Team:Evry/Project/Compounds/Sensing

From 2014.igem.org

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<li><b><u><h5>Advantages of bio-sensing</h5></u></b> <br>
<li><b><u><h5>Advantages of bio-sensing</h5></u></b> <br>
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In response of those recent awareness, different systems of detection have been developed. <br>
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<p>
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But with the approach of bio-sensing, we develop tool which are able to detect pollutant with a very high efficiency, and with a great specificity. <br>
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In response to this recent awareness towards those toxic compounds, different systems of detection have been developed. <br>
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Biological elements necessary to built those tools have a very low cost, are very easy to obtain and the assembling is quite easy and don’t emit any pollutant. <br>
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However with the approach of bio-sensing, we develop tools which are able to detect a pollutant with a very high efficiency, and with a great specificity. <br>
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So besides having effective and cheap systems, biosensors are totally biological and non-polluting tools.<br>
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Biological elements necessary to build those tools are cheap, easily obtained and their production doesn’t emit any pollutant. <br>
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Thus besides being effective and cheap systems, biosensors are totally biological and non-polluting tools.<br>
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<li><b><u><h5>Systems</h5></u></b> <br>
<li><b><u><h5>Systems</h5></u></b> <br>
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To devellop our tools, we search in the scientific litterature, some natural systems based on promoters inducibles by our compounds of interest. It's often promoters wich allow the expression of a set of genes which correspond to the cell's response to the compound.<br>
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<p>
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For phenols, an a set of genes called Dmp operon in <i>Pseudomonas CF600 </i> is able to degrade phenol with the aim to produce acetyl CoA, and use these compounds as an energy source. <br>
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To develop our bio-sensors, we looked for some natural systems based promoters inducibles by our compounds of interest. It is often promoters wich allow the expression of a set of genes which correspond to the cell's response to the compound.<br>
 +
For phenols, a set of genes called Dmp operon in <i>Pseudomonas CF600 </i> is able to degrade phenol to produce acetyl CoA, and use this molecule as an energy source. <br></p>
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<FONT color=#003333><b><u>Figure6: </u></b>The catabolic pathway for degradation of phenol and the organization of Dmp operon. (Powlowski J, Shingler V., 1994)</font><br>
<FONT color=#003333><b><u>Figure6: </u></b>The catabolic pathway for degradation of phenol and the organization of Dmp operon. (Powlowski J, Shingler V., 1994)</font><br>
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<br>
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<br><p>
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The transcription of this operon is regulated by the DmpR regulator element which bind phenol and activate the transcription of the phenol hydroxylase promoter by allowing the fixation of the RNA polymerase (more information, see the section <a href="https://2014.igem.org/Team:Evry/Biology/Sensors">Sensors</a>). <br>
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The transcription of this operon is regulated by the DmpR regulator element which binds phenol and activates the transcription of the phenol hydroxylase enzyme by allowing the fixation of the RNA polymerase (more information, see the section <a href="https://2014.igem.org/Team:Evry/Biology/Sensors">Sensors</a>). <br>
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</p></div>
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<p>
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For PCBs, two distinct classes of bacteria have now been identified as being able to degrade PCBs:<br>
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For PCBs, two distinct classes of bacteria have now been identified as being able to degrade PCBs.<br>
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<li>Aerobic bacteria which live in oxygenated environments </li>
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Aerobic bacteria which live in oxygenated environments and anaerobic bacteria which live in oxygen free environments such as aquatic sediments. They use different mechanisms, aerobes attack PCBs oxidatively, breaking open the carbon ring and destroying the compounds. Anaerobes, on the other hand, leave the biphenyl rings intact while removing the chlorines. <br>
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<li>Anaerobic bacteria which live in oxygen free environments such as aquatic sediments. </li><br>
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They use different mechanisms, aerobes attack PCBs oxidatively, breaking open the carbon ring and destroying the compounds. Anaerobes, on the other hand, leave the biphenyl rings intact while removing the chlorines. <br>
The evidence in the literature suggests that PCDD/F compounds are subject to biodegradation in the environment as part of the natural chlorine cycle.<br>
The evidence in the literature suggests that PCDD/F compounds are subject to biodegradation in the environment as part of the natural chlorine cycle.<br>
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<img src="https://static.igem.org/mediawiki/2014/8/81/PathwayPCB.jpg" alt="text to print if image not found" /><br>
<img src="https://static.igem.org/mediawiki/2014/8/81/PathwayPCB.jpg" alt="text to print if image not found" /><br>
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<FONT color=#003333><b><u>Figure7: </u></b>The catabolic pathway for degradation of biphenyl by aerobic bacteria and the organization of bph gene cluster (Kensuke F., Hidehiko F., 2008) .</font><br>
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<FONT color=#003333><b><u>Figure7: </u></b>The catabolic pathway for degradation of biphenyl by aerobic bacteria and the organization of the bph gene cluster (Kensuke F., Hidehiko F., 2008) .</font><br></p>
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<br><p>
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The transcription of this set of genes is regulated by bphR2 wich bind PCBs and activate the transcription of pbhR1 gene (more information, see the section <a href="https://2014.igem.org/Team:Evry/Biology/Sensors">Sensors</a>). <br>
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The transcription of this set of genes is regulated by bphR2 which binds PCBs and activates the transcription of pbhR1 gene (more information, see the section <a href="https://2014.igem.org/Team:Evry/Biology/Sensors">Sensors</a>). <br>
<br>
<br>
 +
</p>
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<p>
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For nitrites, the degradation pathways are very well known because they belong to the nitrite cycle. As for heavy metals, a lot of operons which allows the cell tolerance to these compounds exist and have promoters reacting specifically to the metal concentration. <br>
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+
However for this project, we chose to develop systems based on promoters presents in our bacteria strain <i>Pseudovibrio denitrificans</i>. <br>
-
For nitrites, degradation pathway are very well known because they belong to the nitrite cycle. And for heavy metals, a lot of operon which allows the cell's tolerance to these compounds exist and have promoter answering specifically to the metal concentration. <br>
+
In this way, we used an RNA sequencing approach to detect promoters able to react to the pollutant presence (more information, see the section <a href="https://2014.igem.org/Team:Evry/Biology/RNAseq">RNAseq</a>). <br>
-
But for this project, we chose to develop systems based on promoters presents in our bacteria strain <i>Pseudovibrio denitrificans</i>. <br>
+
Our bacteria strain is known to live in sponge and may provide them a better tolerance to pollutants like heavy metals. The ability of the bacteria is currently study by the 'Molecules of defence and communication in the microbial ecosystems' team of the National museum of natural history of Paris (their web page <a href="http://mcam.mnhn.fr/MDCEM/index.htm">here</a>)<br>
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In that way, we made an RNA sequencing approach to detect promoter able to answer to the pollutant presence (more information, see the section <a href="https://2014.igem.org/Team:Evry/Biology/RNAseq">RNAseq</a>). <br>
+
-
Our bacteria strain is known to live in sponge and may provide them a better tolerance to pollutants like heavy metals. This fact is actually study by the 'Molecules of defence and communication in the microbial ecosystems' team of the National museum of natural history of Paris (their web page <a href="http://mcam.mnhn.fr/MDCEM/index.htm">here</a>)<br>
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<br>
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</p>
<li><b><u><h5>Futur : degradation?</h5></u></b> <br>
<li><b><u><h5>Futur : degradation?</h5></u></b> <br>
<br><div align="justify">
<br><div align="justify">
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<p>
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For phenol and PCBs => enzyme of degradation pathways<br>
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Sensing constructions are very simple and easy to construct. In a larger framework we can imagine one day being able to clone all the enzymes of the degradation pathways of phenol and PCBs in our bacteria. In fact we can create more than a sensor system based on sponge: a complete filtrating system which can not only sense pollutants, but totally remove them. <br>
<br>
<br>
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for nitrites it exist different biologic denitrification systems to reduce nitrates concentration in water that use bacteria as Pseudomonas with a denitrification yield of 80%. Bacteria are fixated on a mineral support and feed with acetic acid or ethanol (SNIDE). The major drawback is the production of nitrous and nitric oxide that are greenhouse gas. <br>
+
For removing nitrites, it exists different biological denitrification systems to reduce nitrates concentration in water that use bacteria as Pseudomonas with a denitrification yield of 80%. Bacteria are fixed on a mineral support and feed with acetic acid or ethanol (SNIDE). The major drawback is the production of nitrous and nitric oxide that are greenhouse gases. <br>
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To make a bacterium able to transforme nitrite into nitrogen we just have to add two enzymes: <br>
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To make a bacterium able to transform nitrites into nitrogen we just have to add two enzymes: <br>
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<ul>
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-> Hydroxylamine oxydase from Parococcus denitrificans: nitrite + H2O = hydroxylamine<br>
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<li>hydroxylamine oxydase from Parococcus denitrificans: nitrite + H2O = hydroxylamine<br>
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-> Hydrazine oxydoreductase from Candidatus Brocadia anammoxidans: hydroxylamine + NH3 + acceptor = N2 + H2O + reduced acceptor
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<li>hydrazine oxydoreductase from Candidatus Brocadia anammoxidans: hydroxylamine + NH3 + acceptor = N2 + H2O + reduced acceptor
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<FONT color=#003333><b><u>Figure8: </u></b>Nitrogen cycle.</font><br>
<FONT color=#003333><b><u>Figure8: </u></b>Nitrogen cycle.</font><br>
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</p>
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<br>
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<br><p>
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Unfortunately, when we talk about heavy metals we talk about atoms which cannot just be degraded by a biological pathway. But we can imagine some ways of accumulation of these elements in bacteria that we can remove and treated after like chemical waste.<br>
+
Unfortunately, dealing with heavy metals means dealing with atoms which cannot just be degraded by a biological pathway. But we can imagine some ways of accumulation of these elements in bacteria that we can remove and treated after like chemical waste.<br>
<br>
<br>

Latest revision as of 22:16, 17 October 2014

The sensing approach

 Sensing



  • Advantages of bio-sensing

    In response to this recent awareness towards those toxic compounds, different systems of detection have been developed.
    However with the approach of bio-sensing, we develop tools which are able to detect a pollutant with a very high efficiency, and with a great specificity.
    Biological elements necessary to build those tools are cheap, easily obtained and their production doesn’t emit any pollutant.
    Thus besides being effective and cheap systems, biosensors are totally biological and non-polluting tools.

  • Systems

    To develop our bio-sensors, we looked for some natural systems based promoters inducibles by our compounds of interest. It is often promoters wich allow the expression of a set of genes which correspond to the cell's response to the compound.
    For phenols, a set of genes called Dmp operon in Pseudomonas CF600 is able to degrade phenol to produce acetyl CoA, and use this molecule as an energy source.


    text to print if image not found
    Figure6: The catabolic pathway for degradation of phenol and the organization of Dmp operon. (Powlowski J, Shingler V., 1994)


    The transcription of this operon is regulated by the DmpR regulator element which binds phenol and activates the transcription of the phenol hydroxylase enzyme by allowing the fixation of the RNA polymerase (more information, see the section Sensors).


    For PCBs, two distinct classes of bacteria have now been identified as being able to degrade PCBs:

  • Aerobic bacteria which live in oxygenated environments
  • Anaerobic bacteria which live in oxygen free environments such as aquatic sediments.

    • They use different mechanisms, aerobes attack PCBs oxidatively, breaking open the carbon ring and destroying the compounds. Anaerobes, on the other hand, leave the biphenyl rings intact while removing the chlorines.
    The evidence in the literature suggests that PCDD/F compounds are subject to biodegradation in the environment as part of the natural chlorine cycle.


    text to print if image not found
    Figure7: The catabolic pathway for degradation of biphenyl by aerobic bacteria and the organization of the bph gene cluster (Kensuke F., Hidehiko F., 2008) .


    The transcription of this set of genes is regulated by bphR2 which binds PCBs and activates the transcription of pbhR1 gene (more information, see the section Sensors).

    For nitrites, the degradation pathways are very well known because they belong to the nitrite cycle. As for heavy metals, a lot of operons which allows the cell tolerance to these compounds exist and have promoters reacting specifically to the metal concentration.
    However for this project, we chose to develop systems based on promoters presents in our bacteria strain Pseudovibrio denitrificans.
    In this way, we used an RNA sequencing approach to detect promoters able to react to the pollutant presence (more information, see the section RNAseq).
    Our bacteria strain is known to live in sponge and may provide them a better tolerance to pollutants like heavy metals. The ability of the bacteria is currently study by the 'Molecules of defence and communication in the microbial ecosystems' team of the National museum of natural history of Paris (their web page here)

  • Futur : degradation?

    Sensing constructions are very simple and easy to construct. In a larger framework we can imagine one day being able to clone all the enzymes of the degradation pathways of phenol and PCBs in our bacteria. In fact we can create more than a sensor system based on sponge: a complete filtrating system which can not only sense pollutants, but totally remove them.

    For removing nitrites, it exists different biological denitrification systems to reduce nitrates concentration in water that use bacteria as Pseudomonas with a denitrification yield of 80%. Bacteria are fixed on a mineral support and feed with acetic acid or ethanol (SNIDE). The major drawback is the production of nitrous and nitric oxide that are greenhouse gases.
    To make a bacterium able to transform nitrites into nitrogen we just have to add two enzymes:
    -> Hydroxylamine oxydase from Parococcus denitrificans: nitrite + H2O = hydroxylamine
    -> Hydrazine oxydoreductase from Candidatus Brocadia anammoxidans: hydroxylamine + NH3 + acceptor = N2 + H2O + reduced acceptor


    text to print if image not found
    Figure8: Nitrogen cycle.


    Unfortunately, dealing with heavy metals means dealing with atoms which cannot just be degraded by a biological pathway. But we can imagine some ways of accumulation of these elements in bacteria that we can remove and treated after like chemical waste.

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