Difference between revisions of "Team:Kent/Basic Part"

 
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<p>This part encodes Cytochrome <i>b</i><sub>562</sub> in a pSB1C3 backbone. Cytochrome <i>b</i><sub>562</sub> is a single subunit, four-helix bundle protein containing a non-covalently bound b-type haem group with a molecular weight of 25kDa <sup><a href="#r1">[1]</a></sup><sup><a href="#r2">[2]</a></sup>.</p>
 
<p>This part encodes Cytochrome <i>b</i><sub>562</sub> in a pSB1C3 backbone. Cytochrome <i>b</i><sub>562</sub> is a single subunit, four-helix bundle protein containing a non-covalently bound b-type haem group with a molecular weight of 25kDa <sup><a href="#r1">[1]</a></sup><sup><a href="#r2">[2]</a></sup>.</p>
  
<!----<h3> Validation </h3>----->
 
  
 
<a class="anchor" id="top"name="CsgAss Sup35"></a><h2><b>Sup35NM with N-terminal CsgAss signal sequence </b><br><i>Part name: BBa_K1739002 </i></h2>
 
<a class="anchor" id="top"name="CsgAss Sup35"></a><h2><b>Sup35NM with N-terminal CsgAss signal sequence </b><br><i>Part name: BBa_K1739002 </i></h2>
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<p><i>(<b>Figure 3.</b> Illustrates the construction of BBa_K1739002. The image was created using SnapGene Viewer.)</i></p>
 
<p><i>(<b>Figure 3.</b> Illustrates the construction of BBa_K1739002. The image was created using SnapGene Viewer.)</i></p>
  
<p> This part design includes the bipartite CsgA signal sequence that targets the protein to the Sec-export pathway and subsequently to the Curli export pathway via interaction with CsgG <sup><a href="#r6">[6]</a></sup><sup><a href="#r7">[7]</a></sup>. Sup35NM is derived from the yeast prion protein Sup35p from S. cerevisiae (bakers yeast) and excludes the C-terminal domain with the N-terminal domain allowing self-assembly of functional amyloid <sup><a href="#r3">[3]</a></sup><sup><a href="#r4">[4]</a></sup>. This has previously been discussed by Tessier and Lindquist (2009) <sup><a href="#r8">[8]</a></sup> who show that two beta-sheets bond together in a self-complimenting ‘steric zipper’ that excludes water, leaving a highly stable parallel beta-sheet with one molecule every 4.7 Angstroms. The particular advantage of using Sup35NM is that in its native state Sup35p has two functional domains, the N and C terminal, separated by the highly charged M domain <sup><a href="#r3">[3]</a></sup><sup><a href="#r4">[4]</a></sup><sup><a href="#r9">[9]</a></sup> allowing the fusion of a new functional domain. This part has been inserted into the pSB1C3 backbone and uses the promoter BBa_J23104.</p>
+
<p> This part design includes the bipartite CsgA signal sequence that targets the protein to the Sec-export pathway and subsequently to the Curli export pathway via interaction with CsgG <sup><a href="#r6">[6]</a></sup><sup><a href="#r7">[7]</a></sup>. Sup35NM is derived from the yeast prion protein Sup35p from S. cerevisiae (bakers yeast) and excludes the C-terminal domain with the N-terminal domain allowing self-assembly of functional amyloid <sup><a href="#r3">[3]</a></sup><sup><a href="#r4">[4]</a></sup>. This has previously been discussed by Tessier and Lindquist (2009) <sup><a href="#r8">[8]</a></sup> who show that two beta-sheets bond together in a self-complimenting ‘steric zipper’ that excludes water, leaving a highly stable parallel beta-sheet with one molecule every 4.7 Angstroms. The particular advantage of using Sup35NM is that in its native state Sup35p has two functional domains, the N and C terminal, separated by the highly charged M domain <sup><a href="#r3">[3]</a></sup><sup><a href="#r4">[4]</a></sup><sup><a href="#r9">[9]</a></sup> allowing the fusion of a new functional domain. This part has been inserted into the pSB1C3 backbone and uses the promoter <a href="http://parts.igem.org/Part:BBa_J23104">BBa_J23104.</a></p>
  
  
  
<br> <!---- CR images--->
 
<!-----<div>
 
<img src="https://static.igem.org/mediawiki/2015/7/7d/Team_Kent_105and72_congored_cropped.jpg" style="width: 50%">
 
</div>----->
 
<!-----<p> <i>(<b>Figure 4.</b> Shows our Congo red plates. The top plate depicts both our negative control plasmid, PVS105 and our BioBrick containing CsgAss and Sup35NM. Whereas the bottom plate shows only VS45 with our BioBrick. The presence of red colonies illustrates the successful formation of amyloid.)</i></p>
 
<br>----->
 
 
<!----<p>Further validation was achieved by observing the topography of our cell suspension using Atomic Force Microscopy (AFM). As shown in in Fig.X there is clear amyloid formation in the induced VS45 sample. In contrast, there was no amyloid formation in the sample containing the negative control strain VS105.</p>---->
 
<br><br> <!--- AFM image ---->
 
<!----<p>The combination of these results demonstrates that our BioBrick facilitates the export of Sup35 and the subsequent formation of amyloid.
 
</p>---->
 
 
<!----<img src="https://static.igem.org/mediawiki/2015/1/16/Team_Kent_c3_csg_sup35_gel.jpg" style="width:30%">---->
 
  
 
<a class="anchor" id="top"name="CsgAss Sup35 Cytb562"></a><h2><b> Envirowire: Sup35NM with an N-terminal CsgAss signal sequence and a C-terminal Cytochrome <i>b</i><sub>562</sub></b><br><i>Part name: BBa_K1739003</i></h2>
 
<a class="anchor" id="top"name="CsgAss Sup35 Cytb562"></a><h2><b> Envirowire: Sup35NM with an N-terminal CsgAss signal sequence and a C-terminal Cytochrome <i>b</i><sub>562</sub></b><br><i>Part name: BBa_K1739003</i></h2>
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<p><i>(<b>Figure 5. </b> Illustrates the construction of BBa_K1739003. This image was created using SnapGene Viewer.)</i></p>
 
<p><i>(<b>Figure 5. </b> Illustrates the construction of BBa_K1739003. This image was created using SnapGene Viewer.)</i></p>
  
<p> This BioBrick encodes for the Envirowire fusion protein. It contains three segments, CsgA signal sequence, Sup35NM (<a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1739000"> BBa_K1739000</a> and <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1739002"> BBa_K1739002</a>) and Cytochrome <i>b</i><sub>562</sub> (BBa_K1739001) The bipartite CsgA signal sequence targets the Sec protein export pathway followed by the endogenous curli export system of E.coli allowing our protein to be easily exported into an external medium <sup><a href="#r6">[6]</a></sup><sup><a href="#r7">[7]</a></sup>. Sup35NM is derived from the yeast prion protein Sup35p and excludes the C-terminal domain. The N-terminal domain allows self-assembly of functional amyloid <sup><a href="#r3">[3]</a></sup><sup><a href="#r4">[4]</a></sup>. This has previously been discussed by Tessier and Lindquist (2009)<sup><a href="#r8">[8]</a></sup> who show that two beta-sheets bond together in a self-complimenting ‘steric zipper’ that excludes water, leaving a highly stable parallel beta-sheet with one molecule every 4.7Å. The particular advantage of using Sup35-NM is that in its native state Sup35p has two functional domains, the N and C terminal, separated by the highly charged M domain <sup><a href="#r3">[3]</a></sup><sup><a href="#r4">[4]</a></sup><sup><a href="#r9">[9]</a></sup>. Here, with the removal of the functional C domain allows us to add our own functional protein, in this case cytochrome <i>b</i><sub>562</sub>, to form a fusion protein. We chose Cytochrome <i>b</i><sub>562</sub> as the electron carrier to make our amyloid conductive. The structure of cytochrome <i>b</i><sub>562</sub> consists of a single 24kDa subunit containing four nearly parallel alpha helices <sup><a href="#r1">[1]</a></sup><sup><a href="#r5">[5]</a></sup>. B-type cytochromes are a favourable choice because heme binds in a non-ionic fashion to the two ligands Methionine-7 and Histidine-106 <sup><a href="#r10">[10]</a></sup>. Heme binding has been shown to occur in both the native protein and the denatured protein, although the latter exhibits a modest affinity with a dissociation constant (Kd) of 3μM. This allows the cytochrome to be exported in an unfolded state and heme to be added exogenously to initiate correct folding of the cytochrome by burying hydrophobic side chains <sup><a href="#r2">[2]</a></sup>. Furthermore, heme binding to cytochrome <i>b</i><sub>562</sub> has a high affinity interaction with a dissociation constant (Kd) of 9nM at 25°C <sup><a href="#r2">[2]</a></sup>. This BioBrick part has been inserted into the pSB1C3 backbone and uses the promoter BBa_J23104. This part can be used in the VS45 strain of E.coli containing deletions that prevent amyloid from binding to the outside of the cell and increase the rate of protein exiting the cell via the curli export system. </p>
+
<p> This BioBrick encodes for the Envirowire fusion protein. It contains three segments, CsgA signal sequence, Sup35NM (<a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1739000"> BBa_K1739000</a> and <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1739002"> BBa_K1739002</a>) and Cytochrome <i>b</i><sub>562</sub> (BBa_K1739001) The bipartite CsgA signal sequence targets the Sec protein export pathway followed by the endogenous curli export system of <i>E.coli</i> allowing our protein to be easily exported into an external medium <sup><a href="#r6">[6]</a></sup><sup><a href="#r7">[7]</a></sup>. Sup35NM is derived from the yeast prion protein Sup35p and excludes the C-terminal domain. The N-terminal domain allows self-assembly of functional amyloid <sup><a href="#r3">[3]</a></sup><sup><a href="#r4">[4]</a></sup>. This has previously been discussed by Tessier and Lindquist (2009)<sup><a href="#r8">[8]</a></sup> who show that two beta-sheets bond together in a self-complimenting ‘steric zipper’ that excludes water, leaving a highly stable parallel beta-sheet with one molecule every 4.7Å. The particular advantage of using Sup35-NM is that in its native state Sup35p has two functional domains, the N and C terminal, separated by the highly charged M domain <sup><a href="#r3">[3]</a></sup><sup><a href="#r4">[4]</a></sup><sup><a href="#r9">[9]</a></sup>. Here, with the removal of the functional C domain allows us to add our own functional protein, in this case cytochrome <i>b</i><sub>562</sub>, to form a fusion protein. We chose Cytochrome <i>b</i><sub>562</sub> as the electron carrier to make our amyloid conductive. The structure of cytochrome <i>b</i><sub>562</sub> consists of a single 24kDa subunit containing four nearly parallel alpha helices <sup><a href="#r1">[1]</a></sup><sup><a href="#r5">[5]</a></sup>. B-type cytochromes are a favourable choice because heme binds in a non-ionic fashion to the two ligands Methionine-7 and Histidine-106 <sup><a href="#r10">[10]</a></sup>. Heme binding has been shown to occur in both the native protein and the denatured protein, although the latter exhibits a modest affinity with a dissociation constant (Kd) of 3μM. This allows the cytochrome to be exported in an unfolded state and heme to be added exogenously to initiate correct folding of the cytochrome by burying hydrophobic side chains <sup><a href="#r2">[2]</a></sup>. Furthermore, heme binding to cytochrome <i>b</i><sub>562</sub> has a high affinity interaction with a dissociation constant (Kd) of 9nM at 25°C <sup><a href="#r2">[2]</a></sup>. This BioBrick part has been inserted into the pSB1C3 backbone and uses the promoter <a href="http://parts.igem.org/Part:BBa_J23104">BBa_J23104</a>. This part can be used in the VS45 strain of <i>E.coli</i>containing deletions that prevent amyloid from binding to the outside of the cell and increase the rate of protein exiting the cell via the curli export system. </p>
 
<br>
 
<br>
<!------<h3> Validation </h3>
 
<p>Validation of our fusion protein’s export was achieved using two techniques. Firstly, using a segmented diagnostic Congo Red agar plate with the antibiotics chloramphenicol and ampicillin present in order to select the VS45 strains transformed with our plasmid. As a negative control, we used VS45 with PVS105, as it does not have the ability to export amyloid-forming proteins. These strains were plated in 2 quarter segments of the plate and left to incubate for 24 hours at 37°C. This resulted red VS45 with PVS72 colonies due to binding of Congo Red to the amyloid fibres produced by the colonies, and white colonies of VS45 with PVS105 showing no export of amyloid-forming protein (shown in fig.4). These results confirmed that our protein was being produced and targeted to the curli export pathway by csgA, as well as self-assembling into amyloid fibres. </p>---->
 
 
 
<!-----<div>
 
<img src="https://static.igem.org/mediawiki/2015/e/ea/Team_Kent_conductivityimage.jpg" style="width:85%">
 
</div>----->
 
<!---<p><i>(<b>Figure 6.</b> Shows the conductivity testing of the biofilm on the haem plates.) </i></p>----->
 
 
<!----<p>The third method of validation for protein export and amyloid formation was achieved by atomic force microscopy (AFM) imaging to provide a topography of our samples. Using the aforementioned E.coli strains a, 5 day incubation at 25°C was carried out to make sure that the amyloid fibres were stable for the AFM protocol, as suggested by Sivanathan and Hochschild (2012)<sup><a href="#r6">[6]</a></sup>. The resulting images clearly showed the presence of amyloid fibres in the VS45 sample with PVS72 and no amyloid fibres in the VS45 with PVS105 sample.</p>----->
 
 
<!---AFM image--->
 
 
<!-----<img src="https://static.igem.org/mediawiki/2015/e/ea/Team_Kent_AFM_Negativecontrol.jpg" style="width:50%">----->
 
 
  
  

Latest revision as of 00:23, 19 September 2015


iGEM Kent 2015


Basic Parts

Sup35NM
Part name: BBa_K1739000

(Figure 1. Illustrates the construction of BBa_K1739000. The image was created using SnapGene Viewer.)

Sup35 is derived from the yeast prion protein Sup35p and excludes the C-terminal domain. The N-terminal domain allows self-assembly of functional amyloid [3][4]. This BioBrick is an improved version of a previously designed BioBrick (Part:BBa_K401001) from the Valencia 2010 iGEM team that encoded the Sup35 protein from Saccharomyces cerevisiae. The previously designed BioBrick contained illegal BioBrick restriction sites. Our improved BioBrick has optimized in order to remove these cut sites and we have produced a part compatible with the iGEM part submission standards.

Cytochrome b562
Part name: BBa_K1739001

(Figure 2. Illustrates the construction of BBa_K1739001. The image was created using SnapGene Viewer.)

This part encodes Cytochrome b562 in a pSB1C3 backbone. Cytochrome b562 is a single subunit, four-helix bundle protein containing a non-covalently bound b-type haem group with a molecular weight of 25kDa [1][2].

Sup35NM with N-terminal CsgAss signal sequence
Part name: BBa_K1739002

(Figure 3. Illustrates the construction of BBa_K1739002. The image was created using SnapGene Viewer.)

This part design includes the bipartite CsgA signal sequence that targets the protein to the Sec-export pathway and subsequently to the Curli export pathway via interaction with CsgG [6][7]. Sup35NM is derived from the yeast prion protein Sup35p from S. cerevisiae (bakers yeast) and excludes the C-terminal domain with the N-terminal domain allowing self-assembly of functional amyloid [3][4]. This has previously been discussed by Tessier and Lindquist (2009) [8] who show that two beta-sheets bond together in a self-complimenting ‘steric zipper’ that excludes water, leaving a highly stable parallel beta-sheet with one molecule every 4.7 Angstroms. The particular advantage of using Sup35NM is that in its native state Sup35p has two functional domains, the N and C terminal, separated by the highly charged M domain [3][4][9] allowing the fusion of a new functional domain. This part has been inserted into the pSB1C3 backbone and uses the promoter BBa_J23104.

Envirowire: Sup35NM with an N-terminal CsgAss signal sequence and a C-terminal Cytochrome b562
Part name: BBa_K1739003

(Figure 5. Illustrates the construction of BBa_K1739003. This image was created using SnapGene Viewer.)

This BioBrick encodes for the Envirowire fusion protein. It contains three segments, CsgA signal sequence, Sup35NM ( BBa_K1739000 and BBa_K1739002) and Cytochrome b562 (BBa_K1739001) The bipartite CsgA signal sequence targets the Sec protein export pathway followed by the endogenous curli export system of E.coli allowing our protein to be easily exported into an external medium [6][7]. Sup35NM is derived from the yeast prion protein Sup35p and excludes the C-terminal domain. The N-terminal domain allows self-assembly of functional amyloid [3][4]. This has previously been discussed by Tessier and Lindquist (2009)[8] who show that two beta-sheets bond together in a self-complimenting ‘steric zipper’ that excludes water, leaving a highly stable parallel beta-sheet with one molecule every 4.7Å. The particular advantage of using Sup35-NM is that in its native state Sup35p has two functional domains, the N and C terminal, separated by the highly charged M domain [3][4][9]. Here, with the removal of the functional C domain allows us to add our own functional protein, in this case cytochrome b562, to form a fusion protein. We chose Cytochrome b562 as the electron carrier to make our amyloid conductive. The structure of cytochrome b562 consists of a single 24kDa subunit containing four nearly parallel alpha helices [1][5]. B-type cytochromes are a favourable choice because heme binds in a non-ionic fashion to the two ligands Methionine-7 and Histidine-106 [10]. Heme binding has been shown to occur in both the native protein and the denatured protein, although the latter exhibits a modest affinity with a dissociation constant (Kd) of 3μM. This allows the cytochrome to be exported in an unfolded state and heme to be added exogenously to initiate correct folding of the cytochrome by burying hydrophobic side chains [2]. Furthermore, heme binding to cytochrome b562 has a high affinity interaction with a dissociation constant (Kd) of 9nM at 25°C [2]. This BioBrick part has been inserted into the pSB1C3 backbone and uses the promoter BBa_J23104. This part can be used in the VS45 strain of E.colicontaining deletions that prevent amyloid from binding to the outside of the cell and increase the rate of protein exiting the cell via the curli export system.


References

[1] Fujiwara, T., Fnkumori,, Y. and Yamanaka, T. (1993). Halobacterium halobium Cytochrome b-558 and Cytochrome b-562: Purification and Some Properties. J. Biochem., 113, pp.48-54.

[2]Robinson, C., Liu, Y., Thomson, J., Sturtevant, J. and Sligar, S. (1997). Energetics of Heme Binding to Native and Denatured States of Cytochrome b 562 †. Biochemistry, 36(51), pp.16141-16146.

[3] Frederick, K., Debelouchina, G., Kayatekin, C., Dorminy, T., Jacavone, A., Griffin, R. and Lindquist, S. (2014). Distinct Prion Strains Are Defined by Amyloid Core Structure and Chaperone Binding Site Dynamics. Chemistry & Biology, 21(2), pp.295-305.

[4] Glover, J., Kowal, A., Schirmer, E., Patino, M., Liu, J. and Lindquist, S. (1997). Self-Seeded Fibers Formed by Sup35, the Protein Determinant of [PSI+], a Heritable Prion-like Factor of S. cerevisiae. Cell, 89(5), pp.811-819.

[5] Mathews, F. S., Bethge, P. H., & Czerwinski, E. W. (1979). The structure of cytochrome b562 from Escherichia coli at 2.5 A resolution. Journal of Biological Chemistry, 254(5), 1699-1706.

[6] Sivanathan, V. and Hochschild, A. (2012). Generating extracellular amyloid aggregates using E. coli cells. Genes & Development, 26(23), pp.2659-2667

[7] Sivanathan, V. and Hochschild, A. (2013). A bacterial export system for generating extracellular amyloid aggregates. Nat Protoc, 8(7), pp.1381-1390.

[8]Tessier, P. and Lindquist, S. (2009). Unraveling infectious structures, strain variants and species barriers for the yeast prion [PSI+]. Nat Struct Mol Biol, 16(6), pp.598-605.

[9] Wickner, R., Edskes, H., Shewmaker, F. and Nakayashiki, T. (2007). Prions of fungi: inherited structures and biological roles. Nature Reviews Microbiology, 5(8), pp.611-618.

[10]Xavier, A., Czerwinski, E., Bethge, P. and Mathews, F. (1978). Identification of the haem ligands of cytochrome b562 by X-ray and NMR methods. Nature, 275(5677), pp.245-247.