Team:Washington/Our Project

From 2014.igem.org

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   <h1> Background </h1>
   <h1> Background </h1>
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<p align = left> New novel methods must be first tested for viability against other existing methods. Our project is no different. In order, to gauge the effectiveness and accuracy of our method we
 +
choose test proteins that are well studied and characterized. Therefore, Bindi and several of its mutant variants that have been well studied were choosen. The first step of our
 +
project was to replicate the results of the studies on Bindi and its variants by repeating the stability test experiments presented in "the paper." After verifying the results
 +
of "the paper", we proceeded to construct our degron protein constructs and expressed them in yeast cells containing an inducible mechanism for the expression of green fluorescence
 +
protein.Subsequently, the fluorescent emission of each cell is measured as higher fluorescent corresponds to higher test protein stability. </p>
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 +
  <h2> Our System </h2>
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<h3> Components of the Degron Construct </h3>
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<h3> Test Protein </h3>
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   <h1> Our System </h1>
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   <h2> Method </h2>
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  <h1> Method </h1>
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  <p align =left> The essential process of our system involves cloning and manufacturing of a plasmid in <i> E.coli </i>. Once, the plasmids have been constructed and verified in <i> E.Coli </i>
 +
they are transformed into <i>S.Cerevisiae</i>. The plasmid constructs are then expressed. Following several days of growth the yeast cultures are passed through a flow cytometer
 +
and the fluorescence of each cell is measured. Higher fluorescence is associated with higher expression of the protein of interest which in-turn is indicative of higher protein
 +
stability. </p>
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<h3> Analysis of Test Protein Stability </h3>
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<h3> Analysis of Test Protein Stability using established methods</h3>
<h3> Cloning in <i> Escherichia coli </i> </h3>
<h3> Cloning in <i> Escherichia coli </i> </h3>
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<p align = left> There are five possible degron constructs corresponding to five different positions the degron can take in our construct. The first step is to insert our protein into each
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      <h3> Preparation and Passaging of <i> Saccharomyces cerevisiae </i> </h3>
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of the five constructs and verify it. </p>
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 +
<h3> Preparation and Passaging of <i> Saccharomyces cerevisiae </i> </h3>
 +
<p align = left> Once, plasmids of the five possible degron constructs have been cloned with our three test proteins, they are subsequently transformed in PYE1 a strain of
 +
<i> S. Cerevisiae </i> with the ability to produce green fluorescent proteins with the proper promoter protein such as Gal4 which is a part of our degron construct.
 +
Following the transformation, the cells are plated onto plates with on a  Selective Dropout C-Uracil media and incubated at 30<sup>o</sup>C for 2 days. After two days, three
 +
colonies are choosen and added to an overnight culture of 3mL Selective Dropout Media C-Uracil and 2% Glucose then incuabted for another two days at 30<sup>o</sup>C.
 +
After two days of incubation, a 20-50uL aliquot of each culture is "passaged" into another 3mL culture prepared in the same manner as before and incubated for the same
 +
duration and temperature as the previous culture. The passaging is done several times after each passage after the second passage, a glycerol stock is prepare from the
 +
culture and flow cytometry is run on the culture.</p>
 +
<p align = left> The purpose of passaging is to gradually remove excess copies of the plasmid constructs. Excess copies, exceeding one per cell will lead to multiple fold increase in the
 +
expression of the degron protein construct. As a result of this, GFP expression will also be increased thus reducing the viability and accuracy of the Flow Cytometry
 +
measurements conducted on each cell culture.</p> 
 +
 
       <h3> Relative Stability Analyzed via Flow Cytometry </h3>
       <h3> Relative Stability Analyzed via Flow Cytometry </h3>
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       <h3> Mutagenesis through Error Prone Polymerase Chain Reactions </h3>
       <h3> Mutagenesis through Error Prone Polymerase Chain Reactions </h3>
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   <h1> Results </h1>
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   <h2> Results </h2>
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<h3> Protein stability analysis using Thermal and Guanadinium HCl melts </h3>
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<h3> Protein stability analysis using Thermal and Guanidinium Hydrogen Chloride melts </h3>
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<h3> Protein stability analysis using Degron Constructs and Flow Cytometry </h3>
<h3> Protein stability analysis using Degron Constructs and Flow Cytometry </h3>
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<h3> Mutagenesis Results and Mutant Variant Analysis</h3>
<h3> Mutagenesis Results and Mutant Variant Analysis</h3>
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   <h1> Future Plans </h1>
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   <h2> Future Plans </h2>
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        <h1> Examination of more proteins </h1>
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<h3> Examination of more proteins </h3>
 +
 +
<h3> Further evolving more stable variants of existing proteins </h3>
            
            
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   <h1> Submitted Parts </h1>
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   <h2> Submitted Parts </h2>
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Revision as of 22:17, 9 October 2014

UW Homepage Official iGEM website

Background

New novel methods must be first tested for viability against other existing methods. Our project is no different. In order, to gauge the effectiveness and accuracy of our method we choose test proteins that are well studied and characterized. Therefore, Bindi and several of its mutant variants that have been well studied were choosen. The first step of our project was to replicate the results of the studies on Bindi and its variants by repeating the stability test experiments presented in "the paper." After verifying the results of "the paper", we proceeded to construct our degron protein constructs and expressed them in yeast cells containing an inducible mechanism for the expression of green fluorescence protein.Subsequently, the fluorescent emission of each cell is measured as higher fluorescent corresponds to higher test protein stability.

Our System

Components of the Degron Construct

Test Protein

Method

The essential process of our system involves cloning and manufacturing of a plasmid in E.coli . Once, the plasmids have been constructed and verified in E.Coli they are transformed into S.Cerevisiae. The plasmid constructs are then expressed. Following several days of growth the yeast cultures are passed through a flow cytometer and the fluorescence of each cell is measured. Higher fluorescence is associated with higher expression of the protein of interest which in-turn is indicative of higher protein stability.

Analysis of Test Protein Stability using established methods

Cloning in Escherichia coli

There are five possible degron constructs corresponding to five different positions the degron can take in our construct. The first step is to insert our protein into each of the five constructs and verify it.

Preparation and Passaging of Saccharomyces cerevisiae

Once, plasmids of the five possible degron constructs have been cloned with our three test proteins, they are subsequently transformed in PYE1 a strain of S. Cerevisiae with the ability to produce green fluorescent proteins with the proper promoter protein such as Gal4 which is a part of our degron construct. Following the transformation, the cells are plated onto plates with on a Selective Dropout C-Uracil media and incubated at 30oC for 2 days. After two days, three colonies are choosen and added to an overnight culture of 3mL Selective Dropout Media C-Uracil and 2% Glucose then incuabted for another two days at 30oC. After two days of incubation, a 20-50uL aliquot of each culture is "passaged" into another 3mL culture prepared in the same manner as before and incubated for the same duration and temperature as the previous culture. The passaging is done several times after each passage after the second passage, a glycerol stock is prepare from the culture and flow cytometry is run on the culture.

The purpose of passaging is to gradually remove excess copies of the plasmid constructs. Excess copies, exceeding one per cell will lead to multiple fold increase in the expression of the degron protein construct. As a result of this, GFP expression will also be increased thus reducing the viability and accuracy of the Flow Cytometry measurements conducted on each cell culture.

Relative Stability Analyzed via Flow Cytometry

Mutagenesis through Error Prone Polymerase Chain Reactions

Selecting Stable Variants through Fluorescence Activated Cell Sorting

Results

Protein stability analysis using Thermal and Guanadinium HCl melts

Protein stability analysis using Degron Constructs and Flow Cytometry

Mutagenesis Results and Mutant Variant Analysis

Future Plans

Examination of more proteins

Further evolving more stable variants of existing proteins

Submitted Parts

Retrieved from "http://2014.igem.org/Team:Washington/Our_Project"