Difference between revisions of "Team:Evry Paris-Saclay/Description"

 
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<h1>Description</h1>
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<h1 style="font-weight:800; text-align:center;">DESCRIPTION</h1>
  
 
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<p>Our project aims to build a synthetic intercellular communication system. In natural ecosystems, there already exist several mechanisms which bacteria utilize to interact among themselves for latency, reproduction, or survival. Bacteria can produce signaling molecules that are sensed by others of their species, or even of other species, to trigger a molecular response. These communication systems can be engineered to regulate and automatize industrial bioprocesses. An important feature that would help achieve this goal is the orthogonality of the signaling molecules. The more specific the send-sense system is, the more efficiently the response of the targeted microorganism can be engineered.
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<p style="font-size:15px;">The small peptide based signalling system of SPbeta group bacteriophages, also called the “Arbitrium system” [1], is used by phages to regulate their lytic and lysogenic behaviour. In fact, a phage that enters a bacterium early in the infection will follow a lytic cycle by default. This means that the phage will replicate itself inside the cell and then it will lyse the cell to be released back into the environment to infect other bacteria.
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We find the recently described phage communication system to be a good candidate for synthetic cell-cell interaction (Zohar et al., 2017 Nature 541, 488-493). The system uses a secreted peptide called “arbitrium” to control phage-mediated bacterial lysis. The principal genes in charge of this regulated lysis have been validated in phage Phi3T and B. subtilis. However, to our knowledge there are 17 orthologous genes that encode similar peptides and their receptors, which have not yet been characterized. A key part of our project goals is to characterize a library of these different arbitrium peptides and their receptors for orthogonality. This will help identify unique peptide-receptor pairs that do not exhibit cross-talk for future use in engineering of unambiguous cell-cell communication. Additionally, we will test and expand the use of the peptide-based communication system from Bacillus to E. coli, a more widely used model bacterium. This will benefit many academic and industrial projects by enabling multiple parallel channels of communication between cells.
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<p style="font-size:15px;">After a while, a lot of phages will be in the bacterial environment. That represents a risk for the persistence of the bacterial culture, and consequently for the phages’ survival.
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The newly validate communication system will be also be integrated into a co-culture of two different species of bacteria. Co-culturing more than one microorganism has been used as a strategy for mainly industrial process. It has been shown that the engineered co-culture displays robustness, tolerance for toxic metabolic waste and resistance to stress conditions (<i>Goers et al., 2014, J R Soc Interface 11, 20140065</i>). Moreover, engineered co-cultures can be used for many other applications such as biocatalysis or bioremediation, bioproduction of high-valued compound with metabolic engineering, complex protein expression, among others.
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<p style="font-size:15px;">That is why bacteriophages have developed a mechanism to prevent the total exhaustion of their hosts, based on a peptide based signal. The peptide is produced in the cell after an infection and released to the outside. When the extracellular concentration of the peptide reaches high levels, the phages’ behaviour will change and they will be more likely to follow a lysogenic cycle.
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An engineering-ready specific communication system like ours could also be useful within the framework of distributed biological computing. Instead of implementing complex molecular circuits in one cell, it would enable bioengineers to implement simpler circuits in multiple cells of a consortium and integrate circuit outputs later. This would make building large-scale circuits easier to implement, more modular and less noisy, while reducing the expression burden on individual cells (<i>Macía et al., 2012 Trends Biotechnol 30, 342-349</i>). In practical terms, the envisioned bacterial communication system would have numerous benefits, some of them relevant to the fields of biomedicine (Kim et al., 2018, bioRxiv 308734), bioengineering and bioremediation (<i>Macia & Sole, 2014, PLoS ONE 9, e81248</i>). It would also enable new ways of engineering multicellular biomaterials, such as biofilms or tissue architectures (<i>Macia & Sole, 2014, PLoS ONE 9, e81248</i>).
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<img style="margin-left:auto; margin-right:auto; width:100%;" src="https://static.igem.org/mediawiki/2018/6/63/T--Evry_Paris-Saclay--ProjectIntro.png" alt="" /><br/><br/>
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<p style="font-size:15px;">This communication system is made up of three main components: the peptide which is the communication molecule, the receptor which is a transcription factor that is inhibited by the peptide, and the promoter which is activated by the receptor.
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<p style="font-size:15px;">In the paper which initially described this communication system [1], the peptide is six amino acids long and is expressed from a gene called aimP, the receptor is called AimR, and the promoter controls a gene called aimX (so we called it pAimX) which regulates the switch to lysogeny.
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<p style="font-size:15px;">When a phage infects a bacterium, it will express both aimR and aimP. A dimer of AimR then activates aimX which represses lysogeny, resulting in the lytic cycle of the phage. The AimP pre-pro-peptide is secreted to the outside of the cell and afterwards is processed by an extracellular protease to its mature form: SAIRGA. As SAIRGA reaches high concentration levels outside the bacteria it enters bacteria through the OPP transporter. When the bacteriophage infects a bacterium which already contains SAIRGA, AimR binds to the peptide and cannot activate aimX, which results in the activation of lysogeny.</p><br/>
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<video style="margin-left:40px; margin-right:auto;" width="750" height="572" controls="controls" src="https://static.igem.org/mediawiki/2018/b/b2/T--Evry_Paris-Saclay--animation_system.mp4">Vidéo d'animation du système</video><br/><br/>
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<p style="font-size:15px;">As explained <a href="https://2018.igem.org/Team:Evry_Paris-Saclay">previously</a>, the aim of our project is to develop a new system for cell-to-cell communication in <i>E. coli</i>. We chose the Arbitrium system to reach this goal for several reasons. First, the orthogonality of these systems would be better since we are using a bacteriophage system non-native to our bacterium of choice: <i>E. coli</i>. Second, unlike small molecules and their receptors, peptides and their receptor proteins are easier to diversify by directed evolution which is useful for generating new variants of the communication system. More details on the reasons for our choice are presented in the <a href="https://2018.igem.org/Team:Evry_Paris-Saclay/Human_Practices#integrated_human_practices">Integrated Human Practices</a>.</p><br/>
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<h2 class="anchor" style="font-weight:800; text-align:center;" id="references">REFERENCES</h2>
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<p style="font-size:15px;" class="bibliographie">[1] Erez Z, Steinberger-Levy I, Shamir M, Doron S, Stokar-Avihail A, Peleg Y, Melamed S, Leavitt A, Savidor A, Albeck S, Amitai G, Sorek R. Communication between viruses guides lysis-lysogeny decisions. Nature (2017) 541, 488-493.
 
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Latest revision as of 00:27, 18 October 2018


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DESCRIPTION

The small peptide based signalling system of SPbeta group bacteriophages, also called the “Arbitrium system” [1], is used by phages to regulate their lytic and lysogenic behaviour. In fact, a phage that enters a bacterium early in the infection will follow a lytic cycle by default. This means that the phage will replicate itself inside the cell and then it will lyse the cell to be released back into the environment to infect other bacteria.


After a while, a lot of phages will be in the bacterial environment. That represents a risk for the persistence of the bacterial culture, and consequently for the phages’ survival.


That is why bacteriophages have developed a mechanism to prevent the total exhaustion of their hosts, based on a peptide based signal. The peptide is produced in the cell after an infection and released to the outside. When the extracellular concentration of the peptide reaches high levels, the phages’ behaviour will change and they will be more likely to follow a lysogenic cycle.




This communication system is made up of three main components: the peptide which is the communication molecule, the receptor which is a transcription factor that is inhibited by the peptide, and the promoter which is activated by the receptor.


In the paper which initially described this communication system [1], the peptide is six amino acids long and is expressed from a gene called aimP, the receptor is called AimR, and the promoter controls a gene called aimX (so we called it pAimX) which regulates the switch to lysogeny.


When a phage infects a bacterium, it will express both aimR and aimP. A dimer of AimR then activates aimX which represses lysogeny, resulting in the lytic cycle of the phage. The AimP pre-pro-peptide is secreted to the outside of the cell and afterwards is processed by an extracellular protease to its mature form: SAIRGA. As SAIRGA reaches high concentration levels outside the bacteria it enters bacteria through the OPP transporter. When the bacteriophage infects a bacterium which already contains SAIRGA, AimR binds to the peptide and cannot activate aimX, which results in the activation of lysogeny.




As explained previously, the aim of our project is to develop a new system for cell-to-cell communication in E. coli. We chose the Arbitrium system to reach this goal for several reasons. First, the orthogonality of these systems would be better since we are using a bacteriophage system non-native to our bacterium of choice: E. coli. Second, unlike small molecules and their receptors, peptides and their receptor proteins are easier to diversify by directed evolution which is useful for generating new variants of the communication system. More details on the reasons for our choice are presented in the Integrated Human Practices.


REFERENCES

[1] Erez Z, Steinberger-Levy I, Shamir M, Doron S, Stokar-Avihail A, Peleg Y, Melamed S, Leavitt A, Savidor A, Albeck S, Amitai G, Sorek R. Communication between viruses guides lysis-lysogeny decisions. Nature (2017) 541, 488-493.

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