Team:UNITN-Trento/Project/Bacillus

From 2013.igem.org

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Bacillus subtilis
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<i>Bacillus subtilis</i>
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</span>
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</span>
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When we first came up with the idea of <i>B. fruity</i>, we immediatly thought that <i>B .subtilis</i> was the perfect chassis for a possible marketable application:
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When we first came up with the idea of <i>B. fruity</i>, we immediatly thought that <i>B. subtilis</i> was the perfect chassis for a possible marketable application:
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<ol>
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<ol>
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<li>
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<li>
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<i>Bacillus subtilis</i> sporulates and it can be stored in a inactive state;
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<i>Bacillus subtilis</i> sporulates and can be stored in an inactive state;
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</li>
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</li>
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<li>
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<li>
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<i>Bacillus subtilis</i> is not pathogenic and therefore can be used safely for food applications;
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<i>Bacillus subtilis</i> is not pathogenic and therefore can be used safely for food applications.
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</li>
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</li>
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</ol>
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</ol>
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<i>Bacillus subtilis</i> would be the perfect chassis for a fruit-ripening household product that exploit ethylene (or MeSA) production upon spores activation. We designed a <i>B. fruity</i> home edition based on this principle.<br />
-
<i>Bacillus subtilis</i> would be the perfect chassis for a fruit-ripening household product, that exploit ethylene (or MeSA) production upon spores activation. We have designed a <i>B. fruity</i> home edition that exploits this principle. <br/>
+
To achieve this goal we started working with EFE, an ethylene forming enzyme from <i>Pseudomas syringae</i> pv. phaseolicola (<a href="http://parts.igem.org/Part:BBa_K1065002">BBa_K1065002</a>), which were inserted into pSBBs0K-Pspac (IPGT inducible) and  pSBBs4S-Pxyl (xylose inducible) These two bio-brick plasmids were designed for <i>B. subtilis</i> by the iGEM 2012 LMU Munich team (please note that we used the new functional versions of these plasmids that were kindly provided by LMU Munich).
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To achieve this goal we started working with EFE, a ethylene forming enzyme from <i>Pseudomas Syringae</i> pv. phaseolicola (<a href="http://parts.igem.org/Part:BBa_K1065002">BBa_K1065002</a>), which were inserted into pSBBs0K-Pspac (IPGT inducible) and  pSBBs4S-Pxyl (xylose inducible), two biobrick plasmids designed for <i>B. subtilis</i> by the iGEM 2012 LMU Munich team (please note that we used a new functional version of these plasmids, that were kindly sent to us from LMU Munich).
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<img src="http://2013.igem.org/wiki/images/8/85/Tn-2013-project_ethylene-BBa_K1065001.jpg"/>
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<img src="http://2013.igem.org/wiki/images/8/85/Tn-2013-project_ethylene-BBa_K1065001.jpg"/>
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<span class="tn-subtitle">Cloning of BBa_K1065204</span>
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<span class="tn-subtitle">Cloning of BBa_K1065203</span>
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The integrative plasmid pXyl was digested prior transformation in minimal media and the correct integration of the insert into <i>B. subtilis</i> genome was confirmed by threonine assay.
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The integrative plasmid pXyl was digested prior transformation in minimal media and the correct integration of the insert into <i>B. subtilis</i> genome was confirmed with the threonine assay.
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<div class="tn-doublephoto-wrap">
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<div class="tn-doublephoto-wrap">
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<img class="photo" src="http://2013.igem.org/wiki/images/b/b0/Tn-2013_PXyl_digestion.png"/>
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<img class="photo" src="http://2013.igem.org/wiki/images/b/b0/Tn-2013_PXyl_digestion.png"/>
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<img class="photo" src="http://2013.igem.org/wiki/images/3/3b/Tn-2013_thr_assay.jpg"/>
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<img class="photo" src="http://2013.igem.org/wiki/images/3/3b/Tn-2013_thr_assay.jpg"/>
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</div>
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<span class="tn-caption"><b>Figure 1:</b> transformation of <a href="http://parts.igem.org/Part:BBa_K1065204">BBa_1065204</a> in <i>B. subtilis</i>. Transformation of the integrative vector pXyl carrying the EFE gene was achieved by digesting the plasmid with ScaI to obtain a linear DNA (left panel) which was then transformed into <i>B. subtilis</i> 168 using minimal medium.  Correct integration was confirmed with the threonine test: cells that carry the insert in the proper position become auxotrophic and can not longer grow in the absence of threonine.</span>
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-
+
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<span class="tn-subtitle">Toxicity assay</span>
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-
We then measured the optical density of cells induced and non induced for both constructs.
+
-
<div class="tn-doublephoto-wrap">
+
-
<img class="plot" src="http://2013.igem.org/wiki/images/8/8e/Tn-2013_K1065203_plot.png">
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<img class="plot" src="http://2013.igem.org/wiki/images/1/14/Tn-2013_K1065204_plot.png">
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</div>
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<span class="tn-caption"><b>Figure 2:</b> <i>B. subtilis</i> 168 cells transformed with <a href="http://parts.igem.org/Part:BBa_K1065204">BBa_K1065204</a> or <a href="http://parts.igem.org/Part:BBa_K1065203">BBa_K1065203</a> were grown until an OD=0.9 and then splitted in two samples before induction. Cells were induced with 1% xylose for BBa_K1065203 and 0.5 mM of IPTG for BBa_K1065204. In both cases the induced samples (blue trace) grow slightly slower than the controls (red trace).</span>
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-
<span class="tn-subtitle">Sporulation assay</span>
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-
Spores were obtained by growing the transformed <i>B. subtilis</i> 168 cells in DSM medium, subjecting them to a heat shock at 60 &deg;C and plating them on a preheated glass slide. Spores were visualized at the microscope.
+
-
<span class="tn-subtitle">Ethylene detection</span>
+
-
Ethylene production was tested by Gas Chromatography as we previoulsy did for <a href="http://parts.igem.org/Part:BBa_K1065001">BBa_K1065001</a>.  The experiment was performed both from cultures started from fresh plates and from dry spores.<br/>
+
-
We did not observe any production of ethylene after 4 hours, nor after overnight induction. <br/>
+
-
At this point we are not able to confirm that EFE was correctly expressed under these conditions. Surprisingly, induced culture had a strong smell of methane and mercapto compounds. The presence of sulfur compounds was confirmed by exposing the culture to lead acetate paper strips . Hydrogen sulfide and other mercapto compounds react with lead-acetate to form lead(II) sulfate, a black insoluble precipitate that darkens the white strip.
+
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<img src="http://2013.igem.org/wiki/images/6/69/Tn-2013_Lead-acetate_strip_assay.jpg"/>
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<span style="text-align:justify;"class="tn-caption center"><b>Figure 4:</b> detection of sulfur compounds. <i>B. subtilis</i> 168 cells non transformed (1 and 2), transformed with <a href="http://parts.igem.org/Part:BBa_K1065203">BBa_K1065203</a> and transformed with <a href="http://parts.igem.org/Part:BBa_K1065204">BBa_K1065204</a> were grown until O.D. 0.9 was reached. At this O.D. one sample was then supplemented with 1% xylose or with 1 mM IPTG. Cells were left to grow overnight into vials containing a lead acetate strip. The day after, transformed and induced samples showed a darker strip indicating the presence of sulfur compounds. The non trasformed cells supplemented with the inducer did not show that precipitate. </span>
+
-
<span class="tn-subtitle">Future directions</span>
+
-
For future experiments and improvement of the system we have identified additional potential drawbacks, including:
+
-
<ul>
+
-
<li>pXyl could be inhibited by glucose although the threonine test confirmed the correct insertion of the vector;</li>
+
-
<li>the acquisition of pSpac could not be confirmed by colony PCR yet; even if  the growth of colonies in the presence of the  antibiotic indicates that the episomal vector carrying EFE gene is present;</li>
+
-
<li>at present the expression of the EFE gene has not been demonstrated. We plan to perform an additional real-time PCR experiment (to assess transcription).</li>
+
-
</ul>  
+
</div>
</div>
 +
<span class="tn-caption"><b>Figure 1:</b> transformation of <a href="http://parts.igem.org/Part:BBa_K1065204">BBa_1065204</a> in <i>B. subtilis</i>. Transformation of the integrative vector pXyl carrying the EFE gene was achieved by digestion of the plasmid with ScaI to obtain a linear DNA (left panel) which was then transformed into <i>B. subtilis</i> 168 cultured in minimal medium.  Correct integration was confirmed by threonine test: cells that carry the insert in the proper position become auxotrophic and can no longer grow in the absence of threonine.</span>
 +
 +
<span class="tn-subtitle">Toxicity assay</span>
 +
We measured the optical density of cells induced and non induced for both constructs.
 +
<div class="tn-doublephoto-wrap">
 +
<img class="plot" src="http://2013.igem.org/wiki/images/1/14/Tn-2013_K1065204_plot.png">
 +
<img class="plot" src="http://2013.igem.org/wiki/images/8/8e/Tn-2013_K1065203_plot.png">
 +
</div>
 +
<span class="tn-caption"><b>Figure 2:</b> <i>B. subtilis</i> 168 cells transformed with <a href="http://parts.igem.org/Part:BBa_K1065204">BBa_K1065204</a> or <a href="http://parts.igem.org/Part:BBa_K1065203">BBa_K1065203</a> were grown until an OD of 0.9 and then split in two samples before induction. Cells were induced with 1% xylose for BBa_K1065204 and 0.5 mM of IPTG for BBa_K1065203. In both cases the induced samples (blue) grow slightly slower than the controls (red).</span>
 +
 +
<span class="tn-subtitle">Sporulation assay</span>
 +
Spores were obtained growing the transformed <i>B. subtilis</i> 168 cells in DSM medium, subjecting them to a heat shock at 60 &deg;C and plating them on a preheated glass slide. Spores were visualized at the microscope.
 +
 +
<span class="tn-subtitle">Ethylene detection</span>
 +
Ethylene production was tested by Gas Chromatography as we previously did for <a href="http://parts.igem.org/Part:BBa_K1065001">BBa_K1065001</a>. The experiment was performed both from cultures started from fresh plates and from dry spores.<br/>
 +
We did not observe any production of ethylene after 4 hours, nor after overnight induction.<br/>
 +
At this point we are not able to confirm that EFE was correctly expressed under these conditions but, surprisingly, induced culture had a strong smell of methane and mercapto compounds. The presence of sulfur compounds was confirmed by exposing the culture to lead acetate paper strips . Hydrogen sulfide and other mercapto compounds react with lead-acetate to form lead(II) sulfate, a black insoluble precipitate that darkens the white strip.
 +
<img src="http://2013.igem.org/wiki/images/6/69/Tn-2013_Lead-acetate_strip_assay.jpg"/>
 +
<span style="text-align:justify;"class="tn-caption center"><b>Figure 4:</b> detection of sulfur compounds. <i>B. subtilis</i> 168 cells non transformed, transformed with <a href="http://parts.igem.org/Part:BBa_K1065203">BBa_K1065203</a> and transformed with <a href="http://parts.igem.org/Part:BBa_K1065204">BBa_K1065204</a> were grown until O.D. 0.9 was reached. At this O.D. one sample was then supplemented with 1% xylose or with 1 mM IPTG. Cells were left to grow overnight into vials containing a lead acetate strip. The day after, transformed and induced samples showed a darker strip indicating the presence of sulfur compounds. Non transformed cells supplemented with the inducer did not show that precipitate.</span>
 +
<span class="tn-subtitle">Future directions</span>
 +
For future experiments and improvement of the system we have identified additional potential drawbacks, including:
 +
<ul>
 +
<li>pXyl could be inhibited by glucose although the threonine test confirmed the correct insertion of the vector;</li>
 +
<li>the acquisition of pSpac could not be confirmed by colony PCR yet; even if  the growth of colonies in the presence of the  antibiotic indicates that the episomal vector carrying EFE gene is present;</li>
 +
<li>at present the expression of the EFE gene has not been demonstrated. We plan to perform an additional real-time PCR experiment (to assess transcription).</li>
 +
</ul>
 +
</div>
<div class="sheet-2">
<div class="sheet-2">

Latest revision as of 23:16, 4 October 2013

Bacillus subtilis When we first came up with the idea of B. fruity, we immediatly thought that B. subtilis was the perfect chassis for a possible marketable application:
  1. Bacillus subtilis sporulates and can be stored in an inactive state;
  2. Bacillus subtilis is not pathogenic and therefore can be used safely for food applications.
Bacillus subtilis would be the perfect chassis for a fruit-ripening household product that exploit ethylene (or MeSA) production upon spores activation. We designed a B. fruity home edition based on this principle.
To achieve this goal we started working with EFE, an ethylene forming enzyme from Pseudomas syringae pv. phaseolicola (BBa_K1065002), which were inserted into pSBBs0K-Pspac (IPGT inducible) and pSBBs4S-Pxyl (xylose inducible) These two bio-brick plasmids were designed for B. subtilis by the iGEM 2012 LMU Munich team (please note that we used the new functional versions of these plasmids that were kindly provided by LMU Munich). Cloning of BBa_K1065204 The integrative plasmid pXyl was digested prior transformation in minimal media and the correct integration of the insert into B. subtilis genome was confirmed by threonine assay.
Figure 1: transformation of BBa_1065204 in B. subtilis. Transformation of the integrative vector pXyl carrying the EFE gene was achieved by digestion of the plasmid with ScaI to obtain a linear DNA (left panel) which was then transformed into B. subtilis 168 cultured in minimal medium. Correct integration was confirmed by threonine test: cells that carry the insert in the proper position become auxotrophic and can no longer grow in the absence of threonine. Toxicity assay We measured the optical density of cells induced and non induced for both constructs.
Figure 2: B. subtilis 168 cells transformed with BBa_K1065204 or BBa_K1065203 were grown until an OD of 0.9 and then split in two samples before induction. Cells were induced with 1% xylose for BBa_K1065204 and 0.5 mM of IPTG for BBa_K1065203. In both cases the induced samples (blue) grow slightly slower than the controls (red). Sporulation assay Spores were obtained growing the transformed B. subtilis 168 cells in DSM medium, subjecting them to a heat shock at 60 °C and plating them on a preheated glass slide. Spores were visualized at the microscope. Ethylene detection Ethylene production was tested by Gas Chromatography as we previously did for BBa_K1065001. The experiment was performed both from cultures started from fresh plates and from dry spores.
We did not observe any production of ethylene after 4 hours, nor after overnight induction.
At this point we are not able to confirm that EFE was correctly expressed under these conditions but, surprisingly, induced culture had a strong smell of methane and mercapto compounds. The presence of sulfur compounds was confirmed by exposing the culture to lead acetate paper strips . Hydrogen sulfide and other mercapto compounds react with lead-acetate to form lead(II) sulfate, a black insoluble precipitate that darkens the white strip. Figure 4: detection of sulfur compounds. B. subtilis 168 cells non transformed, transformed with BBa_K1065203 and transformed with BBa_K1065204 were grown until O.D. 0.9 was reached. At this O.D. one sample was then supplemented with 1% xylose or with 1 mM IPTG. Cells were left to grow overnight into vials containing a lead acetate strip. The day after, transformed and induced samples showed a darker strip indicating the presence of sulfur compounds. Non transformed cells supplemented with the inducer did not show that precipitate. Future directions For future experiments and improvement of the system we have identified additional potential drawbacks, including:
  • pXyl could be inhibited by glucose although the threonine test confirmed the correct insertion of the vector;
  • the acquisition of pSpac could not be confirmed by colony PCR yet; even if the growth of colonies in the presence of the antibiotic indicates that the episomal vector carrying EFE gene is present;
  • at present the expression of the EFE gene has not been demonstrated. We plan to perform an additional real-time PCR experiment (to assess transcription).