Team:PennState/diauxie/conclusions

We have constructed the xylose-inducible constructs with the GFP reporter and testing is still in progress with newly constructed E. coli cell strains. Eight different tests are being performed to show the effects of sugar induction, XylR expression, and XylE expression. The initial tests were mostly performed with strain DH5α , which contains the entire xyl operon in the chromosome. Xylose metabolism in this strain thus poses a problem during the characterization of our constructs.

Newly constructed strains constitutively express xylR and xylE genes. Intracellular levels of XylR may be too low to accommodate the high copy plasmid used in our studies, and the presence of glucose may alter native XylR expression levels, thereby artificially lowering induction levels. Native xylose transport genes are also subject to glucose repression, so XylE will be independently expressed at high levels to ensure xylose uptake in the presence of glucose. Strain W3110 ∆xylB-G carries deletion in xylose metabolism (xylA and xylB) and transport (xylFGH) genes, and therefore would not cause any unwanted depletion of the xylose during testing of the promoter constructs. The level of induction from the test constructs with and without XylR production will be compared to evaluate the role of XylR levels on induction. Similarly, the effect of having XylE as the sole transporter will be studied. Strain W3110 ∆xylB-R is similar to the ∆xylB-G strain but also does not express XylR, and will serve to further study the role of XylR (no induction should be observed in the absence of XylR).

The W3110 ∆xylB-G cell strain alone will not exhibit any xylose metabolism or transport, and therefore would not cause any unwanted depletion of the xylose available for activation of the test constructs. The level of induction from the test constructs with and without XylR production will be compared to see the significance of XylR levels on induction. Similarly the effect of having XylE as the sole transport mechanism will also be observed.

Understanding the behaviour of these constructs will provide valuable insights into the natural control region and its dependence on both xylose transport and XylR concentration for induction. These studies will also help us further characterize our engineered promoter, and to find the conditions where glucose/xylose diauxie is eliminated.

One of our hypotheses is that XylR interacts with RNA polymerase to strengthen its binding. Xylose-bound XylR should positively regulate transcription, and the hope is that a strengthened promoter sequence will still require activation by XylR (and not just increase constitutivity). If this turns out not to be the case, the we have proposed a third strategy involving the xyl transcriptional control region from Bacillus sp. In this system XylR (which is very different from the XylR produced by E. coli) is known to act as a repressor, such that xylose binding to XylR derepresses and enables RNA polymerase binding and transcriptional activation. The “diauxie” phenotype that occurs for xyl expression in Bacillus is due to the ability of glucose (or glucose phosphate) to directly interact with XylR and influence its repressor functions. To eliminate glucose sensitivity, we are engineering the Bacillus XylR regulatory protein to act independently of glucose or other metabolites resulting from glucose metabolism.

@@ Line 161: / Line 161: @@
   <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>
@@ Line 172: / Line 172: @@
 <td valign="top" id="pagecontent" width="80%"><span style="font-size: 16pt">Conclusions</span>
 <hr/>
-<p class="start">Even though we have created the xylose inducible constructs with the GFP reporter, further testing is in progress with the newly created E. coli cell lines.  There are eight different tests that could be performed to show the effects of sugar induction, xylR production, and xylE production.  The tests previously performed were mostly in DH5α E. coli cells which contain the entire xyl operon in the chromosome.  This means that without our constructs in the cell, xylose would be naturally metabolized.  The fluorescence testing results would reflect the xylose metabolism from the natural behavior instead of the inserted plasmid.</p>
+<p class="start">We have constructed the xylose-inducible constructs with the GFP reporter and testing is still in progress with newly constructed <em>E. coli</em> cell strains.  Eight different tests are being performed to show the effects of sugar induction, XylR expression, and XylE expression. The initial tests were mostly performed with strain DH5α , which contains the entire xyl operon in the chromosome.  Xylose metabolism in this strain thus poses a problem during the characterization of our constructs. </p>
-<p>The W3110 ∆xylB-G cells have no xylose metabolism and should not grow at all with xylose.  The fluorescence results should show altering levels with xylose induction since there is still xylR present.  The W3110 ∆xylB-R cells should show no xylose induction with any of the promoters since there will be no xylR protein present.  Both of these cells will be tested with xylR constitutive production on the plasmid, xylE constitutive production, or a combination of both.  These tests should show different fluorescence strengths for sugar induction.  The strongest effect should occur with xylR and xylE under control of the constitutive promoter on the plasmid, in the W3110 ∆xylB-R cells.  </p>
+<p>Newly constructed strains constitutively express xylR and xylE genes. Intracellular levels of XylR may be too low to accommodate the high copy plasmid used in our studies, and the presence of glucose may alter native XylR expression levels, thereby artificially lowering induction levels. Native xylose transport genes are also subject to glucose repression, so XylE will be independently expressed at high levels to ensure xylose uptake in the presence of glucose. Strain W3110 ∆xylB-G carries deletion in xylose metabolism (<em>xylA</em> and <em>xylB</em>) and transport (<em>xylFGH</em>) genes, and therefore would not cause any unwanted depletion of the xylose during testing of the promoter constructs.  The level of induction from the test constructs with and without XylR production will be compared to evaluate the role of XylR levels on induction.  Similarly, the effect of having XylE as the sole transporter will be studied. Strain W3110 ∆xylB-R is similar to the ∆xylB-G strain but also does not express XylR, and will serve to further study the role of XylR (no induction should be observed in the absence of XylR). </p>
-<p>We hope to see more of a difference in glucose-xylose induction between the natural promoter and our engineered promoters.  Because we are increasing the strength of the RNA polymerase binding site to resemble a constitutive promoter sequence, there is the possibility that XylR binding will have no effect on our system.  We are hoping that XylR interacts with the polymerase to strengthen its binding, therefore causing xylose to positively regulate transcription.  If this turns out to not be the case than we have a third strategy that involves using the xyl transcriptional control region from Bacillus bacteria.  In this system XylR acts as a repressor, only xylose binding to XylR allows transcription to take place.  We would put a constitutive promoter upstream of this region causing the genes to be expressed only in the presence of xylose.</p>
+<p>The W3110 ∆xylB-G cell strain alone will not exhibit any xylose metabolism or transport, and therefore would not cause any unwanted depletion of the xylose available for activation of the test constructs.  The level of induction from the test constructs with and without XylR production will be compared to see the significance of XylR levels on induction.  Similarly the effect of having XylE as the sole transport mechanism will also be observed. </p>
+<p>Understanding the behaviour of these constructs will provide valuable insights into the natural control region and its dependence on both xylose transport and XylR concentration for induction.  These studies will also help us further characterize our engineered promoter, and to find the conditions where glucose/xylose diauxie is eliminated. </p>
+<p>One of our hypotheses is that XylR interacts with RNA polymerase to strengthen its binding. Xylose-bound XylR should positively regulate transcription, and the hope is that a strengthened promoter sequence will still require activation by XylR (and not just increase constitutivity). If this turns out not to be the case, the we have proposed a third strategy involving the xyl transcriptional control region from Bacillus sp.  In this system XylR (which is very different from the XylR produced by E. coli) is known to act as a repressor, such that xylose binding to XylR derepresses and enables RNA polymerase binding and transcriptional activation. The “diauxie” phenotype that occurs for xyl expression in Bacillus is due to the ability of glucose (or glucose phosphate) to directly interact with XylR and influence its repressor functions. To eliminate glucose sensitivity, we are engineering the Bacillus XylR regulatory protein to act independently of glucose or other metabolites resulting from glucose metabolism.</p>