Team:Chiba/Project/uptake

From 2013.igem.org

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<h2 id="uptake" style="background-color:#ff9933"><center>Uptake</center></h2>
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<h2 id="uptake" style="background-color:#ff9933"><center>Reprogramming Iron Homeostasis</center></h2>
<h3 style="background-color:#ffdead ">1.Introduction</h3>
<h3 style="background-color:#ffdead ">1.Introduction</h3>
 +
<p>&nbsp;&nbsp;&nbsp;&nbsp;To maximize the chance of magnetization, we would like to pump as much Fe into the cell as possible, and keep it. To this end, we tried to eliminate the negative controller (encoded by <i>fur</i>) on the <i>Fec</i> system (iron importer). Also, we tried to knock down the Fe exporter <i>fie</i>F. </p>
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<h3 style="background-color:#f0ffff ">Target-1:<i>fur</i></h3>
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<p>&nbsp;&nbsp;&nbsp;&nbsp;<i>Fur</i> (Ferric uptake regulator) controls multiple stages of iron metabolism such as taking iron in or storing iron. Major mode-of-action is in binding to <i>Fur</i> box to regulate transcription of various genes involved in the iron homeostasis.
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When cellular level of iron increase, <i>Fur</i> turns into the activated form, thereby start restricting the reproduction of the iron transporter (Fec system). Long story short, it ends up with down-regulating the iron uptake. At the same time, this active form <i>Fur</i> negatively controls the expression ofRyhB. RyhB is one of the sRNA that represses the expression of endogenous Ferritin.  So, turning <i>Fur</i> in active form (by increasing cellular iron concentration) leads to the induction of ferritin construction.<br><br><br>
<p>
<p>
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<h3 style="background-color:#f0ffff ">1.1.<i>Fur</i></h3>
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When iron level get back, <i>Fur</i> turn back to inactive state, thereby restoring the iron uptaking machineries. RyhB would also work normally, so expression of ferritin is down-regulated to prevent iron depletion. On the other hand, other iron importing system EfeUOB recognizes rather ascorbic type and more specialized in importing Fe(II). EfeUOB is also controlled by <i>Fur</i>:  When the level of Fe(II) becomes too high, <i>Fur</i> restricts EfeUOB and block uptaking the iron (II).
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<p>&nbsp;&nbsp;&nbsp;&nbsp;<i>Fur</i> (Ferric uptake regulator) controls iron metabolism such as taking iron in or storing iron.<br>
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<br><br><br>
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&nbsp;&nbsp;&nbsp;&nbsp;In most cases, it combines with <i>Fur</i> box (which is near the promoter) and regulates transcription.</p>
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</p>
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<p>&nbsp;&nbsp;&nbsp;&nbsp;When iron is rich, <i>Fur</i> becomes active and when <i>Fur</i> becomes active, it restricts the expression of iron transporter, and that means that the iron uptake would stop. At the same time,<i> Fur</i> restricts the expression of <i>Ryh</i>B. <i>RyhB</i> is one of the sRNA that restricts the expression of Ferritin, so making <i>Fur</i> active leads ferritin to express.<br>
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&nbsp;&nbsp;&nbsp;&nbsp;Conversely, when iron is lacking, <i>Fur</i> becomes inactive, and the iron transporter would work normally, so iron would be taken in. <i>Ryh</i>B would also work normally, so expression of ferritin is restricted and Ferritin wouldn't be expressed.<br>
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&nbsp;&nbsp;&nbsp;&nbsp;In short, if we knockdown/knockout <i>Fur</i>, iron transporter would be active so iron would be taken in, but the expression of Ferritin is stopped by <i>Ryh</i>B.</p><br>
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<br>
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<h3 style="background-color:#f0ffff ">1.2.<i>fie</i>F</h3>
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<p>&nbsp;&nbsp;&nbsp;&nbsp;There is a Regulator called <i>fie</i>F (ferric iron efflux). It makes iron and zinc flow out of cell and controls detoxification of cell. When <i>fie</i>F is knocked down/out, the tolerance of cell to iron would be lowered.<br>
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<br>
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&nbsp;&nbsp;&nbsp;&nbsp;<i>Fec</i> has a character that can recognize ferric citrate and taking Fe(III) in. <i>Fec</i> is controlled by <i>Fur</i> and when the density of Fe(III) in the cell is too high, <i>Fur</i> restricts Fec and stops iron uptake.<br>
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&nbsp;&nbsp;&nbsp;&nbsp;In the same way, <i>Efe</i>UOB has a character that can recognize ascorbic acid and taking Fe(II) in. <i>Efe</i>UOB is also controlled by <i>Fur</i> and when the density of Fe(II) in the cell is too high, <i>Fur</i> restricts <i>EfeUOB</i> and stops iron uptake.<br>
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<br>
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&nbsp;&nbsp;&nbsp;&nbsp;Using these characters, and by knocking down/out <i>Fur</i> and <i>fie</i>F, <i>Fec</i>/<i>Efe</i>UOB expression wouldn't be restricted so the amount of iron coming in would increase and the amount of iron going out would decrease. The system would work like when iron is lacking.<br>
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<br>
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&nbsp;&nbsp;&nbsp;&nbsp;As a result, the amount of  iron inside <i>E. coli</i> would increase.</p>
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<br><center><img src="https://static.igem.org/mediawiki/2013/f/f8/Uptake_image.PNG" width="723px"height="305px"></center><br>
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 +
<p>
 +
In summary, fur plays important roles iron homeostasis, and it is by nature a negative regulator for iron update.  We would like to knockdown Fur so that iron transporter system would stay active even at the 'too much' situation.  Possible downside could be that it also reduce the endogenous Ferritin formation, but we are constructing artificial (arabinose-inducible) system to functionally express human ferritins.<br><br><br>
</p>
</p>
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<h3 style="background-color:#ffdead ">2.Materials&Methods</h3>
 
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<h3 style="background-color:#f0ffff ">2.1.plasmid construct</h3>
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<h3 style="background-color:#f0ffff ">Target-2:<i>fie</i>F</h3>
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<p>
<p>
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&nbsp;&nbsp;&nbsp;&nbsp;We constructed four plasmids knocking down <i>fur</i>, <i>fie</i>F, <i>gor</i>, and <i>trx</i>B. at the same time, in order to confirm the function of dCas9, we constructed a plasmid knocking down <i>lacZ</i>.<br>
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There is a Regulator called fieF (ferric iron efflux). It makes iron and zinc flow out of cell and contribute to the detoxification of cell from various chemicals. It is known that the knock out of this fieF result in increase in iron accumulation <a href="https://2013.igem.org/Team:Chiba/Reference"><sup>4</sup></a>
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プラスミドについて書く<br>
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. Interestingly, this efflux pump is reported to be out of the complex regulation network of iron homeostasis (not regulated by fur at all).  <br><br><br>
 +
Thus, by temporary knocking down Fur, the expression of Fec/EfeUOB expression wouldn't be restricted so the amount of iron coming in would increase and the amount of iron going out would decrease. The system would work like when iron is lacking.<br><br>
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<a href="#">Part link</a><br><br>
 
</p>
</p>
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<h3 style="background-color:#f0ffff ">2.2.Evaluation of <i>Fur</i>,<i>fie</i>F knockdown</h3>
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<p>
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&nbsp;&nbsp;&nbsp;&nbsp;We performed two experiments about CRISPRi system in order to confirm the knockdown function as desired. The purpose is a function check for <i>lacZ</i>, <i>Fur</i>, <i>fie</i>F, <i>gor</i>, and <i>trx</i>B. <br>
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<br><center><img src="https://static.igem.org/mediawiki/2013/f/f8/Uptake_image.PNG" width="723px"height="305px"></center><br>
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<h3 style="background-color:#ffdead ">2. Experimental Results</h3>
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 +
 
 +
 
 +
<h3 style="background-color:#f0ffff ">2.1. Toward Blick for temporal/ inducible KO of the target gene</h3>
 +
<P>
 +
Because of the physiological impact to the host cell, we decided not to go for normal, permanent removal of the target genes (fur/ fieF) in the genome. Also, the gene knock-out (via genome editing) is chassis engineering, not the BioBrick construction.  To best enjoy the portability of plasmid (BioBrick), it is ideal to make plasmid-coded gene-knockout system.  To this end, we decided to establish temporal knockdown systems using recently developed CRISPRi system.  <br>
 +
We constructed four plasmids for the knocking down each of fur, fieF, gor, and trxB. Alongside, we also constructed a plasmid knocking down lacZ.<br>
 +
The key regulating molecule (the mutant dCas9) is expressed in trans using another plasmid.  Expression of dCas9 is induced by the addition of anhydro Tetracycline (aTc).<br
 +
</p>
<center><img src="https://static.igem.org/mediawiki/2013/7/7f/Chiba.CRISPRi.kan.png"alt=""align="middle"></center><br>
<center><img src="https://static.igem.org/mediawiki/2013/7/7f/Chiba.CRISPRi.kan.png"alt=""align="middle"></center><br>
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<center><p><b>Fig. 1</b> the method of function check about <i>fur</i></p></center>
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<center><p><b>Fig. 1</b> the method of function check about dCas9</p></center>
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<a href="https://2013.igem.org/Team:Chiba/Assay/uptake">Assay</a>
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<a href="https://2013.igem.org/Team:Chiba/Assay/uptake"><p>Assay</p></a>
</p>
</p>
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<h3 style="background-color:#f0ffff ">2.3.Evaluation of absorbed iron volume</h3>
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<h3 style="background-color:#f0ffff ">2.2. CRISPRi as inducible knockdown platform
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</h3>
<p>
<p>
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<b>Experiment:</b><br>
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We tested CRISPRi system for the aTc-inducing knockdown for the model targeted site lacZ. 
 +
1) In the absence of anhydro Tetracycline (aTc), CRISPRi-medeated lacZ gene transcriptional silencing is not supposed to occur.  Indeed, we observed blue-colored colonies in aTc (-) plate.  This means lacZ is well expressed.
 +
2) In the presence of aTc, CRISPRi-medeated lacZ gene transcriptional silencing should occur.  Yes, we saw drastic decrease in color of colony in aTc (+) plate.  Thus, the expression of lacZ is repressed as we designed.
 +
</P>
 +
<center><img src="https://static.igem.org/mediawiki/2013/a/a6/Chiba.CRISPRi-lacZ.png"alt=""align="middle"></center><br>
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<center><p><b>Fig. 2</b> Function check about CRISPRi-<i>lacZ</i></p></center><br>
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<h3 style="background-color:#f0ffff ">2.3. Inducible knockdown of targeted locus
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</h3>
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<left><img src="https://static.igem.org/mediawiki/2013/3/3f/CRISPRi.PNG" width="409px"height="88px"></left>
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<p>
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<right><img src="https://static.igem.org/mediawiki/2013/2/23/DCas9.PNG" width="306px"height="110px"></right><br>
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Then we tried to knockdown our target site Fur.
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<center><b>Fig. a</b></center>
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<br><p>&nbsp;&nbsp;&nbsp;&nbsp;<i>E. coli</i> stain BL21 was transformed by Plasmid shown in <b>Fig. a</b> .&nbsp;Then we cultured all transformants with atC.&nbsp; atC was added to knock down <i>fur</i> and <i>fie</i>F.&nbsp; After that we cultured it in the presence of ferric citrate, and measured the density of iron that weren’t taken in to <i>E. coli</i> and remained in the medium by measuring Absorbance (Abs 756) with color reagent.</p>
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1) To confirm the effective knock-down of the gene, we engineered a strain that has kanamycin resistance gene right after the target sequence (within the reading frame of fur).: See Fig1.<br>
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 +
2) CRISPRi-medeated fur gene transcriptional silencing was performed by expressing dCas9 together with engineered snRNA targeted to fur. <br>
 +
 
 +
3) The resultant transformant was resistance to kanamysin (see left panel of Fig. 3), but it shows kanamycin sensitivity upon addition of aTc.  This clearly shows that the CRISPRi system is effectively silencing the transcription of the targeted locus (fur).<br>
</p>
</p>
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<h3 style="background-color:#ffdead ">3.Results & Discussion</h3>
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<h3 style="background-color:#f0ffff ">2.4. The effect of knockdown of fur on iron uptake
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</h3>
<p>
<p>
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<h3 style="background-color:#f0ffff ">3.1.plasmid建設の説明</h3>
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Experiment: E. coli stain BL21 transformed with Plasmid shown in Fig. 4 was cultured in the presence of aTc.  Then the transformant was cultured in the media containing ferric citrate.  The conc. of iron left in the media was measured by titration using specialized indicator for irons.<br><br>
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<h3 style="background-color:#f0ffff ">3.2.Function Check</h3>
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 +
Results: In summary, we did not observe any increase in iron uptake, even in the condition that fur or fieF was successfully silenced.  We want to combine all the knock-down guiders for fur and fieF in hope for the synergistic effect on ion uptake/ storage.  Also, we would like to combine these system with ferritin-expressing devices we developed alongside.  Also, putting all systems into Biobrick is also our hope to finish soon (without any problem:  in next couple of weeks, we are done!  -note on Sept 27th).
<br>
<br>
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<center><img src="https://static.igem.org/mediawiki/2013/2/26/Chiba.CRISPRi.spot.png"alt=""align="middle"></center><br>
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</p>
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<center><p><b>Fig. 2</b>CRISPRi efficiently silence transcription</p></center><br>
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<h3 style="background-color:#ffdead ">3.Results & Discussion</h3>
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<br>
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<p>
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<center><img src="https://static.igem.org/mediawiki/2013/a/a6/Chiba.CRISPRi-lacZ.png"alt=""align="middle"></center><br>
 
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<center><p><b>Fig. 3</b> Function check about CRISPRi-<i>lacZ</i></p></center><br>
 
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<h3 style="background-color:#f0ffff ">3.1.Function Check</h3>
 +
<p>
1) In the absence of anhydro Tetracycline (aTc), CRISPRi-medeated <i>lac</i>Z gene transcriptional silencing did not occur, resulting in blue-colored colony in which <i>lac</i>Z was expressed.<br>
1) In the absence of anhydro Tetracycline (aTc), CRISPRi-medeated <i>lac</i>Z gene transcriptional silencing did not occur, resulting in blue-colored colony in which <i>lac</i>Z was expressed.<br>
2) In the presence of aTc, CRISPRi-medeated <i>lac</i>Z gene transcriptional silencing successfully occurred, resulting in colorless colony in which <i>lac</i>Z was not expressed.<br>
2) In the presence of aTc, CRISPRi-medeated <i>lac</i>Z gene transcriptional silencing successfully occurred, resulting in colorless colony in which <i>lac</i>Z was not expressed.<br>
3) CRISPRi-medeated <i>fur</i> gene transcriptional silencing successfully occurred, resulting in the loss of kanamysin resistance.<br>
3) CRISPRi-medeated <i>fur</i> gene transcriptional silencing successfully occurred, resulting in the loss of kanamysin resistance.<br>
 +
</p>
 +
<br>
 +
<center><img src="https://static.igem.org/mediawiki/2013/2/26/Chiba.CRISPRi.spot.png"alt=""align="middle"></center><br>
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<center><p><b>Fig. 3</b>CRISPRi efficiently silence transcription</p></center><br>
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<br>
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<h3 style="background-color:#f0ffff ">3.3.A knockdown of <i>fie</i>F or fur has no effect on iron uptake  </h3>
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<h3 style="background-color:#f0ffff ">3.2.A knockdown of <i>fie</i>F or <i>fur</i> has no effect on iron uptake  </h3>
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<center><img src="https://static.igem.org/mediawiki/2013/f/f0/Chiba_shimamura_special.png"width="800px"></center><br>
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<center>Fig. 4 BL21およびSHuffleでの、各プラスミドを導入した大腸菌の鉄試薬別のabsorbance</center><br>
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<center><img src="https://static.igem.org/mediawiki/2013/5/5e/Chiba_shimamura_kennryousen.png"width="800px"></center><br>
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<center>Fig. 4 BL21およびSHuffleでの、各プラスミドを導入した大腸菌の鉄試薬別のabsorbance</center><br>
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<p>
  Iron uptake was not detectable (iron concentration changes in media were less than micro molar order), even if <i>fur</i> or <i>fie</i>F was successfully knocked down.<br>
  Iron uptake was not detectable (iron concentration changes in media were less than micro molar order), even if <i>fur</i> or <i>fie</i>F was successfully knocked down.<br>
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A future subject is to experiment   
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A future subject is to experiment at more cell number of <i>E. coli</i>.<br>
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今後の課題としては、さらに多い細胞数での定量、または、加える鉄試薬の濃度をさらに調整しなおす必要がある。<br>
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</p>
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<center><img src="https://static.igem.org/mediawiki/2013/0/0d/Chiba_shimamura_super.png"width="800px"></center><br>
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<center><p><b>Fig. 4 </b>Absorbance at each cell number of <i>E. coli</i>(BL21 and <a href="https://www.neb.com/products/c3025-shuffle-competent-e-coli">SHuffle®</a> introduced each plusmid</p></center><br>
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<center><img src="https://static.igem.org/mediawiki/2013/a/a2/Chiba_shimamura_ultra.png"width="800px"></center><br>
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<center><p><b>Fig. 5</b> Absorbance of as a function of each iron concentration</p></center><br>
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<center><img src="https://static.igem.org/mediawiki/2013/7/7f/Chiba_tetui.png"width="387px"height="537px"></center><br>
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<center><p><b>Fig. 6</b></p></center><br>
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<h3 style="background-color:#ffdead ">4.Conclusion</h3>
 
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<p>
 
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それは・・
 
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</p>
 

Latest revision as of 04:16, 28 September 2013

iGEM-2013 Chiba

iGEM-2013 Chiba

Reprogramming Iron Homeostasis

1.Introduction

    To maximize the chance of magnetization, we would like to pump as much Fe into the cell as possible, and keep it. To this end, we tried to eliminate the negative controller (encoded by fur) on the Fec system (iron importer). Also, we tried to knock down the Fe exporter fieF.

Target-1:fur

    Fur (Ferric uptake regulator) controls multiple stages of iron metabolism such as taking iron in or storing iron. Major mode-of-action is in binding to Fur box to regulate transcription of various genes involved in the iron homeostasis. When cellular level of iron increase, Fur turns into the activated form, thereby start restricting the reproduction of the iron transporter (Fec system). Long story short, it ends up with down-regulating the iron uptake. At the same time, this active form Fur negatively controls the expression ofRyhB. RyhB is one of the sRNA that represses the expression of endogenous Ferritin. So, turning Fur in active form (by increasing cellular iron concentration) leads to the induction of ferritin construction.


When iron level get back, Fur turn back to inactive state, thereby restoring the iron uptaking machineries. RyhB would also work normally, so expression of ferritin is down-regulated to prevent iron depletion. On the other hand, other iron importing system EfeUOB recognizes rather ascorbic type and more specialized in importing Fe(II). EfeUOB is also controlled by Fur: When the level of Fe(II) becomes too high, Fur restricts EfeUOB and block uptaking the iron (II).


In summary, fur plays important roles iron homeostasis, and it is by nature a negative regulator for iron update. We would like to knockdown Fur so that iron transporter system would stay active even at the 'too much' situation. Possible downside could be that it also reduce the endogenous Ferritin formation, but we are constructing artificial (arabinose-inducible) system to functionally express human ferritins.


Target-2:fieF

There is a Regulator called fieF (ferric iron efflux). It makes iron and zinc flow out of cell and contribute to the detoxification of cell from various chemicals. It is known that the knock out of this fieF result in increase in iron accumulation 4 . Interestingly, this efflux pump is reported to be out of the complex regulation network of iron homeostasis (not regulated by fur at all).


Thus, by temporary knocking down Fur, the expression of Fec/EfeUOB expression wouldn't be restricted so the amount of iron coming in would increase and the amount of iron going out would decrease. The system would work like when iron is lacking.



2. Experimental Results

2.1. Toward Blick for temporal/ inducible KO of the target gene

Because of the physiological impact to the host cell, we decided not to go for normal, permanent removal of the target genes (fur/ fieF) in the genome. Also, the gene knock-out (via genome editing) is chassis engineering, not the BioBrick construction. To best enjoy the portability of plasmid (BioBrick), it is ideal to make plasmid-coded gene-knockout system. To this end, we decided to establish temporal knockdown systems using recently developed CRISPRi system.
We constructed four plasmids for the knocking down each of fur, fieF, gor, and trxB. Alongside, we also constructed a plasmid knocking down lacZ.
The key regulating molecule (the mutant dCas9) is expressed in trans using another plasmid. Expression of dCas9 is induced by the addition of anhydro Tetracycline (aTc).


Fig. 1 the method of function check about dCas9

Assay

2.2. CRISPRi as inducible knockdown platform

We tested CRISPRi system for the aTc-inducing knockdown for the model targeted site lacZ. 1) In the absence of anhydro Tetracycline (aTc), CRISPRi-medeated lacZ gene transcriptional silencing is not supposed to occur. Indeed, we observed blue-colored colonies in aTc (-) plate. This means lacZ is well expressed. 2) In the presence of aTc, CRISPRi-medeated lacZ gene transcriptional silencing should occur. Yes, we saw drastic decrease in color of colony in aTc (+) plate. Thus, the expression of lacZ is repressed as we designed.


Fig. 2 Function check about CRISPRi-lacZ


2.3. Inducible knockdown of targeted locus

Then we tried to knockdown our target site Fur. 1) To confirm the effective knock-down of the gene, we engineered a strain that has kanamycin resistance gene right after the target sequence (within the reading frame of fur).: See Fig1.
2) CRISPRi-medeated fur gene transcriptional silencing was performed by expressing dCas9 together with engineered snRNA targeted to fur.
3) The resultant transformant was resistance to kanamysin (see left panel of Fig. 3), but it shows kanamycin sensitivity upon addition of aTc. This clearly shows that the CRISPRi system is effectively silencing the transcription of the targeted locus (fur).

2.4. The effect of knockdown of fur on iron uptake

Experiment: E. coli stain BL21 transformed with Plasmid shown in Fig. 4 was cultured in the presence of aTc. Then the transformant was cultured in the media containing ferric citrate. The conc. of iron left in the media was measured by titration using specialized indicator for irons.

Results: In summary, we did not observe any increase in iron uptake, even in the condition that fur or fieF was successfully silenced. We want to combine all the knock-down guiders for fur and fieF in hope for the synergistic effect on ion uptake/ storage. Also, we would like to combine these system with ferritin-expressing devices we developed alongside. Also, putting all systems into Biobrick is also our hope to finish soon (without any problem: in next couple of weeks, we are done! -note on Sept 27th).

3.Results & Discussion

3.1.Function Check

1) In the absence of anhydro Tetracycline (aTc), CRISPRi-medeated lacZ gene transcriptional silencing did not occur, resulting in blue-colored colony in which lacZ was expressed.
2) In the presence of aTc, CRISPRi-medeated lacZ gene transcriptional silencing successfully occurred, resulting in colorless colony in which lacZ was not expressed.
3) CRISPRi-medeated fur gene transcriptional silencing successfully occurred, resulting in the loss of kanamysin resistance.



Fig. 3CRISPRi efficiently silence transcription




3.2.A knockdown of fieF or fur has no effect on iron uptake

Iron uptake was not detectable (iron concentration changes in media were less than micro molar order), even if fur or fieF was successfully knocked down.
A future subject is to experiment at more cell number of E. coli.


Fig. 4 Absorbance at each cell number of E. coli(BL21 and SHuffle® introduced each plusmid



Fig. 5 Absorbance of as a function of each iron concentration



Fig. 6