Difference between revisions of "Part:BBa K1716000"
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===Methods and Experimental Design=== | ===Methods and Experimental Design=== | ||
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| − | <p>For proof of concept we decided to make a single | + | <p>For proof of concept we decided to make a single point mutation in the ribosomal S12 protein in B. subtilis, which results in resistance to the antibiotic streptomycin. The required change is a lysine to arginine substitution at position 56 of the protein. The S12 subunit is coded by the rpsL gene (Barnard et al. 2010). An oligo that could integrate this change was designed using MODEST (Bonde et al., 2014). These oligos were successfully integrated into the two strains: <em>∆mutS::beta-neo<sup>R</sup></em> and <em>∆mutS::GP35-neo<sup>R</sup>.</em></p> |
| − | <p>All the | + | <p>All of the strains were made by homologous recombination. Plasmids containing cassettes that were able to do a double-crossover homologous recombination into the genome of B. subtilis 168 (referred to as knockout (KO) plasmid). These were used to, simultaneously, delete the desired gene (amyE or mutS) and insert the expression cassette for one of the recombinases: beta or GP35.</p> |
<p><img alt="" src="https://static.igem.org/mediawiki/2015/a/a4/DTU-Denmark_pDG268neo_recombinase.png" style="width: 400px; height: 397px;" /><img alt="" src="https://static.igem.org/mediawiki/2015/c/c1/DTU-Denmark_pSB1C3neo_recombinase.png | <p><img alt="" src="https://static.igem.org/mediawiki/2015/a/a4/DTU-Denmark_pDG268neo_recombinase.png" style="width: 400px; height: 397px;" /><img alt="" src="https://static.igem.org/mediawiki/2015/c/c1/DTU-Denmark_pSB1C3neo_recombinase.png | ||
" style="width: 400px; height: 397px;" /></p> | " style="width: 400px; height: 397px;" /></p> | ||
| − | <p><span style="font-size:14px;">Figure 1. Shows the general concepts of the two plasmids pDG268neo_recombinase and pSB1C3_recombinase. Both exist in two versions, one with each of the recombinase proteins CDSs (Beta and GP35). They also have different RBSs since they are optimized for the CDS. Upstream of neoR is a promoter and RBS and downstream of neoR is a terminator, but sequences and positions of these features are not known.</span></p> | + | <p><span style="font-size:14px;">Figure 1. Shows the general concepts of the two plasmids pDG268neo_recombinase and pSB1C3_recombinase. Both exist in two versions, one with each of the recombinase proteins' CDSs (Beta and GP35). They also have different RBSs since they are optimized for the CDS. Upstream of neoR is a promoter and RBS and downstream of neoR is a terminator, but sequences and positions of these features are not known.</span></p> |
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<p>Four different plasmids were assembled to make the four MAGE ready strains:<br /> | <p>Four different plasmids were assembled to make the four MAGE ready strains:<br /> | ||
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pSB1C3_GP35-neoR</p> | pSB1C3_GP35-neoR</p> | ||
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<div class="panel panel-default"> | <div class="panel panel-default"> | ||
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<p><i>Sequence was ordered from IDT as two gblocks (for each recombinase) with overlapping regions, thus they can be assembled with Gibson assembly.</i></p> | <p><i>Sequence was ordered from IDT as two gblocks (for each recombinase) with overlapping regions, thus they can be assembled with Gibson assembly.</i></p> | ||
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| − | <p>pDG268neo was linearized | + | <p>pDG268neo was linearized by PCR with primers, so that the native <i>lacZ </i>was omitted. This linearized plasmid was purified and used in a Gibson assembly reaction with two cognate gblocks.</p> |
<p><img alt="" src="https://static.igem.org/mediawiki/2015/d/d9/DTU-Denmark_pDG268_1.png | <p><img alt="" src="https://static.igem.org/mediawiki/2015/d/d9/DTU-Denmark_pDG268_1.png | ||
" style="width: 700px; height: 835px;" /></p> | " style="width: 700px; height: 835px;" /></p> | ||
| − | <p><span style="font-size:14px;">Figure 2. Gibson assembly of the pDG268neo_GP35, the gblocks | + | <p><span style="font-size:14px;">Figure 2. Gibson assembly of the pDG268neo_GP35, the gblocks were fused to the “gp35 Gblocks fused” in the same reaction. The Gibson assembly of pDG268neo_beta was similar.</span></p> |
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<p>This resulted in two different plasmids pDG268neo_beta and pDG268neo_gp35.</p> | <p>This resulted in two different plasmids pDG268neo_beta and pDG268neo_gp35.</p> | ||
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</div> | </div> | ||
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<p>The two mutS KO plasmids was made of the following DNA fragments:</p> | <p>The two mutS KO plasmids was made of the following DNA fragments:</p> | ||
| − | <p>1. | + | <p>1. Flanking regions upstream and downstream of <i>mutS</i> from <i>B. subtilis</i> genome was amplified to generate the homologous regions for homologous recombination and deletion of <i>mutS</i>.</p> |
| − | <p>2. Recombinase and neoR expression cassettes | + | <p>2. Recombinase and neoR expression cassettes were amplified from the pDG268neo_recombinase</p> |
<p>3. Linearized pSB1C3 was used as template.</p> | <p>3. Linearized pSB1C3 was used as template.</p> | ||
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| − | <p>These fragments | + | <p>These fragments were assembled into two different plasmids pSB1C3_<em>mutS::beta-neo<sup>R</sup></em> and pSB1C3_<em>mutS::gp35-neo<sup>R</sup></em> using Gibson assembly.</p> |
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<p><img alt="" src="https://static.igem.org/mediawiki/2015/d/dc/DTU-Denmark_pDG268_2.png | <p><img alt="" src="https://static.igem.org/mediawiki/2015/d/dc/DTU-Denmark_pDG268_2.png | ||
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| − | <p> | + | <p>Electroporation competent <em>Bacillus subtilis 168. </em>was electroplated with MAGE oligos and plated on nonselective plates. The colonies from the LB plates were transferred to LB + 500y streptomycin (strep) plates. Plates were incubated at 37 degC for 48 hours and CFUs were counted on both the LB and the strep plates in order to determine recombination frequencies.</p> |
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Revision as of 23:08, 26 September 2015
Methods and Experimental Design
Four Bacillus subtilis strains which expressed a recombinase were created by genetically engineering the wild type strain 168:
- ∆amyE::beta-neoR
- ∆amyE::GP35-neoR
- ∆mutS::beta-neoR
- ∆mutS::GP35-neoR
For proof of concept we decided to make a single point mutation in the ribosomal S12 protein in B. subtilis, which results in resistance to the antibiotic streptomycin. The required change is a lysine to arginine substitution at position 56 of the protein. The S12 subunit is coded by the rpsL gene (Barnard et al. 2010). An oligo that could integrate this change was designed using MODEST (Bonde et al., 2014). These oligos were successfully integrated into the two strains: ∆mutS::beta-neoR and ∆mutS::GP35-neoR.
All of the strains were made by homologous recombination. Plasmids containing cassettes that were able to do a double-crossover homologous recombination into the genome of B. subtilis 168 (referred to as knockout (KO) plasmid). These were used to, simultaneously, delete the desired gene (amyE or mutS) and insert the expression cassette for one of the recombinases: beta or GP35.
Figure 1. Shows the general concepts of the two plasmids pDG268neo_recombinase and pSB1C3_recombinase. Both exist in two versions, one with each of the recombinase proteins' CDSs (Beta and GP35). They also have different RBSs since they are optimized for the CDS. Upstream of neoR is a promoter and RBS and downstream of neoR is a terminator, but sequences and positions of these features are not known.
Four different plasmids were assembled to make the four MAGE ready strains:
pDG268neo_Beta-neoR
pDG268neo_GP35-neoR
pSB1C3_Beta-neoR
pSB1C3_GP35-neoR
Insert of recombinase in amyE
For pDG268neo_recobinase a DNA sequence containing following features
● Promoter: PliaG from BBa_K823002 was used.
● RBSs were optimized for the specific CDS using the salis lab RBS calculator (https://www.denovodna.com/software/)
● CDS for recombination protein beta or GP35
● Terminator: we use rho-independent Part:BBa_B0014
Sequence was ordered from IDT as two gblocks (for each recombinase) with overlapping regions, thus they can be assembled with Gibson assembly.
pDG268neo was linearized by PCR with primers, so that the native lacZ was omitted. This linearized plasmid was purified and used in a Gibson assembly reaction with two cognate gblocks.
Figure 2. Gibson assembly of the pDG268neo_GP35, the gblocks were fused to the “gp35 Gblocks fused” in the same reaction. The Gibson assembly of pDG268neo_beta was similar.
This resulted in two different plasmids pDG268neo_beta and pDG268neo_gp35.
mutS deletion
The two mutS KO plasmids was made of the following DNA fragments:
1. Flanking regions upstream and downstream of mutS from B. subtilis genome was amplified to generate the homologous regions for homologous recombination and deletion of mutS.
2. Recombinase and neoR expression cassettes were amplified from the pDG268neo_recombinase
3. Linearized pSB1C3 was used as template.
These fragments were assembled into two different plasmids pSB1C3_mutS::beta-neoR and pSB1C3_mutS::gp35-neoR using Gibson assembly.
Figure 3. Gibson assembly of the pSB1C3_beta. The feature called “mutL” corresponding mutS downstream. The Gibson assembly of pSB1C3_GP35 was similar.
All plasmids were verified by restriction enzyme digestion.
We prepared naturally competent B. subtilis 168 to be transformed. The plasmids were linearized with restriction enzymes. Then transformed into naturally competent B. subtilis 168, transformants were selected on 5ɣ neo. Transformants were verified with colony PCRs.
Electroporation competent Bacillus subtilis 168. was electroplated with MAGE oligos and plated on nonselective plates. The colonies from the LB plates were transferred to LB + 500y streptomycin (strep) plates. Plates were incubated at 37 degC for 48 hours and CFUs were counted on both the LB and the strep plates in order to determine recombination frequencies.