Difference between revisions of "Part:BBa K4806209"

Latest revision as of 14:58, 12 October 2023

POR gene with HA-tag for Chlamydomonas reinhardtii (Phytobrick)

This composite part contains the AβSAP(i)-promotor (BBa_K4806013), the coding sequence of the POR (BBa_K4806003), the HA-tag (BBa_K3002017)^* for detection and the tRPL23-terminator (BBa_K3002006)^*. This part is codon-optimized for Chlamydomonas reinhardtii and was built as part of the CYPurify Collection. This level 2 part leads to expression of the POR

Construct

Fig.1 Construct design
This construct was designed using the modular cloning system (MoClo).

The resistance cassette for hygromycin is already built in the level 2 vector pMBS810 we are using. The usage of this vector allows the direct assembly of level 0 parts to level 2 constructs, facilitating the cloning time (Niemeyer & Schroda, 2022).

Sequence and Features

Assembly Compatibility:

10
INCOMPATIBLE WITH RFC[10]
Illegal PstI site found at 1353
Illegal PstI site found at 2613
Illegal PstI site found at 2673
Illegal PstI site found at 3332
12
INCOMPATIBLE WITH RFC[12]
Illegal NheI site found at 249
Illegal NheI site found at 2538
Illegal PstI site found at 1353
Illegal PstI site found at 2613
Illegal PstI site found at 2673
Illegal PstI site found at 3332
Illegal NotI site found at 2978
21
INCOMPATIBLE WITH RFC[21]
Illegal XhoI site found at 530
23
INCOMPATIBLE WITH RFC[23]
Illegal PstI site found at 1353
Illegal PstI site found at 2613
Illegal PstI site found at 2673
Illegal PstI site found at 3332
25
INCOMPATIBLE WITH RFC[25]
Illegal PstI site found at 1353
Illegal PstI site found at 2613
Illegal PstI site found at 2673
Illegal PstI site found at 3332
Illegal NgoMIV site found at 4261
Illegal AgeI site found at 268
1000
COMPATIBLE WITH RFC[1000]

Results

We detected the expression of the POR with HA-tag via immunoblotting.

Fig.2 Expression of the POR with HA-tag
(a)Level 2 MoClo construct for expression of the POR containing the HA-tag was designed (see Fig.1 for part description)
(b) Picture of resulting western blot. The POR is marked by a black arrow, the white arrow marks a cross reaction of antibodies. For reference, the UVM4 recipient strain and a strain expressing the HA-tagged ribosomal chloroplast 50S protein L5 (RPL5) were used as a negative and positive control, respectively

For detection the UVM4 strain was transformed with the construct in (a). 30 hygromycin-resistant transformants were cultivated in TAP medium and samples were taken after 3 days. Whole-cell proteins were extracted and analyzed by SDS-PAGE and immunoblotting using an anti-HA antibody. The expression of the POR (~ 77 kDa) is visible.

We tried to supertransform this construct into positive CYP3A4 strains.

Fig.5 Supertrafo of the POR into positive CYP3A4 strains
(a) Level 2 MoClo constructs for expression of the enzymes CYP3A4 and the POR containing the HA-tag. (b) The CYP3A4 strain was transformed with the POR construct in (a). 30 hygromomycin-resistant transformants were cultivated in TAP-medium and samples taken after 3 days. Whole-cell proteins were extracted and analyzed by SDS-PAGE and immunoblotting using an anti-HA antibody. In the resultant the white arrow marks a cross reaction of antibodies. The expression of CYP3A4 (~57 kDa) is visible. The expression of the POR (~ 77 kDa) is not visible. For reference, the UVM4 recipient strain and a strain expressing the HA-tagged ribosomal chloroplastic 50S protein L5 (RPL5) were used as a negative and positive control, respectively.

Sadly we were not able to detect the expression of the POR.

Contribution

The ^* marked parts were not created by us. Our results can be found on the experience page of each part.

The CYurify Collection

The world is at a crossroad. We must decide now how we want to continue living in order to survive. To contribute to this cause, we proudly present our CYPURIFY Collection for Chlamydomonas reinhardtii. The contamination of our water with toxic substances is on the rise, damaging ecosystems and eventually impacting us humans. We see it as our duty to take action.

To accomplish this, we designed 23 level 0, 9 level 1 and 24 level 2 parts for bioremediation of toxic wastewater using Modular Cloning. At heart of this collection are the Cytochrome P450 enzymes. Some of these monooxygenases are already used in synthesis or in medicine. We aimed to take a further step in research by expressing these enzymes in Chlamydomonas for the first time.

Chlamydomonas reinhardtii is the perfect fit for our system as a phototrophic organism with cost-effective and sustainable cultivation. Additionally, this organism is well-studied and easy to transform. We have access to a vast library of preexisting parts, all compatible with Modular Cloning.

Modular Cloning is a cloning method based on the Golden Gate System. What makes it unique is the ability to assemble entire genes in a single reaction. This is made possible by using type IIS restriction enzymes, which cut outside their recognition sequence, effectively removing it after ligation into the target vector. Therefore, the reaction proceeds in a specific direction. The parts are divided into level 0,1 and 2. Level 0 parts are basic components such as promotors, terminators or tags. Level 1 parts are combinations of these level 0 parts, forming transcriptional units. Level 2 parts are combinations of level 1 parts, allowing the expression of multiple genes simultaneously. Level 0 parts are assigned one of 10 positions, with standardized overhangs between them, enabling the exchange of parts between laboratories.

With our collection, we aim to contribute to environmental protection. This collection is infinitely expandable with new CYPs that can degrade other toxic substances. So, what are you waiting for?

@@ Line 3: / Line 3: @@
 <partinfo>BBa_K4806209 short</partinfo>
-aaaaaaaaa
+<html>
+<style>
+    .bild {max-width: 100% ; height: auto;}
+    .unterschrift {font-size: 11.5px;}
+</style>
-<!-- Add more about the biology of this part here
-===Usage and Biology===
-<!-- -->
+<p>This composite part contains the AβSAP(i)-promotor (<a href=" https://parts.igem.org/Part:BBa_K4806013">BBa_K4806013</a>), the coding sequence of the POR (<a href=" https://parts.igem.org/Part:BBa_K4806003">BBa_K4806003</a>), the HA-tag (<a href=" https://parts.igem.org/Part:BBa_K3002017">BBa_K3002017</a>)<sup>*</sup> for detection and the tRPL23-terminator (<a href="https://parts.igem.org/Part:BBa_K3002006">BBa_K3002006</a>)<sup>*</sup>. This part is codon-optimized for <i>Chlamydomonas reinhardtii</i> and was built as part of the CYPurify Collection. This level 2 part leads to expression of the POR </p>
-<span class='h3bb'>Sequence and Features</span>
+<br>
-<partinfo>BBa_K4806209 SequenceAndFeatures</partinfo>
+<h2>Construct</h2>
+<p>
+  <img class="bild" src="https://static.igem.wiki/teams/4806/wiki/registry/level2/por-ha-construct.png">
+  <div class="unterschrift"><b>Fig.1 Construct design</b><br>
+   This construct was designed using the modular cloning system (MoClo).</div>
+</p>
+  <p>The resistance cassette for hygromycin is already built in the level 2 vector pMBS810 we are using. The usage of this vector allows the direct assembly of level 0 parts to level 2 constructs, facilitating the cloning time (Niemeyer & Schroda, 2022). </p>
+<p><br></p>
+<h2>Sequence and Features</h2>
+</html>
+<partinfo>BBa_K4806209 SequenceAndFeatures</partinfo>
-<!-- Uncomment this to enable Functional Parameter display
-===Functional Parameters===
 <partinfo>BBa_K4806209 parameters</partinfo>
-<!-- -->
+<html>
+<h2>Results</h2>
+<p>We detected the expression of the POR with HA-tag via immunoblotting.</p>
+<p>
+  <img class="bild" src="https://static.igem.wiki/teams/4806/wiki/registry/level2/por-ha-wb.png">
+  <div class="unterschrift"><b>Fig.2 Expression of the POR with HA-tag</b><br>
+   (a)Level 2 MoClo construct for expression of the POR containing the HA-tag was designed (see Fig.1 for part description) <br> (b) Picture of resulting western blot. The POR is marked by a black arrow, the white arrow marks a cross reaction of antibodies. For reference, the UVM4 recipient strain and a strain expressing the HA-tagged ribosomal chloroplast 50S protein L5 (RPL5) were used as a negative and positive control, respectively
+ </div>
+</p>
+<p>For detection the UVM4 strain was transformed with the construct in (a). 30 hygromycin-resistant transformants were cultivated in TAP medium and samples were taken after 3 days. Whole-cell proteins were extracted and analyzed by SDS-PAGE and immunoblotting using an anti-HA antibody. The expression of the POR (~ 77 kDa) is visible.
+</p><p><br></p>
+<p>We tried to supertransform this construct into positive CYP3A4 strains.</p>
+<p>
+  <img class="bild" src="https://static.igem.wiki/teams/4806/wiki/registry/level2/supertrafo.png">
+  <div class="unterschrift"><b>Fig.5 Supertrafo of the POR into positive CYP3A4 strains</b><br>
+   (a) Level 2 MoClo constructs for expression of the enzymes CYP3A4 and the POR containing the HA-tag. (b) The CYP3A4 strain was transformed with the POR construct in (a). 30 hygromomycin-resistant transformants were cultivated in TAP-medium and samples taken after 3 days. Whole-cell proteins were extracted and analyzed by SDS-PAGE and immunoblotting using an anti-HA antibody. In the resultant the white arrow marks a cross reaction of antibodies. The expression of CYP3A4 (~57 kDa) is visible. The expression of the POR (~ 77 kDa) is not visible. For reference, the UVM4 recipient strain and a strain expressing the HA-tagged ribosomal chloroplastic 50S protein L5 (RPL5) were used as a negative and positive control, respectively.
+  </div>
+</p>
+<p>Sadly we were not able to detect the expression of the POR.</p>
+<h2>Contribution</h2>
+<p>The <sup>*</sup> marked parts were not created by us. Our results can be found on the experience page of each part.</p>
+<p><br></p>
+<h2>The CYurify Collection</h2>
+<p>The world is at a crossroad. We must decide now how we want to continue living in order to survive. To contribute to this cause, we proudly present our CYPURIFY Collection for <i>Chlamydomonas reinhardtii</i>. The contamination of our water with toxic substances is on the rise, damaging ecosystems and eventually impacting us humans. We see it as our duty to take action.</p><p>
+To accomplish this, we designed 23 level 0, 9 level 1 and 24 level 2 parts for bioremediation of toxic wastewater using Modular Cloning. At heart of this collection are the Cytochrome P450 enzymes. Some of these monooxygenases are already used in synthesis or in medicine. We aimed to take a further step in research by expressing these enzymes in <i>Chlamydomonas</i> for the first time. </p><p>
+<i>Chlamydomonas reinhardtii</i> is the perfect fit for our system as a phototrophic organism with cost-effective and sustainable cultivation. Additionally, this organism is well-studied and easy to transform. We have access to a vast library of preexisting parts, all compatible with Modular Cloning.</p><p>
+Modular Cloning is a cloning method based on the Golden Gate System. What makes it unique is the ability to assemble entire genes in a single reaction. This is made possible by using type IIS restriction enzymes, which cut outside their recognition sequence, effectively removing it after ligation into the target vector. Therefore, the reaction proceeds in a specific direction. The parts are divided into level 0,1 and 2. Level 0 parts are basic components such as promotors, terminators or tags. Level 1 parts are combinations of these level 0 parts, forming transcriptional units. Level 2 parts are combinations of level 1 parts, allowing the expression of multiple genes simultaneously. Level 0 parts are assigned one of 10 positions, with standardized overhangs between them, enabling the exchange of parts between laboratories. </p><p>
+With our collection, we aim to contribute to environmental protection. This collection is infinitely expandable with new CYPs that can degrade other toxic substances. So, what are you waiting for?
+</p>
+</html>