Difference between revisions of "Part:BBa K1980003"
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<li>They should be from the prokaryotic domain because eukaryotic proteins can have expression issues in <i>Escherichia coli.</i> </li>
 
<li>They should be from the prokaryotic domain because eukaryotic proteins can have expression issues in <i>Escherichia coli.</i> </li>
 
</ul>
 
</ul>
−
 
+
<p>
−
<p>It is believed that the protein may help the bacterium survive copper toxicity, though deleting the gene had no effect on pathogenicity in mice.</p>
+
MymT is a small prokaryotic metallothein discovered in <i>Mycobacterium tuberculosis</i> by Gold <i>et al.</i><sup>(2)</sup>. It is believed that the protein may help the bacterium survive copper toxicity.</p>
 +
<p> MymT is believed to bind up to 7 copper ions but has a preference for 4-6.<sup>(2)</sup>
 +
</p>
 
<!-- -->
 
<!-- -->
  
−
 
+
==Experience==
−
 
+
<p> We cloned MymTsfGFP from Gblock into the shipping vector then transferred it into the pBAD, arabinose-inducible commercial expression vector.</p>
 +
 +
<p>We were unable however to detect copper chelation activity of MymTsfGFP when expressed from pBAD in MG1655 <i>E. coli</i> strain, using a BCS absorbance assay. Modelling by our team suggested that this was because insufficient protein could be expressed to chelate the amount needed to be detectable on the assay. ( 2 μM detection limit)</p>
 +
<p>We purified this protein but were still unable to detect copper chelation with the assay in our purified extracts.</p>
 +
<p><b>FLIM</b></p>
 +
<p>
 +
We discovered a paper by Hötzer et al<sup>(2)</sup> that described how His-tagged GFP can be quenched by a copper ion binding to this His tag leading to a reduction in the fluorescence lifetime (the time the fluorophore spends in the excited state before returning to the ground state by emitting a photon.) They speculated that this could potentially be used as a <i>in vivo</i> copper assay.
 +
</p>
 +
https://static.igem.org/mediawiki/2016/3/32/FLIM_diagram_sam_oxford_2016.png
 +
<p>
 +
(2) Hötzer B., Ivanov R., Altmeier S., Kappl R., Jung G., (2011) "Determination of copper(II) ion concentration by lifetime measurements of green fluorescent protein."  Journal of Fluorescence, 21(6), pp. 2143-2153. doi: 10.1007/s10895-011-0916-1
 +
</p>
 +
<p>
 +
As we had His-tagged our chelator-sfGFP constructs we were curious to see if this technique could be applied to our parts to measure copper chelation <i>in vivo</i> by our parts. We believe that two possibilities were likely:
 +
</p>
 +
<ol>
 +
<li>Copper chelation by the chelator reduces the free copper concentration inside the cell meaning that less binds to the His tag and the fluorescence lifetime will be greater than a His-tagged sfGFP control</li>
 +
<li>Copper chelation by the chelator would allow additional quenching if copper was bound within the quenching radius of the fluorophore leading to a reduction in fluorescence lifetime compare with a sfGFP control</li>
 +
</ol>
 +
<p>
 +
Lacking access to a fluorescence lifetime microscope ourselves we contacted Cardiff iGEM who had a FLIM machine in their bioimaging unit. They very kindly agreed to run a few samples for us taking up over five hours of microscope time.
 +
</p>
 +
<p>
 +
We sent Cardiff iGEM our parts MymTsfGFP in pBAD and pCopA CueR sfGFP (as a control) in live MG1655 <i>E. coli</i> in agar tubes. Cardiff grew them overnight in 5ml of LB with 5uM copper with and without 2mM arabinose.
 +
</p>
 +
<p>
 +
The imaging unit spread each strain on slides and measured the fluorescence lifetime of three areas on each slide.</p>
 +
<p> (Acquisition parameters: using the x63 water immersion objective with excitation at 483nm (71% intensity, pulse rate 40MHz) and emission via a BP500-550 filter. Scan resolution at 512 x 512 pixels at pixel size of 0.26 microns/pixel, 1AU pinhole.  Counts of >1000 per lifetime recording.)
 +
</p>
 +
<p>FLIM images from one section of each slide:</p>
 +
https://static.igem.org/mediawiki/2016/5/5d/FLIM_images_sam_oxford_2016.png
 +
<p>
 +
As expected the pCopA CueR sfGFP control was fluorescent, with and without arabinose, with the mean fluorescence lifetime a consistent 2.6ns. </p>
 +
<p>
 +
When Csp1-sfGFP was induced the mean lifetime decreased to 2.5ns and the variance was increased. This might be indicate that copper chelation has occurred or may be reflective of the expression problems of Csp1.</p>
 +
<p>sfGFP:</p>
 +
https://static.igem.org/mediawiki/2016/5/5d/SfGFP_FLIM_plot_sam_oxford_2016.jpeg
 +
<p>Csp1-sfGFP:</p>
 +
https://static.igem.org/mediawiki/2016/f/fc/Csp1sfgfp_flim_sam_oxford_2016.jpeg
 
<!-- Uncomment this to enable Functional Parameter display  
 
<!-- Uncomment this to enable Functional Parameter display  
 
===Functional Parameters===
 
===Functional Parameters===
 
<partinfo>BBa_K1980003 parameters</partinfo>
 
<partinfo>BBa_K1980003 parameters</partinfo>
 
<!-- -->
 
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Revision as of 13:21, 20 October 2016


MymT sfGFP

MymT is a small prokaryotic copper metallothein discovered in Mycobacterium tuberculosis. It can bind up to 7 copper ions but has a preference for 4-6. This version has a C terminal sfGFP with a C terminal hexahistidine tag for purification. The MymT and sfGFP are separated by a short hydrophilic, flexible linker. This part has been codon optimised for E. coli.


Sequence and Features:


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal XhoI site found at 595
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Usage and Biology

Our project aimed to detect and chelate dietary copper as a treatment for Wilson's Disease, a copper accumulation disorder. We decided that the ideal copper chelation protein would have these properties:

  • Should be able to bind multiple copper ions per peptide to increase the efficient use of cell resources.
  • They should be from the prokaryotic domain because eukaryotic proteins can have expression issues in Escherichia coli.

MymT is a small prokaryotic metallothein discovered in Mycobacterium tuberculosis by Gold et al.(2). It is believed that the protein may help the bacterium survive copper toxicity.

MymT is believed to bind up to 7 copper ions but has a preference for 4-6.(2)

Experience

We cloned MymTsfGFP from Gblock into the shipping vector then transferred it into the pBAD, arabinose-inducible commercial expression vector.

We were unable however to detect copper chelation activity of MymTsfGFP when expressed from pBAD in MG1655 E. coli strain, using a BCS absorbance assay. Modelling by our team suggested that this was because insufficient protein could be expressed to chelate the amount needed to be detectable on the assay. ( 2 μM detection limit)

We purified this protein but were still unable to detect copper chelation with the assay in our purified extracts.

FLIM

We discovered a paper by Hötzer et al(2) that described how His-tagged GFP can be quenched by a copper ion binding to this His tag leading to a reduction in the fluorescence lifetime (the time the fluorophore spends in the excited state before returning to the ground state by emitting a photon.) They speculated that this could potentially be used as a in vivo copper assay.

FLIM_diagram_sam_oxford_2016.png

(2) Hötzer B., Ivanov R., Altmeier S., Kappl R., Jung G., (2011) "Determination of copper(II) ion concentration by lifetime measurements of green fluorescent protein." Journal of Fluorescence, 21(6), pp. 2143-2153. doi: 10.1007/s10895-011-0916-1

As we had His-tagged our chelator-sfGFP constructs we were curious to see if this technique could be applied to our parts to measure copper chelation in vivo by our parts. We believe that two possibilities were likely:

  1. Copper chelation by the chelator reduces the free copper concentration inside the cell meaning that less binds to the His tag and the fluorescence lifetime will be greater than a His-tagged sfGFP control
  2. Copper chelation by the chelator would allow additional quenching if copper was bound within the quenching radius of the fluorophore leading to a reduction in fluorescence lifetime compare with a sfGFP control

Lacking access to a fluorescence lifetime microscope ourselves we contacted Cardiff iGEM who had a FLIM machine in their bioimaging unit. They very kindly agreed to run a few samples for us taking up over five hours of microscope time.

We sent Cardiff iGEM our parts MymTsfGFP in pBAD and pCopA CueR sfGFP (as a control) in live MG1655 E. coli in agar tubes. Cardiff grew them overnight in 5ml of LB with 5uM copper with and without 2mM arabinose.

The imaging unit spread each strain on slides and measured the fluorescence lifetime of three areas on each slide.

(Acquisition parameters: using the x63 water immersion objective with excitation at 483nm (71% intensity, pulse rate 40MHz) and emission via a BP500-550 filter. Scan resolution at 512 x 512 pixels at pixel size of 0.26 microns/pixel, 1AU pinhole. Counts of >1000 per lifetime recording.)

FLIM images from one section of each slide:

FLIM_images_sam_oxford_2016.png

As expected the pCopA CueR sfGFP control was fluorescent, with and without arabinose, with the mean fluorescence lifetime a consistent 2.6ns.

When Csp1-sfGFP was induced the mean lifetime decreased to 2.5ns and the variance was increased. This might be indicate that copper chelation has occurred or may be reflective of the expression problems of Csp1.

sfGFP:

SfGFP_FLIM_plot_sam_oxford_2016.jpeg

Csp1-sfGFP:

Csp1sfgfp_flim_sam_oxford_2016.jpeg