Difference between revisions of "Part:BBa K3562000"
 
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<partinfo>BBa_K3562000 short</partinfo>
 
<partinfo>BBa_K3562000 short</partinfo>
  
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AHL-lactonase with AHLs (Quorum-sensing factor Acyl Homoserine Lactone) degradation activity.
+
AHL-acylase with AHLs (Quorum-sensing factor Acyl Homoserine Lactone) degradation activity.
  
 
<!-- Add more about the biology of this part here
 
<!-- Add more about the biology of this part here
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===Usage and Biology===
 
===Usage and Biology===
 
<p>
 
<p>
−
AHL-lactonase is a kind of lactonase opened the homoserine lactone ring of AHL in the presence of water to produce N-acly homoserine.(Fig.1) The biological activity of degradation products will be greatly reduced.
+
AHL-acylase is an acylase that cleaves AHL by hydrolyzing the amide linkage between the acyl side chain and HSL moiety.(Fig.1)
 
<br/>
 
<br/>
−
[[Image:AHL-lactonase.png|frame|'''Figure 1:'''Mechanism of AHL-lactonase]]
+
[[Image:AHL-acylase.png|frame|'''Figure 1:'''Mechanism of AHL-acylase]]
 
</p>
 
</p>
 
<p>
 
<p>
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</p>
 
</p>
 
<p>
 
<p>
−
Different AHL degrading enzymes have different substrate preferences and degradation activities.(Fig.2)
+
Different AHL degrading enzymes have different substrate preferences and degradation activities. We try to select suitable ones from a variety of enzymes.
−
[[Image:AHL-lactonase.png|frame|'''Figure 1:'''Mechanism of AHL-lactonase]]
+
</p>
 +
===Protocols===
 +
<p>Combined with the results of experiments this year, we propose a new procedure to characterize the enzyme activity.</p>
 +
<p>1. Cut the plasmid with single enzyme</p>
 +
<p>2. Use Gibson assembly kit to ligate it with the target gene (homologous arms and His tag were added when the genes were synthesized)</p>
 +
<p>3. Transform the ligation products into E.coli BL21 and culture it after spread plate</p>
 +
<p>4. Pick some single colonies into fresh medium</p>
 +
<p>5. Use colony PCR to find the positive ones, and send samples to company to do gene sequencing</p>
 +
<p>6. Amplify the bacteria in larger volume of fresh medium</p>
 +
<p>7. Use IPTG to induce the expression of the enzymes</p>
 +
<p>8. Collect the bacteria and extract the proteins</p>
 +
<p>9. Keep some of the crude bacteria extract and use Ni resins (from commercial kit) to purify others</p>
 +
<p>For the crude extract:</p>
 +
<p>(1) Mix the crude extract and the AHL standard stock solutions in certain buffer (according to the optimal PH of the enzyme) and the control group is added with extract inactivated by high temperature</p>
 +
<p>(2) React in optimal temperature and take one sample per 30 minutes</p>
 +
<p>(3) Extract three times with at least an equal volume of acidified ethyl acetate</p>
 +
<p>(4) The organic layer is separated, collected and dried using anhydrous sodium sulfate</p>
 +
<p>(5) Use a rotary evaporator to remove the organic solvent in the sample under reduced pressure</p>
 +
<p>(6) The residue is reconstituted in chromatographic grade methanol</p>
 +
<p>(7) The sample is analyzed by HPLC to quantify the AHL concentration in the reaction system</p>
 +
<p>For the purified enzymes:</p>
 +
<p>(1) Analyze the protein with SDS-PAGE</p>
 +
<p>(2) Measure the enzyme concentration by BCA kit</p>
 +
<p>If the crude extract can efficiently degrade AHLs, then use the purified enzymes to repeat the former procedure performed on the crude extract; if not, change the conditions of enzyme expression to avoid inclusion-body form of the enzymes</p>
 +
<p>For the standard curve:</p>
 +
<p> (1) Dissolve certain amount of AHL dry powder in chromatographic grade methanol to create a series of AHL solutions with different concentrations</p>
 +
<p>(2) Analyze them by HPLC and draw the standard curve of AHL concentration versus HPLC data.</p>
 +
<p>10. Analyze the data from the experiments of purified enzymes with the help of the standard curve</p>
 +
<p>11. Then use excel to draw the Lineweaver-Burk plot and obtain the Km (Michaelis constant) value of the enzymes towards this kind of AHL</p>
 +
<p>12. The same operation can be done to attain different Km values towards 3-oxo-C12-HSL and C4-HSL in Pseudomonas aeruginosa.</p>
 +
<p>13. Combine the data with our quorum dynamics model to observe the overall effects the enzymes have on the quorum sensing systems of P.aeruginosa</p>
 +
<p>14. Decide whether the enzyme is suitable for our project
 +
 
 +
</p>

Latest revision as of 16:59, 27 October 2020


AiiC (with His-tag)

AHL-acylase with AHLs (Quorum-sensing factor Acyl Homoserine Lactone) degradation activity.

Sequence and Features


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal SpeI site found at 2071
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal SpeI site found at 2071
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal SpeI site found at 2071
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal SpeI site found at 2071
  • 1000
    COMPATIBLE WITH RFC[1000]


Usage and Biology

AHL-acylase is an acylase that cleaves AHL by hydrolyzing the amide linkage between the acyl side chain and HSL moiety.(Fig.1)

Figure 1:Mechanism of AHL-acylase

Quorum sensing factor is closely related to bacterial virulence. Enzymes that degrade AHL can control the concentration of AHL to silence the expression of related genes. In our project, we use these enzymes to control the virulence of Pseudomonas aeruginosa referred to existing experimental therapies.

Different AHL degrading enzymes have different substrate preferences and degradation activities. We try to select suitable ones from a variety of enzymes.

Protocols

Combined with the results of experiments this year, we propose a new procedure to characterize the enzyme activity.

1. Cut the plasmid with single enzyme

2. Use Gibson assembly kit to ligate it with the target gene (homologous arms and His tag were added when the genes were synthesized)

3. Transform the ligation products into E.coli BL21 and culture it after spread plate

4. Pick some single colonies into fresh medium

5. Use colony PCR to find the positive ones, and send samples to company to do gene sequencing

6. Amplify the bacteria in larger volume of fresh medium

7. Use IPTG to induce the expression of the enzymes

8. Collect the bacteria and extract the proteins

9. Keep some of the crude bacteria extract and use Ni resins (from commercial kit) to purify others

For the crude extract:

(1) Mix the crude extract and the AHL standard stock solutions in certain buffer (according to the optimal PH of the enzyme) and the control group is added with extract inactivated by high temperature

(2) React in optimal temperature and take one sample per 30 minutes

(3) Extract three times with at least an equal volume of acidified ethyl acetate

(4) The organic layer is separated, collected and dried using anhydrous sodium sulfate

(5) Use a rotary evaporator to remove the organic solvent in the sample under reduced pressure

(6) The residue is reconstituted in chromatographic grade methanol

(7) The sample is analyzed by HPLC to quantify the AHL concentration in the reaction system

For the purified enzymes:

(1) Analyze the protein with SDS-PAGE

(2) Measure the enzyme concentration by BCA kit

If the crude extract can efficiently degrade AHLs, then use the purified enzymes to repeat the former procedure performed on the crude extract; if not, change the conditions of enzyme expression to avoid inclusion-body form of the enzymes

For the standard curve:

(1) Dissolve certain amount of AHL dry powder in chromatographic grade methanol to create a series of AHL solutions with different concentrations

(2) Analyze them by HPLC and draw the standard curve of AHL concentration versus HPLC data.

10. Analyze the data from the experiments of purified enzymes with the help of the standard curve

11. Then use excel to draw the Lineweaver-Burk plot and obtain the Km (Michaelis constant) value of the enzymes towards this kind of AHL

12. The same operation can be done to attain different Km values towards 3-oxo-C12-HSL and C4-HSL in Pseudomonas aeruginosa.

13. Combine the data with our quorum dynamics model to observe the overall effects the enzymes have on the quorum sensing systems of P.aeruginosa

14. Decide whether the enzyme is suitable for our project