Difference between revisions of "Part:BBa K1716000"

Revision as of 23:15, 26 September 2015

Lambda Beta recombinase optimized for expression in B. subtilis

Recombination-mediated genetic engineering (recombineering) utlises homologous recombination to facilitate genetic modifications at any desired target by flanking the mutated sequence with homologous regions. Multiplex Automated Genome Engineering (MAGE) is a method for rapid and efficient targeted programming and evolution of cells through cyclical recombineering using multiple single-stranded DNA oligonucleotides (oligos). The MAGE protocol utilises the λ Red recombination system in combination with an (temporary) inactivation of the mismatch repair system and consists of 7 steps that can be done with standard laboratory equipment (Wang, 2009). As MAGE utilises oligos, only the Beta protein of the λ Red system is required. This BioBrick encodes an optimised coding sequence for lambda phage derived beta recombinase. When expressed in Bacillus subtilis, oligo recombineering efficiencies were increased. [http://2015.igem.org/Team:DTU-Denmark/Project/MAGE Please see our project page].

Quick Guide: How to use

1. Express lambda beta in B. subtilis (or another organisms) by insertion into must (mismatch repair) gene. Read more about how we did that using standard B. subtilis BioBricks available from the registry under our project [http://2015.igem.org/Team:DTU-Denmark/Project/MAGE here]. 2. Make electro/MAGE-competent B. subtilis cells. Find our protocol here. 3. Design your 90-mer oligo. If you want to design oligos targeting NRPS use our NRPS Oligo Designer (NOD). Otherwise we suggest using [http://modest.biosustain.dtu.dk MODEST]. You can also read more about how to to multiplex engineering to design oligo chips [http://2015.igem.org/Team:DTU-Denmark/Project/Background here] for low-cost library generation. 4. Electroporate the cells. Read more about our optimisation of MAGE in Bacillus subtilis and cos-MAGE for higher efficiencies [http://2015.igem.org/Team:DTU-Denmark/Project/POC_MAGE here].

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 protein substitution in the ribosomal S12 protein in B. subtilis 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 design using MODEST (Bonde et al., 2014). These oligos were successfully integrated into the two strains: ∆mutS::beta-neo^R and ∆mutS::GP35-neo^R.

All the strain were made by homologous recombineering. Plasmids containing cassettes that were able to do a double-crossover homologous recombineering 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 inserting 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 in a 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 was 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. About 500 bp up- and downstream from mutS was amplified, using primers with tails.

2. Recombinase and neoR expression cassettes was amplified from the pDG268neo_recombinase

3. Linearized pSB1C3 was used as template.

These fragments was assembled into two different plasmids pSB1C3_mutS::beta-neo^R and pSB1C3_mutS::gp35-neo^R 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 cells were prepared in following the protocol: Electroporation competent Bacillus subtilis 168. Electropration was carried out according to the MAGE in Bacillus subtilis 168 protocol. The colonies from the LB plates were colonies picked onto an LB and 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.Results

Results

	Total number of CFUs	Number of transformant	Transformation frequency
ΔmutS::beta-neo^R	52	7	0.13
ΔmutS::GP35-neo^R	100	1	0.01

Table 1. shows the data for the MAGE proof of concept.

Second replication of the plates:

Figure 4. Pictures shows the first and second replication of the transformants. From left to right of ΔmutS::GP35-neo^R replicate1, ΔmutS::GP35-neo^Rreplicate2 , ΔmutS::beta-neo^Rreplica1, and ΔmutS::beta-neo^Rreplica2.

References

Barnard, A. M. L., Simpson, N. J. L., Lilley, K. S., & Salmond, G. P. C. (2010). Mutations in rpsL that confer streptomycin resistance show pleiotropic effects on virulence and the production of a carbapenem antibiotic in Erwinia carotovora. Microbiology, 156(4), 1030–1039. Bonde, M. T., Klausen, M. S., Anderson, M. V., Wallin, A. I. N., Wang, H. H., & Sommer, M. O. A. (2014). MODEST: a web-based design tool for oligonucleotide-mediated genome engineering and recombineering. Nucleic Acids Research, 42(W1), W408–W415. doi:10.1093/nar/gku428 Wang, H. H., Isaacs, F. J., Carr, P. A., Sun, Z. Z., Xu, G., Forest, C. R., & Church, G. M. (2009). Programming cells by multiplex genome engineering and accelerated evolution. Nature, 460(7257), 894–898. doi:10.1038/nature08187 Photo credit go MAGE cycle: Michael Schantz Klausen

Sequence and Features

Assembly Compatibility:

10
COMPATIBLE WITH RFC[10]
12
COMPATIBLE WITH RFC[12]
21
COMPATIBLE WITH RFC[21]
23
COMPATIBLE WITH RFC[23]
25
COMPATIBLE WITH RFC[25]
1000
INCOMPATIBLE WITH RFC[1000]
Illegal BsaI site found at 245

@@ Line 1: / Line 1: @@
+__NOTOC__
+<partinfo>BBa_K1716000 short</partinfo>
+Recombination-mediated genetic engineering (recombineering) utlises homologous recombination to facilitate genetic modifications at any desired target by flanking the mutated sequence with homologous regions. Multiplex Automated Genome Engineering (MAGE) is a method for rapid and efficient targeted programming and evolution of cells through cyclical recombineering using multiple single-stranded DNA oligonucleotides (oligos). The MAGE protocol utilises the &#955; Red recombination system in combination with an (temporary) inactivation of the mismatch repair system and consists of 7 steps that can be done with standard laboratory equipment (Wang, 2009). As MAGE utilises oligos, only the Beta protein of the &#955; Red system is required. This BioBrick encodes an optimised coding sequence for lambda phage derived beta recombinase. When expressed in Bacillus subtilis, oligo recombineering efficiencies were increased. [http://2015.igem.org/Team:DTU-Denmark/Project/MAGE Please see our project page].
+<html><div style="float:right;"><img src="https://static.igem.org/mediawiki/2015/9/91/DTU-Denmark_Magecycle.png" style="width:400px" /></div></html>
+===Quick Guide: How to use===
+. Express lambda beta in ''B. subtilis'' (or another organisms) by insertion into must (mismatch repair) gene. Read more about how we did that using standard B. subtilis BioBricks available from the registry under our project [http://2015.igem.org/Team:DTU-Denmark/Project/MAGE here].
+. Make electro/MAGE-competent B. subtilis cells. Find our protocol [https://static.igem.org/mediawiki/2015/2/2e/DTU-Denmark_Electro_competent_protocol.pdf here].
+. Design your 90-mer oligo. If you want to design oligos targeting NRPS use our NRPS Oligo Designer (NOD). Otherwise we suggest using [http://modest.biosustain.dtu.dk MODEST]. You can also read more about how to to multiplex engineering to design oligo chips [http://2015.igem.org/Team:DTU-Denmark/Project/Background here] for low-cost library generation.
+. Electroporate the cells. Read more about our optimisation of MAGE in ''Bacillus subtilis'' and cos-MAGE for higher efficiencies [http://2015.igem.org/Team:DTU-Denmark/Project/POC_MAGE here].
 ===Methods and Experimental Design===
 <html>
@@ Line 10: / Line 23: @@
 </ul>
-<p>For proof of concept we decided to make a&nbsp;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.&nbsp;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).&nbsp;These oligos were successfully integrated into the&nbsp;two&nbsp;strains: <em>∆mutS::beta-neo<sup>R</sup></em>&nbsp;and&nbsp;<em>∆mutS::GP35-neo<sup>R</sup>.</em></p>
+<p>For proof of concept we decided to make a&nbsp;single protein substitution in the ribosomal S12 protein in B. subtilis results in resistance to the antibiotic streptomycin. The required change is a lysine to arginine substitution at position 56 of the protein.&nbsp;The S12 subunit is coded by the rpsL gene (Barnard et al. 2010). An oligo that could integrate this change was design using MODEST (Bonde et al., 2014).&nbsp;These oligos were successfully integrated into the&nbsp;two&nbsp;strains: <em>∆mutS::beta-neo<sup>R</sup></em>&nbsp;and&nbsp;<em>∆mutS::GP35-neo<sup>R</sup>.</em></p>
-<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>All the strain were made by homologous recombineering. Plasmids containing cassettes that were able to do a double-crossover homologous recombineering 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 inserting 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
 " style="width: 400px; height: 397px;" /></p>
-<p><span style="font-size:14px;">Figure 1.&nbsp;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.&nbsp;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>&nbsp;</p>
 <p>Four different plasmids were assembled to make the four MAGE ready strains:<br />
@@ Line 26: / Line 40: @@
 pSB1C3_GP35-neoR</p>
+<p>&nbsp;</p>
 <div class="panel panel-default">
@@ Line 47: / Line 62: @@
 <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>&nbsp;</p>
-<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>pDG268neo was linearized in a 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
 " style="width: 700px; height: 835px;" /></p>
-<p><span style="font-size:14px;">Figure 2.&nbsp;Gibson assembly of the pDG268neo_GP35, the gblocks were fused to the &ldquo;gp35 Gblocks fused&rdquo; in the same reaction. The Gibson assembly of pDG268neo_beta was similar.</span></p>
+<p><span style="font-size:14px;">Figure 2.&nbsp;Gibson assembly of the pDG268neo_GP35, the gblocks was fused to the &ldquo;gp35 Gblocks fused&rdquo; in the same reaction. The Gibson assembly of pDG268neo_beta was similar.</span></p>
+<p>&nbsp;</p>
 <p>This resulted in two different plasmids pDG268neo_beta and pDG268neo_gp35.</p>
+<p>&nbsp;</p>
 </div>
 </div>
@@ Line 72: / Line 90: @@
 <p>The two mutS KO plasmids was made of the following DNA fragments:</p>
-<p>1.&nbsp;&nbsp;&nbsp;&nbsp; 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>1.&nbsp;&nbsp;&nbsp;&nbsp; About 500 bp up- and downstream from <i>mutS</i> was amplified, using primers with tails.</p>
-<p>2.&nbsp;&nbsp;&nbsp;&nbsp; Recombinase and neoR expression cassettes were amplified from the pDG268neo_recombinase</p>
+<p>2.&nbsp;&nbsp;&nbsp;&nbsp; Recombinase and neoR expression cassettes was amplified from the pDG268neo_recombinase</p>
 <p>3. &nbsp; &nbsp; Linearized pSB1C3&nbsp;was used as template.</p>
+<p>&nbsp;</p>
-<p>These fragments were assembled into two different plasmids pSB1C3_<em>mutS::beta-neo<sup>R</sup></em>&nbsp;and pSB1C3_<em>mutS::gp35-neo<sup>R</sup></em>&nbsp;using Gibson assembly.</p>
+<p>These fragments was assembled into two different plasmids pSB1C3_<em>mutS::beta-neo<sup>R</sup></em>&nbsp;and pSB1C3_<em>mutS::gp35-neo<sup>R</sup></em>&nbsp;using Gibson assembly.</p>
+<p>&nbsp;</p>
 <p><img alt="" src="https://static.igem.org/mediawiki/2015/d/dc/DTU-Denmark_pDG268_2.png
@@ Line 94: / Line 114: @@
 </div>
-<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>
+<p>Electroporation competent cells were prepared in following the protocol: Electroporation competent <em>Bacillus subtilis 168. </em>Electropration was carried out according to the MAGE in <em>Bacillus subtilis 168</em> protocol. The colonies from the LB plates were colonies picked onto an LB and 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.Results</p>
 </html>
+===Results===
+<html>
+<div aria-labelledby="headingOne" class="panel-collapse collapse" id="collapseOne" role="tabpanel">
+<div class="panel-body">
+<div class="panel-body">
+<table border="1" cellpadding="1" cellspacing="1" class="table table" style="width:500px;">
+	<thead>
+		<tr>
+			<th scope="col">&nbsp;</th>
+			<th scope="col" style="text-align: center;">Total number of CFUs</th>
+			<th scope="col" style="text-align: center;">Number of transformant</th>
+			<th scope="col" style="text-align: center;">Transformation frequency</th>
+		</tr>
+	</thead>
+	<tbody>
+		<tr>
+			<td>&Delta;<i>mutS::beta-neo</i><i><sup>R</sup></i></td>
+			<td style="text-align: center;">52</td>
+			<td style="text-align: center;">7</td>
+			<td style="text-align: center;">0.13</td>
+		</tr>
+		<tr>
+			<td>&Delta;<i>mutS::GP35-neo</i><i><sup>R</sup></i></td>
+			<td style="text-align: center;">100</td>
+			<td style="text-align: center;">1</td>
+			<td style="text-align: center;">0.01</td>
+		</tr>
+	</tbody>
+</table>
+<p><span style="font-size:14px;">Table 1. shows&nbsp;the data for the&nbsp;MAGE proof of concept.</span></p>
+<p>&nbsp;</p>
+<p>Second replication of the plates:</p>
+<p><img alt="" src="https://static.igem.org/mediawiki/2015/9/9d/DTU-Denmark_POC_mutSgp35.png
+" style="width: 375px; height: 205px;" /><img alt="" src="http://2015.igem.org//wiki/images/c/cc/DTU-Denmark_POC_mutSbeta.png" style="width: 397px; height: 205px;" /></p>
+<p><span style="font-size:14px;">Figure 4. Pictures shows the first and second replication of the transformants. From left to right of &Delta;mutS::GP35-neo<sup>R</sup>&nbsp;<span style="font-size:14px;"> replicate1</span>,&nbsp;<em>&Delta;mutS::GP35-neo</em><sup><em>R</em>&nbsp;</sup><span style="font-size:14px;">replicate2 </span>,&nbsp;&Delta;<i>mutS::beta-neo</i><i><sup>R&nbsp;</sup></i>replica1, and&nbsp;<span style="font-size:14px;">&Delta;<i>mutS::beta-neo</i><i><sup>R&nbsp;</sup></i>replica2.</span></span></p>
+</div>
+</div>
+</div>
+</html>
+===References===
+Barnard, A. M. L., Simpson, N. J. L., Lilley, K. S., &amp;amp; Salmond, G. P. C. (2010). Mutations in rpsL that confer streptomycin resistance show pleiotropic effects on virulence and the production of a carbapenem antibiotic in Erwinia carotovora. Microbiology, 156(4), 1030–1039.
+Bonde, M. T., Klausen, M. S., Anderson, M. V., Wallin, A. I. N., Wang, H. H., & Sommer, M. O. A. (2014). MODEST: a web-based design tool for oligonucleotide-mediated genome engineering and recombineering. Nucleic Acids Research, 42(W1), W408–W415. doi:10.1093/nar/gku428
+Wang, H. H., Isaacs, F. J., Carr, P. A., Sun, Z. Z., Xu, G., Forest, C. R., & Church, G. M. (2009). Programming cells by multiplex genome engineering and accelerated evolution. Nature, 460(7257), 894–898. doi:10.1038/nature08187
+Photo credit go MAGE cycle: Michael Schantz Klausen
+<!-- Add more about the biology of this part here
+===Usage and Biology===
+<!-- -->
+<span class='h3bb'>Sequence and Features</span>
+<partinfo>BBa_K1716000 SequenceAndFeatures</partinfo>
+<!-- Uncomment this to enable Functional Parameter display
+===Functional Parameters===
+<partinfo>BBa_K1716000 parameters</partinfo>
+<!-- -->