Difference between revisions of "Part:BBa K2916029"
 
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<partinfo>BBa_K2916029 short</partinfo>
 
<partinfo>BBa_K2916029 short</partinfo>
  
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This part is used for expression of SerRS needed for the PURE and OnePot PURE cell-free systems.
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This part is used for expression of Seryl-tRNA synthetase (SerRS) needed for the OnePot PURE cell-free system.
  
 
<!-- 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===
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===Biology===
 +
 
 +
Transfer RNA (tRNA) is the molecule that enables the Genetic Code contained in the nucleotide sequence of a messenger RNA (mRNA) molecule to be translated into the amino acid sequence of a polypeptide chain. This function is catalysed by a group of enzymes called aminoacyl-tRNA synthetase (aaRS) which attach the appropriate amino acid onto its tRNA. This group consists of 20 different types of aminoacyl-tRNA synthetases, one for each amino acid of the genetic code. Those enzymes, in presence of Adenosine triphosphate (ATP) and Amino Acids, produces aminoacyl-tRNA (tRNA charged with an Amino Acid) that can be used by the ribosome to transfer the amino acid from the tRNA to the polypeptide being synthesised, according of course to the genetic code.
 +
Aminoacyl-tRNA therefore play a major role in RNA translation.
 +
 
 +
 
 +
Seryl-tRNA synthetase (SerRS) attaches to Serine (codons: UCU, UCC, UCA, UCG, AGU and AGC)
 +
 
 +
In our part, besides the sequence encoding for the protein we also have a hexahistidine-tag to allow us purify the protein.
 +
 
 +
 
 +
===Usage===
 +
 
 +
In our project we used SerRS as a part of the protein solution needed for <html><a style="padding: 0px; margin: 0px;" href="https://2019.igem.org/Team:EPFL/OnePot_Pure"> OnePot PURE cell-free system </a></html> using the method of gravity flow affinity chromatography, as described in the <html><a style="padding: 0px; margin: 0px;" href="https://www.protocols.io/view/protein-purification-for-onepot-pure-cell-free-sys-8auhsew"> protocol </a></html> we designed.
 +
 
 +
 
 +
 
 +
 
 +
===Characterization===
 +
 
 +
=='''Expression and purification of SerRS'''==
 +
 
 +
<br/>
 +
 
 +
SerRS is one of the proteins we used for the OnePot PURE cell-free system. We expressed it in BL21(DE3) E.coli strain using a pET21a vector. The expression system has a T7 promoter, a lac operator, RBS and a T7 Terminator, enabling us to regulate the expression with IPTG.<br/><br/>
 +
'''Methods'''
 +
<br/>
 +
 
 +
SerRS was purified using our <html><a style="padding: 0px; margin: 0px;" href="https://www.protocols.io/view/protein-purification-for-onepot-pure-cell-free-sys-8auhsew"> protocol </a></html>. To test if the protein was actually expressed, we performed a SDS-PAGE that is presented below. On the left side we can see the results included in the initial OnePot PURE paper (<i>Lavickova et al, 2019</i>) while on the right (batch1_a,b and batch2_a,b) are the solutions we produced ourselves. (The procedure we followed and the conditions of the experiment can be found <html><a style="padding: 0px; margin: 0px;" href="https://www.protocols.io/view/sps-page-protein-electrophoresis-775hrq6"> here</a></html>).
 +
<br/>
 +
 
 +
<html>
 +
<figure style="text-align:center;">
 +
                <img style="max-width:700px;" src="https://2019.igem.org/wiki/images/b/bb/T--EPFL--ProteinMolec.png" alt="control">
 +
                <figcaption><b>Figure 1:</b> SDS-PAGE of OnePot PURE protein solution.</figcaption>
 +
              </figure>
 +
</html>
 +
 
 +
'''Conclusion'''
 +
<br/> SerRS has a molecular weight of around 49kDa, but even though we cannot be absolutely sure if the band shown is only due to it, we may assume that it is expressed. To verify the existence and functionality of this protein we need to proceed with more experiments that would be mainly focused on the efficiency of the system.
 +
<br/>
 +
<br/>
 +
 
 +
=='''OnePot PURE functionality test'''==
 +
 
 +
 
 +
<br/>
 +
To make sure that we have all the proteins in our OnePot PURE protein solution, and that they all function properly we need check if proteins can be expressed in our OnePot PURE cell-free system. <br/>
 +
 
 +
'''Methods'''<br/>
 +
 
 +
We expressed <html><a style="padding: 0px; margin: 0px;" href="https://parts.igem.org/Part:BBa_I746909"> superfolding GFP</a></html> following the <html><a style="padding: 0px; margin: 0px;" href="https://www.protocols.io/view/protein-expression-in-onepot-pure-cell-free-system-8avhse6"> protocol</a></html> we designed in 10μl reactions, and measured the fluorescence on a plate reader at excitation wavelength of 535nm. We tested the expression using different concentrations of the sf GFP DNA template and also compared it with the fluorescence produced in PURExpress from NEB.
 +
<br/>
 +
 
 +
 
 +
<html>
 +
<figure style="text-align:center;">
 +
                <img style="max-width:700px;" src="https://2019.igem.org/wiki/images/b/b2/T--EPFL--resultsOnePot10.png" alt="control">
 +
                <figcaption><b>Figure 2:</b> sf GFP expression using 10nM DNA template.</figcaption>
 +
              </figure>
 +
</html>
 +
<html>
 +
<figure style="text-align:center;">
 +
                <img style="max-width:700px;" src="https://2019.igem.org/wiki/images/7/75/T--EPFL--resultsOnePot5.png" alt="control">
 +
                <figcaption><b>Figure 3:</b> sf GFP expression using 5nM DNA template.</figcaption>
 +
              </figure>
 +
</html>
 +
<html>
 +
<figure style="text-align:center;">
 +
                <img style="max-width:700px;" src="https://2019.igem.org/wiki/images/e/e7/T--EPFL--resultsOnePot25.png" alt="control">
 +
                <figcaption><b>Figure 4:</b> sf GFP expression using 2.5nM DNA template.</figcaption>
 +
              </figure>
 +
</html>
 +
<html>
 +
<figure style="text-align:center;">
 +
                <img style="max-width:700px;" src="https://2019.igem.org/wiki/images/7/70/T--EPFL--resultsOnePot.png" alt="control">
 +
                <figcaption><b>Figure 5:</b> Comparison between OnePot PURE and PURExpress at saturation.</figcaption>
 +
              </figure>
 +
</html>
 +
 
 +
'''Conclusion'''
 +
<br/> The expression was successful so we can confirm that SerRS exists in our protein solution and is also functioning properly.
 +
<br/>
  
−
Used in OnePot PURE
 
  
  

Latest revision as of 01:31, 22 October 2019


Expression of SerRS in E.coli

This part is used for expression of Seryl-tRNA synthetase (SerRS) needed for the OnePot PURE cell-free system.


Biology

Transfer RNA (tRNA) is the molecule that enables the Genetic Code contained in the nucleotide sequence of a messenger RNA (mRNA) molecule to be translated into the amino acid sequence of a polypeptide chain. This function is catalysed by a group of enzymes called aminoacyl-tRNA synthetase (aaRS) which attach the appropriate amino acid onto its tRNA. This group consists of 20 different types of aminoacyl-tRNA synthetases, one for each amino acid of the genetic code. Those enzymes, in presence of Adenosine triphosphate (ATP) and Amino Acids, produces aminoacyl-tRNA (tRNA charged with an Amino Acid) that can be used by the ribosome to transfer the amino acid from the tRNA to the polypeptide being synthesised, according of course to the genetic code. Aminoacyl-tRNA therefore play a major role in RNA translation.


Seryl-tRNA synthetase (SerRS) attaches to Serine (codons: UCU, UCC, UCA, UCG, AGU and AGC)

In our part, besides the sequence encoding for the protein we also have a hexahistidine-tag to allow us purify the protein.


Usage

In our project we used SerRS as a part of the protein solution needed for OnePot PURE cell-free system using the method of gravity flow affinity chromatography, as described in the protocol we designed.



Characterization

Expression and purification of SerRS


SerRS is one of the proteins we used for the OnePot PURE cell-free system. We expressed it in BL21(DE3) E.coli strain using a pET21a vector. The expression system has a T7 promoter, a lac operator, RBS and a T7 Terminator, enabling us to regulate the expression with IPTG.

Methods

SerRS was purified using our protocol . To test if the protein was actually expressed, we performed a SDS-PAGE that is presented below. On the left side we can see the results included in the initial OnePot PURE paper (Lavickova et al, 2019) while on the right (batch1_a,b and batch2_a,b) are the solutions we produced ourselves. (The procedure we followed and the conditions of the experiment can be found here).

control
Figure 1: SDS-PAGE of OnePot PURE protein solution.

Conclusion
SerRS has a molecular weight of around 49kDa, but even though we cannot be absolutely sure if the band shown is only due to it, we may assume that it is expressed. To verify the existence and functionality of this protein we need to proceed with more experiments that would be mainly focused on the efficiency of the system.

OnePot PURE functionality test


To make sure that we have all the proteins in our OnePot PURE protein solution, and that they all function properly we need check if proteins can be expressed in our OnePot PURE cell-free system.

Methods

We expressed superfolding GFP following the protocol we designed in 10μl reactions, and measured the fluorescence on a plate reader at excitation wavelength of 535nm. We tested the expression using different concentrations of the sf GFP DNA template and also compared it with the fluorescence produced in PURExpress from NEB.


control
Figure 2: sf GFP expression using 10nM DNA template.
control
Figure 3: sf GFP expression using 5nM DNA template.
control
Figure 4: sf GFP expression using 2.5nM DNA template.
control
Figure 5: Comparison between OnePot PURE and PURExpress at saturation.

Conclusion
The expression was successful so we can confirm that SerRS exists in our protein solution and is also functioning properly.


Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 1440
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal SapI.rc site found at 194