Team:St Andrews/metal-binding

From 2012.igem.org

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     <ul class="nav nav-pills">
     <ul class="nav nav-pills">
       <li><a href="#content-container">Introduction</a></li>
       <li><a href="#content-container">Introduction</a></li>
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      <li><a href="#project-description">Project Description</a></li>
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       <li><a href="#synthesizing-metal-binding-peptides">Synthesizing metal binding peptides</a></li>
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       <li><a href="#synthesizing-metal-binding-peptides">Synthesizing metal-binding peptides</a></li>
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       <li><a href="#biobricks">Biobricks</a></li>
       <li><a href="#biobricks">Biobricks</a></li>
       <li><a href="#references">References</a></li>
       <li><a href="#references">References</a></li>
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<img src="https://static.igem.org/mediawiki/2012/9/9f/MetalBindingLogo_100.png" align="left"></img>
<img src="https://static.igem.org/mediawiki/2012/9/9f/MetalBindingLogo_100.png" align="left"></img>
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<p>Precious and toxic metals frequently find their way into the environment. As their names suggest this is wasteful and damaging respectively. St Andrews iGEM '12 plans to take the first steps towards solving this problem using synthetic biology.
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<blockquote class="span4 pull-right"><p>Precious and toxic metals frequently find their way into the environment. As their names suggest, such leaks are wasteful and damaging respectively. St Andrews iGEM '12 plans to take on this challenge using synthetic biology.
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<br>
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</p></blockquote>
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<br>
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 +
<h2>Inspiration</h2>
 +
<p>Our project was inspired by the work done identifying the platinum and palladium particles present on roads, primarily emitted from catalytic converters (Deplanche et al. 2011).  In 2010, 50% of the world's platinum and palladium production was used for catalytic converters, with the largest use in Europe (Jollie 2010).  Platinum and palladium appear on road surfaces in small concentrations and in minute particles, < 3 μm (Prichard, Fisher 2012).  These precious elements are a finite resource!  However, their eventual exhaustion can be postponed by collecting and recycling them.</p>
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</p>
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<h2>Collection</h2>
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<br>
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<p>We have focused on the collection process.  We have worked in a similar way to Chung et al., in that we have produced a protein with a metal binding peptide on the terminus of an easily expressible protein (Chan Chung, Cao et al. 2008).  The difference is that we used glutathione S-transferase (GST tag) rather than ubiquitin, and instead of adding the binding peptide chemically to the protein we expressed both the protein and the peptide in <i>E. coli</i> BL21 (DE3) cells.  These cells are particularly suited to large scale protein production.  The peptides sequences were taken from various sources (Seker, Demir 2011, Bae, Chen et al. 2000, Song, Caguiat et al. 2004, White, Liljestrand et al. 2007) and codon optimised for <i>E. coli</i>.  The nucleotide sequence that code for the peptides were modified so they could be produced by <i>E. coli</i> using an online program <a href="http://molbiol.ru/eng/scripts/01_19.html">Protein to DNA</a>.</p>
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</section>
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<p>We decided to go down two different routes.  The first was making an array of peptides incorporated into GST-protein that bind specific metals, and the second was to make a protein with multiple metal binding sites for multiple metals.  </p>
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<section id="project-description">
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<h2>Metal Binding Peptides</h2>
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<br>
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<p>With the first of the two ideas we thought that it would be possible use a column to immobilise the protein by its GST tag.  A solution containing multiple metal ions would then be passed through the column, which would bind each metal ion specifically.  Initially, we decided to take a look at palladium, platinum and nickel (Seker, Demir 2011).  The reason for choosing these metals was twofold: firstly, because platinum and palladium are particularly precious metals, which provides an economic argument; and secondly, because nickel columns were readily available to test this idea. </p>
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  <h2>Project Description</h2>
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<p> The human race moved from the stone of the Neolithic period and into the metallurgy of the Chalcolithic period with the widespread use of metal tools in their every day work regime (Gale 1991).  From here little changed over the next 6,000 years where metals are still a massive part of our everyday lives but in quantities that dwarf previous usages.  These high levels of metal requirements have left the landscape scarred.</p>
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<p>Our project was inspired by the work done in the identification of platinum and palladium particles that are present on roads; emitted from catalytic converters (Deplanche, Murray et al. ).  In 2010 50% of the worlds production of platinum and palladium were used for catalytic converters, with the highest amount being in Europe (Jollie 2010).  Platinum and palladium appear ion the roads in small concentrations and in minute particles, < 3 μm (Prichard, Fisher 2012).  These precious elements are a finite resource meaning that once its gone its gone.  This doesn’t have to be the case, as the metals can be collected up and recycled. </p>
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<h2>gBlock Scavengers</h2>
 +
<p>The second route would produce a protein that would act as a general metal scavenging protein.  gBlocks (≤ 500 bps) were specifically designed and inserted into a pGEX-6P-1.  One of them was designed to bind toxic metals: cadmium, mercury and cobalt (Seker, Demir 2011, Bae, Chen et al. 2000, Song, Caguiat et al. 2004, White, Liljestrand et al. 2007).  This was done by inserting flexible linkers between the metal binding sites (Hu, Wang et al. 2007).  This prevented hairpins in the structure.  The second gBlock designed was for precious metals, not including platinum and palladium.  The corresponding gene sequences specific for gold, silver, aluminum and titanium peptides (Seker, Demir 2011) were usedThe design of this differed from the other gBlock as myoglobin was hijacked, the loops removed and replaced with our metal binding peptides. </p>
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<p>The collection process is what we have been focussing on specifically.  We have worked in a similar way to Chung et al, in that we have produced a protein with a metal binding peptide on the N-terminus of an easily expressible protein (Chan Chung, Cao et al. 2008).  The difference is that we used glutathione S-transferase (GST tag) rather than ubiquitin, and instead of adding the binding peptide chemically to the protein we expressed both the protein and the peptide in E. Coli BL21 (DE3) cells.  The peptides were taken from various sources (Seker, Demir 2011, Bae, Chen et al. 2000, Song, Caguiat et al. 2004, White, Liljestrand et al. 2007) and back translated specifically for E. coli using an online program <a href="http://molbiol.ru/eng/scripts/01_19.html">Protein to DNA</a>.</p>
 
-
<p>We decided to go down two different routes.  The first was making an array of protein that bind a specific metal, and the second was to make a protein that has multiple metal binding sites.  </p>
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<section id="synthesizing-metal-binding-peptides">
 +
<div class="page-header">
 +
<h1>Synthesizing Metal Binding Proteins</h1>
 +
</div>
-
<p>With the first of the two ideas we thought that it would be possible to make a column, using the GST tag to bind the proteins in place. A solution containing multiple metal ions would then be passed through the column and bind each metal ion specifically.  We initially looked at binding palladium, platinum and nickel (Seker, Demir 2011).  The choice to use these metals was  first, because platinum and palladium are the precious metals we were initially looking at, and second, because nickel columns were readily available to test this idea. </p>
+
<p>For detail on our laboratory procedures, please refer to our <a href="https://2012.igem.org/Team:St_Andrews/Lab-book">Protocols</a>.
-
<p>The second Idea is more of a scavenging protein.  gBlocks (≤ 500 bps) were specifically designed and inserted into a pGEX-6P-1. One of them was designed to bind toxic metals; cadmium, mercury and cobalt (Seker, Demir 2011, Bae, Chen et al. 2000, Song, Caguiat et al. 2004, White, Liljestrand et al. 2007).  This was done by inserting flexible linkers between the metal binding sites (Hu, Wang et al. 2007).  The linkers were used because they were quite flexible. This prevented hairpins in the structure. The second gBlock designed was for precious metals, not including platinum and palladium.  The corresponding base pairs for gold, silver, aluminum and titanium peptides (Seker, Demir 2011) were used.  The design of this differed from the other gBlock as myoglobin was hijacked, the loops removed and replaced with our metal binding peptides. .</p>
+
<h2>Metal binding peptide procedure</h2>
-
 
+
<p>Sequences were found for metal binding peptides. The gene sequences for the production of the metal binding peptides were very short. Therefore we were able to have each peptide gene synthesised as two complementary oligonucleotides. We then annealed the primers together. The product of this reaction had the relevant sticky ends for insertion of the sequence into the plasmid vector. </p>
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<section id="synthesizing-metal-binding-peptides">
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<h3>Primers</h3>
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<br>
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-
<h2>Synthesizing metal-binding peptides</h2>
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-
 
+
-
 
+
-
<p>For detail on our laboratory procedures, please refer to our <a href="https://2012.igem.org/Team:St_Andrews/Lab-book">Protocols</a>.
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-
<p>Sequences were found for short metal binding peptides. To insert these sequences into a plasmid vector in the form of double stranded, functioning piece of DNA, we designed short complementary pairs of primers that would anneal. </p>
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-
<BR>&nbsp;</BR>
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<a name="primers"><span class="label label-info">Primers</span></a>
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<p>All primers are notated 5' to 3'.</p>
<p>All primers are notated 5' to 3'.</p>
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<p> </p>
 
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    Ni1 reverse
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    <span class="caret"></span>
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  <p><div class="span3">TCGAGGTGGTGATCGTGATGATGG</div></p> 
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     Ni2</sub> forward
     Ni2</sub> forward
     <span class="caret"></span>
     <span class="caret"></span>
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</div>
-
<div class="btn-group">
 
-
  <a class="btn btn-mini dropdown-toggle" data-toggle="dropdown" href="#">
 
-
    Ni2</sub> reverse
 
-
    <span class="caret"></span>
 
-
  </a>
 
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  <ul class="dropdown-menu">
 
-
      <div class="span4">TCGAGGCCTTCACCGCAACCGCATGTTGTACACATG</div>
 
-
  </ul>
 
-
</div>.
 
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-
 
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<p>
 
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</div>
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<div class="btn-group">
<div class="btn-group">
   <a class="btn btn-mini dropdown-toggle" data-toggle="dropdown" href="#">
   <a class="btn btn-mini dropdown-toggle" data-toggle="dropdown" href="#">
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     Pd reverse
+
     Ni1 reverse
     <span class="caret"></span>
     <span class="caret"></span>
   </a>
   </a>
   <ul class="dropdown-menu">
   <ul class="dropdown-menu">
-
      <div class="span3">ATATTTGTTCTGGGTCACGCT</div>
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  <p><div class="span3">TCGAGGTGGTGATCGTGATGATGG</div></p> 
   </ul>
   </ul>
</div>
</div>
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   <a class="btn btn-mini dropdown-toggle" data-toggle="dropdown" href="#">
   <a class="btn btn-mini dropdown-toggle" data-toggle="dropdown" href="#">
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     Pt forward
+
     Ni2</sub> reverse
     <span class="caret"></span>
     <span class="caret"></span>
   </a>
   </a>
   <ul class="dropdown-menu">
   <ul class="dropdown-menu">
-
<div class="span3">GATCGCACCAGCACCTGGCGC</div>
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      <div class="span4">TCGAGGCCTTCACCGCAACCGCATGTTGTACACATG</div>
   </ul>
   </ul>
</div>
</div>
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<div class="btn-group">
   <a class="btn btn-mini dropdown-toggle" data-toggle="dropdown" href="#">
   <a class="btn btn-mini dropdown-toggle" data-toggle="dropdown" href="#">
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     Pt reverse
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     Pd reverse
     <span class="caret"></span>
     <span class="caret"></span>
   </a>
   </a>
   <ul class="dropdown-menu">
   <ul class="dropdown-menu">
-
  <div class="span3">GCGCCAGGTGCTGGTGCGATC</div>
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      <div class="span3">ATATTTGTTCTGGGTCACGCT</div>
   </ul>
   </ul>
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</div></p>
 
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<li><strong>GST Forward</strong> and <strong>Pt Reverse</strong></li></ul>
<li><strong>GST Forward</strong> and <strong>Pt Reverse</strong></li></ul>
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<span class="label label-info">Vector</span>
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<h3>Vector</h3>
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<BR>&nbsp;</BR>
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<div class="row-fluid">
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<div class="span7">
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                <ul>
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<p>Our vector of choice was pGEX-6p-1, as it contains the genetic information needed to produce GST (258, 992) and is ampicillin-resistant.</p>
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                <li class="span4">
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                    <div class="thumbnail">
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                        <img src="https://static.igem.org/mediawiki/2012/7/78/450px-PGEX-6P-1.jpg" alt=""><br>   
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            </li>
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                </ul>
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<li class="span6">
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<p>Our vector of choice was pGEX-6p-1, as it contains the genetic information needed to produce GST (258, 992) and is ampicillin-resistant. </p>
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<p>pGEX was digested with EcoR1(955) and Xho1(970). </p>
<p>pGEX was digested with EcoR1(955) and Xho1(970). </p>
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</li>
 
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</div>
 
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<BR>&nbsp;</BR>
 
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<span class="label label-info"> Short metal binding peptides</span>
 
<p>The primers designed to create our short Ni1, Ni2, Pd and Pt binding inserts were annealed. </p>
<p>The primers designed to create our short Ni1, Ni2, Pd and Pt binding inserts were annealed. </p>
<p>The primer dimers were ligated into the cut pGEX vector on the N terminus of GST. </p>
<p>The primer dimers were ligated into the cut pGEX vector on the N terminus of GST. </p>
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<p>The miniprep product was used to transform the engineered pGEX vector into BL21 gold <i>E. coli</i> cells. </p>
<p>The miniprep product was used to transform the engineered pGEX vector into BL21 gold <i>E. coli</i> cells. </p>
<p>These cells were induced and GST+Ni1, Ni2, Pd or Pt was overexpressed. </p>
<p>These cells were induced and GST+Ni1, Ni2, Pd or Pt was overexpressed. </p>
-
<p>GST+ Ni1 and Ni2 were used to prove functionality in our engineered protein.  They bound to nickel beads successfully, and further characterisation was carried out by the University Geology department using ICP-MS. </p>
+
<p>GST+ Ni1 and Ni2 were used to prove functionality in our engineered protein.  They bound to nickel beads successfully, and further characterisation was carried out by the University Geology department using their Inductively coupled plasma mass spectrometer. </p>
<p>The Pd and Pt constructs were not fully characterised . </p>
<p>The Pd and Pt constructs were not fully characterised . </p>
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<BR>&nbsp;</BR>
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</div>
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<a name=" gblocks "><span class="label label-info">gBlocks<sup>TM</sup></span></a>
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<div class="span5">
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<p>Two gBlocks<sup>TM</sup> were designed and ordered from IDT. </p>
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<a href="#modal-vector" data-toggle="modal" class="thumbnail">
 +
<img src="https://static.igem.org/mediawiki/2012/7/78/450px-PGEX-6P-1.jpg" alt="" />
 +
</a>
 +
</div>
 +
</div>
 +
 
 +
<h2>gBlock procedure</h2>
 +
<p>Two gBlock sequences were designed and ordered from IDT. </p>
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   <span style="background-color:#8A4117"> Cd1 </span>
   <span style="background-color:#8A4117"> Cd1 </span>
   <span style="background-color:#0000FF"> Linker 2 </span>
   <span style="background-color:#0000FF"> Linker 2 </span>
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   Co1 </span>
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   <span style="background-color:#52D017"> Co1 </span>
   <span style="background-color:#0000A0"> Linker 3 </span>
   <span style="background-color:#0000A0"> Linker 3 </span>
   <span style="background-color:#E77471"> Hg1 </span>
   <span style="background-color:#E77471"> Hg1 </span>
   <span style="background-color:#ADD8E6"> Linker 1 </span>
   <span style="background-color:#ADD8E6"> Linker 1 </span>
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   Co1 </span>
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   <span style="background-color:#8BB381"> Co2 </span>
   <span style="background-color:#0000FF"> Linker 2 </span>
   <span style="background-color:#0000FF"> Linker 2 </span>
   <span style="background-color:#FFA500"> Ni1 </span>
   <span style="background-color:#FFA500"> Ni1 </span>
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   <span style="background-color:#8A4117"> TTTGGATCCATGGAATGTGAATGTGAATGTGAATGTGAATGTGAATGTGAATGTGAGTGTGAATGTGAGTGCGAATGCGAA <br/>  
   <span style="background-color:#8A4117"> TTTGGATCCATGGAATGTGAATGTGAATGTGAATGTGAATGTGAATGTGAATGTGAGTGTGAATGTGAGTGCGAATGCGAA <br/>  
   <span style="background-color:#0000FF"> CTGATTGCGTCCCTGCAGGGC <br/>
   <span style="background-color:#0000FF"> CTGATTGCGTCCCTGCAGGGC <br/>
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   CACTCTGTTCGTTGGCTGCTGCCGGGTGCGCACCCG <br/>
+
   <span style="background-color:#52D017">CACTCTGTTCGTTGGCTGCTGCCGGGTGCGCACCCG <br/>
   <span style="background-color:#0000A0"> ATGCCGCCGTCCCAGCTGGAAGGCATT <br/>
   <span style="background-color:#0000A0"> ATGCCGCCGTCCCAGCTGGAAGGCATT <br/>
   <span style="background-color:#E77471"> ggcggcacccuggcggugccgggcaugaccugcgcggcgugcccgauuaccgugaaaaaaggcggcugg <br/>
   <span style="background-color:#E77471"> ggcggcacccuggcggugccgggcaugaccugcgcggcgugcccgauuaccgugaaaaaaggcggcugg <br/>
   <span style="background-color:#ADD8E6">TccaTgcagcTgTcccagcTggaaggcaTT <br/>
   <span style="background-color:#ADD8E6">TccaTgcagcTgTcccagcTggaaggcaTT <br/>
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   AAACTGCACTCTTCTCCGCACACCCTGCCGGTTCAG <br/>
+
   <span style="background-color:#8BB381"> AAACTGCACTCTTCTCCGCACACCCTGCCGGTTCAG <br/>
   <span style="background-color:#0000FF"> CTGATTGCGTCCCTGCAGGGC <br/>
   <span style="background-color:#0000FF"> CTGATTGCGTCCCTGCAGGGC <br/>
   <span style="background-color:#FFA500"> CATCATCACCATCACCAC <br/>
   <span style="background-color:#FFA500"> CATCATCACCATCACCAC <br/>
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</div>
</div>
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<p>The gBlocks alone were ligated into the iGEM pSB1C3 vector for submission. </p>
+
<p>The gBlocks alone were ligated into the iGEM pSB1C3 vector for submission.</p>
-
<p>The ligation was successful but the BioBricks remain uncharacterised. </p>
+
<p>The ligation was successful but the BioBricks remain uncharacterised.</p>
 +
 
 +
<h2>Results</h2>
 +
<p>We have been able to submit two fully characterised BioBricks into the Registry of Standard Biological Parts as well as three functioning, yet uncharacterised, BioBricks.</p>
 +
 
 +
<p>We were first able to see the Ni1 and Ni2 proteins had been expressed as they were able to be purified on Ni beads.  This meant that any protein that was eluted from the beads would then be a Ni binding protein.  Both Ni binding proteins were seen after elution.</p>
 +
 
 +
<p>Using the results obtained by the UV-vis spectrum, seen on the graphs below, we were able to decipher that both of the Ni binding proteins, Ni1 and Ni2, had bound to Ni once again.  This time it was shown using the shift in the λ<sub>max</sub> of the Ni solution.</p>
 +
 
 +
<p>As a further characterisation step we looked at the proteins using an ICP-MS.  This will allow us to see, in parts per billion, how much Ni was bound to the proteins.  The results from this method of characterisation are not yet available to us, but will be ready in time for the European iGEM Jamboree 2012 presentation and poster.</p>
 +
 
 +
 
 +
<h2>Graphs</h2>
 +
 
 +
<div class="well">
 +
 
 +
<div class="row-fluid">
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 +
    <ul class="thumbnails">
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    <li class="span4">
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    <a href="#nisol" data-toggle="modal" class="thumbnail">
 +
<img src="https://static.igem.org/mediawiki/2012/8/8e/NiCl2_soln.jpeg" alt="" />
 +
<h5>Graph  1: <em>NiCl<sub>2</sub> solution</em></h5>
 +
    <p>This graph shows the λ<sub>max</sub> of the NiCl<sub>2</sub> solution in water with a peak at 394 nm.  The λ<sub>max</sub> of this peak will not change regardless of concentration.  The concentration of 25 mM was used so the absorbance was under one, and so that the amide bonds were not intruding with their absorbances, 190-230 nm. </p>
 +
    </a>
 +
    </li>
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 +
    <li class="span4">
 +
    <a href="#nicl2" data-toggle="modal" class="thumbnail">
 +
    <img src="https://static.igem.org/mediawiki/2012/4/4a/New_Ni_binding_protein_graph.jpeg" alt="" />
 +
    <h5>Graph 2: <em>Metal binding protein</em></h5>
 +
    <p>This graph shows the absorbance of the metal binding protein Ni2.  We can see that in the regions where the NiCl<sub>2</sub> will be unobstructed by any absorbance of the NiCl<sub>2</sub>.</p>
 +
    </a>
 +
    </li>
 +
 
 +
<li class="span4">
 +
    <a href="#protein" data-toggle="modal" class="thumbnail">
 +
    <img src="https://static.igem.org/mediawiki/2012/3/3e/6_His_protein_in_water.jpeg" alt="" />
 +
    <h5>Graph 3: <em>Ni binding protein with Ni bound</em></h5>
 +
    <p>This graph shows the change in the  λ<sub>max</sub> to 390 nm.  As stated previously, the λ<sub>max</sub> will not change with changes of concentrations, and there aren't any absorbances in this region of the Ni2 protein to obstruct the readings.  This, therefore, must mean the Ni is bound to the protein.</p>
 +
    </a>
 +
    </li>
 +
 
 +
</ul>
 +
 
 +
</div>
 +
</div>
</section>
</section>
 +
<section id="biobricks">
<section id="biobricks">
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<br>
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<div class="page-header">
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<h2>Biobricks</h2>
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<h1>Biobricks</h1>
 +
</div>
 +
<table class="table table-striped">
 +
    <thead>
 +
        <tr>
 +
            <th>Biobrick</th>
 +
            <th>Short name</th>
 +
            <th>Description</th>
 +
            <th>Length</th>
 +
        </tr>
 +
    </thead>
 +
    <tbody>
 +
        <tr>
 +
            <td><a href="http://partsregistry.org/Part:BBa_K925002">BBa_K925002</a></td>
 +
            <td>HisTagGST</td>
 +
            <td>This part codes for glutathione S-transferase (GST) protein with a histidine tag attached to the end. This provides a double ended tag protein and proof that the concept of attaching small metal binding peptides to the end of GST can create a protein with two active binding sites. This part is fully characterised.</td>
 +
            <td>669</td>
 +
        </tr>
 +
        <tr>
 +
            <td><a href="http://partsregistry.org/Part:BBa_K925004">BBa_K925004</a></td>
 +
            <td>NiTagGST</td>
 +
            <td>This part codes for GST and has a alternative nickel binding peptide attached to the end of the protein. This double ended protein binds to both GST and to nickel and is fully characterised.</td>
 +
            <td>681</td>
 +
        </tr>
 +
        <tr>
 +
            <td><a href="http://partsregistry.org/Part:BBa_K925005">BBa_K925005</a></td>
 +
            <td>PdTagGST</td>
 +
            <td>This part codes for GST with a palladium binding peptide attached to the end of the protein. The part is not yet characterised.</td>
 +
            <td>666</td>
 +
        </tr>
 +
        <tr>
 +
            <td><a href="http://partsregistry.org/Part:BBa_K925006">BBa_K925006</a></td>
 +
            <td>MyPrecious </td>
 +
            <td>This part codes for a gBlock that was designed by hijacking the structure of myoglobin and replacing the loops of the structure with precious metal binding peptides. The part was designed to bind gold, silver, aluminium and titanium. The part is not yet characterised.</td>
 +
            <td>479</td>
 +
        </tr>
 +
        <tr>
 +
            <td><a href="http://partsregistry.org/Part:BBa_K925007">BBa_K925007</a></td>
 +
            <td>MyToxic </td>
 +
            <td>This part codes for a gBlock that was designed by building flexible linker sequences around peptide binding sequences for toxic metals. The part was intended to scavenge cobalt, cadmium and mercury. The part is not yet characterised.</td>
 +
            <td>888</td>
 +
        </tr>
 +
    </tbody>
 +
</table>
</section>
</section>
<section id="references">
<section id="references">
-
<br>
 
<b><u>References</u></b>
<b><u>References</u></b>
-
<p>BAE, W., CHEN, W., MULCHANDANI, A. and MEHRA, R.K., 2000. <i>Enhanced bioaccumulation of heavy metals by bacterial cells displaying synthetic phytochelatins. Biotechnology and bioengineering</i>, <b>70</b>(5), pp. 518-524.</p>
+
 
-
<p>CHAN CHUNG, K.C., CAO, L., DIAS, A.V., PICKERING, I.J., GEORGE, G.N. and ZAMBLE, D.B., 2008. A high-affinity metal-binding peptide from Escherichia coli HypB. <i>Journal of the American Chemical Society</i>, <b>130</b>(43), pp. 14056-14057.</p>
+
<p><a href="http://onlinelibrary.wiley.com/doi/10.1002/1097-0290(20001205)70:5%3C518::AID-BIT6%3E3.0.CO;2-5/abstract">Bae, W., Chen, W., Mulchandani, A. and Mehra, R.K., 2000. Enhanced bioaccumulation of heavy metals by bacterial cells displaying synthetic phytochelatins. <i>Biotechnology and bioengineering</i>, 70(5), p.518-524.</a></p>
-
<p>DEPLANCHE, K., MURRAY, A., MENNAN, C., TAYLOR, S. and MACASKIE, L., Biorecycling of Precious Metals and Rare Earth Elements. </p>
+
 
-
<p>GALE, N.H., 1991. Metals and metallurgy in the Chalcolithic period. <i>Bulletin of the American Schools of Oriental Research</i>, , pp. 37-61.</p>
+
<p><a href="http://pubs.acs.org/doi/abs/10.1021/ja8055003">Chan Chung, K.C., Cao, L., Dias, A.V., Pickering, I.J., George, G.N. and Zamble, D.B., 2008. A high-affinity metal-binding peptide from Escherichia coli HypB. <i>Journal of the American Chemical Society</i>, 130(43), p.14056-14057.</a></p>
-
<p>HU, X., WANG, H., KE, H. and KUHLMAN, B., 2007. High-resolution design of a protein loop. <i>Proceedings of the National Academy of Sciences</i>, <b>104</b>(45), pp. 17668.</p>
+
 
-
<p>JOLLIE, D., 2010. <i>Platinum 2010</i>. Johnson Matthey.</p>
+
<p><a href="http://www.intechopen.com/books/nanomaterials/biorecycling-of-precious-metals-and-rare-earth-elements" title="Biorecycling of Precious Metals and Rare Earth Elements">Deplanche, K., Murray, A., Mennan, C., Taylor, S. and Macaskie, L., Biorecycling of Precious Metals and Rare Earth Elements</a>. </p>
-
<p>PRICHARD, H.M. and FISHER, P.C., 2012. Identification of platinum and palladium particles emitted from vehicles and dispersed into the surface environment. <i>Environmental science & technology</i>, .</p>
+
 
-
<div id="random"><p>SEKER, U.O.S. and DEMIR, H.V., 2011. Material binding peptides for nanotechnology. <i>Molecules</i>, <b>16</b>(2), pp. 1426-1451.</p></div>
+
<p><a href="http://www.pnas.org/content/104/45/17668.short">Hu, X., Wang, H., Ke, H. and Kuhlman, B., 2007. High-resolution design of a protein loop. <i>Proceedings of the National Academy of Sciences</i>, 104(45), p.17668.</a></p>
-
<p>SONG, L., CAGUIAT, J., LI, Z., SHOKES, J., SCOTT, R.A., OLLIFF, L. and SUMMERS, A.O., 2004. Engineered single-chain, antiparallel, coiled coil mimics the MerR metal binding site. <i>Journal of Bacteriology</i>, <b>186</b>(6), pp. 1861-1868.</p>
+
 
-
<p>WHITE, B.R., LILJESTRAND, H.M. and HOLCOMBE, J.A., 2007. A ‘turn-on’FRET peptide sensor based on the mercury binding protein MerP. <i>Analyst</i>, <b>133</b>(1), pp. 65-70.</p>
+
<p><a href="http://www.platinum.matthey.com/uploaded_files/Pt_2010/10completepublication.pdf"> Jollie, D., 2010. <i>Platinum 2010</i>. Johnson Matthey.</a></p>
 +
 
 +
<p><a href="http://pubs.acs.org/doi/abs/10.1021/es203666h">Pritchard, H.M. and Fisher, P.C., 2012. Identification of platinum and palladium particles emitted from vehicles and dispersed into the surface environment. <i>Environmental science & technology</i>.</a></p>
 +
 
 +
<div id="random"><a href="http://www.mdpi.com/1420-3049/16/2/1426"><p>Seker, U.O.S. and Demir, H.V., 2011. Material binding peptides for nanotechnology. <i>Molecules</i>, 16(2), p.1426-1451.</a></p></div>
 +
 
 +
<p><a href="http://jb.asm.org/content/186/6/1861.short">Song, L., Caguiat, J., Li, Z., Shokes, J., Scott, R.A., Olliff, L. and Summers, A.O., 2004. Engineered single-chain, antiparallel, coiled coil mimics the MerR metal binding site. <i>Journal of Bacteriology</i>, 186(6), p.1861-1868.</a></p>
 +
 
 +
<p><a href="http://pubs.rsc.org/en/content/articlelanding/2007/AN/b711777a">White, B.R., Liljestrand, H.M. and Holcombe, J.A., 2007. A ‘turn-on’FRET peptide sensor based on the mercury binding protein MerP. <i>Analyst</i>, 133(1), p.65-70.</a></p>
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Latest revision as of 01:09, 27 September 2012

Metal binding protein

Precious and toxic metals frequently find their way into the environment. As their names suggest, such leaks are wasteful and damaging respectively. St Andrews iGEM '12 plans to take on this challenge using synthetic biology.

Inspiration

Our project was inspired by the work done identifying the platinum and palladium particles present on roads, primarily emitted from catalytic converters (Deplanche et al. 2011). In 2010, 50% of the world's platinum and palladium production was used for catalytic converters, with the largest use in Europe (Jollie 2010). Platinum and palladium appear on road surfaces in small concentrations and in minute particles, < 3 μm (Prichard, Fisher 2012). These precious elements are a finite resource! However, their eventual exhaustion can be postponed by collecting and recycling them.

Collection

We have focused on the collection process. We have worked in a similar way to Chung et al., in that we have produced a protein with a metal binding peptide on the terminus of an easily expressible protein (Chan Chung, Cao et al. 2008). The difference is that we used glutathione S-transferase (GST tag) rather than ubiquitin, and instead of adding the binding peptide chemically to the protein we expressed both the protein and the peptide in E. coli BL21 (DE3) cells. These cells are particularly suited to large scale protein production. The peptides sequences were taken from various sources (Seker, Demir 2011, Bae, Chen et al. 2000, Song, Caguiat et al. 2004, White, Liljestrand et al. 2007) and codon optimised for E. coli. The nucleotide sequence that code for the peptides were modified so they could be produced by E. coli using an online program Protein to DNA.

We decided to go down two different routes. The first was making an array of peptides incorporated into GST-protein that bind specific metals, and the second was to make a protein with multiple metal binding sites for multiple metals.

Metal Binding Peptides

With the first of the two ideas we thought that it would be possible use a column to immobilise the protein by its GST tag. A solution containing multiple metal ions would then be passed through the column, which would bind each metal ion specifically. Initially, we decided to take a look at palladium, platinum and nickel (Seker, Demir 2011). The reason for choosing these metals was twofold: firstly, because platinum and palladium are particularly precious metals, which provides an economic argument; and secondly, because nickel columns were readily available to test this idea.

gBlock Scavengers

The second route would produce a protein that would act as a general metal scavenging protein. gBlocks (≤ 500 bps) were specifically designed and inserted into a pGEX-6P-1. One of them was designed to bind toxic metals: cadmium, mercury and cobalt (Seker, Demir 2011, Bae, Chen et al. 2000, Song, Caguiat et al. 2004, White, Liljestrand et al. 2007). This was done by inserting flexible linkers between the metal binding sites (Hu, Wang et al. 2007). This prevented hairpins in the structure. The second gBlock designed was for precious metals, not including platinum and palladium. The corresponding gene sequences specific for gold, silver, aluminum and titanium peptides (Seker, Demir 2011) were used. The design of this differed from the other gBlock as myoglobin was hijacked, the loops removed and replaced with our metal binding peptides.

For detail on our laboratory procedures, please refer to our Protocols.

Metal binding peptide procedure

Sequences were found for metal binding peptides. The gene sequences for the production of the metal binding peptides were very short. Therefore we were able to have each peptide gene synthesised as two complementary oligonucleotides. We then annealed the primers together. The product of this reaction had the relevant sticky ends for insertion of the sequence into the plasmid vector.

Primers

All primers are notated 5' to 3'.

Ni1 forward
Ni2 forward
Pd forward
Ni1 reverse
Ni2 reverse
Pd reverse

For primer annealing in the PCR, the primer sequences were combined in the following way:

  • GST Forward and Ni1 Reverse
  • GST Forward and Ni2 Reverse
  • GST Forward and Pd Reverse
  • GST Forward and Pt Reverse

Vector

Our vector of choice was pGEX-6p-1, as it contains the genetic information needed to produce GST (258, 992) and is ampicillin-resistant.

pGEX was digested with EcoR1(955) and Xho1(970).

The primers designed to create our short Ni1, Ni2, Pd and Pt binding inserts were annealed.

The primer dimers were ligated into the cut pGEX vector on the N terminus of GST.

The ligated vector was transformed into DH5-α E. coli cells.

These cells were grown up and a miniprep was carried out.

The primer dimer insert was too small to detect using a diagnostic digest.

The miniprep product was used to transform the engineered pGEX vector into BL21 gold E. coli cells.

These cells were induced and GST+Ni1, Ni2, Pd or Pt was overexpressed.

GST+ Ni1 and Ni2 were used to prove functionality in our engineered protein. They bound to nickel beads successfully, and further characterisation was carried out by the University Geology department using their Inductively coupled plasma mass spectrometer.

The Pd and Pt constructs were not fully characterised .

gBlock procedure

Two gBlock sequences were designed and ordered from IDT.

Precious metal scavenging Toxic metal scavenging

The gBlocks alone were ligated into the iGEM pSB1C3 vector for submission.

The ligation was successful but the BioBricks remain uncharacterised.

Results

We have been able to submit two fully characterised BioBricks into the Registry of Standard Biological Parts as well as three functioning, yet uncharacterised, BioBricks.

We were first able to see the Ni1 and Ni2 proteins had been expressed as they were able to be purified on Ni beads. This meant that any protein that was eluted from the beads would then be a Ni binding protein. Both Ni binding proteins were seen after elution.

Using the results obtained by the UV-vis spectrum, seen on the graphs below, we were able to decipher that both of the Ni binding proteins, Ni1 and Ni2, had bound to Ni once again. This time it was shown using the shift in the λmax of the Ni solution.

As a further characterisation step we looked at the proteins using an ICP-MS. This will allow us to see, in parts per billion, how much Ni was bound to the proteins. The results from this method of characterisation are not yet available to us, but will be ready in time for the European iGEM Jamboree 2012 presentation and poster.

Graphs

Biobrick Short name Description Length
BBa_K925002 HisTagGST This part codes for glutathione S-transferase (GST) protein with a histidine tag attached to the end. This provides a double ended tag protein and proof that the concept of attaching small metal binding peptides to the end of GST can create a protein with two active binding sites. This part is fully characterised. 669
BBa_K925004 NiTagGST This part codes for GST and has a alternative nickel binding peptide attached to the end of the protein. This double ended protein binds to both GST and to nickel and is fully characterised. 681
BBa_K925005 PdTagGST This part codes for GST with a palladium binding peptide attached to the end of the protein. The part is not yet characterised. 666
BBa_K925006 MyPrecious This part codes for a gBlock that was designed by hijacking the structure of myoglobin and replacing the loops of the structure with precious metal binding peptides. The part was designed to bind gold, silver, aluminium and titanium. The part is not yet characterised. 479
BBa_K925007 MyToxic This part codes for a gBlock that was designed by building flexible linker sequences around peptide binding sequences for toxic metals. The part was intended to scavenge cobalt, cadmium and mercury. The part is not yet characterised. 888
References

Bae, W., Chen, W., Mulchandani, A. and Mehra, R.K., 2000. Enhanced bioaccumulation of heavy metals by bacterial cells displaying synthetic phytochelatins. Biotechnology and bioengineering, 70(5), p.518-524.

Chan Chung, K.C., Cao, L., Dias, A.V., Pickering, I.J., George, G.N. and Zamble, D.B., 2008. A high-affinity metal-binding peptide from Escherichia coli HypB. Journal of the American Chemical Society, 130(43), p.14056-14057.

Deplanche, K., Murray, A., Mennan, C., Taylor, S. and Macaskie, L., Biorecycling of Precious Metals and Rare Earth Elements.

Hu, X., Wang, H., Ke, H. and Kuhlman, B., 2007. High-resolution design of a protein loop. Proceedings of the National Academy of Sciences, 104(45), p.17668.

Jollie, D., 2010. Platinum 2010. Johnson Matthey.

Pritchard, H.M. and Fisher, P.C., 2012. Identification of platinum and palladium particles emitted from vehicles and dispersed into the surface environment. Environmental science & technology.

Song, L., Caguiat, J., Li, Z., Shokes, J., Scott, R.A., Olliff, L. and Summers, A.O., 2004. Engineered single-chain, antiparallel, coiled coil mimics the MerR metal binding site. Journal of Bacteriology, 186(6), p.1861-1868.

White, B.R., Liljestrand, H.M. and Holcombe, J.A., 2007. A ‘turn-on’FRET peptide sensor based on the mercury binding protein MerP. Analyst, 133(1), p.65-70.

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University of St Andrews, 2012.

Contact us: igem2012@st-andrews.ac.uk, Twitter, Facebook

This iGEM team has been funded by the MSD Scottish Life Sciences Fund. The opinions expressed by this iGEM team are those of the team members and do not necessarily represent those of Merck Sharp & Dohme Limited, nor its Affiliates.