Difference between revisions of "Team:UiOslo Norway/Collaborations"
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<div style="float:left; width:50%;"> | <div style="float:left; width:50%;"> | ||
<h1> Experiments </h1> | <h1> Experiments </h1> | ||
| + | <h2> 1. Obtaining the genes </h2> | ||
| + | <p>The first project part pursues the goal to get or clone all genes that are involved in our project into a plasmid, which allows a rapid and easy amplification of those genes for further experiments. </br> | ||
| + | For the soluble methane monooxygenase (sMMO) from <i>Methylococcus capsulatus</i> (Bath) we got the genes for the subunits (<i>mmoXYZBCD</i>) cloned into the BioBrick standard vector pSC1B3 from the | ||
| − | < | + | <a href="https://2014.igem.org/Team:Braunschweig/Achievements-content#parts" > |
| − | + | iGEM 2014 team from Braunschweig, Germany. | |
| − | < | + | </a> |
| + | Those six parts are registered as BioBrick parts under the names; Bba_K1390001 (<i>mmoB</i>), Bba_K1390002 (<i>mmoC</i>), Bba_K1390003 (<i>mmoD</i>), Bba_K1390004 (<i>mmoX</i>), Bba_K1390005 (<i>mmoY</i>), and Bba_K1390006 (<i>mmoZ</i>). </br> | ||
| + | Genes encoding the enzymes for the conversion of methanol into biomass (<i>medh2</i>, <i>hps</i>, and <i>phi</i>) were amplified by PCR from <i>Bacillus methanolicus</i> (MGA3) genomic DNA and TOPO blunt end cloning into the pCR4 vector was performed. Primers were designed in a way that they bind in the 5’ and 3’ untranslated region (UTR) of each gene.</br> | ||
| + | TOPO blunt end cloning of <i>mmoG</i> did not succeed. Instead <i>mmoG</i> was synthesized by IDT as a gBlock gene fragment, codon optimized for protein expression in <i>E. coli</i>. | ||
| + | </p> | ||
| − | </ | + | <h2> 2. Construction of BioBrick parts</h2> |
| + | <p>The second project part had the intention to create four new basic BioBrick parts. Those basic parts consist of the coding sequences (CDS) of a gene. The codonoptimized <i>mmoG</i> as well as all three genes encoding the enzymes for the methanol to biomass conversion (<i>medh2</i>, <i>hps</i>, and <i>phi</i>) were created as | ||
| + | <a href="https://2015.igem.org/Team:UiOslo_Norway/Basic_Part" > | ||
| + | BioBrick parts. | ||
| + | </a> </br> | ||
| − | + | The CDS of the <i>hps</i> gene, encoding the 3-hexulose-6-phosphate synthase, contains PstI and XbaI restriction sites making it not compatible with the BioBrick system. In two rounds of <i>in vitro</i> mutagenesis both restriction sites were removed and <i>hps</i> was cloned into pSC1B3 and submitted as a | |
| − | < | + | <a href="https://2015.igem.org/Team:UiOslo_Norway/Basic_Part" > |
| − | + | BioBrick part. | |
| − | < | + | </a> |
| − | + | ||
</p> | </p> | ||
| − | < | + | <h2>3. Generation of expression constructs</h2> |
| − | < | + | <p>Before assembling the final constructs we wanted to show that each individual protein could be expressed in <i>E. coli</i>. The pET system has been chosen as our preferred system for overexpression of each individual protein. The vector backbones pET-28 and pET-30 were chosen as potential expression vector.</br> |
| − | < | + | </br> |
| − | + | </br> | |
| + | Figure about construct: T7 prom—RBS—GENE Coming soon | ||
| + | </br> | ||
| + | </br> | ||
| + | With PCR we added restriction enzyme sites at the 5’ and 3’ end of CDS of each gene. Afterwards the gene was cloned either into pET-30 or pET-28 with the use of the listed restriction enzymes (Table 1 coming soon). | ||
</p> | </p> | ||
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</div> | </div> | ||
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| − | < | + | <h1> Protocols </h1> |
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Revision as of 11:14, 1 September 2015
Experiments
1. Obtaining the genes
The first project part pursues the goal to get or clone all genes that are involved in our project into a plasmid, which allows a rapid and easy amplification of those genes for further experiments. For the soluble methane monooxygenase (sMMO) from Methylococcus capsulatus (Bath) we got the genes for the subunits (mmoXYZBCD) cloned into the BioBrick standard vector pSC1B3 from the iGEM 2014 team from Braunschweig, Germany. Those six parts are registered as BioBrick parts under the names; Bba_K1390001 (mmoB), Bba_K1390002 (mmoC), Bba_K1390003 (mmoD), Bba_K1390004 (mmoX), Bba_K1390005 (mmoY), and Bba_K1390006 (mmoZ). Genes encoding the enzymes for the conversion of methanol into biomass (medh2, hps, and phi) were amplified by PCR from Bacillus methanolicus (MGA3) genomic DNA and TOPO blunt end cloning into the pCR4 vector was performed. Primers were designed in a way that they bind in the 5’ and 3’ untranslated region (UTR) of each gene. TOPO blunt end cloning of mmoG did not succeed. Instead mmoG was synthesized by IDT as a gBlock gene fragment, codon optimized for protein expression in E. coli.
2. Construction of BioBrick parts
The second project part had the intention to create four new basic BioBrick parts. Those basic parts consist of the coding sequences (CDS) of a gene. The codonoptimized mmoG as well as all three genes encoding the enzymes for the methanol to biomass conversion (medh2, hps, and phi) were created as BioBrick parts. The CDS of the hps gene, encoding the 3-hexulose-6-phosphate synthase, contains PstI and XbaI restriction sites making it not compatible with the BioBrick system. In two rounds of in vitro mutagenesis both restriction sites were removed and hps was cloned into pSC1B3 and submitted as a BioBrick part.
3. Generation of expression constructs
Before assembling the final constructs we wanted to show that each individual protein could be expressed in E. coli. The pET system has been chosen as our preferred system for overexpression of each individual protein. The vector backbones pET-28 and pET-30 were chosen as potential expression vector. Figure about construct: T7 prom—RBS—GENE Coming soon With PCR we added restriction enzyme sites at the 5’ and 3’ end of CDS of each gene. Afterwards the gene was cloned either into pET-30 or pET-28 with the use of the listed restriction enzymes (Table 1 coming soon).