Difference between revisions of "Part:BBa K1890002"
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Silicatein is an enzyme natively found in demosponges and diatoms,  
 
Silicatein is an enzyme natively found in demosponges and diatoms,  
 
where it catalyzes the condensation of silica to form the typical skeletal elements.  
 
where it catalyzes the condensation of silica to form the typical skeletal elements.  
−
Here, we use the enzyme to create a polysilicate layer around the host organism <i>E. coli</i>.
+
Here, we use the enzyme to create a polysilicate layer around the host organism <i>E. coli</i> (Figure 1).
 +
The gene is fused to the transmembrane domain of INP in order to display the protein at the cell membrane.
 +
This biobrick was expressed in a backbone containing the inducible Lac-promoter.
 +
<html>
 +
    <figure>
 +
        <center><img src="https://static.igem.org/mediawiki/2016/4/43/T--TU_Delft--Silicate_layer.png">
 +
            <figcaption>
 +
                <b>Figure 1</b>: Silicatein is able to convert monosilicate to polysilicate, allowing the cell to cover itself in polysilicate.
 +
            </figcaption></center>
 +
    </figure>
 +
</html>
  
 
<h2>Characterization</h2>
 
<h2>Characterization</h2>
 +
This biobrick was expressed in <i>E. coli</i> BL21. Cells were grown overnight in selective LB.
 +
They were transfered to fresh medium and grown until in exponential phase.
 +
Then IPTG was added to induce expression. After a subsequent incubation of three hours,
 +
the medium was supplemented with silicic acid as substrate for silicatein.
 +
After another three hours, the silicate layer was considered to be formed.
 +
A change in structure was observed for these cultures (Figure 2).
 +
 +
<html>
 +
    <figure>
 +
        <center><img src="https://static.igem.org/mediawiki/2016/7/76/T--TU_Delft--silicate_culture_structure.jpeg">
 +
            <figcaption>
 +
                <b>Figure 2</b>: Structure of <i>E. coli</i> culture with polysilicate.
 +
            </figcaption></center>
 +
    </figure>
 +
</html>
 +
 
In order to characterize the formation of a polysilicate layer around <i>E. coli</i>, we performed multiple experiments.  
 
In order to characterize the formation of a polysilicate layer around <i>E. coli</i>, we performed multiple experiments.  
 
<ul><li>Rhodamine 123 staining</li>
 
<ul><li>Rhodamine 123 staining</li>
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Cells were stained according to the protocol based on Li <i>et al.</i> and Müller <i>et al.</i> [4][5].
 
Cells were stained according to the protocol based on Li <i>et al.</i> and Müller <i>et al.</i> [4][5].
 
Rhodamine was excited with a wavelength of 395 nm.
 
Rhodamine was excited with a wavelength of 395 nm.
 +
 +
<html>
 +
    <figure>
 +
        <center><img src="">
 +
            <figcaption>
 +
                <b>Figure 3</b>: Widefield and fluorescence images of <i>E. coli</i> expressing OmpA-silicatein, treated
 +
                with silicic acid (top) and without silicic acid (bottom). The cells were stained with Rhodamine 123
 +
                and excited at 395 nm.
 +
                Of the widefield and fluorescence images an overlay was made to show the fraction of fluorescent cells.
 +
            </figcaption></center>
 +
    </figure>
 +
</html>
 +
 +
<h3>Viability</h3>
 +
Since the silicatein expressing cells are to cover themselves in polysilicate, their nutrient supply might be limited by diffusion, which can eventually result in cell death. To investigate whether this is indeed the case, a growth study was performed (Figure 4).
 +
Cells were grown overnight in selective LB. They were transfered to fresh medium and grown until in exponential phase. Then IPTG was added to induce expression. After a subsequent incubation of three hours, the medium was supplemented with silicic acid as substrate for silicatein. During the following five hours samples were taken, of which a 10<sup>-6</sup> dilution was plated on selective LB plates. Colony forming units (cfu) were counted the day after. As a negative control, cells expressing another type of silicatein <partinfo>K1890002</partinfo>, not supplemented with silicic acid were used.
 +
<html>
 +
    <figure>
 +
        <center><img src="">
 +
            <figcaption>
 +
                <b>Figure 4</b>: Number of colony forming units (cfu) during incubation with silicic acid.
 +
            </figcaption></center>
 +
    </figure>
 +
</html>
 +
 +
This figure suggests that either the polysilicate layer inhibits nutrient diffusion into the cell, or the sodium silicate has a detrimental effect on growth.
  
 
<h2>References</h2>
 
<h2>References</h2>

Revision as of 21:23, 17 October 2016

Silicatein gene, fused to transmembrane domain of OmpA, with strong RBS

Introduction

Silicatein, originating from the demosponge Tethya aurantium, catalyzes the formation of polysilicate. As described by Curnow et al, the silicatein gene was fused to the transmembrane domain of outer membrane protein A (OmpA), in order to display it at the surface of the cell [1][2]. The fusion of silicatein and OmpA is constructed according to Francisco et al, consisting of the transmembrane domain of OmpA together with the signaling peptide and the first nine N-terminal amino acids of lipoprotein (Lpp), both of which are native proteins from Escherichia coli [3]. The coding sequence in this BioBrick is combined with the strong RBS BBa_B0034.

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BamHI site found at 192
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]

Usage and Biology

Silicatein is an enzyme natively found in demosponges and diatoms, where it catalyzes the condensation of silica to form the typical skeletal elements. Here, we use the enzyme to create a polysilicate layer around the host organism E. coli (Figure 1). The gene is fused to the transmembrane domain of INP in order to display the protein at the cell membrane. This biobrick was expressed in a backbone containing the inducible Lac-promoter.

Figure 1: Silicatein is able to convert monosilicate to polysilicate, allowing the cell to cover itself in polysilicate.

Characterization

This biobrick was expressed in E. coli BL21. Cells were grown overnight in selective LB. They were transfered to fresh medium and grown until in exponential phase. Then IPTG was added to induce expression. After a subsequent incubation of three hours, the medium was supplemented with silicic acid as substrate for silicatein. After another three hours, the silicate layer was considered to be formed. A change in structure was observed for these cultures (Figure 2).

Figure 2: Structure of E. coli culture with polysilicate.

In order to characterize the formation of a polysilicate layer around E. coli, we performed multiple experiments.

  • Rhodamine 123 staining
  • Growth study
  • SEM imaging
  • TEM imaging

Staining with Rhodamine 123

In this experiment we imaged the silicatein expressing cells with a fluorescence microscope, after treating them with a fluorescent dye. The fluorescent dye Rhodamine 123 (Sigma) has shown to bind specifically to polysilicate [4]. Cells were stained according to the protocol based on Li et al. and Müller et al. [4][5]. Rhodamine was excited with a wavelength of 395 nm.

Figure 3: Widefield and fluorescence images of E. coli expressing OmpA-silicatein, treated with silicic acid (top) and without silicic acid (bottom). The cells were stained with Rhodamine 123 and excited at 395 nm. Of the widefield and fluorescence images an overlay was made to show the fraction of fluorescent cells.

Viability

Since the silicatein expressing cells are to cover themselves in polysilicate, their nutrient supply might be limited by diffusion, which can eventually result in cell death. To investigate whether this is indeed the case, a growth study was performed (Figure 4). Cells were grown overnight in selective LB. They were transfered to fresh medium and grown until in exponential phase. Then IPTG was added to induce expression. After a subsequent incubation of three hours, the medium was supplemented with silicic acid as substrate for silicatein. During the following five hours samples were taken, of which a 10-6 dilution was plated on selective LB plates. Colony forming units (cfu) were counted the day after. As a negative control, cells expressing another type of silicatein BBa_K1890002, not supplemented with silicic acid were used.

Figure 4: Number of colony forming units (cfu) during incubation with silicic acid.

This figure suggests that either the polysilicate layer inhibits nutrient diffusion into the cell, or the sodium silicate has a detrimental effect on growth.

References

[1] Curnow, P., Kisailus, D., & Morse, D. E. (2006). Biocatalytic synthesis of poly(L-lactide) by native and recombinant forms of the silicatein enzymes. Angewandte Chemie - International Edition, 45(4), 613–616.

[2] Curnow, P., Bessette, P. H., Kisailus, D., Murr, M. M., Daugherty, P. S., & Morse, D. E. (2005). Enzymatic synthesis of layered titanium phosphates at low temperature and neutral pH by cell-surface display of silicatein-?? Journal of the American Chemical Society, 127(45), 15749–15755.

[3] Francisco, J. a, Earhart, C. F., & Georgiou, G. (1992). Transport and anchoring of beta-lactamase to the external surface of Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America, 89(April), 2713–2717.

[4] Li, C. W., Chu, S., & Lee, M. (1989). Characterizing the silica deposition vesicle of diatoms. Protoplasma, 151(2-3), 158–163.

[5] Müller, W. E. G., Rothenberger, M., Boreiko, A., Tremel, W., Reiber, A., & Schröder, H. C. (2005). Formation of siliceous spicules in the marine demosponge Suberites domuncula. Cell and Tissue Research, 321(2), 285–297.