Team:CIDEB-UANL Mexico/project union

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<p><i>E. coli</i> needs to resist saline environments, UV rays and temperature changes in order to capture Na+ ions, and produce an aroma as a reporter, everything in the water. That is why it is necessary to remove <i>E. coli</i> from the water in order to obtain usable water; through a biofilter it was easy to do.</p>
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<p>We choose silica as the material for our biofilter, so we make that <i>E. coli</i> expressed a membrane protein which could have the ability for binding silica, and in that way remove <i>E. coli</i> from the water. This was possible for the circuit created by UANL Mexico 2012 team; they created a circuit to make <i>E. coli</i> attached to silica, but as they did not prove it, we want to determine if it really works or not.</p>
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<p>After E.CARU performs its other tasks, in order to remove <i>E. coli</i> from the salty water for making it useful, the ability for binding to silica was introduced to the bacteria. Using this ability, it would be easy to clean the water free of bacterium through a biological filter.</p>
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<td style="padding-left:12px;"><img width=200 height=200 src="https://static.igem.org/mediawiki/2014hs/c/cf/Logo_silica.png"/></td>
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<td style="padding-left:12px;"><img width=154 height=133 src="https://static.igem.org/mediawiki/2014hs/c/cf/Logo_silica.png"/>
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<p><b>How is composed?</b></p>
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<p><b><h2>Description</h2></b></p>
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<p>The binding circuit consists mainly in a fusion protein (a set which includes the CDS L2 with its peptide signal and AIDA) in order to make the protein for binding silica, a membrane protein. In that way <i>E. coli</i> would attach to silica.</p>
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<p><b>L2</b></p>
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<p>The gene L2 encodes for a protein that is able to attach to silica. Taniguchi et al. reported in 2007 that the L2 ribosomal protein from <i>E. coli</i> strongly binds to silica surfaces, even up to 200 times tighter than poliarginine tags commonly used for protein purification. In their work, Taniguchi et al. (2007) constructed a fusion protein containing L2 and green fluorescent protein (GFP) which kept attached to a silica surface even after been washed for 24 hours with a buffer containing 1 M NaCl (<b>Figure 1</b>). <a href="https://2012.igem.org/Team:UANL_Mty-Mexico">UANL Mexico 2012</a> did not have this piece in stock, so we decided to synthetize L2 along with a peptide signal.</p>
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<center><p><img width=704 height=202 src="https://static.igem.org/mediawiki/2014hs/9/92/Composicion_silica.png"
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<center><p><img width=237 height=140 src="https://static.igem.org/mediawiki/2014hs/0/05/Silica_washed.png"align=center hspace=12 alt="IMG_0317"></p>
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align=center hspace=12 alt="IMG_0317"></p></center>
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<p><b>How act L2 and AIDA together?</b></p>
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<p><b>Figure 1.</b> Proteins absorbed to a silica slide and washed for 24 hours a)GFP b) L2-GFP fusion c) R9-GFP fusion. Taken from Taniguchi (2007)</p></center>
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<br>
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<p>The gene L2 encodes for a protein able to attach to silica. Taniguchi et al. reported in 2007 that the L2 ribosomal protein from <i>E. coli</i> strongly adsorbs to silica surfaces, up to 200 times tighter than poliarginine tags commonly used for protein purification. In their work, Taniguchiet al. 2007, constructed a fusion protein of L2 and green fluorescent protein (GFP) which adsorbed to a silica surface even after washing for 24 hours with a buffer containing 1 M NaCl (Figure 3).</p>
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<P><b>AIDA</b></p>
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<p>AIDA-I is an <i>E. coli</i> membrane protein with a passenger domain of 76 kDa exposed to the extracellular space and a transmembrane beta-barrel domain of 45 kDa; the latter has been used to express functional proteins in the cell-membrane of up to 65 kDa (van Bloois et al., 2011). Furthermore passengers coupled to AIDA-I have been reported to reach an expression level of more than 100,000 copies per cell in the outer membrane (Jose and Meyer, 2007). </p><center>
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<center><p><img width=300 height=302 src="https://static.igem.org/mediawiki/2014hs/9/9e/Silica_test.png"
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<p><img width=226 height=251 src="https://static.igem.org/mediawiki/2014hs/a/a2/Aida_system.png"align=center hspace=12 alt="IMG_0317"></p>
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align=center hspace=12 alt="IMG_0317"></p></center>
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<p>AIDA-I is an <i>E. coli</i> membrane protein with a passenger domain of 76 kDa exposed to the extracellular space and a transmembrane beta-barrel domain of 45 kDa; the latter has been used to express functional proteins in the cell-membrane of up to 65 kDa (van Bloois et al., 2011). Furthermore passengers coupled to AIDA-I have been reported to reach an expression level of more than 100,000 copies per cell in the outer membrane (Jose and Meyer, 2007). AIDA-1 allows the expression of proteins larger than small peptides in the outer membrane what makes it the best option to use with L2.</p>
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<p><b>Figure 2.</b> Schematic representation of AIDA-I carrier protein</p></center>
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<br>
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<p><b>How much is important to use BgIII and BamHI to link L2 and AIDA-I?</b></p>
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<p><b>How do L2 and AIDA act together?</b></p>
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<p>As AIDA is a membrane protein producer and L2 produces a protein for making possible the attachment to silica, the team decided to make a fusion protein, so that the protein produced by L2 can be translocated to the membrane of the bacteria with the help of AIDA, and in that way, binding the E.CARU to silica pearls for being filtered.</p>
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<p>In order to make a fusion protein we cannot use SpeI and XbaI to join them because the reading frame would change making a completely different protein. So in order to avoid such problem we use BgIII and BamHI instead which can join AIDA and L2 without changing the reading frame. The scar produced between BamHI and BgIII, as is shown in the figure 2, is formed by six bases respecting the reading frame from both proteins in order to synthetize the correct protein.</p>
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<p><b>Why is it important to use BgIII and BamHI to link L2 and AIDA-I?</b></p>
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<center><p><img width=504 height=302 src="https://static.igem.org/mediawiki/2014hs/5/51/BgIII_y_BamHI.png"
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<p>It was needed to join both proteins in order to make a fusion protein, but SpeI and XbaI could not be used to join them because the reading frame would change, coding for a completely different protein. In order to avoid such problem, BgIII and BamHI were used instead, which could join AIDA and L2 without changing the reading frame. The scar produced between BamHI and BgIII, as it is shown in <b>Figure 3</b>, is formed by six bases, respecting the reading frame from both proteins in order to synthetize the correct protein.</p>
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align=center hspace=12 alt="IMG_0317"></p></center>
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<p><b>Parts of the module</b></p>
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<p><img width=397 height=222 src="https://static.igem.org/mediawiki/2014hs/b/b5/Bg_y_bam_III.png"align=center hspace=12 alt="IMG_0317"></p>
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<center><p><img width=621 height=682 src="https://static.igem.org/mediawiki/2014hs/a/a1/Tabla3CIDEB.jpg"
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<p><b>Figure 3.</b> Example of a ligation using BamHI and BgIII</p></center>
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align=center hspace=12 alt="IMG_0317"></p></center>
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<p><b>Other teams that used it:</b></p>
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<p><b><h2>Device</h2></b></p>
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<p>UANL México 2012: They proposed the fusion protein for using it to binding silica after detect and capture arsenic acid in groundwater, and in that way removed the pollutant arsenic acid from the water, as part of water bioremediation, but they did not finish it. That is why we want to determine if it will work.</p>
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<p>Initially, L2+AIDA and IrrE, protein for giving resistance to <i>E. coli</i> to adverse conditions (<a href="https://2014hs.igem.org/Team:CIDEB-UANL_Mexico/project_resistance">Resistance module</a>), were joined together in only one circuit, but we needed to separate them because L2+AIDA has not been tested and it could affect the production of IrrE (see <b>Figure 4.</b>) as well as for testing each module alone.</p>
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<p><b>How to create a biofilter?</b></p>
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<center><p><img width=529 height=322 src="https://static.igem.org/mediawiki/2014hs/0/05/Circuit_l2_and_irre.png"align=center hspace=12 alt="IMG_0317"></p>
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<p>Although <i>E. coli</i> could acquire the ability for binding silica, we need to create a biofilter to remove bacteria from water. Our proposal as biofilter is shown in the next figure:</p>
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<p><b>Figure 4.</b> Circuit for our project and for testing resistance and union modules. </p></center>
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<br>
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<center><p><img width=204 height=502 src="https://static.igem.org/mediawiki/2014hs/e/e2/Biofiltro.png"
+
<p>The union circuit consists mainly of a constitutive promoter, an RBS, a peptide signal attached to L2 and this attached to AIDA by a scar and a terminator. The device is designed this way in order to produce a protein that helps the bacteria to bind to silica.</p>
-
align=center hspace=12 alt="IMG_0317"></p></center>
+
-
<p><b>References</b></p>
+
<center><p><img width=463 height=101 src="https://static.igem.org/mediawiki/2014hs/9/92/Composicion_silica.png"align=center hspace=12 alt="IMG_0317"></p></center><center>
-
<p>Part BBa_K888000 (2012). Retrieved on March 29th, 2014, from: http://parts.igem.org/wiki/index.php?title=Part:BBa_K888000.</p>
+
<p><b>Figure 5.</b> Union Device</p></center>
-
<p>Part BBa_K888001 (2012). Retrieved on March 29th, 2014, from: http://parts.igem.org/wiki/index.php?title=Part:BBa_K888001.</p>
+
<br>
-
<p>Part:BBa_B0034. (2013). Retrieved on March 30th, 2014, from: http://parts.igem.org/wiki/index.php?title=Part:BBa_B0034.</p>
+
-
<p>Part:BBa_J23119. (2006). Retrieved on April 30, 2014, from: http://parts.igem.org/wiki/index.php?title=Part:BBa_J23119.</p>
+
-
<p>Part BBa_K888005 (2012). Retrieved on March 29th, from: http://parts.igem.org/wiki/index.php?title=Part:BBa_K888005.</p>
+
-
<p>UANL Mexico (2012). Recovery module. Retrieved on March 28th, from: https://2012.igem.org/Team:UANL_Mty-Mexico/Project/recovery.</p>
+
-
<div style="text-align: right;"><a href="https://2014hs.igem.org/Team:CIDEB-UANL_Mexico/project_union#"><font color="blue">Return to the Top</font></a></p></div>
+
<p><b><h2>Parts of the module</h2></b></p>
 +
<br><center>
 +
 +
<div>
 +
<table border=0 cellspacing=0 cellpadding=0 width=700 style='width:441.4pt;margin-left:25.5pt;border-collapse: collapse;mso-yfti-tbllook:1184;mso-padding-alt:0cm 5.4pt 0cm 5.4pt;mso-border-insideh: .5pt solid windowtext;mso-border-insidev:.5pt solid windowtext'>
 +
<tr style='mso-yfti-irow:-1;mso-yfti-firstrow:yes;mso-yfti-lastfirstrow:yes'>
 +
<td width=120 valign=top style='width:89.95pt;border:none;border-bottom:solid #AE78D6 1.0pt; mso-border-bottom-alt:solid #AE78D6 .5pt;background:white;mso-background-themecolor: background1;padding:0cm 5.4pt 0cm 5.4pt'>
 +
 +
<p class=MsoNormal align=center style='margin-bottom:0cm;margin-bottom:.0001pt; text-align:center;line-height:normal;mso-yfti-cnfc:517'><b style='mso-bidi-font-weight: normal'>
 +
 +
<span lang=ES-MX style='font-size:12.0pt;font-family:Oxygen; mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:major-fareast; mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:major-bidi; mso-bidi-font-style:italic'>IMAGE<o:p></o:p>
 +
</span></b></p>
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</td>
 +
<td width=122 valign=top style='width:91.85pt;border:none;border-bottom:solid #934BC9 1.0pt; mso-border-bottom-alt:solid #934BC9 .5pt;background:white;mso-background-themecolor: background1;padding:0cm 5.4pt 0cm 5.4pt'>
 +
 +
<p class=MsoNormal align=center style='margin-bottom:0cm;margin-bottom:.0001pt; text-align:center;line-height:normal;mso-yfti-cnfc:1'><b style='mso-bidi-font-weight: normal'>
 +
 +
<span lang=ES-MX style='font-size:12.0pt;font-family:Oxygen; mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font:major-fareast; mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font:major-bidi; mso-bidi-font-style:italic'>CODE<o:p></o:p>
 +
</span></b></p>
 +
</td>
 +
<td width=346 valign=top style='width:259.6pt;border:none;border-bottom:solid #AE78D6 1.0pt; mso-border-bottom-alt:solid #AE78D6 .5pt;background:white;mso-background-themecolor: background1;padding:0cm 5.4pt 0cm 5.4pt'>
 +
 +
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;line-height: normal;tab-stops:85.15pt center 130.35pt;mso-yfti-cnfc:1'><b style='mso-bidi-font-weight:normal'>
 +
 +
<span lang=ES-MX style='font-size:12.0pt; font-family:Oxygen;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font: major-fareast;mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font: major-bidi;mso-bidi-font-style:italic'>
 +
 +
<span style='mso-tab-count:2'>
 +
</span>DESCRIPTION<o:p></o:p>
 +
</span></b></p>
 +
</td>
 +
</tr>
 +
<tr style='mso-yfti-irow:0'>
 +
<td width=120 valign=top style='width:89.95pt;border:none;border-right:solid #AE78D6 1.0pt; mso-border-top-alt:solid #AE78D6 .5pt;mso-border-top-alt:solid #AE78D6 .5pt; mso-border-right-alt:solid #AE78D6 .5pt;background:white;mso-background-themecolor: background1;padding:0cm 5.4pt 0cm 5.4pt'>
 +
 +
<p class=MsoNormal align=right style='margin-bottom:0cm;margin-bottom:.0001pt; text-align:right;line-height:normal;mso-yfti-cnfc:68'>
 +
<!--[if gte vml 1]><v:shape id="_x0000_s1062" type="#_x0000_t75" style='position:absolute;left:0; text-align:left;margin-left:11.6pt;margin-top:3.55pt;width:54.05pt;height:41.3pt; z-index:251671552;mso-position-horizontal-relative:text; mso-position-vertical-relative:text;mso-width-relative:page; mso-height-relative:page'> <v:imagedata src="Tablas%20Capture%20y%20Binding_archivos/image013.png" o:title=""/> <w:wrap type="square"/> </v:shape><![if gte mso 9]><o:OLEObject Type="Embed" ProgID="PBrush" ShapeID="_x0000_s1062" DrawAspect="Content" ObjectID="_1464162125"> </o:OLEObject> <![endif]><![endif]--><![if !vml]><img width=72 height=55 src="https://static.igem.org/mediawiki/2014hs/e/e0/PromoterCIDEB.jpg" align=left hspace=12 v:shapes="_x0000_s1062"><![endif]>
 +
 +
<span style='font-size:12.0pt;font-family:Oxygen;mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:major-fareast;mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:major-bidi;mso-ansi-language:EN-US;mso-bidi-font-style: italic'><o:p></o:p>
 +
</span></p>
 +
</td>
 +
<td width=122 valign=top style='width:91.85pt;border-top:none;border-left: none;border-bottom:solid #AE78D6 1.0pt;border-right:solid #AE78D6 1.0pt; mso-border-top-alt:solid #934BC9 .5pt;mso-border-left-alt:solid #AE78D6 .5pt; mso-border-alt:solid #AE78D6 .5pt;mso-border-top-alt:solid #934BC9 .5pt; background:#F3DEFC;padding:0cm 5.4pt 0cm 5.4pt'>
 +
 +
<p class=MsoNormal align=center style='margin-bottom:0cm;margin-bottom:.0001pt; text-align:center;line-height:normal;mso-yfti-cnfc:64'>
 +
 +
<span style='font-size:12.0pt;font-family:Oxygen;mso-ansi-language:EN-US'><a href="http://parts.igem.org/Part:_BBa_J23119">BBa_J23119</a>
 +
</span>
 +
 +
<span style='font-size:7.0pt;mso-bidi-font-size:12.0pt;font-family:Oxygen; color:red;mso-ansi-language:EN-US'>
 +
</span></p>
 +
</td>
 +
<td width=346 valign=top style='width:259.6pt;border-top:none;border-left: none;border-bottom:solid #AE78D6 1.0pt;border-right:solid #AE78D6 1.0pt; mso-border-top-alt:solid #AE78D6 .5pt;mso-border-left-alt:solid #AE78D6 .5pt; mso-border-alt:solid #AE78D6 .5pt;background:#F3DEFC;padding:0cm 5.4pt 0cm 5.4pt'>
 +
 +
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align: justify;line-height:normal;mso-yfti-cnfc:64'>
 +
 +
<span lang=ES-MX style='font-size:12.0pt;font-family:Oxygen'>The J23119 is the most effective and common constitutive promoter used. It has a length of 35bp.<o:p></o:p>
 +
</span></p>
 +
</td>
 +
</tr>
 +
<tr style='mso-yfti-irow:1'>
 +
<td width=120 valign=top style='width:89.95pt;border:none;border-right:solid #AE78D6 1.0pt; mso-border-right-alt:solid #AE78D6 .5pt;background:white;mso-background-themecolor: background1;padding:0cm 5.4pt 0cm 5.4pt'>
 +
 +
<p class=MsoNormal align=center style='margin-bottom:0cm;margin-bottom:.0001pt; text-align:center;line-height:normal;mso-yfti-cnfc:4'>
 +
<!--[if gte vml 1]><v:shape id="Picture_x0020_11" o:spid="_x0000_s1067" type="#_x0000_t75" style='position:absolute; left:0;text-align:left;margin-left:12.55pt;margin-top:1.55pt;width:52.6pt; height:49.9pt;z-index:251669504;visibility:visible;mso-wrap-style:square; mso-width-percent:0;mso-height-percent:0;mso-wrap-distance-left:9pt; mso-wrap-distance-top:0;mso-wrap-distance-right:9pt; mso-wrap-distance-bottom:0;mso-position-horizontal:absolute; mso-position-horizontal-relative:text;mso-position-vertical:absolute; mso-position-vertical-relative:text;mso-width-percent:0; mso-height-percent:0;mso-width-relative:page;mso-height-relative:page'> <v:imagedata src="Tablas%20Capture%20y%20Binding_archivos/image015.png" o:title=""/> <w:wrap type="square"/> </v:shape><![endif]--><![if !vml]><img width=70 height=67 src="https://static.igem.org/mediawiki/2014hs/3/30/CDSCIDEB.jpg" align=left hspace=12 v:shapes="Picture_x0020_11"><![endif]></p>
 +
</td>
 +
<td width=122 valign=top style='width:91.85pt;border-top:none;border-left: none;border-bottom:solid #934BC9 1.0pt;border-right:solid #AE78D6 1.0pt; mso-border-top-alt:solid #AE78D6 .5pt;mso-border-left-alt:solid #AE78D6 .5pt; mso-border-alt:solid #AE78D6 .5pt;mso-border-bottom-alt:solid #934BC9 .5pt; padding:0cm 5.4pt 0cm 5.4pt'>
 +
 +
<p class=MsoNormal align=center style='margin-bottom:0cm;margin-bottom:.0001pt; text-align:center;line-height:normal'>
 +
 +
<span style='font-size:12.0pt; font-family:Oxygen;mso-ansi-language:EN-US'><a href="http://parts.igem.org/Part:_BBa%C2%AD_B0034">BBa­_B0034</a>
 +
</span></p>
 +
</td>
 +
<td width=346 valign=top style='width:259.6pt;border-top:none;border-left: none;border-bottom:solid #AE78D6 1.0pt;border-right:solid #AE78D6 1.0pt; mso-border-top-alt:solid #AE78D6 .5pt;mso-border-left-alt:solid #AE78D6 .5pt; mso-border-alt:solid #AE78D6 .5pt;padding:0cm 5.4pt 0cm 5.4pt'>
 +
 +
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align: justify;line-height:normal'>
 +
 +
<span lang=ES-MX style='font-size:12.0pt; font-family:Oxygen'>This specific RBS is based on Elowitz repressilator. It has a length of 12bp.<o:p></o:p>
 +
</span></p>
 +
</td>
 +
</tr>
 +
<tr style='mso-yfti-irow:2'>
 +
<td width=120 valign=top style='width:89.95pt;border:none;border-right:solid #AE78D6 1.0pt; mso-border-right-alt:solid #AE78D6 .5pt;background:white;mso-background-themecolor: background1;padding:0cm 5.4pt 0cm 5.4pt'>
 +
 +
<p class=MsoNormal align=right style='margin-bottom:0cm;margin-bottom:.0001pt; text-align:right;line-height:normal;mso-yfti-cnfc:68'>
 +
<!--[if gte vml 1]><v:shape id="_x0000_s1063" type="#_x0000_t75" style='position:absolute;left:0; text-align:left;margin-left:8.4pt;margin-top:2.55pt;width:52.8pt;height:39.05pt; z-index:251673600;mso-position-horizontal-relative:text; mso-position-vertical-relative:text;mso-width-relative:page; mso-height-relative:page'> <v:imagedata src="Tablas%20Capture%20y%20Binding_archivos/image017.png" o:title=""/> <w:wrap type="square"/> </v:shape><![if gte mso 9]><o:OLEObject Type="Embed" ProgID="PBrush" ShapeID="_x0000_s1063" DrawAspect="Content" ObjectID="_1464162126"> </o:OLEObject> <![endif]><![endif]--><![if !vml]><img width=70 height=52 src="https://static.igem.org/mediawiki/2014hs/5/54/CDS2CIDEB.jpg" align=left hspace=12 v:shapes="_x0000_s1063"><![endif]></p>
 +
</td>
 +
<td width=122 valign=top style='width:91.85pt;border-top:none;border-left: none;border-bottom:solid #AE78D6 1.0pt;border-right:solid #AE78D6 1.0pt; mso-border-top-alt:solid #934BC9 .5pt;mso-border-left-alt:solid #AE78D6 .5pt; mso-border-alt:solid #AE78D6 .5pt;mso-border-top-alt:solid #934BC9 .5pt; background:#F3DEFC;padding:0cm 5.4pt 0cm 5.4pt'>
 +
 +
<p class=MsoNormal align=center style='margin-bottom:0cm;margin-bottom:.0001pt; text-align:center;line-height:normal;mso-yfti-cnfc:64'>
 +
 +
<span style='font-size:12.0pt;font-family:Oxygen;mso-ansi-language:EN-US'><a href="http://parts.igem.org/Part:_BBa_K888000">BBa_K888000</a>
 +
</span></p>
 +
</td>
 +
<td width=346 valign=top style='width:259.6pt;border-top:none;border-left: none;border-bottom:solid #AE78D6 1.0pt;border-right:solid #AE78D6 1.0pt; mso-border-top-alt:solid #AE78D6 .5pt;mso-border-left-alt:solid #AE78D6 .5pt; mso-border-alt:solid #AE78D6 .5pt;background:#F3DEFC;padding:0cm 5.4pt 0cm 5.4pt'>
 +
 +
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align: justify;line-height:normal;mso-yfti-cnfc:64'>
 +
 +
<span style='font-size:12.0pt; font-family:Oxygen;mso-ansi-language:EN-US'>L2. This CDS gives the property for binding silica and glass surfaces to <i>E. coli</i>, it has a length of 819 bp.<o:p></o:p>
 +
</span></p>
 +
</td>
 +
</tr>
 +
<tr style='mso-yfti-irow:3'>
 +
<td width=120 valign=top style='width:89.95pt;border:none;border-right:solid #AE78D6 1.0pt; mso-border-right-alt:solid #AE78D6 .5pt;background:white;mso-background-themecolor: background1;padding:0cm 5.4pt 0cm 5.4pt'>
 +
 +
<p class=MsoNormal align=right style='margin-bottom:0cm;margin-bottom:.0001pt; text-align:right;line-height:normal;mso-yfti-cnfc:4'>
 +
<!--[if gte vml 1]><v:shape id="_x0000_s1064" type="#_x0000_t75" style='position:absolute;left:0; text-align:left;margin-left:8.65pt;margin-top:2.15pt;width:52.55pt;height:40.65pt; z-index:251675648;mso-position-horizontal-relative:text; mso-position-vertical-relative:text;mso-width-relative:page; mso-height-relative:page'> <v:imagedata src="Tablas%20Capture%20y%20Binding_archivos/image019.png" o:title=""/> <w:wrap type="square"/> </v:shape><![if gte mso 9]><o:OLEObject Type="Embed" ProgID="PBrush" ShapeID="_x0000_s1064" DrawAspect="Content" ObjectID="_1464162127"> </o:OLEObject> <![endif]><![endif]--><![if !vml]><img width=70 height=54 src="https://static.igem.org/mediawiki/2014hs/f/f2/CDS3CIDEB.jpg" align=left hspace=12 v:shapes="_x0000_s1064"><i>
 +
 +
<span style='font-size:12.0pt;font-family:Oxygen;mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:major-fareast;mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:major-bidi;mso-ansi-language:EN-US'> <o:p></o:p>
 +
</span></i></p>
 +
</td>
 +
<td width=122 valign=top style='width:91.85pt;border-top:none;border-left: none;border-bottom:solid #AE78D6 1.0pt;border-right:solid #AE78D6 1.0pt; mso-border-top-alt:solid #AE78D6 .5pt;mso-border-left-alt:solid #AE78D6 .5pt; mso-border-alt:solid #AE78D6 .5pt;padding:0cm 5.4pt 0cm 5.4pt'>
 +
 +
<p class=MsoNormal align=center style='margin-bottom:0cm;margin-bottom:.0001pt; text-align:center;line-height:normal'>
 +
 +
<span style='font-size:12.0pt; font-family:Oxygen;mso-ansi-language:EN-US'><a href="http://parts.igem.org/Part:_BBa_K888001">BBa_K888001 </a>
 +
</span></p>
 +
</td>
 +
<td width=346 valign=top style='width:259.6pt;border-top:none;border-left: none;border-bottom:solid #AE78D6 1.0pt;border-right:solid #AE78D6 1.0pt; mso-border-top-alt:solid #AE78D6 .5pt;mso-border-left-alt:solid #AE78D6 .5pt; mso-border-alt:solid #AE78D6 .5pt;padding:0cm 5.4pt 0cm 5.4pt'>
 +
 +
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align: justify;line-height:normal'>
 +
 +
<span lang=ES-MX style='font-size:12.0pt; font-family:Oxygen'>AIDA-I is synthetized as a 132 kDa pre-protein featuring a signal peptide which is cleaved during transport trough the inner membrane, a 78 kDa adhesin (passenger) domain, and a 45 kDa translocator. This autotransporter has a large capability in translocating relatively large passengers from 12-65 kDa by showing a N-terminal type of fusion. Coupled with a passenger domain and a signal peptide (<a href="http://parts.igem.org/Part:BBa_K888005">K888005</a>), it is possible to express functional proteins in the outer membrane of <i>E. coli</i>.
 +
 +
<span style='mso-spacerun:yes'>
 +
</span>It has a length of 1482 bp.<o:p></o:p>
 +
</span></p>
 +
</td>
 +
</tr>
 +
<tr style='mso-yfti-irow:4;height:122.1pt'>
 +
<td width=120 valign=top style='width:89.95pt;border:none;border-right:solid #AE78D6 1.0pt; mso-border-right-alt:solid #AE78D6 .5pt;background:white;mso-background-themecolor: background1;padding:0cm 5.4pt 0cm 5.4pt;height:122.1pt'>
 +
 +
<p class=MsoNormal align=right style='margin-bottom:0cm;margin-bottom:.0001pt; text-align:right;line-height:normal;mso-yfti-cnfc:68'>&nbsp;</p>
 +
 +
<p class=MsoNormal align=right style='margin-bottom:0cm;margin-bottom:.0001pt; text-align:right;line-height:normal;mso-yfti-cnfc:68'>
 +
<!--[if gte vml 1]><v:shape id="_x0000_s1065" type="#_x0000_t75" style='position:absolute;left:0; text-align:left;margin-left:9.8pt;margin-top:3.6pt;width:50.05pt;height:38.05pt; z-index:251677696;mso-position-horizontal-relative:text; mso-position-vertical-relative:text;mso-width-relative:page; mso-height-relative:page'> <v:imagedata src="Tablas%20Capture%20y%20Binding_archivos/image021.png" o:title=""/> <w:wrap type="square"/> </v:shape><![if gte mso 9]><o:OLEObject Type="Embed" ProgID="PBrush" ShapeID="_x0000_s1065" DrawAspect="Content" ObjectID="_1464162128"> </o:OLEObject> <![endif]><![endif]--><![if !vml]><img width=67 height=51 src="https://static.igem.org/mediawiki/2014hs/d/d5/CIDEBCDS5.jpg" align=left hspace=12 v:shapes="_x0000_s1065"><![endif]><i>
 +
 +
<span style='font-size:12.0pt; font-family:Oxygen;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font: major-fareast;mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font: major-bidi;mso-ansi-language:EN-US'><o:p></o:p>
 +
</span></i></p>
 +
</td>
 +
<td width=122 valign=top style='width:91.85pt;border-top:none;border-left: none;border-bottom:solid #AE78D6 1.0pt;border-right:solid #AE78D6 1.0pt; mso-border-top-alt:solid #AE78D6 .5pt;mso-border-left-alt:solid #AE78D6 .5pt; mso-border-alt:solid #AE78D6 .5pt;background:#F3DEFC;padding:0cm 5.4pt 0cm 5.4pt; height:122.1pt'>
 +
 +
<p class=MsoNormal align=center style='margin-bottom:0cm;margin-bottom:.0001pt; text-align:center;line-height:normal;mso-yfti-cnfc:64'>
 +
 +
<span style='font-size:12.0pt;font-family:Oxygen;mso-ansi-language:EN-US'><a href="http://parts.igem.org/Part:_BBa_K888005">BBa_K888005</a>
 +
</span></p>
 +
</td>
 +
<td width=346 valign=top style='width:259.6pt;border-top:none;border-left: none;border-bottom:solid #AE78D6 1.0pt;border-right:solid #AE78D6 1.0pt; mso-border-top-alt:solid #AE78D6 .5pt;mso-border-left-alt:solid #AE78D6 .5pt; mso-border-alt:solid #AE78D6 .5pt;background:#F3DEFC;padding:0cm 5.4pt 0cm 5.4pt; height:122.1pt'>
 +
 +
<p class=MsoNormal style='margin-bottom:0cm;margin-bottom:.0001pt;text-align: justify;line-height:normal;mso-yfti-cnfc:64'>
 +
 +
<span lang=ES-MX style='font-size:12.0pt;font-family:Oxygen'>When this part is coupled with a passenger attached to AIDA-I translocator domain (<a href="http://parts.igem.org/Part:BBa_K888005">K888001</a>), it is possible to express functional proteins in the outer membrane of <i>E. coli</i>. The signal peptide is naturally cleaved during transport trough the inner membrane (Li et al. 2007; van Bloois et al. 2011).It has a length of 147 bp.<o:p></o:p>
 +
</span></p>
 +
</td>
 +
</tr>
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<!--[if gte vml 1]><v:shape id="_x0000_s1066" type="#_x0000_t75" style='position:absolute;left:0; text-align:left;margin-left:17.8pt;margin-top:3.2pt;width:32.25pt;height:44.6pt; z-index:251679744;mso-position-horizontal-relative:text; mso-position-vertical-relative:text;mso-width-relative:page; mso-height-relative:page'> <v:imagedata src="Tablas%20Capture%20y%20Binding_archivos/image023.png" o:title=""/> <w:wrap type="square"/> </v:shape><![if gte mso 9]><o:OLEObject Type="Embed" ProgID="PBrush" ShapeID="_x0000_s1066" DrawAspect="Content" ObjectID="_1464162130"> </o:OLEObject> <![endif]><![endif]--><![if !vml]><img width=43 height=59 src="https://static.igem.org/mediawiki/2014hs/d/d7/STOP.jpg" align=left hspace=12 v:shapes="_x0000_s1066"><![endif]><i>
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<span style='font-size:12.0pt; font-family:Oxygen;mso-fareast-font-family:"Times New Roman";mso-fareast-theme-font: major-fareast;mso-bidi-font-family:"Times New Roman";mso-bidi-theme-font: major-bidi;mso-ansi-language:EN-US'> <o:p></o:p>
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<td width=122 valign=top style='width:91.85pt;border-top:none;border-left: none;border-bottom:solid #AE78D6 1.0pt;border-right:solid #AE78D6 1.0pt; mso-border-top-alt:solid #AE78D6 .5pt;mso-border-left-alt:solid #AE78D6 .5pt; mso-border-alt:solid #AE78D6 .5pt;padding:0cm 5.4pt 0cm 5.4pt;height:51.65pt'>
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<span style='font-size:12.0pt; font-family:Oxygen;mso-ansi-language:EN-US'><a href="http://parts.igem.org/Part:_BBa_B1002">BBa_B1002</a>
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<td width=346 valign=top style='width:259.6pt;border-top:none;border-left: none;border-bottom:solid #AE78D6 1.0pt;border-right:solid #AE78D6 1.0pt; mso-border-top-alt:solid #AE78D6 .5pt;mso-border-left-alt:solid #AE78D6 .5pt; mso-border-alt:solid #AE78D6 .5pt;padding:0cm 5.4pt 0cm 5.4pt;height:51.65pt'>
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<span style='font-size:12.0pt;font-family:Oxygen; mso-ansi-language:EN-US'>Part made of 6bp, responsible for stopping transcription.<o:p></o:p>
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<br>
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<p><b><h2>Justifications</h2></b></p>
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<p>Although <i>E. coli</i> could acquire the ability to bind to silica, a biological filter was designed to remove bacteria from water. The team´s proposed biofilter is shown next:</p>
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<center><p><img width=236 height=346 src="https://static.igem.org/mediawiki/2014hs/e/e2/Biofiltro.png"align=center hspace=12 alt="IMG_0317"></p></center><center>
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<p><b>Figure 6.</b> The team's proposed biofilter model</p></center>
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<p>Silica was chosen as the ideal material because it is cheap and it is commonly found and also because the team wanted to give this material a new use. It was also chosen in order to finish the <a href="https://2012.igem.org/Team:UANL_Mty-Mexico">UANL Mexico 2012</a> team work. They created a circuit to make <i>E. coli</i> bind to silica, but as they did not prove it, we wanted to determine if it is functional.</p>
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<p>AIDA-1 allows the expression of proteins larger than small peptides in the outer membrane, which is why it is the best option to use with L2. AIDA-I was obtained by PCR by <a href="https://2012.igem.org/Team:UANL_Mty-Mexico">UANL Mexico 2012</a>, so we decided use their piece for our project, as it was easy for the team to obtain it because both of the teams are in the same city.</p>
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<p><b><h2>Other teams that used it</h2></b></p>
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<p><b><a href="https://2012.igem.org/Team:UANL_Mty-Mexico">UANL México 2012</a>:</b> They proposed the fusion protein for using it to binding silica after detect and capture arsenic acid in groundwater, and in that way removed the pollutant arsenic acid from the water, as part of water bioremediation. However, their project was not finished.</p>
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<p><h2><b>Union Module Zoom In</b></h2></p></br><center><iframe width="640" height="390" src="//www.youtube.com/embed/PC6pQ6gfT9A" frameborder="0" allowfullscreen></iframe></center>
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<br>
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<p><b><h2>Bibliography/References</h2></b></p><font size="2">
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<p>● Antiquity. (2003). <i>Part:BBa_B0034</i>. Retrieved March 30th, 2014, from <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_B0034">http://parts.igem.org/wiki/index.php?title=Part:BBa_B0034</a>.</p>
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<p>● iGEM2006_Berkeley. (2006). <i>Part:BBa_J23119</i>. Retrieved April 30, 2014, from <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_J23119">http://parts.igem.org/wiki/index.php?title=Part:BBa_J23119</a>.</p>
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<p>● iGEM12_UANL_Mty-Mexico. (2012). <i>Part BBa_K888000</i>. Retrieved March 29th, 2014, from <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K888000">http://parts.igem.org/wiki/index.php?title=Part:BBa_K888000</a>.</p>
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<p>● iGEM12_UANL_Mty-Mexico. (2012). <i>Part BBa_K888001</i>. Retrieved March 29th, 2014, from <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K888001">http://parts.igem.org/wiki/index.php?title=Part:BBa_K888001</a>.</p>
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<p>● iGEM12_UANL_Mty-Mexico. (2012) <i>Part BBa_K888005</i>. Retrieved March 29th,2014, from <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K888005">http://parts.igem.org/wiki/index.php?title=Part:BBa_K888005</a>.</p>
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<p>● UANL Mexico. (2012). <i>Recovery module</i>. Retrieved March 28th,2014, from <a href="https://2012.igem.org/Team:UANL_Mty-Mexico/Project/recovery">https://2012.igem.org/Team:UANL_Mty-Mexico/Project/recovery</a>.</p> </p></font>
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<div style="text-align: right;"><a href="https://2014hs.igem.org/Team:CIDEB-UANL_Mexico/project_union#"><font color="blue">Return to the Top</font></a></p>
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Latest revision as of 23:03, 20 June 2014

iGEM CIDEB 2014 - Project

Union Module

After E.CARU performs its other tasks, in order to remove E. coli from the salty water for making it useful, the ability for binding to silica was introduced to the bacteria. Using this ability, it would be easy to clean the water free of bacterium through a biological filter.

Description

L2

The gene L2 encodes for a protein that is able to attach to silica. Taniguchi et al. reported in 2007 that the L2 ribosomal protein from E. coli strongly binds to silica surfaces, even up to 200 times tighter than poliarginine tags commonly used for protein purification. In their work, Taniguchi et al. (2007) constructed a fusion protein containing L2 and green fluorescent protein (GFP) which kept attached to a silica surface even after been washed for 24 hours with a buffer containing 1 M NaCl (Figure 1). UANL Mexico 2012 did not have this piece in stock, so we decided to synthetize L2 along with a peptide signal.

IMG_0317

Figure 1. Proteins absorbed to a silica slide and washed for 24 hours a)GFP b) L2-GFP fusion c) R9-GFP fusion. Taken from Taniguchi (2007)


AIDA

AIDA-I is an E. coli membrane protein with a passenger domain of 76 kDa exposed to the extracellular space and a transmembrane beta-barrel domain of 45 kDa; the latter has been used to express functional proteins in the cell-membrane of up to 65 kDa (van Bloois et al., 2011). Furthermore passengers coupled to AIDA-I have been reported to reach an expression level of more than 100,000 copies per cell in the outer membrane (Jose and Meyer, 2007).

IMG_0317

Figure 2. Schematic representation of AIDA-I carrier protein


How do L2 and AIDA act together?

As AIDA is a membrane protein producer and L2 produces a protein for making possible the attachment to silica, the team decided to make a fusion protein, so that the protein produced by L2 can be translocated to the membrane of the bacteria with the help of AIDA, and in that way, binding the E.CARU to silica pearls for being filtered.

Why is it important to use BgIII and BamHI to link L2 and AIDA-I?

It was needed to join both proteins in order to make a fusion protein, but SpeI and XbaI could not be used to join them because the reading frame would change, coding for a completely different protein. In order to avoid such problem, BgIII and BamHI were used instead, which could join AIDA and L2 without changing the reading frame. The scar produced between BamHI and BgIII, as it is shown in Figure 3, is formed by six bases, respecting the reading frame from both proteins in order to synthetize the correct protein.


IMG_0317

Figure 3. Example of a ligation using BamHI and BgIII

Device

Initially, L2+AIDA and IrrE, protein for giving resistance to E. coli to adverse conditions (Resistance module), were joined together in only one circuit, but we needed to separate them because L2+AIDA has not been tested and it could affect the production of IrrE (see Figure 4.) as well as for testing each module alone.

IMG_0317

Figure 4. Circuit for our project and for testing resistance and union modules.


The union circuit consists mainly of a constitutive promoter, an RBS, a peptide signal attached to L2 and this attached to AIDA by a scar and a terminator. The device is designed this way in order to produce a protein that helps the bacteria to bind to silica.

IMG_0317

Figure 5. Union Device


Parts of the module


IMAGE

CODE

DESCRIPTION

BBa_J23119

The J23119 is the most effective and common constitutive promoter used. It has a length of 35bp.

BBa­_B0034

This specific RBS is based on Elowitz repressilator. It has a length of 12bp.

BBa_K888000

L2. This CDS gives the property for binding silica and glass surfaces to E. coli, it has a length of 819 bp.

BBa_K888001

AIDA-I is synthetized as a 132 kDa pre-protein featuring a signal peptide which is cleaved during transport trough the inner membrane, a 78 kDa adhesin (passenger) domain, and a 45 kDa translocator. This autotransporter has a large capability in translocating relatively large passengers from 12-65 kDa by showing a N-terminal type of fusion. Coupled with a passenger domain and a signal peptide (K888005), it is possible to express functional proteins in the outer membrane of E. coli. It has a length of 1482 bp.

 

BBa_K888005

When this part is coupled with a passenger attached to AIDA-I translocator domain (K888001), it is possible to express functional proteins in the outer membrane of E. coli. The signal peptide is naturally cleaved during transport trough the inner membrane (Li et al. 2007; van Bloois et al. 2011).It has a length of 147 bp.

BBa_B1002

Part made of 6bp, responsible for stopping transcription.


Justifications

Although E. coli could acquire the ability to bind to silica, a biological filter was designed to remove bacteria from water. The team´s proposed biofilter is shown next:

IMG_0317

Figure 6. The team's proposed biofilter model

Silica was chosen as the ideal material because it is cheap and it is commonly found and also because the team wanted to give this material a new use. It was also chosen in order to finish the UANL Mexico 2012 team work. They created a circuit to make E. coli bind to silica, but as they did not prove it, we wanted to determine if it is functional.

AIDA-1 allows the expression of proteins larger than small peptides in the outer membrane, which is why it is the best option to use with L2. AIDA-I was obtained by PCR by UANL Mexico 2012, so we decided use their piece for our project, as it was easy for the team to obtain it because both of the teams are in the same city.

Other teams that used it

UANL México 2012: They proposed the fusion protein for using it to binding silica after detect and capture arsenic acid in groundwater, and in that way removed the pollutant arsenic acid from the water, as part of water bioremediation. However, their project was not finished.

Union Module Zoom In



Bibliography/References

● Antiquity. (2003). Part:BBa_B0034. Retrieved March 30th, 2014, from http://parts.igem.org/wiki/index.php?title=Part:BBa_B0034.

● iGEM2006_Berkeley. (2006). Part:BBa_J23119. Retrieved April 30, 2014, from http://parts.igem.org/wiki/index.php?title=Part:BBa_J23119.

● iGEM12_UANL_Mty-Mexico. (2012). Part BBa_K888000. Retrieved March 29th, 2014, from http://parts.igem.org/wiki/index.php?title=Part:BBa_K888000.

● iGEM12_UANL_Mty-Mexico. (2012). Part BBa_K888001. Retrieved March 29th, 2014, from http://parts.igem.org/wiki/index.php?title=Part:BBa_K888001.

● iGEM12_UANL_Mty-Mexico. (2012) Part BBa_K888005. Retrieved March 29th,2014, from http://parts.igem.org/wiki/index.php?title=Part:BBa_K888005.

● UANL Mexico. (2012). Recovery module. Retrieved March 28th,2014, from https://2012.igem.org/Team:UANL_Mty-Mexico/Project/recovery.


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