Difference between revisions of "Team:Marburg/Composite Part"

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<div class="btn_e_title">Best Composite Part</div>
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As best composite part we extended our best basic part TfoX, the inducer of natural competence in Vibrio species. We could successfully combine it with one of the inducible promoters from our Marburg Collection.
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<figure style="width:50%; float:left; margin:0.5em;"><img style="display:block; margin:0 auto 0 auto; width:100%;" src="https://static.igem.org/mediawiki/2018/3/3e/T--Marburg--tfoxsequencing.svg" alt="Relative promoter strength of Anderson promoters">
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<figcaption><b>Figure 1:</b>Alignment of sequencing results of our first constructed Lvl1 <i>tfoX</i> plasmids showing missing basepairs at places at which black fragments are missing.</figcaption>
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            </figure>
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<p>As an extension of our basic part <i>tfoX</i> we created a full transcriptional unit enabling you to perform natural transformation in <i>V. natriegens</i>.
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First we started assembling a  full transcriptional unit using a constitutive promoter. Therefore, we assembled <i>tfoX</i> together with the constitutive promoters J23100 or J23110 into a transcriptional unit by golden gate assembly. After transformation of this reactions into <i>E. coli</i> we were able to get colonies that seemed to be positive for the Lvl1 plasmids encoding <i>tfoX</i> because they showed the right size of fragment after plasmid preparation and test digestion, whenever we sent them for sequencing, some basepairs of the <i>tfox</i> gene were always missing (Figure 1).</p>
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<figure style="width: 50%; float: right; margin: 0.5em;"><img style="display:block; margin:0 auto 0 auto; width:100%;" src="https://static.igem.org/mediawiki/2018/4/4d/T--Marburg--pTet.png" alt="Alignment of sequencing results of our first constructed Lvl1 <i>tfoX</i> plasmids showing missing basepairs.">
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<figcaption><b>Figure 2:</b> Relative promoter strength of Anderson promoters
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Data were normalized over the strongest construct J23100. Error bars represent the standard deviation of the measurements of three independent experiments</figcaption>
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            </figure>
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We suggest that these problems could be caused because Tfox could somehow ne toxic to <i>E. coli</i> cells. At this point of our project we realized how important it is to have well characterized, tight, inducible promoters for the usage in <i>V. natriegens</i>.
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In addition to constitutive promoters, the Marburg Collection contains the inducible promoters, pTet and pTrc. From our measurements of the promoter characterization, we learned that the pTet promoter is the tightest one showing the lowest value of Luminescence without induction (Figure 2).
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The pTet promoter can be induced by the tetracycline derivative anhydrotetracycline (ATc). ATc is much less cytotoxic than IPTG but still capable of binding and altering the structure of the repressor TetR, leading to release of the promoter and enabling transcription.
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<figure style="width: 25%; float:left; margin: 0.5em;"><img style="width: 100%;" src="https://static.igem.org/mediawiki/2018/6/64/T--Marburg--Testdigesttfoxlevel1.svg" alt="1 %- Agarose gel of the test digest.">
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<figcaption><b>Figure 3:</b>1 %- Agarose gel of the test digest. 2-logDNA ladder is used as marker on agarose gels.</figcaption>
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            </figure>
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<p>Using this suitable promoter for <i>V. natriegens</i> we successfully assembled a plasmid containing a full transcriptional unit with a pTet promoter and did not had any problems during the cloning process. By Test Digestion and sequencing we could prove, that now the sequence of Tfox was correct (Figure 3 and 4).</p>
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<figure style="width: 50%; margin: 0.5em; float:right;"><img style="width: 100%;" src="https://static.igem.org/mediawiki/2018/a/a8/T--Marburg--sequencingtfox.png" alt="Alignment of sequencing results of our final constructed Lvl1 <i>tfoX</i> plasmid showing the correct sequence.">
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<figcaption><b>Figure 4:</b>Alignment of sequencing results of our final constructed Lvl1 <i>tfoX</i> plasmid showing the correct sequence.</figcaption>
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            </figure>
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As we have already shown in the chapter of our basic part, we were able to perform natural transformation using this plasmid and could demonstrate, that GFP which is encoded on pYTK is expressed by <i>V. natriegens</i>.
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<figure style=" width: 50%; margin: 0.5em;"><img style="width: 100%;" src="https://static.igem.org/mediawiki/2018/e/ed/T--Marburg--pYTKtransformation.svg" alt="Plates showing successful transformation of pYTK.">
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<figcaption><b>Figure 5:</b>Plate showing a successful transformation of pYTK using natural transformation.</figcaption>
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            </figure>
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      <figure style="width: 50%; margin: 0.5em;"><img style="width: 100%;"src="https://static.igem.org/mediawiki/2018/6/6d/T--Marburg--pYTKnaturaltransformation2.png" alt="Plates showing successful transformation of pYTK.">
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<figcaption><b>Figure 6:</b>Plate showing a successful transformation of pYTK using natural transformation with functioning pYTK.</figcaption>
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            </figure>
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Click here to learn more about how we used our best composite part in our project on the following sites in the Strain Engineering sub-project:<br>
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<ul>
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<li><a href="https://2018.igem.org/Team:Marburg/Description">Description</a></li>
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    <li><a href="https://2018.igem.org/Team:Marburg/Design">Design</a></li>
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    <li><a href="https://2018.igem.org/Team:Marburg/Results">Results</a></li>
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</ul>
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Revision as of 22:50, 17 October 2018

Composite Part
Best Composite Part
As best composite part we extended our best basic part TfoX, the inducer of natural competence in Vibrio species. We could successfully combine it with one of the inducible promoters from our Marburg Collection.
Relative promoter strength of Anderson promoters
Figure 1:Alignment of sequencing results of our first constructed Lvl1 tfoX plasmids showing missing basepairs at places at which black fragments are missing.

As an extension of our basic part tfoX we created a full transcriptional unit enabling you to perform natural transformation in V. natriegens. First we started assembling a full transcriptional unit using a constitutive promoter. Therefore, we assembled tfoX together with the constitutive promoters J23100 or J23110 into a transcriptional unit by golden gate assembly. After transformation of this reactions into E. coli we were able to get colonies that seemed to be positive for the Lvl1 plasmids encoding tfoX because they showed the right size of fragment after plasmid preparation and test digestion, whenever we sent them for sequencing, some basepairs of the tfox gene were always missing (Figure 1).

Alignment of sequencing results of our first constructed Lvl1 <i>tfoX</i> plasmids showing missing basepairs.
Figure 2: Relative promoter strength of Anderson promoters Data were normalized over the strongest construct J23100. Error bars represent the standard deviation of the measurements of three independent experiments
We suggest that these problems could be caused because Tfox could somehow ne toxic to E. coli cells. At this point of our project we realized how important it is to have well characterized, tight, inducible promoters for the usage in V. natriegens. In addition to constitutive promoters, the Marburg Collection contains the inducible promoters, pTet and pTrc. From our measurements of the promoter characterization, we learned that the pTet promoter is the tightest one showing the lowest value of Luminescence without induction (Figure 2). The pTet promoter can be induced by the tetracycline derivative anhydrotetracycline (ATc). ATc is much less cytotoxic than IPTG but still capable of binding and altering the structure of the repressor TetR, leading to release of the promoter and enabling transcription.
1 %- Agarose gel of the test digest.
Figure 3:1 %- Agarose gel of the test digest. 2-logDNA ladder is used as marker on agarose gels.

Using this suitable promoter for V. natriegens we successfully assembled a plasmid containing a full transcriptional unit with a pTet promoter and did not had any problems during the cloning process. By Test Digestion and sequencing we could prove, that now the sequence of Tfox was correct (Figure 3 and 4).

Alignment of sequencing results of our final constructed Lvl1 <i>tfoX</i> plasmid showing the correct sequence.
Figure 4:Alignment of sequencing results of our final constructed Lvl1 tfoX plasmid showing the correct sequence.
As we have already shown in the chapter of our basic part, we were able to perform natural transformation using this plasmid and could demonstrate, that GFP which is encoded on pYTK is expressed by V. natriegens.
Plates showing successful transformation of pYTK.
Figure 5:Plate showing a successful transformation of pYTK using natural transformation.
Plates showing successful transformation of pYTK.
Figure 6:Plate showing a successful transformation of pYTK using natural transformation with functioning pYTK.
Click here to learn more about how we used our best composite part in our project on the following sites in the Strain Engineering sub-project:
B. Marchal