Difference between revisions of "Team:ZJU-China/BasicPart"

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<a href="#" class="dropdown-toggle" data-toggle="dropdown">Project</a>
 
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<li><a href="https://2018.igem.org/Team:ZJU-China/LogicGate">Logic Gate</a></li>
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<li><a href="https://2018.igem.org/Team:ZJU-China/Matrix">Matrix</a></li>
<li><a href="#">Curli</a></li>
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<li><a href="https://2018.igem.org/Team:ZJU-China/Electrodes">Electrodes</a></li>
<li><a href="#">Tag/Catcher System</a></li>
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<li><a href="#">Basic Parts</a></li>
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">Composite Parts</a></li>
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<div class="tl" style="font-weight: .8em !important; font-size: 4.5em !important;">BEST&nbsp;&nbsp;<h5>BASIC PART&nbsp;&nbsp;</h5></div>
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<div class="tl" style="font-weight: .8em !important; font-size: 4.5em !important;">BEST BASIC PART&nbsp;&nbsp;<h5>&nbsp;&nbsp;</h5></div>
 
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<div class="intro">
 
<div class="intro">
 
<!--p></br></br>The injury detector we made is based on a cell-free device with three connected enzymes.  HRP(Horseradish Peroxidase) is a commonly used enzyme as clinical testing reagent which catalyzes the reductive cleavage of hydrogen peroxide by an electron donor. As one of the three enzymes for diagnosis, it is of vital importance. </p>
 
<!--p></br></br>The injury detector we made is based on a cell-free device with three connected enzymes.  HRP(Horseradish Peroxidase) is a commonly used enzyme as clinical testing reagent which catalyzes the reductive cleavage of hydrogen peroxide by an electron donor. As one of the three enzymes for diagnosis, it is of vital importance. </p>
 
<p></br>Meanwhile, we found that SpyTag forms a spontaneous isopeptide bond to SpyCatcher, and SdyTag/SdyCatcher, SnoopTag/SnoopCatcher are the same[1][2][3]. The tag/catcher system is a useful tool to link HRP with other protein via covalent bond.</p-->
 
<p></br>Meanwhile, we found that SpyTag forms a spontaneous isopeptide bond to SpyCatcher, and SdyTag/SdyCatcher, SnoopTag/SnoopCatcher are the same[1][2][3]. The tag/catcher system is a useful tool to link HRP with other protein via covalent bond.</p-->
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<span class="psg_ttl"></br>Usage and Biology</span>
 
<span class="psg_ttl"></br>Usage and Biology</span>
  
<p style="padding-left: 2em !important; margin-bottom: .7em !important;">This part consists of BBa_J64997, BBa_B0034, BBa_B0010, BBa_B0012(previous parts) and BBa_K2721029(new part) which codes for HRP, SnoopTag and SdyCatcher. Flanked by SnoopTag and SdyCatcher, HRP can be connected with the other two enzymes to form multienzyme complex. We obtain the original DNA sequence of HRP, SnoopTag and SdyCatcehr from the references below[2][3][4]. After optimizing and synthesizing, we cloned the target sequence into vector PET-26b(+) and successfully detected the production. </p>
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<p style="padding-left: 2em !important; margin-bottom: .7em !important;">CsgA is the monomer of curli, which is an important component of excellular matrix of Enterobacteriaceae[1]. Curli fibers are involved in adhesion to surfaces, cell aggregation, and biofilm formation, they are also used for studies of amyloid fiber formation in human diseases, such as Alzheimer’s, Huntington’s, and prion diseases. </p>
<span class="psg_ttl"></br>Result</span>
+
<p style="padding-left: 2em !important; margin-bottom: .7em !important;">In consideration of curli is an important component of excellular matrix and biofilms, confer diverse artificial functions to the biofilm matrix, such as nanoparticle biotemplating, substrate adhesion, covalent immobilization of proteins or a combination thereof.to the biofilm matrix.[2]In our project, we modified csgA to construct a brand new enzyme fixation matrix or surface display platform, which works as expected and proved the great biological potential.Furthermore, the cell-surface display has many potential applications, including biodegradation,live vaccine development, peptide library screening, bioconversion using whole cell biocatalyst and bioadsorption. </p>
<img style="width: 80% !important;" src="https://static.igem.org/mediawiki/2018/1/19/T--ZJU-China--Part01.png" />
+
<p style="padding-left: 2em !important; margin-bottom: .7em !important;">In short, csgA provides huge potentials for future igem communicity and we are so glad to see the future application! </p>
<h5><span style="width: 5% !important; vertical-align: top;">Fig. 1 </span><span style="width: 92% !important; text-align: left !important; padding-left: 3% !important;">SdyCatcher-HRP-SnoopTag| (A) SDS-PAGE, Lane M1 is protein marker, Lane 1 is BSA (2.00 &micro;g), Lane 2 is SdyCatcher-HRP-SnoopTag. (B) Western Blot, Lane M2 is protein marker, Lane 3 is SdyCatcher-HRP-SnoopTag.</span></h5>
+
 
<p style="margin-top: .9em !important;">Besides, we used BSA Standard Curve to qualifity the expression of SdyCatcher-HRP-SnoopTag. </p>
+
 
<img style="width: 60% !important;" src="https://static.igem.org/mediawiki/2018/d/d4/T--ZJU-China--Part02.png" />
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<span class="psg_ttl">Design </span>
<h5>Fig. 2 Standard curve for Bradford assay</h5>
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<p style="padding-left: 2em !important; margin-bottom: .7em !important;">This year we made use of the design of cell-surface display and modified the csgA protein by fusing spytag to the N-terminal, making it a dorable platform to form enzyme complex and increasd the electrical conductivity because of the histag in the C-terminal. Therefore, we finally constructed our available platform for protein scaffolding, which has been proved more stronger to fix enzymes on electrodes. </p>
<table class="table" style="font-family: 'trebuchet ms'; border: 1px solid black !important;">
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<span class="psg_ttl">Approach and Results </span>
<thead style="background-color: #3b3737 !important;"><tr>
+
<p style="padding-left: 2em !important; margin-bottom: .7em !important;">Cango Red(CR) dye plates and deletion assay shows success induction of over-expressing and the amploid protein characteristic.To see the results, please click here to change to part page.</p>
<th><p style=" font-weight: normal !important; color: white !important;">Sample</p></th>
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<th><p style=" font-weight: normal !important; color: white !important;">OD595</p></th>
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<img style="width: 80% !important;" src="https://static.igem.org/mediawiki/2018/d/dc/T--ZJU-China--matrix5.png" />
<th><p style=" font-weight: normal !important; color: white !important;">Concentration</p></th>
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<h5><h5 style="vertical-align: top; width: 5% !important; display: inline-block;">Fig. 1</h5><h5 style="font-weight: 300 !important; text-align: left; padding-left: 2% !important; width: 93% !important; display: inline-block;"><span style="font-weight: bolder !important;">Quantitative Congo Red (CR) Binding Assays to verify the successful expression of Curli. (A) a is a wild-type E.coli strain that normally expresses csgA protein. b is the PHL628-△csgA cells (csgA knock out) strain. It can be seen that there is almost no expression of csgA after knocking out.  (B) a is the wild type strain, b is the csgA overexpressing strain (a plasmid carrying a csga protein is expressed in wild type E.coli), and c is the csga KO cell. By adding Congo red dye to the bacteria mixture, centrifugation and shaking, we can compare the expression level of curli by observing the color depth of the precipitate.  (C) Figure C is an inverted view of the EP tube in Figure B, showing the color of the sediment at the bottom of the centrifuge tube. a – WT.  b – csgA KO, c – csgA overexpressing.</h5></h5>
</tr></thead>
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<tbody >
+
 
<tr>
+
 
<td style="background-color: #afaaaa !important; font-weight: lighter !important;"><p>SdyCatcher-HRP-SnoopTag</p></td>
+
 
<td style="font-weight: lighter !important;"><p>0.398</p></td>
+
 
<td style="font-weight: lighter !important;"><p>0.80mg/ml</p></td>
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</tr>
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</tbody>
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</table>
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<h5>Table. 1  qualification result of three complex.</h5>
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<span class="psg_ttl"></br>References</span>
 
<span class="psg_ttl"></br>References</span>
<p style=" padding-left: .9em !important;"><span style="width: 5% !important; display: inline-block; vertical-align: top;">[1]</span><span style="width: 93% !important; display: inline-block; text-align: left;">Zakeri (B) Fierer JO, Celik E, Chittock EC, Schwarz-Linek U, Moy VT, Howarth M. Peptide tag forming a rapid covalent bond to a protein, through engineering a bacterial adhesin. Proc Natl Acad Sci U S A. 2012 Mar 20;109(12):E690-7.</span></p>
+
<p style=" padding-left: .9em !important;"><span style="width: 5% !important; display: inline-block; vertical-align: top;">[1]</span><span style="width: 93% !important; display: inline-block; text-align: left;">Barnhart, M.M. and M.R. Chapman, Curli Biogenesis and Function - Annual Review of Microbiology, 60(1):131. Amyloid Cellulose Enteric Biofilm Extracellular Matrix.</span></p>
<p style=" padding-left: .9em !important;"><span style="width: 5% !important; display: inline-block; vertical-align: top;">[2]</span><span style="width: 93% !important; display: inline-block; text-align: left;">Veggiani G, Nakamura T, Brenner MD, Gayet RV, Yan J, Robinson CV, Howarth M.Programmable polyproteams built using twin peptide superglues. Proc Natl Acad Sci U S A. 2016 Feb 2;113(5):1202-7.</span></p>
+
<p style=" padding-left: .9em !important;"><span style="width: 5% !important; display: inline-block; vertical-align: top;">[2]</span><span style="width: 93% !important; display: inline-block; text-align: left;">Nguyen, P.Q., et al., Programmable biofilm-based materials from engineered curli nanofibres. Nature Communications, 2014. 5: p. 4945.</span></p>
<p style=" padding-left: .9em !important;"><span style="width: 5% !important; display: inline-block; vertical-align: top;">[3]</span><span style="width: 93% !important; display: inline-block; text-align: left;">Tan LL, Hoon SS, Wong FT. Kinetic Controlled Tag-Catcher Interactions for Directed Covalent Protein Assembly. PLoS ONE 11(10): e0165074. </span></p>
+
<p style=" padding-left: .9em !important;"><span style="width: 5% !important; display: inline-block; vertical-align: top;">[4]</span><span style="width: 93% !important; display: inline-block; text-align: left;">Edwards,R. SYNTHETIC GENE. British Bio-Technology Ltd.</span></p>
+
<p style=" padding-left: .9em !important;"><span style="width: 5% !important; display: inline-block; vertical-align: top;">[5]</span><span style="width: 93% !important; display: inline-block; text-align: left;">P Hengen. Purification of His-Tag fusion proteins from Escherichia coli. Trends in Biochemical Sciences, 1995,20(7): 285-286.</span></p>
+
 
</br></br>
 
</br></br>
 
</div>
 
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Latest revision as of 23:56, 17 October 2018

<!DOCTYPE html>

BEST BASIC PART  
  


Usage and Biology

CsgA is the monomer of curli, which is an important component of excellular matrix of Enterobacteriaceae[1]. Curli fibers are involved in adhesion to surfaces, cell aggregation, and biofilm formation, they are also used for studies of amyloid fiber formation in human diseases, such as Alzheimer’s, Huntington’s, and prion diseases.

In consideration of curli is an important component of excellular matrix and biofilms, confer diverse artificial functions to the biofilm matrix, such as nanoparticle biotemplating, substrate adhesion, covalent immobilization of proteins or a combination thereof.to the biofilm matrix.[2]In our project, we modified csgA to construct a brand new enzyme fixation matrix or surface display platform, which works as expected and proved the great biological potential.Furthermore, the cell-surface display has many potential applications, including biodegradation,live vaccine development, peptide library screening, bioconversion using whole cell biocatalyst and bioadsorption.

In short, csgA provides huge potentials for future igem communicity and we are so glad to see the future application!

Design

This year we made use of the design of cell-surface display and modified the csgA protein by fusing spytag to the N-terminal, making it a dorable platform to form enzyme complex and increasd the electrical conductivity because of the histag in the C-terminal. Therefore, we finally constructed our available platform for protein scaffolding, which has been proved more stronger to fix enzymes on electrodes.

Approach and Results

Cango Red(CR) dye plates and deletion assay shows success induction of over-expressing and the amploid protein characteristic.To see the results, please click here to change to part page.

Fig. 1
Quantitative Congo Red (CR) Binding Assays to verify the successful expression of Curli. (A) a is a wild-type E.coli strain that normally expresses csgA protein. b is the PHL628-△csgA cells (csgA knock out) strain. It can be seen that there is almost no expression of csgA after knocking out. (B) a is the wild type strain, b is the csgA overexpressing strain (a plasmid carrying a csga protein is expressed in wild type E.coli), and c is the csga KO cell. By adding Congo red dye to the bacteria mixture, centrifugation and shaking, we can compare the expression level of curli by observing the color depth of the precipitate. (C) Figure C is an inverted view of the EP tube in Figure B, showing the color of the sediment at the bottom of the centrifuge tube. a – WT. b – csgA KO, c – csgA overexpressing.

References

[1]Barnhart, M.M. and M.R. Chapman, Curli Biogenesis and Function - Annual Review of Microbiology, 60(1):131. Amyloid Cellulose Enteric Biofilm Extracellular Matrix.

[2]Nguyen, P.Q., et al., Programmable biofilm-based materials from engineered curli nanofibres. Nature Communications, 2014. 5: p. 4945.