Difference between revisions of "Part:BBa K1934020"
 
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<partinfo>BBa_K1934020 short</partinfo>
 
<partinfo>BBa_K1934020 short</partinfo>
  
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This part contains the sequence coding for the streptavidin protein linked to two cellulose binding domains, one located in C and one located in N-terminal.
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This part contains the sequence coding for the streptavidin protein linked to two cellulose-binding domains, one located at the N-terminus ([[Part:BBa_K1934080|CBD1 - BBa_K1934080]]) and one located at the C-terminus ([[Part:BBa_K1934090|CBD2 - BBa_K1934090]]) of the protein sequence.
  
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Streptavidin is a 52,8 kDa protein which has the ability to bind to biotin with high affinity. Indeed, this can be explained by its structure and the formation of an extensive network of intramolecular interactions when biotin is in the binding site. This strong noncovalent link is used in many biotechnologies especially in purification and detection assays. The combination of streptavidin with other proteins thus enables to confer new properties such as a cellulose-binding activity with the integration of two CBDs [1]. The part [[Part:BBa_K1499004-BBa_K1499004]] was submitted to the iGEM registry in 2014 but without any experimental data. Therefore, the part BBa_K1934020 was designed as a streptavidin-CBDs generator.
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<p>Streptavidin is a 52.8 kDa protein which has the ability to bind to biotin with high affinity. Indeed, this can be explained by its structure and the formation of an extensive network of intramolecular interactions when biotin is in the binding site. This strong noncovalent link is used in many biotechnologies especially in purification and detection assays. The combination of streptavidin with other proteins moreover enables to confer new properties such as a cellulose-binding activity with the integration of two CBDs<sup>[1]</sup>. The part [[Part:BBa_K1499004|BBa_K1499004]], cellulose binding domains with streptavidin domain generator, was submitted to the iGEM registry in 2014, but was missing transcriptional and translational signals, and  experimental data. Therefore, the part BBa_K1934020 was designed as a complete streptavidin-CBDs generator displaying a promoter, RBS and terminator. </p>
  
 
[1] Bayer, E. A., Chanzy, H., Lamed, R., & Shoham, Y. (1998). Cellulose, cellulases and cellulosomes. Current opinion in structural biology, 8(5), 548-557.
 
[1] Bayer, E. A., Chanzy, H., Lamed, R., & Shoham, Y. (1998). Cellulose, cellulases and cellulosomes. Current opinion in structural biology, 8(5), 548-557.
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<h3 id="CBD">Purification Using Cellulose Affinity</h3>
 
<h3 id="CBD">Purification Using Cellulose Affinity</h3>
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<p>The BBa_K1934020 part conceived by the 2016 INSA-Lyon team and synthesized by IDT was cloned into pSB1C3 and transformed into the  E. <i>coli</i> NM522 strain. One recombinant clone was grown overnight in LB at 24°C, with IPTG 1 mM and glucose 5 mM. Cells were harvested and resuspended in 1 mL lysis buffer (50 mM Tris, 300 mM NaCl, 10% glycerol). Then the mix was sonicated 5 times 30 seconds on ice at moderate power. The lysate was centrifuged at 14.000 g for 10 min. The supernatant was treated as follow:   
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<p>The BBa_K1934020 part conceived by the 2016 INSA-Lyon team and synthesized by IDT was cloned into pSB1C3 and transformed into the  <i>E. coli</i> NM522 strain. One recombinant clone was grown overnight in LB at 24°C, with IPTG 1 mmol.L<sup>-1</sup> and glucose 5 mmol.L<sup>-1</sup>. Cells were harvested and resuspended in 1 mL lysis buffer (50 mmol.L<sup>-1</sup> Tris, 300 mmol.L<sup>-1</sup> NaCl, 10% glycerol). Then the mix was sonicated 5 times 30 seconds on ice at moderate power. The lysate was centrifuged at 14,000 g for 10 min. The supernatant was treated as follow:   
 
<ul style="list-style-type:circle">
 
<ul style="list-style-type:circle">
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   <li>Wash microcrystaline Cellulose five time in water. Then equilibrate in wash buffer (Amonium Sulfate 1M). Pack the cellulose (10x10 mm) in small chromatography columns (we used syringes barrels). </li>
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   <li>Wash microcrystalline cellulose five times in water. Then equilibrate in washing buffer (ammonium sulfate 1 mol.L<sup>-1</sup>). Pack the cellulose (10x10mm) in small chromatography columns (we used syringes barrels).</li>
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   <li> Gently pour the lysate supernatant on the column. Once the liquid starts to flow out regularly measure the OD280 of the different fractions. Continue pouring wash buffer until the OD280 stabilizes around zero. </li>
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   <li>Gently pour the lysate supernatant on the column. Once the liquid starts flowing through evenly, measure the OD<sub>280</sub> of the different fractions. Continue pouring washing buffer until the OD<sub>280</sub>  stabilizes around zero.</li>
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   <li> Change the washing buffer to water. OD280 shortly rises. Keep the fractions with highest OD280. They should contain the protein. </li>
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   <li>Change the washing buffer to water. OD<sub>280</sub>  shortly rises. Keep the fractions with the highest OD<sub>280</sub>. They should contain the protein.</li>
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<li> Analyse collected fractions on an SDS PAGE.  
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  <li>Analyse collected fractions on an SDS-PAGE.</li></ul>
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Optionally, proteins may be concentrated using ultrafiltration.</li>
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Optionally, proteins may be concentrated using ultrafiltration.
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</ul></p>  
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</p>  
  
  
  
  
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<figure><p style="text-align:center;"><img src="https://static.igem.org/mediawiki/2016/8/8b/INSA-Lyon_SCBD_elution.jpeg" width = "800"/><figcaption><b>Figure 1. Purification of the chimeric Streptavidin-CBD protein on a cellulose column</b> This elution graph shows a first peak, present for both the control and our expression culture.This first peak corresponds to unbound proteins. In presence of water, only one peak was observed: it’s the elution peak of our protein. </figcaption></figure>
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<figure><p style="text-align:center;"><img src="https://static.igem.org/mediawiki/parts/b/b3/INSA-Lyon_SCBD-NM522.jpg" width = "800"/><figcaption><b>Figure 1. Purification of the chimeric Streptavidin-CBD protein on a cellulose column.</b> This elution graph shows a first peak, present for both the control and our expression culture. This first peak corresponds to unbound proteins. In the presence of water, only one peak was observed: it’s the elution peak of our protein.</figcaption></figure>
  
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<h3 id="RT">2. BBa_K1934020 encodes a protein able to bind both biotin and cellulose</h3>
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<h3 id="RT">2. BBa_K1934020 encodes a protein able to bind both biotin and cellulose</h3>
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<figure><p style="text-align:center;"><img src= "https://static.igem.org/mediawiki/2016/f/f2/INSA-Lyon_principle_SCBD.jpeg" width = "400"/><figcaption>
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<figure><p style="text-align:center;"><img src= "https://static.igem.org/mediawiki/2016/f/f2/INSA-Lyon_principle_SCBD.jpeg" width = "400"/></figure>
  
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The  affinity to cellulose of the CBD-streptavidin encoded by BBa_K1934020 was compared to the one of commercial streptavidin. A molecule of Fluorescein was grafted at the 5’ end of a DNA oligo  carrying a molecule of biotin at its 3’ end. This DNA oligo constitutes the reporter system. Such modified oligo was mixed either with the engineered streptavidin-CBD or with commercial Streptavidin. The resulting mix was incubated with microcrystalline cellulose in presence of PBS for 1 hour.The cellulose was then washed twice with fresh PBS and the fluorescence was measured. Every experiment was done in triplicate.  
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Affinity of the streptavidin-CBD encoded by BBa_K1934020 to cellulose was compared to the one of commercial streptavidin. A molecule of fluorescein was grafted at the 5’ end of a DNA oligo  carrying a molecule of biotin at its 3’ end. This DNA oligo constitutes the reporter system. Such modified oligo was mixed either with the engineered streptavidin-CBD or with commercial streptavidin. The resulting mix was incubated with microcrystalline cellulose in presence of PBS for 1 hour. The cellulose was then washed twice with fresh PBS and fluorescence was measured. Every experiment was done in triplicate.  
  
  
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<figure><p style="text-align:center;"><img src= "https://static.igem.org/mediawiki/2016/f/fa/INSA-Lyon_SCBD_linking.jpeg" width = "400"/><figcaption><b>Figure 2. The Streptavidin-CBD  is able to bind biotin and cellulose.</b> The raw cellulose mixed with our report system shows no fluorescence (first bar). The measured fluorescence indicates that commercial streptavidin was able to bind our reporter system and sticks at a low extent to cellulose. We conclude that this results from none-specific adsorption. For the CBD-Streptavidin part (BBa_K1934020), a high fluorescent signal was recorded. </figcaption></figure>
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<figure><p style="text-align:center;"><img src= "https://static.igem.org/mediawiki/2016/f/fa/INSA-Lyon_SCBD_linking.jpeg" width = "400"/><figcaption><b>Figure 2. The Streptavidin-CBD  is able to bind biotin and cellulose.</b> Mixed raw cellulose with our report system shows no fluorescence (first bar). The measured fluorescence indicates that commercial streptavidin was able to bind our reporter system and sticks at a low extent to cellulose. We concluded that this results from non-specific adsorption. For the streptavidin-CBD part (BBa_K1934020), a high fluorescent signal was recorded. </figcaption></figure>
 
<strong>This experiment shows that this streptavidin-CBD protein is able to bind efficiently biotin and cellulose at the same time. </strong>
 
<strong>This experiment shows that this streptavidin-CBD protein is able to bind efficiently biotin and cellulose at the same time. </strong>
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The same experiment was done for the <a href="https://parts.igem.org/Part:BBa_K1934030">BBa_K1934030</a>: part (using a different cellulose binding domain: CBD-CipA,). The binding efficiency of streptavidin-CBDs tend to be slightly lower compared to streptavidin-CipA (x1,1) but was not statistically demonstrated.  
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The same experiment was done for the <a href="https://parts.igem.org/Part:BBa_K1934030">BBa_K1934030</a>: part displaying a different cellulose binding domain, namely CBD-CipA. The binding efficiency of streptavidin-CBDs tends to be slightly lower compared to streptavidin-CipA (x1.1) but was not statistically demonstrated.  
  
 
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Latest revision as of 16:29, 25 October 2016

Streptavidin with Cellulose Binding Domains (CBDs)

This part contains the sequence coding for the streptavidin protein linked to two cellulose-binding domains, one located at the N-terminus (CBD1 - BBa_K1934080) and one located at the C-terminus (CBD2 - BBa_K1934090) of the protein sequence.

Streptavidin is a 52.8 kDa protein which has the ability to bind to biotin with high affinity. Indeed, this can be explained by its structure and the formation of an extensive network of intramolecular interactions when biotin is in the binding site. This strong noncovalent link is used in many biotechnologies especially in purification and detection assays. The combination of streptavidin with other proteins moreover enables to confer new properties such as a cellulose-binding activity with the integration of two CBDs[1]. The part BBa_K1499004, cellulose binding domains with streptavidin domain generator, was submitted to the iGEM registry in 2014, but was missing transcriptional and translational signals, and experimental data. Therefore, the part BBa_K1934020 was designed as a complete streptavidin-CBDs generator displaying a promoter, RBS and terminator.

[1] Bayer, E. A., Chanzy, H., Lamed, R., & Shoham, Y. (1998). Cellulose, cellulases and cellulosomes. Current opinion in structural biology, 8(5), 548-557.

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 779
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal NgoMIV site found at 380
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal SapI.rc site found at 727

Characterization

Purification Using Cellulose Affinity

The BBa_K1934020 part conceived by the 2016 INSA-Lyon team and synthesized by IDT was cloned into pSB1C3 and transformed into the E. coli NM522 strain. One recombinant clone was grown overnight in LB at 24°C, with IPTG 1 mmol.L-1 and glucose 5 mmol.L-1. Cells were harvested and resuspended in 1 mL lysis buffer (50 mmol.L-1 Tris, 300 mmol.L-1 NaCl, 10% glycerol). Then the mix was sonicated 5 times 30 seconds on ice at moderate power. The lysate was centrifuged at 14,000 g for 10 min. The supernatant was treated as follow:

  • Wash microcrystalline cellulose five times in water. Then equilibrate in washing buffer (ammonium sulfate 1 mol.L-1). Pack the cellulose (10x10mm) in small chromatography columns (we used syringes barrels).
  • Gently pour the lysate supernatant on the column. Once the liquid starts flowing through evenly, measure the OD280 of the different fractions. Continue pouring washing buffer until the OD280 stabilizes around zero.
  • Change the washing buffer to water. OD280 shortly rises. Keep the fractions with the highest OD280. They should contain the protein.
  • Analyse collected fractions on an SDS-PAGE.
Optionally, proteins may be concentrated using ultrafiltration.

Figure 1. Purification of the chimeric Streptavidin-CBD protein on a cellulose column. This elution graph shows a first peak, present for both the control and our expression culture. This first peak corresponds to unbound proteins. In the presence of water, only one peak was observed: it’s the elution peak of our protein.

2. BBa_K1934020 encodes a protein able to bind both biotin and cellulose

Affinity of the streptavidin-CBD encoded by BBa_K1934020 to cellulose was compared to the one of commercial streptavidin. A molecule of fluorescein was grafted at the 5’ end of a DNA oligo carrying a molecule of biotin at its 3’ end. This DNA oligo constitutes the reporter system. Such modified oligo was mixed either with the engineered streptavidin-CBD or with commercial streptavidin. The resulting mix was incubated with microcrystalline cellulose in presence of PBS for 1 hour. The cellulose was then washed twice with fresh PBS and fluorescence was measured. Every experiment was done in triplicate.

Figure 2. The Streptavidin-CBD is able to bind biotin and cellulose. Mixed raw cellulose with our report system shows no fluorescence (first bar). The measured fluorescence indicates that commercial streptavidin was able to bind our reporter system and sticks at a low extent to cellulose. We concluded that this results from non-specific adsorption. For the streptavidin-CBD part (BBa_K1934020), a high fluorescent signal was recorded.
This experiment shows that this streptavidin-CBD protein is able to bind efficiently biotin and cellulose at the same time. The same experiment was done for the BBa_K1934030: part displaying a different cellulose binding domain, namely CBD-CipA. The binding efficiency of streptavidin-CBDs tends to be slightly lower compared to streptavidin-CipA (x1.1) but was not statistically demonstrated.