Difference between revisions of "Team:NPU-China/Proofofconcept"

 
(18 intermediate revisions by 6 users not shown)
Line 158: Line 158:
 
                     <h3>1.1 construction of pET-28a-ceaS2 plasmid:</h3>
 
                     <h3>1.1 construction of pET-28a-ceaS2 plasmid:</h3>
 
                     <h4>First, we constructed pET-28a-ceaS2 plasmid with pET-28a plasmid skeleton as vector.
 
                     <h4>First, we constructed pET-28a-ceaS2 plasmid with pET-28a plasmid skeleton as vector.
                         <br> [Plasmid figure + nucleic acid glue figure]</h4>
+
  <div class="col-md-12" style="padding-top:30px">
 +
 
 +
 
 +
                    <div class="col-md-6">
 +
                         <img src="https://static.igem.org/mediawiki/2017/4/44/%28%E5%B0%8F%29%E5%A4%A7%E8%82%A03_pETDuet-NOX-CAT_7451.png" class="img-responsive">
 +
                        <h4> </h4>
 +
                    </div>
 +
                    <div class="col-md-6">
 +
                        <img src="https://static.igem.org/mediawiki/2017/9/94/NPU-ceaS2jiaotu.png" class="img-responsive">
 +
                        <h4> </h4>
 +
                   
 +
                        <h4> </h4>
 +
                    </div>
 +
                </div>
 +
 
 +
                    </h4>
 +
 
 +
 
 
                     <h3>1.2 Expression and Purification of ceaS2 Protein:</h3>
 
                     <h3>1.2 Expression and Purification of ceaS2 Protein:</h3>
 
                     <h4>We transferred the pET-28a-ceaS2 plasmid constructed into E.coli BL21 (DE3) strain and induced E. coli
 
                     <h4>We transferred the pET-28a-ceaS2 plasmid constructed into E.coli BL21 (DE3) strain and induced E. coli
Line 164: Line 181:
 
                         we used the affinity chromatography nickel column to separate and purify the ceaS2 protein and identified
 
                         we used the affinity chromatography nickel column to separate and purify the ceaS2 protein and identified
 
                         it by 12% SDS-PAGE electrophoresis. The results were as follows:</h4>
 
                         it by 12% SDS-PAGE electrophoresis. The results were as follows:</h4>
                     <img src="https://static.igem.org/mediawiki/2017/7/7f/Proof-%E5%9F%BA%E4%BA%8E%E7%94%98%E6%B2%B9%E7%9A%84%E4%B8%99%E7%83%AF%E9%85%B8%E7%BB%86%E8%83%9E%E5%B7%A5%E5%8E%82%E7%9A%84%E5%AE%9E%E7%8E%B0_ENG_%E5%9B%BE%E4%B8%80.png"
+
                     <center><img src="https://static.igem.org/mediawiki/2017/7/7f/Proof-%E5%9F%BA%E4%BA%8E%E7%94%98%E6%B2%B9%E7%9A%84%E4%B8%99%E7%83%AF%E9%85%B8%E7%BB%86%E8%83%9E%E5%B7%A5%E5%8E%82%E7%9A%84%E5%AE%9E%E7%8E%B0_ENG_%E5%9B%BE%E4%B8%80.png"
                         class="img-responsive">
+
                         class="img-responsive"></center>
  
                     <h4>Fig XX Purified CeaS2 after Ni-NTA affinity chromatography
+
                     <h4> Purified ceaS2 after Ni-NTA affinity chromatography
 
                         <br> (M, protein marker (from top to bottom is 25、35、48、63、75、100、135、180 kDa);Lane1, precipitation samples
 
                         <br> (M, protein marker (from top to bottom is 25、35、48、63、75、100、135、180 kDa);Lane1, precipitation samples
 
                         in the cell lysates; 2, supernatant samples in the cell lysates; 3, supernatant flow through Ni-NTA
 
                         in the cell lysates; 2, supernatant samples in the cell lysates; 3, supernatant flow through Ni-NTA
Line 173: Line 190:
 
                         eluent; 7, 300 mM imidazole eluent)
 
                         eluent; 7, 300 mM imidazole eluent)
 
                         <br><br> According to the information in the Uniprot database, the ceaS2 protein has 573 amino acids and
 
                         <br><br> According to the information in the Uniprot database, the ceaS2 protein has 573 amino acids and
                         the molecular weight of the protein is 62.34 kDa. In Figure XX, electrophoretic display of recombinant
+
                         the molecular weight of the protein is 62.34 kDa. In Figure, electrophoretic display of recombinant
 
                         protein molecular weight is consistent with the theoretical molecular weight of the protein, which
 
                         protein molecular weight is consistent with the theoretical molecular weight of the protein, which
 
                         leads to the conclusion that this is the expression of our target protein. The results show that
 
                         leads to the conclusion that this is the expression of our target protein. The results show that
Line 182: Line 199:
 
                     <h4>In order to ensure the reliability and accuracy of the experiment, we first examined the concentration
 
                     <h4>In order to ensure the reliability and accuracy of the experiment, we first examined the concentration
 
                         of the purified protein. Proteins were quantified using the Thermol Scientific BCA Protein Quantification
 
                         of the purified protein. Proteins were quantified using the Thermol Scientific BCA Protein Quantification
                         Kit. The standardized curve of protein concentration of OD562 interval measured(Figure XX).
+
                         Kit. The standardized curve of protein concentration of OD562 interval measured.
 
                     </h4>
 
                     </h4>
                     <img src="https://static.igem.org/mediawiki/2017/e/e0/Proof-%E5%9F%BA%E4%BA%8E%E7%94%98%E6%B2%B9%E7%9A%84%E4%B8%99%E7%83%AF%E9%85%B8%E7%BB%86%E8%83%9E%E5%B7%A5%E5%8E%82%E7%9A%84%E5%AE%9E%E7%8E%B0_ENG_%E5%9B%BE%E4%BA%8C.png"
+
                     <center><img src="https://static.igem.org/mediawiki/2017/e/e0/Proof-%E5%9F%BA%E4%BA%8E%E7%94%98%E6%B2%B9%E7%9A%84%E4%B8%99%E7%83%AF%E9%85%B8%E7%BB%86%E8%83%9E%E5%B7%A5%E5%8E%82%E7%9A%84%E5%AE%9E%E7%8E%B0_ENG_%E5%9B%BE%E4%BA%8C.png"
                         class="img-responsive">
+
                         class="img-responsive"></center>
 
                     <h4>
 
                     <h4>
                         Figure XX Standardized curve of protein concentration
+
                         <center>Standardized curve of protein concentration</center>
 
                         <br> The purified and quantified protein was used for enzymatic activity reaction. The control group
 
                         <br> The purified and quantified protein was used for enzymatic activity reaction. The control group
 
                         was not add ceaS2 enzyme, and the protein buffer was used to make up the volume. The reaction system
 
                         was not add ceaS2 enzyme, and the protein buffer was used to make up the volume. The reaction system
Line 197: Line 214:
 
                       We used high performance liquid chromatography (HPLC) to determine the reaction solution. Determination conditions and parameters:
 
                       We used high performance liquid chromatography (HPLC) to determine the reaction solution. Determination conditions and parameters:
 
                         87H chromatographic column, 5 mM H2SO4 mobile phase, flow rate 0.6 mL / min, UV absorbance 210 nm.
 
                         87H chromatographic column, 5 mM H2SO4 mobile phase, flow rate 0.6 mL / min, UV absorbance 210 nm.
                         Figure XX for the liquid phase determination results.
+
                         Figure for the liquid phase determination results.
 
                     </h4>
 
                     </h4>
  
                     <img src="https://static.igem.org/mediawiki/2017/b/bc/Proof-%E5%9F%BA%E4%BA%8E%E7%94%98%E6%B2%B9%E7%9A%84%E4%B8%99%E7%83%AF%E9%85%B8%E7%BB%86%E8%83%9E%E5%B7%A5%E5%8E%82%E7%9A%84%E5%AE%9E%E7%8E%B0_ENG_%E5%9B%BE%E4%B8%89.png"
+
                     <center><img src="https://static.igem.org/mediawiki/2017/b/bc/Proof-%E5%9F%BA%E4%BA%8E%E7%94%98%E6%B2%B9%E7%9A%84%E4%B8%99%E7%83%AF%E9%85%B8%E7%BB%86%E8%83%9E%E5%B7%A5%E5%8E%82%E7%9A%84%E5%AE%9E%E7%8E%B0_ENG_%E5%9B%BE%E4%B8%89.png"
                         class="img-responsive">
+
                         class="img-responsive"></center>
  
  
 
                     <h4>
 
                     <h4>
                         Fig XX Identification function of Ceas2 by liquid chromatogram
+
                         <center>Identification function of ceaS2 by liquid chromatogram</center>
 
                         <br> (The black line is acrylic acid standard, green line is control, blue line is reaction of D-G3P
 
                         <br> (The black line is acrylic acid standard, green line is control, blue line is reaction of D-G3P
 
                         as substrate, red line is reaction DHAP as substrate)
 
                         as substrate, red line is reaction DHAP as substrate)
Line 211: Line 228:
 
                         minutes presenting a single and satisfying peak shape. The samples in the control group did not correspond
 
                         minutes presenting a single and satisfying peak shape. The samples in the control group did not correspond
 
                         with the treatment group. D-G3P and DHAP reaction group samples both had peaks, in line with the
 
                         with the treatment group. D-G3P and DHAP reaction group samples both had peaks, in line with the
                         standard sample of acrylic acid. Therefore, we can initially determine that Ceas2 is able to catalyze
+
                         standard sample of acrylic acid. Therefore, we can initially determine that ceas2 is able to catalyze
 
                         D-G3P and DHAP to generate acrylic acid.
 
                         D-G3P and DHAP to generate acrylic acid.
 
                     </h4>
 
                     </h4>
Line 219: Line 236:
 
                         <br>
 
                         <br>
 
                     </h4>
 
                     </h4>
                     <img src="https://static.igem.org/mediawiki/2017/9/9d/Proof-%E5%9F%BA%E4%BA%8E%E7%94%98%E6%B2%B9%E7%9A%84%E4%B8%99%E7%83%AF%E9%85%B8%E7%BB%86%E8%83%9E%E5%B7%A5%E5%8E%82%E7%9A%84%E5%AE%9E%E7%8E%B0_ENG_%E5%9B%BE%E5%9B%9B.png"
+
                     <center><img src="https://static.igem.org/mediawiki/2017/9/9d/Proof-%E5%9F%BA%E4%BA%8E%E7%94%98%E6%B2%B9%E7%9A%84%E4%B8%99%E7%83%AF%E9%85%B8%E7%BB%86%E8%83%9E%E5%B7%A5%E5%8E%82%E7%9A%84%E5%AE%9E%E7%8E%B0_ENG_%E5%9B%BE%E5%9B%9B.png"
                         class="img-responsive">
+
                         class="img-responsive"></center>
 +
 
 +
                    <br>
 +
 
 +
                    <center><img src="https://static.igem.org/mediawiki/2017/f/f9/Proof-%E5%9F%BA%E4%BA%8E%E7%94%98%E6%B2%B9%E7%9A%84%E4%B8%99%E7%83%AF%E9%85%B8%E7%BB%86%E8%83%9E%E5%B7%A5%E5%8E%82%E7%9A%84%E5%AE%9E%E7%8E%B0_ENG_%E5%9B%BE%E4%BA%94.png"
 +
                        class="img-responsive"></center>
 +
 
 +
                  <br>
  
                    <img src="https://static.igem.org/mediawiki/2017/f/f9/Proof-%E5%9F%BA%E4%BA%8E%E7%94%98%E6%B2%B9%E7%9A%84%E4%B8%99%E7%83%AF%E9%85%B8%E7%BB%86%E8%83%9E%E5%B7%A5%E5%8E%82%E7%9A%84%E5%AE%9E%E7%8E%B0_ENG_%E5%9B%BE%E4%BA%94.png"
+
                  <center> <img src="https://static.igem.org/mediawiki/2017/7/74/Proof-%E5%9F%BA%E4%BA%8E%E7%94%98%E6%B2%B9%E7%9A%84%E4%B8%99%E7%83%AF%E9%85%B8%E7%BB%86%E8%83%9E%E5%B7%A5%E5%8E%82%E7%9A%84%E5%AE%9E%E7%8E%B0_ENG_%E5%9B%BE%E5%85%AD.png"
                         class="img-responsive">
+
                         class="img-responsive"></center>
  
                     <img src="https://static.igem.org/mediawiki/2017/7/74/Proof-%E5%9F%BA%E4%BA%8E%E7%94%98%E6%B2%B9%E7%9A%84%E4%B8%99%E7%83%AF%E9%85%B8%E7%BB%86%E8%83%9E%E5%B7%A5%E5%8E%82%E7%9A%84%E5%AE%9E%E7%8E%B0_ENG_%E5%9B%BE%E5%85%AD.png"
+
                     <br>
                        class="img-responsive">
+
  
                     <img src="https://static.igem.org/mediawiki/2017/2/25/Proof-%E5%9F%BA%E4%BA%8E%E7%94%98%E6%B2%B9%E7%9A%84%E4%B8%99%E7%83%AF%E9%85%B8%E7%BB%86%E8%83%9E%E5%B7%A5%E5%8E%82%E7%9A%84%E5%AE%9E%E7%8E%B0_ENG_%E5%9B%BE%E4%B8%83.png"
+
                     <center><img src="https://static.igem.org/mediawiki/2017/2/25/Proof-%E5%9F%BA%E4%BA%8E%E7%94%98%E6%B2%B9%E7%9A%84%E4%B8%99%E7%83%AF%E9%85%B8%E7%BB%86%E8%83%9E%E5%B7%A5%E5%8E%82%E7%9A%84%E5%AE%9E%E7%8E%B0_ENG_%E5%9B%BE%E4%B8%83.png"
                         class="img-responsive">
+
                         class="img-responsive"></center>
  
  
Line 235: Line 258:
  
 
                     <h4>
 
                     <h4>
                        Fig XX LC-MS of Ceas2 generated acrylic acid
+
                        <center>LC-MS of ceaS2 generated acrylic acid</center>
                         <br> (From top to bottom is acrylic acid standard, control, Ceas2 reaction by DHAP as substrate, secondary
+
                         <br> (From top to bottom is acrylic acid standard, control, ceas2 reaction by DHAP as substrate, secondary
 
                         mass spectrum of acrylic acid)
 
                         mass spectrum of acrylic acid)
                         <br> According to the liquid chromatogram XX, the control group had no peaks, and the retention time
+
                         <br> According to the liquid chromatogram, the control group had no peaks, and the retention time
 
                         and molecular weight of the sample group were consistent with the standard sample of acrylic acid.
 
                         and molecular weight of the sample group were consistent with the standard sample of acrylic acid.
 
                         Also, the molecular ion peaks and fragment ion peaks in the secondary mass spectrum of the sample
 
                         Also, the molecular ion peaks and fragment ion peaks in the secondary mass spectrum of the sample
                         also fully demonstrated that Ceas2 catalyzed DHAP or ceaS2 to produce the acrylic acid.
+
                         also fully demonstrated that ceas2 catalyzed DHAP or ceaS2 to produce the acrylic acid.
 
                         <br>
 
                         <br>
 
                     </h4>
 
                     </h4>
Line 251: Line 274:
 
                         must pass through, according to which we designed a new approach to acrylic acid biosynthesis based
 
                         must pass through, according to which we designed a new approach to acrylic acid biosynthesis based
 
                         on glycerol.
 
                         on glycerol.
                         <br> 【The new pathway, as shown below】
+
                         <br> The new pathway, as shown below
 
                     </h4>
 
                     </h4>
  
                     <img src="https://static.igem.org/mediawiki/2017/3/39/Proof-%E5%9F%BA%E4%BA%8E%E7%94%98%E6%B2%B9%E7%9A%84%E4%B8%99%E7%83%AF%E9%85%B8%E7%BB%86%E8%83%9E%E5%B7%A5%E5%8E%82%E7%9A%84%E5%AE%9E%E7%8E%B0_ENG_%E5%9B%BE%E5%85%AB_%282%29.png"
+
                     <center><img src="https://static.igem.org/mediawiki/2017/2/21/%E5%A4%A7%E8%82%A0%E5%8E%9F%E5%A7%8B%E4%BB%A3%E8%B0%A2.png"
                         class="img-responsive">
+
                         class="img-responsive"></center>
  
  
  
 
                     <h4>
 
                     <h4>
                        Figure XX The acrylic biosynthetic pathway based on E. coli glycerol aerobic metabolic pathway
+
                        <center>The acrylic biosynthetic pathway based on E. coli glycerol aerobic metabolic pathway</center>
 
                         <br> This new approach is the shortest compared to other known acrylic pathways, where only three enzymes
 
                         <br> This new approach is the shortest compared to other known acrylic pathways, where only three enzymes
 
                         are needed to achieve the synthesis of acrylic acid from glycerol, so this pathway not merely has
 
                         are needed to achieve the synthesis of acrylic acid from glycerol, so this pathway not merely has
Line 271: Line 294:
 
                         inducing the expression of ceaS2 enzyme in E. coli, the reaction system was prepared and carried
 
                         inducing the expression of ceaS2 enzyme in E. coli, the reaction system was prepared and carried
 
                         out. The reaction solution was filtered and the acrylic acid content was determined by high performance
 
                         out. The reaction solution was filtered and the acrylic acid content was determined by high performance
                         liquid chromatography (HPLC). The results are as follows:
+
                         liquid chromatography (HPLC). The results are as follows:<br>
                         <br> [Primitive peak figure of liquid phase, with standard control sample. Shown as follows]
+
                         <br> <center>Primitive peak figure of liquid phase, with standard control sample. Shown as follows</center>
 
                         <br>
 
                         <br>
  
  
  
                         <img src="https://static.igem.org/mediawiki/2017/d/d4/Proof-%E5%9F%BA%E4%BA%8E%E7%94%98%E6%B2%B9%E7%9A%84%E4%B8%99%E7%83%AF%E9%85%B8%E7%BB%86%E8%83%9E%E5%B7%A5%E5%8E%82%E7%9A%84%E5%AE%9E%E7%8E%B0_ENG_%E5%9B%BE%E4%B9%9D.png"
+
                         <center><img src="https://static.igem.org/mediawiki/2017/d/d4/Proof-%E5%9F%BA%E4%BA%8E%E7%94%98%E6%B2%B9%E7%9A%84%E4%B8%99%E7%83%AF%E9%85%B8%E7%BB%86%E8%83%9E%E5%B7%A5%E5%8E%82%E7%9A%84%E5%AE%9E%E7%8E%B0_ENG_%E5%9B%BE%E4%B9%9D.png"
                             class="img-responsive"> Figure 3.7 Whole Cell Catalytic Acrylic de novo Synthesis of Liquid Chromatography
+
                             class="img-responsive"> Whole Cell Catalytic Acrylic de novo Synthesis of Liquid Chromatography</center>
 
                         <br>
 
                         <br>
 
                         <br> From the peak chromatogram, it can be seen that the goal of de novo synthesis of acrylic acid from
 
                         <br> From the peak chromatogram, it can be seen that the goal of de novo synthesis of acrylic acid from
 
                         the cells have been realized.
 
                         the cells have been realized.
 
                         <br> We have achieved the prototype of the glycerol-based acrylic cell factory based on the E. coli BL21
 
                         <br> We have achieved the prototype of the glycerol-based acrylic cell factory based on the E. coli BL21
                         (DE3) strain as the chassis cell !!!
+
                         (DE3) strain as the chassis cell.
 
                         <br>
 
                         <br>
 
                     </h4>
 
                     </h4>

Latest revision as of 20:58, 1 November 2017

In this part, we validate how ceaS2 works as expected and how we construct GAACF1.0.

1.Verification of Synthesis of acrylic acid catalyzed by ceaS2 enzyme

1.1 construction of pET-28a-ceaS2 plasmid:

First, we constructed pET-28a-ceaS2 plasmid with pET-28a plasmid skeleton as vector.

1.2 Expression and Purification of ceaS2 Protein:

We transferred the pET-28a-ceaS2 plasmid constructed into E.coli BL21 (DE3) strain and induced E. coli expression of ceaS2 protein by IPTG. Harnessing the His protein tag from the pET-28a plasmid skeleton, we used the affinity chromatography nickel column to separate and purify the ceaS2 protein and identified it by 12% SDS-PAGE electrophoresis. The results were as follows:

Purified ceaS2 after Ni-NTA affinity chromatography
(M, protein marker (from top to bottom is 25、35、48、63、75、100、135、180 kDa);Lane1, precipitation samples in the cell lysates; 2, supernatant samples in the cell lysates; 3, supernatant flow through Ni-NTA affinity chromatography; 4, 50 mM imidazole eluent; 5, 100 mM imidazole eluent; 6, 200 mM imidazole eluent; 7, 300 mM imidazole eluent)

According to the information in the Uniprot database, the ceaS2 protein has 573 amino acids and the molecular weight of the protein is 62.34 kDa. In Figure, electrophoretic display of recombinant protein molecular weight is consistent with the theoretical molecular weight of the protein, which leads to the conclusion that this is the expression of our target protein. The results show that ceaS2 has good expression and high purity after Ni-NTA affinity chromatography.

1.3 ceaS2 enzymatic reaction:

In order to ensure the reliability and accuracy of the experiment, we first examined the concentration of the purified protein. Proteins were quantified using the Thermol Scientific BCA Protein Quantification Kit. The standardized curve of protein concentration of OD562 interval measured.

Standardized curve of protein concentration

The purified and quantified protein was used for enzymatic activity reaction. The control group was not add ceaS2 enzyme, and the protein buffer was used to make up the volume. The reaction system was mixed and reacted at 30 ° C for 10 h.

1.4 Determination of Acrylic Acid by Liquid Chromatography

We used high performance liquid chromatography (HPLC) to determine the reaction solution. Determination conditions and parameters: 87H chromatographic column, 5 mM H2SO4 mobile phase, flow rate 0.6 mL / min, UV absorbance 210 nm. Figure for the liquid phase determination results.

Identification function of ceaS2 by liquid chromatogram

(The black line is acrylic acid standard, green line is control, blue line is reaction of D-G3P as substrate, red line is reaction DHAP as substrate)
The liquid chromatogram results show that the acrylic acid standardized peak time was in 19.304 minutes presenting a single and satisfying peak shape. The samples in the control group did not correspond with the treatment group. D-G3P and DHAP reaction group samples both had peaks, in line with the standard sample of acrylic acid. Therefore, we can initially determine that ceas2 is able to catalyze D-G3P and DHAP to generate acrylic acid.

1.5 Determination of Acrylic Acid by Liquid Chromatography-Mass Spectrometry (LC-MS)

For the reliable and persuasive results, we also carried out the determination of LC-MS samples. The results are shown below.




LC-MS of ceaS2 generated acrylic acid

(From top to bottom is acrylic acid standard, control, ceas2 reaction by DHAP as substrate, secondary mass spectrum of acrylic acid)
According to the liquid chromatogram, the control group had no peaks, and the retention time and molecular weight of the sample group were consistent with the standard sample of acrylic acid. Also, the molecular ion peaks and fragment ion peaks in the secondary mass spectrum of the sample also fully demonstrated that ceas2 catalyzed DHAP or ceaS2 to produce the acrylic acid.

2. GAACF 1.0: de novo synthesis of acrylic acid

2.1 A New Approach to Acrylic Biosynthesis

G3P are common secondary products of the E. coli central metabolic pathway. By introducing the ceaS2 enzyme directly into the chassis cells, we can construct a new pathway of acrylic biosynthesis based on any carbon source. DHAP and G3P are the carbon flow nodes that E. coli glycerol metabolic pathway must pass through, according to which we designed a new approach to acrylic acid biosynthesis based on glycerol.
The new pathway, as shown below

The acrylic biosynthetic pathway based on E. coli glycerol aerobic metabolic pathway

This new approach is the shortest compared to other known acrylic pathways, where only three enzymes are needed to achieve the synthesis of acrylic acid from glycerol, so this pathway not merely has a better malleability, but also a more promising development prospect.

2.2 Realization of de novo synthesis of acrylic acid


We use the whole cell catalytic method to verify whether the new pathway works in E.coli. After inducing the expression of ceaS2 enzyme in E. coli, the reaction system was prepared and carried out. The reaction solution was filtered and the acrylic acid content was determined by high performance liquid chromatography (HPLC). The results are as follows:

Primitive peak figure of liquid phase, with standard control sample. Shown as follows

Whole Cell Catalytic Acrylic de novo Synthesis of Liquid Chromatography


From the peak chromatogram, it can be seen that the goal of de novo synthesis of acrylic acid from the cells have been realized.
We have achieved the prototype of the glycerol-based acrylic cell factory based on the E. coli BL21 (DE3) strain as the chassis cell.