Team:Bielefeld-CeBiTec/Notebook/StrainsAndConstructs

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<h1> Strains and Constructs </h1>
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<h1> Strains </h1>
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   <td style="font-family:Georgia"><div class="element" style="margin:0px; text-align:center"><a href="#General"><img src="https://static.igem.org/mediawiki/2014/3/35/Bielefeld_CeBiTec_2014-08-25_ecoliGeneral.png" width="150px" height="150px" align="center"><br>General</a></div></td>
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                <a href="#DH5&alpha;">DH5&alpha;</a>
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  <td style="font-family:Georgia"><div class="element" style="margin:0px; text-align:center"><a href="#Module1"><img src="https://static.igem.org/mediawiki/2014/3/35/Bielefeld_CeBiTec_2014-08-14_ecoliM1.jpg"  width="150px" height="150px" align="center"><br>Module 1</div></a></td>
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<a href="https://static.igem.org/mediawiki/2014/ .pdf" target="_blank"> <img src="https://static.igem.org/mediawiki/2014/b/bd/Bielefeld-CeBiTec_2014-08-12_pdf_Icon.png" height="30px"> </a>
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  <td style="font-family:Georgia"><div class="element" style="margin:0px; text-align:center"><a href="#Module2"><img src="https://static.igem.org/mediawiki/2014/6/69/Bielefeld_CeBiTec_2014-10-06_ecoliM2.jpg" width="150px" height="150px" align="center"><br>Module 2</div></a></td>
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            </div>
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  <td style="font-family:Georgia"><div class="element" style="margin:0px; text-align:center"><a href="#Module3"><img src="https://static.igem.org/mediawiki/2014/d/d7/Bielefeld_CeBiTec_2014-08-14_ecoliM3.jpg" width="150px" height="150px" align="center"><br>Module 3</div></a></td>
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  <td style="font-family:Georgia"><div class="element" style="margin:0px; text-align:center"><a href="#Biosafety"><img src="https://static.igem.org/mediawiki/2014/8/8a/Bielefeld_CeBiTec_2014-08-26_ecoliBiosafety.png"  width="150px" height="150px" align="center"><br>Biosafety</div></a></td>
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                <a  style="font-size:24px" href="#"><h6>DH5&alpha;  <a href="https://static.igem.org/mediawiki/2014/ .pdf" target="_blank"> <img src="https://static.igem.org/mediawiki/2014/b/bd/Bielefeld-CeBiTec_2014-08-12_pdf_Icon.png" height="30px"> </a></h6></a>
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<table width="100%" border="1" cellpadding="5" style="background-color:transparent">
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<tr width="100%" bgcolor="#006b60">
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  <th width="30%" align="center">Name</th>
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  <th width="40%" align="center">Properties / Genotype</th>
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  <th width="30%" align="center">BioBrick / Reference</th>
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</tr>
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<tr bgcolor="#3fb498">
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  <th colspan="3" align="left" id="General">General</th>
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</tr>
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<tr>
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<td width="30%" id=""> <a href=http://www.promega.de/resources/protocols/technical-bulletins/101/single-step-krx-competent-cells-protocol> <i>Escherichia coli</i> KRX </a></td>
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<td width="40%">[F ́,traD36,ΔompP,proA+B+,lacIq,Δ(lacZ)M15]ΔompT,endA1,recA1,gyrA96(Nalr),thi-1,hsdR17 (rK–, mK+), e14–(McrA–),relA1,supE44,Δ(lac-proAB),Δ(rhaBAD)::T7 RNA polymerase</td>
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<td width="30%">Promega</td>
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</tr>
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 +
<tr>
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<td width="30%" id=""> <a href=http://tools.lifetechnologies.com/content/sfs/manuals/11319019.pdf> <i>E. coli</i> DH5&alpha; </a></td>
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<td width="40%">F-φ80lacZ∆M15∆(lacZYA-argF) U169recA1endA1hsdR17(rk-, mk+)gal-phoAsupE44λ-thi-1gyrA96relA1 </td>
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<td width="30%">invitrogen</td>
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</tr>
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<tr bgcolor="#3fb498">
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  <th colspan="3" align="left" id="Module1">Module 1</th>
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</tr>
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<tr>
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<td width="30%" id="KRXdeltadcuB"> <i>E.coli</i> KRX &Delta;dcuB::oprF</td>
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<td width="40%">[F ́,traD36,ΔompP,proA+B+,lacIq,Δ(lacZ)M15]ΔompT,endA1,recA1,gyrA96(Nalr),thi-1,hsdR17 (rK–, mK+), e14–(McrA–),relA1,supE44,Δ(lac-proAB),Δ(rhaBAD)::T7 RNA polymerase, &Delta;dcuB::oprF </td>
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<td width="30%"> <a href="http://parts.igem.org/Part:BBa_K1172507">BBa_K1172507</a></td>
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</tr>
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 +
 
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<tr>
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<td width="30%" id="deltadcuBKEIO"><a href="http://cgsc.biology.yale.edu/Strain.php?ID=109221">JW4084-1</a></td>
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<td width="40%">&Delta;dcuB749::kan</td>
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<td width="30%"><a href="#baba2006"> Baba et al., 2006 </a></td>
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</tr>
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 +
 
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<tr>
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<td width="30%" id="deltafrdKEIO"><a href="http://cgsc.biology.yale.edu/Strain.php?ID=106931">JW0506-1</a></td>
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<td width="40%">&Delta;fdrA730::kan</td>
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<td width="30%"><a href="#baba2006"> Baba et al., 2006 </a></td>
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</tr>
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 +
 
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<tr>
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<td width="30%" id=""><a href="http://www.dsmz.de/catalogues/details/culture/DSM-22257.html"><i> Actinobacillus succinogenes 130Z </i></a></td>
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<td width="40%">wild type</td>
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<td width="30%"><a href="#guettler1999">Guettler et al., 1999</a></td>
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</tr>
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 +
<tr>
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<td width="30%" id=""><i><a href="http://www.dsmz.de/catalogues/details/culture/DSM-12127.html"> Geobacter sulfurreducens PCA </i> </a></td>
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<td width="40%">wild type</td>
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<td width="30%"><a href="#viulu2013">Viulu et al., 2013</a></td>
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</tr>
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<tr bgcolor="#3fb498">
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  <th colspan="3" align="left" id="Module2">Module 2</th>
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</tr>
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<tr>
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<td width="30%" id=""> <a href="http://www.neb.com/products/c2530-bl21-competent-e-coli#tabselect0"> <i>E.coli</i> BL21</td>
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<td width="40%">F– ompT gal dcm lon hsdSB(rB- mB-) λ(DE3 [lacI lacUV5-T7 gene 1 ind1 sam7 nin5]) </td>
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<td width="30%">NEB</td>
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</tr>
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<tr bgcolor="#3fb498">
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  <th colspan="3" align="left" id="Module3">Module 3</th>
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</tr>
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 +
<tr>
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<td width="30%" id="DeltaAdh"> <a href=http://cgsc.biology.yale.edu/Strain.php?ID=107394> JW1228-1 </a> </td>
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<td width="40%">&Delta;adhE748::kan</td>
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<td width="30%"><a href="#baba2006"> Baba et al., 2006 </a> </td>
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</tr>
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 +
<tr bgcolor="#3fb498">
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  <th colspan="3" align="left" id="Biosafety">Biosafety</th>
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</tr>
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<tr>
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<td width="30%" id=""> <i>E. coli</i> KRX Δalr</td>
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<td width="40%">[F ́,traD36,ΔompP,proA+B+,lacIq,Δ(lacZ)M15]ΔompT,endA1,recA1,gyrA96(Nalr),thi-1,hsdR17 (rK–, mK+), e14–(McrA–),relA1,supE44,Δ(lac-proAB),Δ(rhaBAD)::T7 RNA polymerase, Δalr</td>
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<td width="30%"></td>
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</tr>
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 +
<tr>
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<td width="30%" id=""> <i>E. coli</i> KRX ΔdadX </td>
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<td width="40%">[F ́,traD36,ΔompP,proA+B+,lacIq,Δ(lacZ)M15]ΔompT,endA1,recA1,gyrA96(Nalr),thi-1,hsdR17 (rK–, mK+), e14–(McrA–),relA1,supE44,Δ(lac-proAB),Δ(rhaBAD)::T7 RNA polymerase, ΔdadX</td>
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<td width="30%"></td>
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</tr>
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 +
<tr>
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<td width="30%" id=""> <i>E. coli</i> KRX Δalr ΔdadX </td>
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<td width="40%">[F ́,traD36,ΔompP,proA+B+,lacIq,Δ(lacZ)M15]ΔompT,endA1,recA1,gyrA96(Nalr),thi-1,hsdR17 (rK–, mK+), e14–(McrA–),relA1,supE44,Δ(lac-proAB),Δ(rhaBAD)::T7 RNA polymerase, ΔdadX, Δalr</td>
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<td width="30%"></td>
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</tr>
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 +
 
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<tr>
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<td width="30%" id=""> <i>E. coli</i> DH5&alpha; Δalr</td>
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<td width="40%">F-φ80lacZ∆M15∆(lacZYA-argF) U169recA1endA1hsdR17(rk-, mk+)gal-phoAsupE44λ-thi-1gyrA96relA1 Δalr</td>
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<td width="30%"></td>
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</tr>
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<tr>
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<td width="30%" id=""> <i>E. coli</i> DH5&alpha; ΔdadX</td>
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<td width="40%">F-φ80lacZ∆M15∆(lacZYA-argF) U169recA1endA1hsdR17(rk-, mk+)gal-phoAsupE44λ-thi-1gyrA96relA1 ΔdadX</td>
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<td width="30%"></td>
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</tr>
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<tr>
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<td width="30%" id=""> <i>E. coli</i> DH5&alpha; Δalr ΔdadX</td>
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<td width="40%">F-φ80lacZ∆M15∆(lacZYA-argF) U169recA1endA1hsdR17(rk-, mk+)gal-phoAsupE44λ-thi-1gyrA96relA1 Δalr ΔdadX</td>
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<td width="30%"></td>
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</tr>
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</table>
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<br><br><br><br>
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<h1>Additional Constructs </h1>
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  <td style="font-family:Georgia"><div class="element" style="margin:0px; text-align:center"><a href="#cGeneral"><img src="https://static.igem.org/mediawiki/2014/3/35/Bielefeld_CeBiTec_2014-08-25_ecoliGeneral.png"  width="150px" height="150px" align="center"><br>General</a></div></td>
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  <td style="font-family:Georgia"><div class="element" style="margin:0px; text-align:center"><a href="#cModule1"><img src="https://static.igem.org/mediawiki/2014/3/35/Bielefeld_CeBiTec_2014-08-14_ecoliM1.jpg"  width="150px" height="150px" align="center"><br>Module 1</div></a></td>
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  <td style="font-family:Georgia"><div class="element" style="margin:0px; text-align:center"><a href="#cModule2"><img src="https://static.igem.org/mediawiki/2014/6/69/Bielefeld_CeBiTec_2014-10-06_ecoliM2.jpg" width="150px" height="150px" align="center"><br>Module 2</div></a></td>
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  <td style="font-family:Georgia"><div class="element" style="margin:0px; text-align:center"><a href="#cModule3"><img src="https://static.igem.org/mediawiki/2014/d/d7/Bielefeld_CeBiTec_2014-08-14_ecoliM3.jpg" width="150px" height="150px" align="center"><br>Module 3</div></a></td>
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  <td style="font-family:Georgia"><div class="element" style="margin:0px; text-align:center"><a href="#cBiosafety"><img src="https://static.igem.org/mediawiki/2014/8/8a/Bielefeld_CeBiTec_2014-08-26_ecoliBiosafety.png"  width="150px" height="150px" align="center"><br>Biosafety</div></a></td>
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  <th width="30%" align="center">Name</th>
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  <th width="40%" align="center">Properties</th>
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  <th width="30%" align="center">BioBrick / Reference</th>
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<tr bgcolor="#3fb498">
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  <th colspan="3" align="left" id="cGeneral">General</th>
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<td width="30%" id="">_</td>
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<td width="40%"></td>
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<td width="30%"></td>
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<tr bgcolor="#3fb498">
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  <th colspan="3" align="left" id="cModule1">Module 1</th>
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<td width="30%" id="">_</td>
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<td width="40%"></td>
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<td width="30%"></td>
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  <th colspan="3" align="left" id="cModule2">Module 2</th>
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<td width="30%" id="pHnCBS1D"><a href="http://www.addgene.org/52065/">pHnCBS1D</a></td>
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<td width="40%"><i>cbbL-cbbS-csoS2-csoS3-csoS4A-csoS4B-csoS1C-csoS1A-csoS1B-csoS1D</i>, Cm<sup>R<sup> </td>
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<td width="30%"><a href="#bonacci2012"> Bonacci et al., 2012 </a></td>
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</tr>
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<tr>
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<td width="30%" id=""> <i>pET16b-glpX<sup>C</sup></i> </td>
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<td width="40%">Amp<sup>R</sup>, <i>glpX<sup>C</sup></i> encodes FBPase/SBPase of <i>Bacillus methanolicus</i></td>
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<td width="30%"><a href="#stolzenberger2013">Stolzenberger al.,2013</a></td>
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</tr>
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<tr>
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<td width="30%" id=""> <i>pSB1A2-T7:prkA</i> </td>
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<td width="40%">Amp<sup>R</sup>, CDS of phosphoribulokinase (<i>prkA</i>) from <i>Synechococcus elongatus</i> under the T7 promoter</td>
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<td width="30%"></td>
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</tr>
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<tr>
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<td width="30%" id=""> <i>pSB1A2-T7:Hneap</i> </td>
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<td width="40%">Amp<sup>R</sup>, CDS of RubisCO (<i>Hneap</i>) from <i>Halothiobacillus neapolitanus</i> under the T7 promoter</td>
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<td width="30%"></td>
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</tr>
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<tr>
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<td width="30%" id=""> <i>pSB1A2-T7:Hneap-prkA</i> </td>
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<td width="40%">Amp<sup>R</sup>, CDS of RubisCO (<i>Hneap</i>) from <i>Halothiobacillus neapolitanus</i> and CDS of prkA from <i>S.elongatus</i> under the T7 promoter</td>
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<td width="30%"></td>
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</tr>
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<tr bgcolor="#3fb498">
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  <th colspan="3" align="left" id="cModule3">Module 3</th>
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</tr>
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<tr>
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<td width="30%" id="pSB1A2_T7_IB"> <i>pSB1A2_T7_alsS_ilvC_ilvD_kivD </td>
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<td width="40%">Isobutanol production pathway under the T7 promoter</td>
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<td width="30%"></td>
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</tr>
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<tr>
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<td width="30%" id="pSB1A2_T7_IB_adhA"> <i>pSB1A2_T7_alsS_ilvC_ilvD_kivD </td>
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<td width="40%">Isobutanol production pathway including the <i>adhA</i> from <i>L. lactis</i> under the T7 promoter</td>
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<td width="30%"></td>
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</tr>
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<tr bgcolor="#3fb498">
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  <th colspan="3" align="left" id="cBiosafety">Biosafety</th>
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</tr>
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<td width="30%" id=""> --- </td>
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  <h6>References</h6>
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<ul>
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                <a href="#KRX">KRX</a>
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<a href="https://static.igem.org/mediawiki/2014/.pdf" target="_blank"> <img src="https://static.igem.org/mediawiki/2014/b/bd/Bielefeld-CeBiTec_2014-08-12_pdf_Icon.png" height="30px"> </a>
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                <a  style="font-size:24px" href="#"><h6>KRX <a href="https://static.igem.org/mediawiki/2014/.pdf"  target="_blank"> <img src="https://static.igem.org/mediawiki/2014/b/bd/Bielefeld-CeBiTec_2014-08-12_pdf_Icon.png" height="30px"> </a></h6></a>
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Stolzenberger, J., Lindner, S.N., Persicke, M., Brautaset, T., and Wendisch, V.F. (2013). Characterization of Fructose 1,6-Bisphosphatase and Sedoheptulose 1,7-Bisphosphatase from the Facultative Ribulose Monophosphate Cycle Methylotroph Bacillus methanolicus. <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3811596/">J Bacteriol</a> 195, 5112–5122.
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Baba, T., T. Ara, M. Hasegawa, Y. Takai, Y. Okumura, M. Baba, K.A. Datsenko, M. Tomita, B.L. Wanner, H. Mori 2006. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. <a href="http://www.ncbi.nlm.nih.gov/pubmed/16738554"> Mol Syst Biol </a> 2:1-11
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<li id="guettler1999">
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Guettler, M. V., Rumler, D., Jain, M. K. (1999). Actinobacillus succinogenes sp. nov., a novel succinic-acid-producing bacterium from the bovine rumen. <a href="http://ijs.sgmjournals.org/content/49/1/207">Int.J.Syst.Bacteriol.</a> 49 : 207-216.
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Viulu, S., Nakamura, K., Kojima, A., Yoshiyasu, Y., Saitou, S., Takamizawa, K. (2013). Geobacter sulfurreducens subsp. ethanolicus, subsp. nov., an ethanol-utilizing dissimilatory Fe(III)-reducing bacterium from a lotus field. <a href="http://www.ncbi.nlm.nih.gov/pubmed/24201144"> J Gen Appl Microbiol </a> 59 ( 5 ): 325-34.
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Latest revision as of 21:49, 17 October 2014


Strains


General

Module 1

Module 2

Module 3

Biosafety

Name Properties / Genotype BioBrick / Reference
General
Escherichia coli KRX [F ́,traD36,ΔompP,proA+B+,lacIq,Δ(lacZ)M15]ΔompT,endA1,recA1,gyrA96(Nalr),thi-1,hsdR17 (rK–, mK+), e14–(McrA–),relA1,supE44,Δ(lac-proAB),Δ(rhaBAD)::T7 RNA polymerase Promega
E. coli DH5α F-φ80lacZ∆M15∆(lacZYA-argF) U169recA1endA1hsdR17(rk-, mk+)gal-phoAsupE44λ-thi-1gyrA96relA1 invitrogen
Module 1
E.coli KRX ΔdcuB::oprF [F ́,traD36,ΔompP,proA+B+,lacIq,Δ(lacZ)M15]ΔompT,endA1,recA1,gyrA96(Nalr),thi-1,hsdR17 (rK–, mK+), e14–(McrA–),relA1,supE44,Δ(lac-proAB),Δ(rhaBAD)::T7 RNA polymerase, ΔdcuB::oprF BBa_K1172507
JW4084-1 ΔdcuB749::kan Baba et al., 2006
JW0506-1 ΔfdrA730::kan Baba et al., 2006
Actinobacillus succinogenes 130Z wild type Guettler et al., 1999
Geobacter sulfurreducens PCA wild type Viulu et al., 2013
Module 2
E.coli BL21 F– ompT gal dcm lon hsdSB(rB- mB-) λ(DE3 [lacI lacUV5-T7 gene 1 ind1 sam7 nin5]) NEB
Module 3
JW1228-1 ΔadhE748::kan Baba et al., 2006
Biosafety
E. coli KRX Δalr [F ́,traD36,ΔompP,proA+B+,lacIq,Δ(lacZ)M15]ΔompT,endA1,recA1,gyrA96(Nalr),thi-1,hsdR17 (rK–, mK+), e14–(McrA–),relA1,supE44,Δ(lac-proAB),Δ(rhaBAD)::T7 RNA polymerase, Δalr
E. coli KRX ΔdadX [F ́,traD36,ΔompP,proA+B+,lacIq,Δ(lacZ)M15]ΔompT,endA1,recA1,gyrA96(Nalr),thi-1,hsdR17 (rK–, mK+), e14–(McrA–),relA1,supE44,Δ(lac-proAB),Δ(rhaBAD)::T7 RNA polymerase, ΔdadX
E. coli KRX Δalr ΔdadX [F ́,traD36,ΔompP,proA+B+,lacIq,Δ(lacZ)M15]ΔompT,endA1,recA1,gyrA96(Nalr),thi-1,hsdR17 (rK–, mK+), e14–(McrA–),relA1,supE44,Δ(lac-proAB),Δ(rhaBAD)::T7 RNA polymerase, ΔdadX, Δalr
E. coli DH5α Δalr F-φ80lacZ∆M15∆(lacZYA-argF) U169recA1endA1hsdR17(rk-, mk+)gal-phoAsupE44λ-thi-1gyrA96relA1 Δalr
E. coli DH5α ΔdadX F-φ80lacZ∆M15∆(lacZYA-argF) U169recA1endA1hsdR17(rk-, mk+)gal-phoAsupE44λ-thi-1gyrA96relA1 ΔdadX
E. coli DH5α Δalr ΔdadX F-φ80lacZ∆M15∆(lacZYA-argF) U169recA1endA1hsdR17(rk-, mk+)gal-phoAsupE44λ-thi-1gyrA96relA1 Δalr ΔdadX




Additional Constructs


General

Module 1

Module 2

Module 3

Biosafety

Name Properties BioBrick / Reference
General
_
Module 1
_
Module 2
pHnCBS1D cbbL-cbbS-csoS2-csoS3-csoS4A-csoS4B-csoS1C-csoS1A-csoS1B-csoS1D, CmR Bonacci et al., 2012
pET16b-glpXC AmpR, glpXC encodes FBPase/SBPase of Bacillus methanolicus Stolzenberger al.,2013
pSB1A2-T7:prkA AmpR, CDS of phosphoribulokinase (prkA) from Synechococcus elongatus under the T7 promoter
pSB1A2-T7:Hneap AmpR, CDS of RubisCO (Hneap) from Halothiobacillus neapolitanus under the T7 promoter
pSB1A2-T7:Hneap-prkA AmpR, CDS of RubisCO (Hneap) from Halothiobacillus neapolitanus and CDS of prkA from S.elongatus under the T7 promoter
Module 3
pSB1A2_T7_alsS_ilvC_ilvD_kivD Isobutanol production pathway under the T7 promoter
pSB1A2_T7_alsS_ilvC_ilvD_kivD Isobutanol production pathway including the adhA from L. lactis under the T7 promoter
Biosafety
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References
  • Stolzenberger, J., Lindner, S.N., Persicke, M., Brautaset, T., and Wendisch, V.F. (2013). Characterization of Fructose 1,6-Bisphosphatase and Sedoheptulose 1,7-Bisphosphatase from the Facultative Ribulose Monophosphate Cycle Methylotroph Bacillus methanolicus. J Bacteriol 195, 5112–5122.
  • Baba, T., T. Ara, M. Hasegawa, Y. Takai, Y. Okumura, M. Baba, K.A. Datsenko, M. Tomita, B.L. Wanner, H. Mori 2006. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2:1-11
  • Guettler, M. V., Rumler, D., Jain, M. K. (1999). Actinobacillus succinogenes sp. nov., a novel succinic-acid-producing bacterium from the bovine rumen. Int.J.Syst.Bacteriol. 49 : 207-216.
  • Viulu, S., Nakamura, K., Kojima, A., Yoshiyasu, Y., Saitou, S., Takamizawa, K. (2013). Geobacter sulfurreducens subsp. ethanolicus, subsp. nov., an ethanol-utilizing dissimilatory Fe(III)-reducing bacterium from a lotus field. J Gen Appl Microbiol 59 ( 5 ): 325-34.

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