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Background

In our project we developed a system to fight pathogens in the gut, which is not a unique idea. Except we wanted our systems key attribute to be specificity. To do so, we needed to find a unique quorum sensing language that we could hijack and utilize. We found the Yen system, from Yersinia enterocolitica. A homologous sytem to the well known Lux system, from Vibrio fischeri.

System design

From the Yen system we stole the activator YenR and the recognition region, the yenbox, fused with a wild type promoter. YenR was synthesized with the RBS B0034 and codon optimized for E. coli. A customized version of the yenbox-promoter was also created.

Result

We managed to get a five-fold induction relative to the base level of expression. The cells that were used during the measurements were double transformed with the yenbox-promoter complex with GFP and a plasmid producing the activator YenR.

Parts

Assembly Plan

Figure 1. The assembly plan of the killing construct. The green arrow is the promotor, the red circle is the RBS and the yellow box is the gene which consist of an export tag, USP45 and the bacteriocin, colicin FyA fused together.

Bacteriocin

With the growing problem of antibiotic resistance spreading, we decided to use bacteriocins as our antimicrobial agent. A bacteriocin is a peptide that is produced naturally by certain bacteria and targets its close relatives. Unlike general antibiotics,the target of bacteriocins are very specific. The bacteriocin, colicin Fy is produced by Y. frederiksenii and it should mostly target other yersinia species. Bacteriocins will either attack the cell membrane or a mechanism inside the cell such as gene expression or protein production.^[1] One of colicins Fy main target is Y. enterocolitica. It kills Y. enterocolitica by creating pores in its cell membrane. Y. enterocolitica is also one among the common pathogens that infects the gut and cause some serious symptoms^[2]. These were some of the reasons to chose colicin as the bacteriocin we want to express.

Spot42 RNA

Our goal was to design a seek and kill system. This implies that we only want to express the bacteriocin when our bacteria is close to the target. We chose this strategy because the cell would stress out to express bacteriocin all the time, even when not in close proximity to Yersinia. In order to make our bacteria only express the colicin when we want, we have included a sRNA system. We used the system that Team Uppsala iGEM 2012 designed. The sRNA consists of an antisense region that recognizes a specific RNA sequence to interact with and another region that recruits the protein Hfq. The HFq protein blocks and prevent mRNA to bind to a ribosome. We have redesigned the antisense region so it will specifically recognize our USP45. This will make it bind to our USP45 and recruit the Hfq protein to stick on that region.^[3] USP45 is the secretion tag that we have coupled to the colicin. The sRNA will stick to Hfq and bind to the mRNA of USP45-Colicin gene and that will block the translation. But when our bacteria is in proximity to y.entercolitica we want it to express the collicin Fy. Therefore, the sensing group have been working on a Yen system which will inactivate the promotor that regulates the spot42 when it is close to Y.enterocolitica.

Figure 2. The spot42 system

[1] http://www.nature.com/nrmicro/journal/v11/n2/full/nrmicro2937.html
[2] http://jb.asm.org/content/194/8/1950.long
[3] https://2012.igem.org/Team:Uppsala_University/Project

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@@ Line 59: / Line 59: @@
 </div>
-<h2>Assembly Plan</h2><img class="schedule" src="https://static.igem.org/mediawiki/2014/8/8b/Uppsala2014_TheKillingsystemV2.png"</img><p>Figure 1. The assembly plan of the killing construct. The green arrow is the promotor, the red circle is the RBS and the yellow box is the gene which consist of an export tag, USP45 and the bacteriocin, colicin FyA fused together.</p><br><br><br><br><h2>Bacteriocin</h2><p>With the growing problem of antibiotic resistance spreading, we decided to use bacteriocins as our antimicrobial agent. A bacteriocin is a peptide that is produced naturally by certain bacteria and targets its close relatives. Unlike general antibiotics,the target of bacteriocins are very specific. The bacteriocin, colicin Fy is produced by Y. frederiksenii and it should mostly target other yersinia species.  Bacteriocins will either attack the cell membrane or a mechanism inside  the cell such as gene expression or protein production.[1] One of colicins Fy main target is Y. enterocolitica. It kills Y. enterocolitica by creating pores in its cell membrane. Y. enterocolitica is also one among the common pathogens that infects the gut and cause some serious symptoms[2]. These were some of the reasons to chose colicin as the bacteriocin we want to express.
+<h2>Assembly Plan</h2><img class="schedule" src="https://static.igem.org/mediawiki/2014/8/8b/Uppsala2014_TheKillingsystemV2.png"</img><p>Figure 1. The assembly plan of the killing construct. The green arrow is the promotor, the red circle is the RBS and the yellow box is the gene which consist of an export tag, USP45 and the bacteriocin, colicin FyA fused together.</p><br><br><br><br><h2>Bacteriocin</h2><p>With the growing problem of antibiotic resistance spreading, we decided to use bacteriocins as our antimicrobial agent. A bacteriocin is a peptide that is produced naturally by certain bacteria and targets its close relatives. Unlike general antibiotics,the target of bacteriocins are very specific. The bacteriocin, colicin Fy is produced by Y. frederiksenii and it should mostly target other yersinia species.  Bacteriocins will either attack the cell membrane or a mechanism inside  the cell such as gene expression or protein production.<sup><a href="#reference1">[1]</a></sup> One of colicins Fy main target is Y. enterocolitica. It kills Y. enterocolitica by creating pores in its cell membrane. Y. enterocolitica is also one among the common pathogens that infects the gut and cause some serious symptoms<sup><a href="#reference2">[2]</a></sup>. These were some of the reasons to chose colicin as the bacteriocin we want to express.
-</p><br><br><h2>Spot42 RNA</h2><p>Our goal was to design a seek and kill system. This implies that we only want to express the bacteriocin when our bacteria is close to the target. We chose this strategy because the cell would stress out to express bacteriocin all the time, even when not in close proximity to Yersinia. In order to make our bacteria only express the colicin when we want, we have included a sRNA system. We used the system that Team Uppsala iGEM 2012 designed. The sRNA consists of an antisense region that recognizes a specific RNA sequence to interact with and another region that recruits the protein Hfq. The HFq protein blocks and prevent mRNA to bind to a ribosome. We have redesigned the antisense region so it will specifically recognize our USP45. This will make it bind to our USP45 and recruit the Hfq protein to stick on that region.[3] USP45 is the secretion tag that we have coupled to the colicin. The sRNA will stick to Hfq and bind to the mRNA of USP45-Colicin gene and that will block the translation.
+</p><br><br><h2>Spot42 RNA</h2><p>Our goal was to design a seek and kill system. This implies that we only want to express the bacteriocin when our bacteria is close to the target. We chose this strategy because the cell would stress out to express bacteriocin all the time, even when not in close proximity to Yersinia. In order to make our bacteria only express the colicin when we want, we have included a sRNA system. We used the system that Team Uppsala iGEM 2012 designed. The sRNA consists of an antisense region that recognizes a specific RNA sequence to interact with and another region that recruits the protein Hfq. The HFq protein blocks and prevent mRNA to bind to a ribosome. We have redesigned the antisense region so it will specifically recognize our USP45. This will make it bind to our USP45 and recruit the Hfq protein to stick on that region.<sup><a href="#reference3">[3]</a></sup> USP45 is the secretion tag that we have coupled to the colicin. The sRNA will stick to Hfq and bind to the mRNA of USP45-Colicin gene and that will block the translation.
 But when our bacteria is in proximity to y.entercolitica we want it to express the collicin Fy. Therefore, the sensing group have been working on a Yen system which will inactivate the promotor that regulates the spot42 when it is close to Y.enterocolitica.
 <p><img class="figure2" src="https://static.igem.org/mediawiki/2014/4/41/Uppsala-igem2014Spot42_system.png"><p>Figure 2. The spot42 system</p>
+<ul class="reference">
+<li><a id="reference">[1]</a> http://www.nature.com/nrmicro/journal/v11/n2/full/nrmicro2937.html</li>
+<li><a id="reference">[2]</a> http://jb.asm.org/content/194/8/1950.long</li>
+<li><a id="reference">[3]</a> https://2012.igem.org/Team:Uppsala_University/Project</li>
+</ul>
 <script>

Team:Uppsala/Project Killing

From 2014.igem.org