Team:PennState/diauxie/TheSystem

In wild-type E. coli the xyl operon controls xylose transport and metabolism. The left facing xylAB genes code for xylose isomerase and kinase. The other set of genes, xylFGH, are right facing and code for active xylose transport proteins. A bidirectional operator controls expression of xylAB and xylFGH. The xylR gene encoding the xylose-inducible regulator XylR is located downstream of xylH and is controlled by its own weak promoter. Full transcriptional activation requires binding of cAMP-CRP to a single CRP binding site. From a “biological circuit” perspective, xylose-bound XylR and cAMP-CRP are the two inputs for this “and” logic gate. In the simplest approximation, this is identical to the presence of xylose and the absence of glucose, since cAMP levels generally vary inversely with the cellular glucose concentration. Another protein called XylE is a passive xylose transporter and exists elsewhere in the E. coli chromosome. Overexpression of the xylE gene may help xylose enter the cell and begin its metabolism cycle.

Natural Xylose Operon (E. coli)

The left facing xylAB genes code for xylose isomerase and kinase.
The other set of genes, xylFGH are right facing and code for active xylose transport proteins.
A bidirectional operator is necessary because of the opposite directions of transcriptional control for xylAB and xylFGH.
XylR is located downstream of xylH but is controlled by its own weak promoter and is involved in regulation. Transcription is initiated when the protein XylR binds to xylose; this complex then binds to the XylR binding site located at both ends of the operator.

The presence of xylose and the absence of glucose are required for natural transcriptional activation in the xyl operon. Our goal was to have activation only dependent on the presence of xylose, independently of glucose.

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   <h4><acronym title="Nuclear Hormone Receptor">NHR Biosensors</acronym><br/></h4>
   <dl id="denav">
-   <dd><a href="hbintro" title="Intro to Endocrine Disruption, pseudoestrogens, pthalates, nuclear hormone receptors, and our goals">Introduction</a></dd>
+   <dd><a href="https://2008.igem.org/Team:PennState/NHR/introduction">NHR Introduction</a></dd>
    <dd><a href="https://2008.igem.org/Team:PennState/smartfold/overview">Phthalate Biosensor</a></dd>
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 <hr/>
-<p class="start">In wild-type <em>E. coli</em> the xyl operon controls xylose transport and metabolism.</p>
+<p>In wild-type <em>E. coli</em> the xyl operon controls xylose transport and metabolism.  The left facing <em>xylAB</em> genes code for xylose isomerase and kinase.  The other set of genes, <em>xylFGH</em>, are right facing and code for active xylose transport proteins.  A bidirectional operator controls expression of <em>xylAB</em> and <em>xylFGH</em>.  The <em>xylR</em> gene encoding the xylose-inducible regulator XylR is located downstream of <em>xylH</em> and is controlled by its own weak promoter. Full transcriptional activation requires binding of cAMP-CRP to a single CRP binding site.  From a “biological circuit” perspective, xylose-bound XylR and cAMP-CRP are the two inputs for this “and” logic gate. In the simplest approximation, this is identical to the presence of xylose and the absence of glucose, since cAMP levels generally vary inversely with the cellular glucose concentration. Another protein called XylE is a passive xylose transporter and exists elsewhere in the <em>E. coli</em> chromosome.  Overexpression of the <em>xylE</em> gene may help xylose enter the cell and begin its metabolism cycle.</p>
+<h6>Natural Xylose Operon (<em>E. coli</em>)</h6>
+<img src="https://static.igem.org/mediawiki/2008/0/0a/Xylrplasmidmap.jpg" alt="[Plasmid Map]" title="" style="width: 100%; border: solid 1px #000" />
 <ul>
-  <li>The left facing <b>xylAB</b> genes code for xylose isomerase and kinase.</li>
+  <li>The left facing <em><b>xylAB</b></em> genes code for xylose isomerase and kinase.</li>
-  <li>The other set of genes, <b>xylFGH</b> are <em>right</em> facing and code for active xylose transport proteins.</li>
+  <li>The other set of genes, <em><b>xylFGH</b></em> are <em>right</em> facing and code for active xylose transport proteins.</li>
-  <li>A bidirectional operator is necessary because of the opposite directions of transcriptional control for xylAB and xylFGH.</li>
+  <li>A bidirectional operator is necessary because of the opposite directions of transcriptional control for <em>xylAB</em> and <em>xylFGH</em>.</li>
   <li><b>XylR</b> is located downstream of xylH but is controlled by its own weak promoter and is involved in regulation.  Transcription is initiated when the protein XylR binds to xylose; this complex then binds to the XylR binding site located at both ends of the operator.
 </ul>
-<p>The system also requires binding of the activated complex cAMP-CRP (Cyclic adenosine monophosphate - cAMP Receptor Protein) to the individual CRP binding site to activate transcription.  In terms of circuits, XylR and cAMP-CRP are the two inputs for this “and” logic gate.  The protein cAMP is an indicator of the glucose concentration in the cell and becomes more abundant with glucose depletion.  Another protein called XylE is a passive xylose transporter and exists elsewhere in the <em>E. coli</em> chromosome.  Over expression of the xylE gene may help xylose enter the cell and begin its metabolism cycle.</p>
-<h6>Natural Operation - PN plasmid (see Implementation)</h6>
-<img src="https://static.igem.org/mediawiki/2008/2/21/Xylrplasmidmap.png" alt="[Plasmid Map]" title="" style="width: 100%; border: solid 1px #000" />
 <p>The presence of xylose and the absence of glucose are required for natural transcriptional activation in the xyl operon.  Our goal was to have activation only dependent on the presence of xylose, independently of glucose.</p>