Team:Copenhagen/Project

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Latest revision as of 14:26, 18 September 2011

Table of Contents

CyperMan to the

Rescue

CyperMan

A CYP is an enzyme with hydroxylation powers. The hydroxylation performed by CYPs are expensive to produce with conventional chemical methods and it can therefore be greatly beneficial to utilize our CyperMans as little synthetic biology factories. Read more.

We have been working on two parallel projects, with two different aims. They are described in more detail below. The project regarding the human p450's was unfortunately put to a halt. This is why our focus has been on the project involving the cytochrome p450's from plants (the "Kill fungi" project).

CyperMan - Kills fungus

We hope to be able to develop bacteria that can kill fungus.
We will introduce a biological system to ''E.coli'' utilizing the plant cytochrome p450 79’s ability to produce small molecules called oximes which are toxic to fungus, as they inhibit the ability of the mitochondrial peroxidases to breakdown potentially harmful hydrogen peroxides. The oximes are produced from aminoacids - phenylalanine, tyrosine and tryptophan. Read more.

CyperMan - Saves the Fish

We hope to find and possibly optimize a biological system which can be introduced in bacteria and lead to the removal of PPCP (pharmaceutical and personal care products) pollutants in water. We intend to transform E.coli bacteria with different combinations of the several membrane bound human cytochrome p450 and examine our different cytochrome p450 transformed E.coli bacteria and their ability to impede estrogenic activity water. Read more.

Impact factors:

Our project has the aim to characterize different subfamilies of Cytochrome p450 as a BioBrick and thus add it to the partsregistry of BioBricks, a continuously growing collection of genetic parts that can be mixed and matched to build synthetic biology devices and systems (partsregistry.org). Hence our project contributes to the expansion of the partsregistry, benefitting all researchers with interest in these particular proteins. The partsregistry is founded on an open source philosophy, a philosophy we see as a great advantage for development and improvement of the number BioBricks already existing. The addition of different cytochrome p450 to this catalogue will perhaps encourage other groups to look at other aspects of the many functions of p450's and thus contribute to the formation of new biological systems – further expanding the field of synthetic biology.

iGEM Medals Requirements

Bronze

Team registration

Complete Judgment form.

Team Wiki.

Plan to present a poster and a talk at the iGEM Jamboree

At least one new submitted and well-characterized standard BioBrick Part or Device.

Silver

Demonstrate that at least one new BioBrick Part of your own design and construction works as expected.
Characterize the operation of at least one new BioBrick Part..

Gold

For Gold Medal, either of the following must be checked

Improve an existing BioBrick Part or Device.
Help another iGEM team
Outline and detail a new approach to an issue of Human Practice in synthetic biology as it relates to your project, such as safety, security, ethics, or ownership, sharing, and innovation .

Comments or questions to the team? Please mail us at igemcopenhagen@gmail.com

Retrieved from "http://2011.igem.org/Team:Copenhagen/Project"

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      <li><a href="https://2011.igem.org/Team:Copenhagen/Protocol" CLASS=leftbar>Protocols</a></li>
      <li><a href="https://2011.igem.org/Team:Copenhagen/Notebook" CLASS=leftbar>Notebook</a></li>
+<li><a href="https://2011.igem.org/Team:Copenhagen/Project/Data" CLASS=leftbar>Data Page</a></li>
 <li><a href="https://2011.igem.org/Team:Copenhagen/Parts" CLASS=leftbar>Parts</a></li>
+<li><a href="https://2011.igem.org/Team:Copenhagen/Results" CLASS=leftbar>Results</a></li>
+<li><a href="https://2011.igem.org/Team:Copenhagen/Collaboration" CLASS=leftbar>Collaboration</a></li>
 <li><a href="https://2011.igem.org/Team:Copenhagen/Attributions" CLASS=leftbar>Attribution</a></li>
 </ul>
     </font>
 <br>
-<center><b>Sponsors</b></center>
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+<br>
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+<br>
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-<table class="https://static.igem.org/mediawiki/2011/4/4c/Evolva.jpg" align="center">
-<tr><td><img src="https://static.igem.org/mediawiki/2011/4/4c/Evolva.jpg"  width="100px"></td></tr>
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 <p>&nbsp;</p>
 <p align="justify">
+<p align = left><strong>CyperMan</strong></p>
+<p>A CYP is an enzyme with hydroxylation powers. The hydroxylation performed by CYPs are expensive to produce with conventional chemical methods and it can therefore be greatly beneficial to utilize our CyperMans as little synthetic biology factories.<a href="https://2011.igem.org/Team:Copenhagen/Project/Cytochrome" style="text-decoration:none; color:blue;"> Read more.</a><br></p>
-<br>
 <br>
-<p align = right><strong>CyperMan - Kills fungus</strong></p>
+We have been working on two parallel projects, with two different aims. They are described in more detail below. The project regarding the human p450's was unfortunately put to a halt. This is why our focus has been on the project involving the cytochrome p450's from plants (the "Kill fungi" project).
-<table class="https://static.igem.org/mediawiki/2011/4/4e/CyperMan_svampe.jpg" align="right">
+<br>
-<tr><td><img src="https://static.igem.org/mediawiki/2011/4/4e/CyperMan_svampe.jpg"  width="175px"></td></tr>
+<br>
+<p align = left><strong>CyperMan - Kills fungus</strong></p>
+<table class="https://static.igem.org/mediawiki/2011/4/4e/Til_siden.png" align="left">
+<tr><td><img src="https://static.igem.org/mediawiki/2011/4/4e/Til_siden.png"  width="175px"></td></tr>
 </table>
-<br>
+<p align = "right">We hope to be able to develop bacteria that can kill fungus.<br>We will introduce a biological system to ''E.coli'' utilizing the plant cytochrome p450 79’s ability to produce small molecules called oximes which are toxic to fungus, as they inhibit the ability of the mitochondrial peroxidases to breakdown potentially harmful hydrogen peroxides. The oximes are produced from aminoacids - phenylalanine, tyrosine and tryptophan.
-<p align = "right">We hope to be able to develop bacteria that can kill fungus.<br>We will introduce a biological system to ''E.coli'' utilizing the plant cytochrome p450 79’s ability to produce small molecules called oximes which are toxic to fungus, as they inhibit the ability of the mitochondrial peroxidases to breakdown potentially harmful hydrogen peroxides. The oximes are produced from natural metabolites in plants.</p>
+<a href="https://2011.igem.org/Team:Copenhagen/Project/Fungus" style="text-decoration:none; color:blue;"> Read more.</a><br></p>
 <br>
-<strong>CyperMan - Saves the Fish</strong>
+<p align = right><strong>CyperMan - Saves the Fish</strong>
-<br>
+<table class="https://static.igem.org/mediawiki/2011/8/88/CyperMan_fisk.jpg" align="right">
-<br>
+<tr><td><img src="https://static.igem.org/mediawiki/2011/8/88/CyperMan_fisk.jpg"  width="180px"></td></tr>
-<table class="https://static.igem.org/mediawiki/2011/8/88/CyperMan_fisk.jpg" align="left">
-<tr><td><img src="https://static.igem.org/mediawiki/2011/8/88/CyperMan_fisk.jpg"  width="175px"></td></tr>
 </table>
-We intend to transform E.coli bacteria with different combinations of the several membrane bound human cytochrome p450. Furthermore, our intension is to use different constitutive promoters in order to express the cytochromes at different levels.
+We hope to find and possibly optimize a biological system which can be introduced in bacteria and lead to the removal of PPCP (pharmaceutical  and personal care products) pollutants in water.
-The next step will be to examine our different cytochrome p450 transformed E.coli bacteria and their ability to impede estrogenic activity water. We hope to find and possibly optimize a biological system which can be introduced in bacteria and lead to the removal of PPCP (pharmaceutical  and personal care products) pollutants in water.
+We intend to transform E.coli bacteria with different combinations of the several membrane bound human cytochrome p450 and examine our different cytochrome p450 transformed E.coli bacteria and their ability to impede estrogenic activity water. <a href="https://2011.igem.org/Team:Copenhagen/Project/Water" style="text-decoration:none; color:blue;"> Read more.</a><br></p>
-<br>
-<br>
-<br>
-<br>
-<strong>Cytochrome p450 CYP 1 & 2 - the source of CyperMans water cleansing power</strong>
-<br>
-<br>
-Cytochromes p450 is one of the largest gene superfamilies coding for enzymes present in the genomes in all biological kingdoms [1]. The enzymatic activities of these proteins are extremely diverse with activity in biotransformation of drugs, bioconversion of xenobiotics, biosynthesis of compounds as steroids, fatty acids, eicosanoids, fat soluble vitamins and bile acids. Furthermore, cytochrome p450’s are involved in the conversion of alkanes, terpenes and aromatic compounds as well as degradation of herbecides and insecticides [1]. </p>
-<p>We will exploit this activity of cytochromes p450 in the bioconversion of xenobiotics to neutralize damaging medical residues in waste water.</p>
-<p>Cytochromes p450 are defined as heme-thiolate proteins featuring a particular spectral signature at 450 nm, thus the name [2]. Despite the label as cytochromes, these proteins are not involved in electron transfers, but act as monooxygenases in a wide range of reactions such as epoxidation, N-dealkylation, O-dealkylation, S-oxidation and hydroxylation [3]. </p>
-<p>We will focus on the hydroxylating property of the cytochromes, which is also the defining reaction for these enzymes.  The reductive activation of molecular oxygen reduces one of the oxygen atoms to a molecule of water, as the other is inserted into the substrate [2].</p>
-<p>
-Fig 1
 <br>
 <br>
-		<strong>RH + NAD(P)H + O2 + H+ -> ROH + NAD(P)+ + H2O</strong>
-<br>
-<br>
-</p>
-<p>A key donor of electrons for the reduction of molecular oxygen is the NADPH dependent cytochrome p450 reductase (CPR). This protein shuttles electrons from NADPH through the FAD and FMN- coenzymes into the iron of the prosthetic heme group of cytochrome p450 [4]. </p>
-<p>A characterization of the cytochromes p450 is the main objective with this project. We will exploit the wide specificity of these cytochromes to target many different damaging agents continuously by hydroxylation, which can reduce the damaging activity of e.g. estrogen. </p>
-<br>
-<table class="https://static.igem.org/mediawiki/2011/c/cc/CYP_catalystisk_circle.PNG" align="center">
- <caption align="bottom"><p align="justify"><b>Figure 1</b>The P450 catalytic cycle in hydroxylation</p></caption>
-<tr><td><img src="https://static.igem.org/mediawiki/2011/c/cc/CYP_catalystisk_circle.PNG" width="500px"></td></tr>
-</table><br>
-<br>
-<strong>Cytochrome p450 CYP 79 - the source of CyperMans fungus destroying power</strong>
-<br>
-<br>
-Background information:
-<br>
-It has been proposed in the article Dynamic Metabolons [5] that the assembly and disassembly of enzymes complexes, so-called metabolons, may differentiate plant defense responses to insect attack and fungal infection.
-The two CYP79 and CYP71 subfamilies are part of a metabolon complex that shifts between assembly and disassembly, according to interactions with proteins or from specific metabolic demands. The CYP79 subfamily can by itself produce a substance called 4-hydroxyphenyl-acetaldeyde oxime. This substance is generally toxic to fungi and frequently used as chemical fungicides. They function by inhibiting mitochondrial oxidases and thereby promote lipid peroxidation and the production of toxic reactive oxygen species[5].
-The CYP79A1 and CYP79A2 proteins use L-Tyrosine as a substrate, which it hydroxylates twice on the amino-group in the presence of NADPH and O2. The products of these reactions are quite unstable and dehydration and decarboxylation will then produce 4-hydroxyphenyl-acetaldeyde oxime. [6] The CYP79B1 isoform is specific for tryptophan and therefore it produces indole 3-acetaldoxime instead.
-<br>
-<br>
-<table class="https://static.igem.org/mediawiki/2011/3/37/Modificeret_model_2.png" align="center">
-<tr><td><img src="https://static.igem.org/mediawiki/2011/3/37/Modificeret_model_2.png"  width="500px"></td></tr>
-</table>
-<br>
-The Project: <br>
-Our goal is to express different CYP79’s (more specifically from the subfamilies A1, A2 and B1) in E. Coli, to determine whether they can actually be expressed as working proteins in them. Then our idea is introduce a promoter to the system, which reacts to a specific chemical signal that is sent out by fungi.  We are also working with both the iGEM teams from DTU. To ensure that the protein only will be expressed in the presence of fungi, we plan to incorporate a regulating system that uses RNA-RNA interactions. A constitutive promoter will make sure that a small 9 bp piece of RNA is constantly expressed. This piece of RNA is complimentary to the ribosomal binding site of our plasmid-RNA and will therefore bind to it. This will prevent our gene of interest from being translated into protein. Another promoter that is induced by a fungal elicitor will start the production of another small 9 bp piece of RNA that is complimentary to the first 9 bp RNA when these bind there is no inhibition of the gene translation. This is a system developed by DTU-DENMARK1.
-<br>
-<br>
 <strong>Impact factors:</strong>
-<br>
-<br>
-<u>Open source BioBricks:</u>
 <br>
 <br>
-Our project has the aim to characterize Cytochrome p450 as a BioBrick and thus add it to the partsregistry of BioBricks, a continuously growing collection of genetic parts that can be mixed and matched to build synthetic biology devices and systems (partsregistry.org). Hence our project contributes to the expansion of the partsregistry, benefitting all researchers with interest in this particular protein, since cytochrome p450 doesn’t exist in the partsregistry. The partsregistry is founded on an open source philosophy, a philosophy we see as a great advantage for development and improvement of the number BioBricks already existing. The addition of cytochrome p450 to this catalogue will perhaps encourage other groups to look at other aspects of the many functions of p450 and thus contribute to the formation of new biological systems – further expanding the field of synthetic biology.
+Our project has the aim to characterize different subfamilies of Cytochrome p450 as a BioBrick and thus add it to the partsregistry of BioBricks, a continuously growing collection of genetic parts that can be mixed and matched to build synthetic biology devices and systems (partsregistry.org). Hence our project contributes to the expansion of the partsregistry, benefitting all researchers with interest in these particular proteins. The partsregistry is founded on an open source philosophy, a philosophy we see as a great advantage for development and improvement of the number BioBricks already existing. The addition of different cytochrome p450 to this catalogue will perhaps encourage other groups to look at other aspects of the many functions of p450's and thus contribute to the formation of new biological systems – further expanding the field of synthetic biology.
-<br>
-<br>
-<u>Ecological and economical prospects:</u>
-<br>
-<br>
-Our future aim with our project is to determine whether it would be a viable solution to use an oxime producing agent as a type of fungicide. The best scenario would be if the plants themselves was able to produce the oximes and thus protect themselves and eliminating the need for fungicides.
-<br>
-<br>
-Another future aim with our project is to improve wastewater treatments and thus contribute to a cleaner and uncontaminated drinking water for everyone. With this scientific project, we will move towards this realization, but more research is needed. Our belief is that further research on the use of cytochrome p450 will give a valid and an inexpensive product for use in wastewater treatment plants, thus benefitting the environment and our planet.
- <br><br>
-<strong>References</strong>
-<br><br>
-[1] F. Hannemann, A. Bichet, K. M. Ewen, R. Bernhardt: Cytochrome p450 systems – biological variations of electron transport chains. Biochemica et Biophysica Acta 1770 (2007) 330 - 344
-<br>
-[2] Paul R. Ortiz de Montellano. Hydrocarbon Hydroxylation by Cytochrome P450 Enzymes. Chem Rev. 2010 February 10; 110(2): 932
-<br>
-[3] http://www.anaesthetist.com/physiol/basics/metabol/cyp/Findex.htm
-<br>
-[4] T. Laursen, K. Jensen,B. L. Møller: Conformational changes of the NADPH dependent cytochrome P450 reductase in the course of electron transfer to cytochromes P450. Biochemica et Biophysica Acta 1814 (2011) 132-138
-<br>
-[5]Moller, B. L. (2010) Plant science. Dynamic metabolons, Science 330, 1328-1329.
-<br>
-[6]Koch, B. M., Sibbesen, O., Halkier, B. A., Svendsen, I., and Moller, B. L. (1995) The primary sequence of cytochrome P450tyr, the multifunctional N-hydroxylase catalyzing the conversion of L-tyrosine to p-hydroxyphenylacetaldehyde oxime in the biosynthesis of the cyanogenic glucoside dhurrin in Sorghum bicolor (L.) Moench, Arch Biochem Biophys 323, 177-186.
 </p>
-<table align="center">
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 <IMG SRC="http://lh5.ggpht.com/_Uc3bmii-yi0/TMhTZEsQBQI/AAAAAAAAAoI/Wlkf0vghuGk/caseCocherOK.PNG"/> Team registration<br>
-<IMG SRC="http://lh4.ggpht.com/_Uc3bmii-yi0/TMhTqQbWTSI/AAAAAAAAAoQ/tU6xh9B91iw/caseCocherEmpty.PNG"/> Complete Project Summary form<br>
+<IMG SRC="http://lh5.ggpht.com/_Uc3bmii-yi0/TMhTZEsQBQI/AAAAAAAAAoI/Wlkf0vghuGk/caseCocherOK.PNG"/> Complete Judgment form.<br>
-<IMG SRC="http://lh5.ggpht.com/_Uc3bmii-yi0/TMhTZEsQBQI/AAAAAAAAAoI/Wlkf0vghuGk/caseCocherOK.PNG"/> Team Wiki
+<IMG SRC="http://lh5.ggpht.com/_Uc3bmii-yi0/TMhTZEsQBQI/AAAAAAAAAoI/Wlkf0vghuGk/caseCocherOK.PNG"/><a href="https://2011.igem.org/Team:Copenhagen" style="text-decoration:none; color:black;"> Team Wiki.</a>
 <br>
-<IMG SRC="http://lh4.ggpht.com/_Uc3bmii-yi0/TMhTqQbWTSI/AAAAAAAAAoQ/tU6xh9B91iw/caseCocherEmpty.PNG"/> Present a poster and a talk at the iGEM Jamboree<br>
+<IMG SRC="http://lh5.ggpht.com/_Uc3bmii-yi0/TMhTZEsQBQI/AAAAAAAAAoI/Wlkf0vghuGk/caseCocherOK.PNG"/> Plan to present a poster and a talk at the iGEM Jamboree<br>
-<IMG SRC="http://lh4.ggpht.com/_Uc3bmii-yi0/TMhTqQbWTSI/AAAAAAAAAoQ/tU6xh9B91iw/caseCocherEmpty.PNG"/><a href="https://2010.igem.org/Team:INSA-Lyon/Project" style="text-decoration:none; color:black;"> At least one new submitted and well-characterized standard BioBrick Part or Device.</a><br>
+<IMG SRC="http://lh5.ggpht.com/_Uc3bmii-yi0/TMhTZEsQBQI/AAAAAAAAAoI/Wlkf0vghuGk/caseCocherOK.PNG"/><a href="https://2011.igem.org/Team:Copenhagen/Parts" style="text-decoration:none; color:black;"> At least one new submitted and well-characterized standard BioBrick Part or Device.</a><br>
 <br></p>
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 <p style="text-indent:0px;">
-<IMG SRC="http://lh4.ggpht.com/_Uc3bmii-yi0/TMhTqQbWTSI/AAAAAAAAAoQ/tU6xh9B91iw/caseCocherEmpty.PNG"/> Demonstrate that at least one new BioBrick Part of your own design and construction works as expected<br>
+<IMG SRC="http://lh5.ggpht.com/_Uc3bmii-yi0/TMhTZEsQBQI/AAAAAAAAAoI/Wlkf0vghuGk/caseCocherOK.PNG"/> <a href="https://2011.igem.org/Team:Copenhagen/Results" style="text-decoration:none; color:black;">Demonstrate that at least one new BioBrick Part of your own design and construction works as expected.</a><br>
-<IMG SRC="http://lh4.ggpht.com/_Uc3bmii-yi0/TMhTqQbWTSI/AAAAAAAAAoQ/tU6xh9B91iw/caseCocherEmpty.PNG"/> Characterize the operation of at least one new BioBrick Part.<br>
+<IMG SRC="http://lh5.ggpht.com/_Uc3bmii-yi0/TMhTZEsQBQI/AAAAAAAAAoI/Wlkf0vghuGk/caseCocherOK.PNG"/> <a href="https://2011.igem.org/Team:Copenhagen/Results" style="text-decoration:none; color:black;">Characterize the operation of at least one new BioBrick Part..</a><br>
 </p>
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 <IMG SRC="http://lh4.ggpht.com/_Uc3bmii-yi0/TMhTqQbWTSI/AAAAAAAAAoQ/tU6xh9B91iw/caseCocherEmpty.PNG"/> Improve an existing BioBrick Part or Device. <br>
-<IMG SRC="http://lh4.ggpht.com/_Uc3bmii-yi0/TMhTqQbWTSI/AAAAAAAAAoQ/tU6xh9B91iw/caseCocherEmpty.PNG"/><a href="https://2010.igem.org/Team:INSA-Lyon/Acknowledgements#collaboCheck" style="text-decoration:none; color:black;"> Help another iGEM team </a><br>
+<IMG SRC="http://lh5.ggpht.com/_Uc3bmii-yi0/TMhTZEsQBQI/AAAAAAAAAoI/Wlkf0vghuGk/caseCocherOK.PNG"/><a href="https://2011.igem.org/Team:Copenhagen/Collaboration" style="text-decoration:none; color:black;"> Help another iGEM team </a><br>
-<IMG SRC="http://lh4.ggpht.com/_Uc3bmii-yi0/TMhTqQbWTSI/AAAAAAAAAoQ/tU6xh9B91iw/caseCocherEmpty.PNG"/> Outline and detail a new approach to an issue of Human Practice in synthetic biology as it relates to your project, such as safety, security, ethics, or ownership, sharing, and innovation.<br>
+<IMG SRC="http://lh5.ggpht.com/_Uc3bmii-yi0/TMhTZEsQBQI/AAAAAAAAAoI/Wlkf0vghuGk/caseCocherOK.PNG"/><a href="https://2011.igem.org/Team:Copenhagen/Ethics" style="text-decoration:none; color:black;"> Outline and detail a new approach to an issue of Human Practice in synthetic biology as it relates to your project, such as safety, security, ethics, or ownership, sharing, and innovation </a> .<br>
 <br>
 </p>