 mmol.L-1 and 5 mmol.L-1. OD600 of each culture was measured every hour over six hours. E. coli NM522 strain was grown overnight in LB at 37°C in the same three induction conditions as control.
Results
  • Noise of the pTAC: fluorescence in absence of IPTG

We studied the noise of the promoter by comparing the normalized fluorescence between the construction and the NM522 strain without any induction of IPTG.

Figure 1. Fluorescence/OD600 comparison between NM522 with or without the plasmid (RFP). Fluorescence of each sample was measured every hour over six hours with ChemiDoc Imaging system and was normalized by dividing by the OD600. After one hour, a significant expression difference was noticed; NM522 strain with plasmid revealed a higher protein expression.

An ANOVA was made to see if there was a time effect between the two populations. We obtained a p-value of 0.61, suggesting that time had no effect on pTAC-RFP expression in absence of IPTG (α<0.05). Given this result, we gathered data to analyze if there was a significant difference between the two strains. A Student test was performed with the variance not equal. The p-value of 5.44*10-4 indicated that the strain carrying pTAC-RFP transcriptional fusion displayed a higher fluorescence than the control strain.

  • pTAC induction by increasing concentration of IPTG

Then we studied the induction of the promoter by comparing the normalized fluorescence of the construction under the induction of [IPTG] = 0 and 1 mmol.L-1.

Figure 2. Fluorescence/OD600 comparison between NM522 strains with plasmid (RFP) and with IPTG induction of 0 or 1 mmol.L-1. Fluorescence of each sample was measured every hour over six hours with ChemiDoc Imaging system and was normalized by dividing by the OD600. After one hour, a significant expression difference was noticed; IPTG induction enables a higher protein expression rate.

An ANOVA test was made to see if there was a time effect between the two populations. A p-value of 0.21 indicated that time had no effect on the fluorescence induction (α<0.05). Data was therefore gathered in order to compare the strain fluorescence with 1 mmol.L-1 IPTG and no IPTG. We realized a Student test with the variance not equal and obtained a p-value of 8.57*10-3, showing a difference of fluorescence due to the presence of IPTG in the medium.

Finally, we compared the expression of the pTAC-RFP transcriptional fusion in 2 concentrations of IPTG: 1 and 5 mmol.L-1.

Figure 3. Fluorescence/OD600 comparison between NM522 strains with plasmid (RFP) and with IPTG induction of 1 or 5 mmol.L-1 Fluorescence of each sample was measured every hour over six hours with ChemiDoc Imaging system and was normalized by dividing by the OD600. Even after six hours of incubation, no significant expression difference was observed, protein expression rate was not correlated with the concentration of IPTG.

An ANOVA was made to see if there was a time effect between the two populations. A p-value of 0.06 indicated that time had no effect (α<0.05). From there, we could gather the data to analyze if there was a significant difference between the two concentrations of IPTG.

We realized a Student test with the variance not equal and obtained a p-value of 0.61, indicating that no significant difference of fluorescence was observed with the rise of IPTG concentration.

Conclusion

In the case of RFP, the pTAC promoter seemed to not enable a gene tune because statistics showed that there was a significant noise, even in the absence of IPTG.