Difference between revisions of "Part:BBa K5071016"

 
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<partinfo>BBa_K5071016 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K5071016 SequenceAndFeatures</partinfo>
  
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    <title>BBa_K5071016 (pETDuet-BGCI-gene123)</title>
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    <h2>Composite part BBa_K5071016 (pETDuet-BGCI-gene123)</h2>
  
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<!-- Uncomment this to enable Functional Parameter display
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    <h3>Construction Design</h3>
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===Functional Parameters===
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    <p>
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<partinfo>BBa_K5071016 parameters</partinfo>
+
        First, we obtained 4 target fragments using PCR technology. In order to improve the success rate of plasmid construction, we connected the 4 target fragments pairwise (by Overlap PCR), resulting in two fragments. Subsequently, we constructed a new plasmid by ligating the fragments with a vector using enzymatic digestion and ligation.
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<!-- -->
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    </p>
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 +
    <div style="text-align:center;">
 +
        <img src="https://static.igem.wiki/teams/5071/bba-k5071016/1.jpg" alt="Fig 1. The plasmid map of pETDuet-BGCI-gene123">
 +
        <div class="caption">Fig 1. The plasmid map of pETDuet-BGCI-gene123</div>
 +
    </div>
 +
 
 +
    <h3>Engineering Principle</h3>
 +
    <p>
 +
        Firstly, the target fragments were obtained using PCR technology and the vector was linearized. Then, the four target fragments were overlapped pairwise to form two fragments. Subsequently, they were connected to the backbone using enzyme digestion and ligation methods to construct an expression plasmid containing three target genes. This was used to validate the impact of the relevant genes on the products.
 +
    </p>
 +
 
 +
    <h3>Experimental Approach</h3>
 +
    <p>
 +
        Firstly, we utilized PCR technology to obtain three target genes, BGCI-1, BGCI-2, BGCI-3 (synthesized by a biotech company), with band lengths of 150 bp, 1200 bp, and 500 bp, respectively, for connection to the plasmid. We then performed PCR to amplify the terminator of the first reading frame and the promoter of the second reading frame along with the intervening sequence in plasmid pETD (named as 123-mid), resulting in a 200 bp band. Figure 2 demonstrates bands of the expected sizes, confirming the successful acquisition of these four fragments. Gel electrophoresis was then conducted for gel extraction, which will be used in subsequent experiments.
 +
    </p>
 +
 
 +
    <div style="text-align:center;">
 +
        <img src="https://static.igem.wiki/teams/5071/bba-k5071016/2.jpg" alt="Fig 2. The purpose segment of plasmid pETDuet-BGCI-gene123">
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        <div class="caption">Fig 2. The purpose segment of plasmid pETDuet-BGCI-gene123</div>
 +
    </div>
 +
 
 +
    <p>
 +
        Subsequently, we used overlap PCR technology to connect fragment BGCI-1 with BGCI-2, and 123-mid with BGCI-3, resulting in band lengths of 1300bp and 700bp, respectively. Figure 3A displays bands of the expected sizes, confirming successful connection. Following this, we performed double enzyme digestion on the plasmid using BamH1 and Xho1 restriction enzymes to linearize the plasmid, resulting in a band length of 4000bp. Figure 3B shows bands of the expected size, confirming successful linearization. We recovered the gel from both of these steps of gel electrophoresis and performed the connection, followed by transformation into E. coli DH5α.
 +
    </p>
 +
 
 +
    <div style="text-align:center;">
 +
        <img src="https://static.igem.wiki/teams/5071/bba-k5071016/3.jpg" alt="Fig 3. The results of the overlap connection and plasmid linearization">
 +
        <div class="caption">Fig 3. The results of the overlap connection and plasmid linearization</div>
 +
    </div>
 +
 
 +
    <p>
 +
        We selected multiple colonies for PCR verification, and the bands matched the expected length (1200 bp). We sent the validated bacterial strains to a biotech company for sequencing (Figure 4), selected plasmids without mutations, and successfully obtained the constructed plasmid pETDuet-BGCI-gene123.
 +
    </p>
 +
 
 +
    <div style="text-align:center;">
 +
        <img src="https://static.igem.wiki/teams/5071/bba-k5071016/4.jpg" alt="Fig 4. Single clone verification of pETDuet-BGCI-gene123 transformed E. coli DH5α. A. The results of colony PCR; B: The clones on the plate; C: Sequencing results">
 +
        <div class="caption">Fig 4. Single clone verification of pETDuet-BGCI-gene123 transformed E. coli DH5α</div>
 +
    </div>
 +
 
 +
    <h3>Characterization/Measurement</h3>
 +
 
 +
    <h4>1: Transformation of E. coli BL21-Strain-BGCI</h4>
 +
    <p>
 +
        In our target genes, the 6 genes of BGCI represent metabolic pathway 1, which are the 6 genes contained in plasmids pETDuet-BGCI-gene123 and pRSFDuet-BGCI-gene456. We simultaneously transformed these two plasmids into E. coli BL21 for the production of terpenoid compounds. The experimental results, as shown in Figure 5, depict the transformed E. coli BL21. We conducted single colony verification to confirm the presence of both plasmids, as illustrated in Figure 16. We obtained bacterial strains that correctly harbored both transformed plasmids, which we named as BGCI.
 +
    </p>
 +
 
 +
    <div style="text-align:center;">
 +
        <img src="https://static.igem.wiki/teams/5071/bba-k5071016/5.jpg" alt="Fig 5. Colony PCR results of strain BGCI">
 +
        <div class="caption">Fig 5. Colony PCR results of strain BGCI</div>
 +
    </div>
 +
 
 +
    <h4>2: Protein expression-Strain-BGCI</h4>
 +
    <p>
 +
        To assess the gene expression in the bacterial strains, we lysed the cells. To run a protein gel, start by preparing protein samples with a loading buffer and loading them into the gel wells. Run the gel at a constant voltage to separate proteins by size, then stain the gel to visualize the separated proteins. Finally, analyze the protein bands to interpret the results. We performed protein electrophoresis at different time points after IPTG induction, as shown in Figure 6, to detect the proteins expressing our target genes (BGCI-2 is 43.3kDa, BGCI-1 is 3.1kDA, BGCI-2 is 18.4kDa, BGCI-5 is 26.1kDa, BGCI-4 is 48.4kDA, BGCI-6 is 29.2kDa).
 +
    </p>
 +
 
 +
    <div style="text-align:center;">
 +
        <img src="https://static.igem.wiki/teams/5071/bba-k5071016/6.jpg" alt="Fig 6. Protein gel results of strain BGCI">
 +
        <div class="caption">Fig 6. Protein gel results of strain BGCI</div>
 +
    </div>
 +
 
 +
    <h4>3: The test results for Total Antioxidant Capacity (T-AOC)</h4>
 +
    <p>
 +
        Various antioxidants and antioxidant enzymes in the fermentation broth contribute to the total antioxidant level. We used a Total Antioxidant Capacity assay kit (colorimetric method) for detection. The main principle is that DPPH is a stable free radical with maximum absorption at 515nm. Upon addition of antioxidants to the DPPH solution, a decolorization reaction occurs. Therefore, the change in absorbance can be quantified using Trolox as a control system to measure the antioxidant capacity of antioxidants. We first subjected the fermentation broth after 48 hours of fermentation to ultrasonic disruption: power 200W, ultrasound 3s, interval 10s, repeated 30 times, centrifuged at 10000rpm for 10 minutes at 4℃, followed by detection. The experimental results, as shown in Figure 7 and Table 1, revealed a significant increase in the DPPH scavenging rate for our genetically modified strains, from 4.58% to 40.80% and 49.45%, respectively. This demonstrates the success of our modification.
 +
    </p>
 +
 
 +
    <table>
 +
        <tr>
 +
            <th>Strain</th>
 +
            <th>Absorbance</th>
 +
            <th>STD</th>
 +
            <th>DPPH Free Radical Clearance (%)</th>
 +
        </tr>
 +
        <tr>
 +
            <td>Control</td>
 +
            <td>0.146</td>
 +
            <td>0.0191</td>
 +
            <td>4.58</td>
 +
        </tr>
 +
        <tr>
 +
            <td>BGCI</td>
 +
            <td>0.089</td>
 +
            <td>0.0039</td>
 +
            <td>40.80</td>
 +
        </tr>
 +
    </table>
 +
 
 +
    <div style="text-align:center;">
 +
        <img src="https://static.igem.wiki/teams/5071/bba-k5071016/7.jpg" alt="Fig 7. DPPH scavenging rates of the genetically modified strains">
 +
        <div class="caption">Fig 7. DPPH scavenging rates of the genetically modified strains</div>
 +
    </div>
 +
 
 +
    <h4>4: The test of the fermentation product antibacterial experiment</h4>
 +
    <p>
 +
        For the antibacterial activity testing of the fermentation broth, we utilized the double-layer agar plate method, with the bottom layer containing 1.5% LB solid medium and the top layer containing 0.8% LB solid medium poured after the bottom layer had cooled. Once the top layer reached an appropriate temperature, it was mixed with the cultured K-12 strain and poured into petri dishes. As shown in Figure 8, 4μL of the respective liquid was pipetted into each position. Each column represents three parallels of the same experimental group:
 +
        1. Positive control with ciprofloxacin concentration of 1g/L;
 +
        2. Positive control with ciprofloxacin concentration of 0.5g/L;
 +
        3. Concentrated 5-fold lysate supernatant after cell disruption;
 +
        4. Original lysate supernatant after cell disruption;
 +
        5. Squalene at 200mg/L.
 +
        Our experimental results indicate that the concentrated 5-fold fermentation broth of strain BGCI exhibits some antibacterial effects, but we cannot determine the identity of this substance.
 +
    </p>
 +
 
 +
    <div style="text-align:center;">
 +
        <img src="https://static.igem.wiki/teams/5071/bba-k5071016/8.jpg" alt="Fig 8. Results of the antibacterial experiment on the bacterial strains">
 +
        <div class="caption">Fig 8. Results of the antibacterial experiment on the bacterial strains</div>
 +
    </div>
 +
 
 +
    <h4>5: Determination of squalene in the fermentation broth by HPLC</h4>
 +
    <p>
 +
        To determine if our target terpenoid compound is squalene, we conducted testing on the fermentation broth of the bacterial strains. The detection method involved the following steps: Fermentation was carried out using a biphasic fermentation method, with 10% volume of normal heptane added on top of the LBG medium. After fermentation, 1 mL of the 24-hour whole-cell catalytic liquid was taken, centrifuged at 13,000×g for 10 minutes, and the supernatant was discarded. Then, 400 μL of saline solution was added to wash the fermentation cells, centrifuged at 13,000×g for 10 minutes, and the supernatant was discarded. Next, ddH2O was added, thoroughly mixed, and brought to a volume of 400 μL. The cells were disrupted by ultrasonication at a working power of 20%, for 2 minutes with 3-second on and 5-second off cycles. Subsequently, 600 μL of ethyl acetate was added, mixed well, and subjected to ultrasonic cleaning twice for 15 minutes each. The mixture was then centrifuged, and 400 μL of the extract phase was obtained. The extract was concentrated using a vacuum centrifuge to evaporate the solvent, then re-dissolved in 200 μL of methanol, filtered through a 0.22 μm filter membrane, and ready for analysis.
 +
    </p>
 +
 
 +
    <div style="text-align:center;">
 +
        <img src="https://static.igem.wiki/teams/5071/bba-k5071016/9.jpg" alt="Fig 9. Detection results of squalene in the fermentation broth of the bacterial strains">
 +
        <div class="caption">Fig 9. Detection results of squalene in the fermentation broth of the bacterial strains</div>
 +
    </div>
 +
 
 +
    <h4>6: Determination of squalene in the fermentation broth by LC-MS</h4>
 +
    <p>
 +
        The squalene content was measured in the bacterial strain through LC-MS, with a yield of 6.60 mg/L. Due to the higher detection accuracy of LC-MS compared to HPLC, it is more precise and suitable for testing substances at low concentrations.
 +
    </p>
 +
 
 +
    <table>
 +
        <tr>
 +
            <th>Strain</th>
 +
            <th>Squalene Concentration (mg/L)</th>
 +
            <th>STD</th>
 +
        </tr>
 +
        <tr>
 +
            <td>BGCI</td>
 +
            <td>6.60</td>
 +
            <td>0.5056</td>
 +
        </tr>
 +
        <tr>
 +
            <td>BGCII</td>
 +
            <td>0.00</td>
 +
            <td>0.0000</td>
 +
        </tr>
 +
    </table>
 +
 
 +
    <div style="text-align:center;">
 +
        <img src="https://static.igem.wiki/teams/5071/bba-k5071016/10.jpg" alt="Fig 10. Detection results of squalene in the fermentation broth of the bacterial strains">
 +
        <div class="caption">Fig 10. Detection results of squalene in the fermentation broth of the bacterial strains</div>
 +
    </div>
 +
 
 +
</body>
 +
</html>

Revision as of 05:51, 30 September 2024


pETDuet-BGCI-gene123

pETDuet-BGCI-gene123

Sequence and Features


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal PstI site found at 5636
    Illegal PstI site found at 5853
    Illegal PstI site found at 5943
    Illegal PstI site found at 6263
    Illegal PstI site found at 6699
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    INCOMPATIBLE WITH RFC[12]
    Illegal PstI site found at 5636
    Illegal PstI site found at 5853
    Illegal PstI site found at 5943
    Illegal PstI site found at 6263
    Illegal PstI site found at 6699
    Illegal NotI site found at 149
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 305
    Illegal BamHI site found at 106
    Illegal XhoI site found at 354
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal PstI site found at 5636
    Illegal PstI site found at 5853
    Illegal PstI site found at 5943
    Illegal PstI site found at 6263
    Illegal PstI site found at 6699
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal PstI site found at 5636
    Illegal PstI site found at 5853
    Illegal PstI site found at 5943
    Illegal PstI site found at 6263
    Illegal PstI site found at 6699
    Illegal NgoMIV site found at 324
    Illegal NgoMIV site found at 671
    Illegal NgoMIV site found at 5348
    Illegal AgeI site found at 6543
  • 1000
    COMPATIBLE WITH RFC[1000]

<!DOCTYPE html> BBa_K5071016 (pETDuet-BGCI-gene123)

Composite part BBa_K5071016 (pETDuet-BGCI-gene123)

Construction Design

First, we obtained 4 target fragments using PCR technology. In order to improve the success rate of plasmid construction, we connected the 4 target fragments pairwise (by Overlap PCR), resulting in two fragments. Subsequently, we constructed a new plasmid by ligating the fragments with a vector using enzymatic digestion and ligation.

Fig 1. The plasmid map of pETDuet-BGCI-gene123
Fig 1. The plasmid map of pETDuet-BGCI-gene123

Engineering Principle

Firstly, the target fragments were obtained using PCR technology and the vector was linearized. Then, the four target fragments were overlapped pairwise to form two fragments. Subsequently, they were connected to the backbone using enzyme digestion and ligation methods to construct an expression plasmid containing three target genes. This was used to validate the impact of the relevant genes on the products.

Experimental Approach

Firstly, we utilized PCR technology to obtain three target genes, BGCI-1, BGCI-2, BGCI-3 (synthesized by a biotech company), with band lengths of 150 bp, 1200 bp, and 500 bp, respectively, for connection to the plasmid. We then performed PCR to amplify the terminator of the first reading frame and the promoter of the second reading frame along with the intervening sequence in plasmid pETD (named as 123-mid), resulting in a 200 bp band. Figure 2 demonstrates bands of the expected sizes, confirming the successful acquisition of these four fragments. Gel electrophoresis was then conducted for gel extraction, which will be used in subsequent experiments.

Fig 2. The purpose segment of plasmid pETDuet-BGCI-gene123
Fig 2. The purpose segment of plasmid pETDuet-BGCI-gene123

Subsequently, we used overlap PCR technology to connect fragment BGCI-1 with BGCI-2, and 123-mid with BGCI-3, resulting in band lengths of 1300bp and 700bp, respectively. Figure 3A displays bands of the expected sizes, confirming successful connection. Following this, we performed double enzyme digestion on the plasmid using BamH1 and Xho1 restriction enzymes to linearize the plasmid, resulting in a band length of 4000bp. Figure 3B shows bands of the expected size, confirming successful linearization. We recovered the gel from both of these steps of gel electrophoresis and performed the connection, followed by transformation into E. coli DH5α.

Fig 3. The results of the overlap connection and plasmid linearization
Fig 3. The results of the overlap connection and plasmid linearization

We selected multiple colonies for PCR verification, and the bands matched the expected length (1200 bp). We sent the validated bacterial strains to a biotech company for sequencing (Figure 4), selected plasmids without mutations, and successfully obtained the constructed plasmid pETDuet-BGCI-gene123.

Fig 4. Single clone verification of pETDuet-BGCI-gene123 transformed E. coli DH5α. A. The results of colony PCR; B: The clones on the plate; C: Sequencing results
Fig 4. Single clone verification of pETDuet-BGCI-gene123 transformed E. coli DH5α

Characterization/Measurement

1: Transformation of E. coli BL21-Strain-BGCI

In our target genes, the 6 genes of BGCI represent metabolic pathway 1, which are the 6 genes contained in plasmids pETDuet-BGCI-gene123 and pRSFDuet-BGCI-gene456. We simultaneously transformed these two plasmids into E. coli BL21 for the production of terpenoid compounds. The experimental results, as shown in Figure 5, depict the transformed E. coli BL21. We conducted single colony verification to confirm the presence of both plasmids, as illustrated in Figure 16. We obtained bacterial strains that correctly harbored both transformed plasmids, which we named as BGCI.

Fig 5. Colony PCR results of strain BGCI
Fig 5. Colony PCR results of strain BGCI

2: Protein expression-Strain-BGCI

To assess the gene expression in the bacterial strains, we lysed the cells. To run a protein gel, start by preparing protein samples with a loading buffer and loading them into the gel wells. Run the gel at a constant voltage to separate proteins by size, then stain the gel to visualize the separated proteins. Finally, analyze the protein bands to interpret the results. We performed protein electrophoresis at different time points after IPTG induction, as shown in Figure 6, to detect the proteins expressing our target genes (BGCI-2 is 43.3kDa, BGCI-1 is 3.1kDA, BGCI-2 is 18.4kDa, BGCI-5 is 26.1kDa, BGCI-4 is 48.4kDA, BGCI-6 is 29.2kDa).

Fig 6. Protein gel results of strain BGCI
Fig 6. Protein gel results of strain BGCI

3: The test results for Total Antioxidant Capacity (T-AOC)

Various antioxidants and antioxidant enzymes in the fermentation broth contribute to the total antioxidant level. We used a Total Antioxidant Capacity assay kit (colorimetric method) for detection. The main principle is that DPPH is a stable free radical with maximum absorption at 515nm. Upon addition of antioxidants to the DPPH solution, a decolorization reaction occurs. Therefore, the change in absorbance can be quantified using Trolox as a control system to measure the antioxidant capacity of antioxidants. We first subjected the fermentation broth after 48 hours of fermentation to ultrasonic disruption: power 200W, ultrasound 3s, interval 10s, repeated 30 times, centrifuged at 10000rpm for 10 minutes at 4℃, followed by detection. The experimental results, as shown in Figure 7 and Table 1, revealed a significant increase in the DPPH scavenging rate for our genetically modified strains, from 4.58% to 40.80% and 49.45%, respectively. This demonstrates the success of our modification.

Strain Absorbance STD DPPH Free Radical Clearance (%)
Control 0.146 0.0191 4.58
BGCI 0.089 0.0039 40.80
Fig 7. DPPH scavenging rates of the genetically modified strains
Fig 7. DPPH scavenging rates of the genetically modified strains

4: The test of the fermentation product antibacterial experiment

For the antibacterial activity testing of the fermentation broth, we utilized the double-layer agar plate method, with the bottom layer containing 1.5% LB solid medium and the top layer containing 0.8% LB solid medium poured after the bottom layer had cooled. Once the top layer reached an appropriate temperature, it was mixed with the cultured K-12 strain and poured into petri dishes. As shown in Figure 8, 4μL of the respective liquid was pipetted into each position. Each column represents three parallels of the same experimental group: 1. Positive control with ciprofloxacin concentration of 1g/L; 2. Positive control with ciprofloxacin concentration of 0.5g/L; 3. Concentrated 5-fold lysate supernatant after cell disruption; 4. Original lysate supernatant after cell disruption; 5. Squalene at 200mg/L. Our experimental results indicate that the concentrated 5-fold fermentation broth of strain BGCI exhibits some antibacterial effects, but we cannot determine the identity of this substance.

Fig 8. Results of the antibacterial experiment on the bacterial strains
Fig 8. Results of the antibacterial experiment on the bacterial strains

5: Determination of squalene in the fermentation broth by HPLC

To determine if our target terpenoid compound is squalene, we conducted testing on the fermentation broth of the bacterial strains. The detection method involved the following steps: Fermentation was carried out using a biphasic fermentation method, with 10% volume of normal heptane added on top of the LBG medium. After fermentation, 1 mL of the 24-hour whole-cell catalytic liquid was taken, centrifuged at 13,000×g for 10 minutes, and the supernatant was discarded. Then, 400 μL of saline solution was added to wash the fermentation cells, centrifuged at 13,000×g for 10 minutes, and the supernatant was discarded. Next, ddH2O was added, thoroughly mixed, and brought to a volume of 400 μL. The cells were disrupted by ultrasonication at a working power of 20%, for 2 minutes with 3-second on and 5-second off cycles. Subsequently, 600 μL of ethyl acetate was added, mixed well, and subjected to ultrasonic cleaning twice for 15 minutes each. The mixture was then centrifuged, and 400 μL of the extract phase was obtained. The extract was concentrated using a vacuum centrifuge to evaporate the solvent, then re-dissolved in 200 μL of methanol, filtered through a 0.22 μm filter membrane, and ready for analysis.

Fig 9. Detection results of squalene in the fermentation broth of the bacterial strains
Fig 9. Detection results of squalene in the fermentation broth of the bacterial strains

6: Determination of squalene in the fermentation broth by LC-MS

The squalene content was measured in the bacterial strain through LC-MS, with a yield of 6.60 mg/L. Due to the higher detection accuracy of LC-MS compared to HPLC, it is more precise and suitable for testing substances at low concentrations.

Strain Squalene Concentration (mg/L) STD
BGCI 6.60 0.5056
BGCII 0.00 0.0000
Fig 10. Detection results of squalene in the fermentation broth of the bacterial strains
Fig 10. Detection results of squalene in the fermentation broth of the bacterial strains