Difference between revisions of "Part:BBa K3570006"

 
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<h2>Usage</h2>
 
<h2>Usage</h2>
 
<p style="text-indent: 40px">
 
<p style="text-indent: 40px">
DPP1 upstream homology arm part shall be used together with DPP1 downstream homology arm part ([https://parts.igem.org/Part:BBa_K3570007 BBa_K3570007]) to target a functional yeast integration locus. When DPP1 up put to 5' of the biobrick together with DPP1 downstream to the 3', the biobrick can be integrated into the <i>S. cerevisiae's</i> genome. It will do homologous recombination within the Diacylglycerol pyrophosphate phosphatase 1 (DPP1) gene. </p>
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DPP1 upstream homology arm part shall be used together with DPP1 downstream homology arm part ([https://parts.igem.org/Part:BBa_K3570007 BBa_K3570007]) to target a functional yeast integration locus. When DPP1 up put to 5' of the biobrick together with DPP1 downstream to the 3', the biobrick can be integrated into the <i>S. cerevisiae's</i> genome. It will target an homologous recombination within the Diacylglycerol pyrophosphate phosphatase 1 (DPP1) gene. </p>
 
<p style="text-indent: 40px">
 
<p style="text-indent: 40px">
 
This sequence was identified from a personal communication with Dr. Gilles Truan. </p>
 
This sequence was identified from a personal communication with Dr. Gilles Truan. </p>
  
 
<h2>Experiments</h2>
 
<h2>Experiments</h2>
<p> We used this part in the insertion of the tHMG1 and CrtE genes (part [https://parts.igem.org/Part:BBa_K3570000 BBa_K3570000]) in the yeast genome. Below is our yeast transformation protocol and our results which show that we have successfully integrated this part and that the BBa_K3570006 and [https://parts.igem.org/Part:BBa_K3570007 BBa_K3570007] parts work.</p><br>
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<p> We used this part in the insertion of the tHMG1 and CrtE genes (part [https://parts.igem.org/Part:BBa_K3570000 BBa_K3570000]) in the yeast genome. Below is our yeast transformation protocol and our results which show that we have successfully integrated this part and that BBa_K3570006 and [https://parts.igem.org/Part:BBa_K3570007 BBa_K3570007] parts work.</p><br>
  
 
<p> <strong>A. Protocols </strong></p><br>
 
<p> <strong>A. Protocols </strong></p><br>
  
<li><strong>Preparation of yeast competent cells</strong></li><br>
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<li><strong>Preparation of yeast competent cells</strong></li>
<p>Fresh yeast were grown in 25ml of YPD medium overnight. This preculture was diluted to low OD600nm (e.g. 0.05) in 50ml of fresh YPD medium. The biomass concentration was measured every two hours until it reaches an OD600nm of around 0.8. The 50ml of culture was transfered in a 50ml falcon-tube and was centrifuged 5 minutes at 3000rpm at room temperature. The supernatant was removed and 25ml of LiAc/TE was added. The tube had to be thoroughly inverting 10 times. The tube was centrifuged 5 minutes at 3000rpm at room temperature. The supernatante was removed and 400µl of LiAc/TE was added. The tube had to be thoroughly inverting 10 times. Yeast competent cells should be used on the same day that they have been prepared.</p><br>
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<p>Fresh yeast were grown in 25 ml of YPD medium overnight. This preculture was diluted to low OD<sub>600 nm</sub> (e.g. 0.05) in 50 ml of fresh YPD medium. The biomass concentration was measured every two hours until it reaches an OD<sub>600 nm</sub> of around 0.8. 50 ml of culture were transfered in a 50 ml falcon-tube and were centrifuged 5 minutes at 3000 rpm at room temperature. The supernatant was removed and 25 ml of LiAc/TE was added. The tube had to be thoroughly inverted 10 times. The tube was centrifuged 5 minutes at 3000 rpm at room temperature. The supernatant was removed and 400 µl of LiAc/TE was added. The tube had to be thoroughly inverted 10 times. Yeast competent cells should be used on the same day that they have been prepared.</p><br>
  
<li><strong>Yeast transformation</strong></li><br>
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<li><strong>Yeast transformation</strong></li>
<p>A mix in 1.5ml microcentrifuge tube was prepared with 2µl of transforming DNA (BBa_K3570000), 40µl of competente yeast cells , 25µg of carrier DNA (SS-DNA) and 168µl of 50% PEG in 100mM LiAc/TE.<br>
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<p>A mix in a 1.5 ml microcentrifuge tube was prepared with 2 µl of transforming DNA (BBa_K3570000), 40 µl of competent yeast cells, 25 µg of carrier DNA (SS-DNA) and 168 µl of 50% PEG in 100 mM LiAc/TE.<br>
Positive control was the same mixture but the transforming DNA was replaced by 1uL of pR313. The negative control was the same mixture but had no transforming DNA.
+
Positive control was the same mixture but the transforming DNA was replaced by 1 µL of pR313. The negative control was the same mixture but had no transforming DNA.
After vortexing, the solution was incubated 45 minutes at 30°C. Then 13µl of DMS0 was added and the solution was vortexed again. It was centrifuged at 10,000 rpm for 1 minute. The supernatante was removed and the pellet was resuspended in 80µl of NaCl. The solution was seeded on petri dishe of YNB with all amino acids expect histidine. Our selectable marker was histidine. The petri dishe was incubated at 30°C for three days.</p><br>
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After vortexing, the solution was incubated 45 minutes at 30°C. 13 µl of DMS0 were added and the solution was vortexed again. It was centrifuged at 10,000 rpm for 1 minute. The supernatant was removed and the pellet was resuspended in 80 µl of NaCl. The solution was seeded on YNB Petri dish with all amino acids expect histidine since histidine was our selection marker. The Petri dish was incubated at 30°C for three days.</p><br>
  
<li><strong>Integration verification PCR</strong></li><br>
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<li><strong>Validation</strong></li>
<p>The integration of BBa_K3570000 using the DPP1 homoly sequence (BBa_K3570006 and BBa_K3570007) was performed by a genomic PCR using the TaKaRa PCR amplification Kit. Our insert was to big to be amplified by PCR. We therefore decided to amplified a part of 1200kb in the genome. The following primers have been used. The primer 1 (forward hybridizes on our selectable marker HIS3 . The primer 2 (reverse) hybridizes on the 1,039,876 pb of the chromosome IV of the strain BY4741 (upstream of the DPP1 gene).</p><br>
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<p>Verification of integration of BBa_K3570000 using the DPP1 homology sequence (BBa_K3570006 and BBa_K3570007) was performed by a genomic PCR using the TaKaRa PCR amplification Kit and the following primers: primer 1 (forward) hybridizes on our selectable marker HIS3 while primer 2 (reverse) hybridizes upstream of the DPP1 gene.</p>
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<p> Primer 1: ATCAGGATTTGCGCCTTT</p>
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<p> Primer 2: GCCGCCGAGGGTATTTTACTTCCG</p><br>
  
 
<strong>B. Results and discussion</strong><br>
 
<strong>B. Results and discussion</strong><br>
  
<p>Since the construction of the part BBa_K3570000 was successful, we proceeded to the next step: integration in the yeast genome. The plasmid was digested with enzymes SbfI and EcoRI and purified to transform the yeast Saccharomyces cerevisiae resulting in th strain BY4741 DPP::tHMG1-crtE. The yeast was then grown on YNB with all amino acids expect histidine for 3 days. At the third try, we were able to observe around 20 colonies in our yeast transformation, about the same on the positive control and none on the negative control plate. We randomly chose eight clones from our transformation and one from the positive control plate (see on the figure 1 below) for PCR verification integration.</p>
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<p>After 3 days, we were able to observe around 20 colonies in our yeast transformation, about the same amount on the positive control and none on the negative control plate. Eight clones were randomly chosen from our transformation and one from the positive control plate (figure 1) for PCR validation of the integration.</p>
  
[[File:T--Toulouse_INSA-UPS--2020_CB-F7.png|500px|thumb|center|Figure1: Verification of the integration of the part BBa_K3570000 in the yeast genome using DPP1 homology sequence (BBa_3570006 and BBa_3570007). The expected size is 1.2kb.]]
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[[File:T--Toulouse_INSA-UPS--2020_CB-F7.png|500px|thumb|center|Figure 1: validation of the integration of the part BBa_K3570000 in the yeast genome using DPP1 homology sequence (BBa_3570006 and BBa_3570007). The expected correct size is 1.2kb.]]
  
<p>All clones have the expected size (1.2kb), and the control where we inserted pRS313 does not show any band.<br>
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<p>All clones have the expected size (1.2kb), and the control where we inserted pRS313 does not show any band, proving that we have successfully integrated our construction into the yeast using DPP1 homology sequence.<br>
The integration of BBa_K3570000 should results in an increase of the GGPP quantity. For further verification, we analyzed the quantity of GGPP in the strain BY4741 DPP::tHMG1-crtE and in the wild type.</p><br>
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</p><br>
  
[[File:T--Toulouse_INSA-UPS--2020_CB-F7.png|500px|thumb|center|Figure 2: Results of the GGPP analysis from culture on YNB with 2% Glucose by LC-MS]]
 
  
<p>According to the figure 2, our strain BY4741 DPP::tHMG1-crtE showed a five-fold increase in GGPP concentration in comparison with the wild type yeast.
 
These two verifications proved that we have successfully integrated tHmg1 and CrtE into the yeast using DPP1 homology sequence!</p>
 
  
 
<h2>References</h2>
 
<h2>References</h2>

Latest revision as of 12:10, 26 October 2020


DPP1 upstream homologous sequence

Usage

DPP1 upstream homology arm part shall be used together with DPP1 downstream homology arm part (BBa_K3570007) to target a functional yeast integration locus. When DPP1 up put to 5' of the biobrick together with DPP1 downstream to the 3', the biobrick can be integrated into the S. cerevisiae's genome. It will target an homologous recombination within the Diacylglycerol pyrophosphate phosphatase 1 (DPP1) gene.

This sequence was identified from a personal communication with Dr. Gilles Truan.

Experiments

We used this part in the insertion of the tHMG1 and CrtE genes (part BBa_K3570000) in the yeast genome. Below is our yeast transformation protocol and our results which show that we have successfully integrated this part and that BBa_K3570006 and BBa_K3570007 parts work.


A. Protocols


  • Preparation of yeast competent cells
  • Fresh yeast were grown in 25 ml of YPD medium overnight. This preculture was diluted to low OD600 nm (e.g. 0.05) in 50 ml of fresh YPD medium. The biomass concentration was measured every two hours until it reaches an OD600 nm of around 0.8. 50 ml of culture were transfered in a 50 ml falcon-tube and were centrifuged 5 minutes at 3000 rpm at room temperature. The supernatant was removed and 25 ml of LiAc/TE was added. The tube had to be thoroughly inverted 10 times. The tube was centrifuged 5 minutes at 3000 rpm at room temperature. The supernatant was removed and 400 µl of LiAc/TE was added. The tube had to be thoroughly inverted 10 times. Yeast competent cells should be used on the same day that they have been prepared.


  • Yeast transformation
  • A mix in a 1.5 ml microcentrifuge tube was prepared with 2 µl of transforming DNA (BBa_K3570000), 40 µl of competent yeast cells, 25 µg of carrier DNA (SS-DNA) and 168 µl of 50% PEG in 100 mM LiAc/TE.
    Positive control was the same mixture but the transforming DNA was replaced by 1 µL of pR313. The negative control was the same mixture but had no transforming DNA. After vortexing, the solution was incubated 45 minutes at 30°C. 13 µl of DMS0 were added and the solution was vortexed again. It was centrifuged at 10,000 rpm for 1 minute. The supernatant was removed and the pellet was resuspended in 80 µl of NaCl. The solution was seeded on YNB Petri dish with all amino acids expect histidine since histidine was our selection marker. The Petri dish was incubated at 30°C for three days.


  • Validation
  • Verification of integration of BBa_K3570000 using the DPP1 homology sequence (BBa_K3570006 and BBa_K3570007) was performed by a genomic PCR using the TaKaRa PCR amplification Kit and the following primers: primer 1 (forward) hybridizes on our selectable marker HIS3 while primer 2 (reverse) hybridizes upstream of the DPP1 gene.

    Primer 1: ATCAGGATTTGCGCCTTT

    Primer 2: GCCGCCGAGGGTATTTTACTTCCG


    B. Results and discussion

    After 3 days, we were able to observe around 20 colonies in our yeast transformation, about the same amount on the positive control and none on the negative control plate. Eight clones were randomly chosen from our transformation and one from the positive control plate (figure 1) for PCR validation of the integration.

    Figure 1: validation of the integration of the part BBa_K3570000 in the yeast genome using DPP1 homology sequence (BBa_3570006 and BBa_3570007). The expected correct size is 1.2kb.

    All clones have the expected size (1.2kb), and the control where we inserted pRS313 does not show any band, proving that we have successfully integrated our construction into the yeast using DPP1 homology sequence.



    References

    • S. cerevisiae genome, chromosome IV, DPP1 gene. GenBank: CP046084.1

    Sequence and Features


    Assembly Compatibility:
    • 10
      INCOMPATIBLE WITH RFC[10]
      Illegal PstI site found at 50
    • 12
      INCOMPATIBLE WITH RFC[12]
      Illegal PstI site found at 50
    • 21
      COMPATIBLE WITH RFC[21]
    • 23
      INCOMPATIBLE WITH RFC[23]
      Illegal PstI site found at 50
    • 25
      INCOMPATIBLE WITH RFC[25]
      Illegal PstI site found at 50
    • 1000
      COMPATIBLE WITH RFC[1000]