Difference between revisions of "Team:Chalmers Gothenburg/Project/Constructs"

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             <a class="sub-level" href="#koandins">Simultaneous knock-out and insertion</a>
 
             <a class="sub-level" href="#koandins">Simultaneous knock-out and insertion</a>
 
             <a class="sub-level" href="#ko">Knock-out</a>
 
             <a class="sub-level" href="#ko">Knock-out</a>
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             <a href="#ecoli"><i>E.Coli</i></a>
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             <a href="#bs"><i>Bacillus subtilis</i></a>
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             <a href="#sce"><i>Saccharomyces cerevisiae</i></a>
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            <a href="#yar"><i>Yarrowia lipolytica</i></a>
 
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           </figure>  
 
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<div class="target" id="ecoli">
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<div class="target" id="bs">
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<h2><i>Bacillus subtilis</i></h2>
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<p class="text">The purpose of the constructs in <i>B. subtilis</i> is to enable it to grow on acetate and overproduce arginine. Both constructs are based on the vectors from the bacillus box made by the <a href="https://2012.igem.org/Team:LMU-Munich">2012 LMU-Munich iGEM-team</a> [6]. </p>
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<h3 class="sidetitle">1. Glyoxylate shunt</h3>
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<p class="text"><i>B. subtilis</i> cannot utilize acetate as a carbon source, which can be solved by inserting the glyoxylate shunt from <i>Bacillus licheniformis</i> into <i>B. subtilis</i>, see Figure X. The shunt consists of two enzymes in an operon, aceA and aceB, under the control of a native <i>B. licheniformis</i> promoter, which have been shown to be active in <i>B. subtilis</i> as well [7].</p>
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<figure>
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<img src="https://static.igem.org/mediawiki/2016/f/f4/T--Chalmers_Gothenburg--shunt.png" width="700px">
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<div><b>Figure X</b>Construct for the glyoxylate shunt</div>
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</figure>
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<p class="text">The glyoxylate shunt was amplified from extracted genomic DNA from with the primers in Table X. Both the product and the vector pBs4S were cut with Xba1 and Spe1 before ligation and transformation into <i>E. coli</i>. This was not optimal as there is a risk of vector-only clones due to overlaps of Xba1 and Spe1 sticky ends, but had to be done anyway because the shunt contained both EcoR1 and Pst1 sites. They could have been removed through mutagenic PCR, but this was not done due to time limitations. </p>
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          <figure>
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            <figcaption class="table-caption"><b>Table X.</b> Primers used for generating the fragments glyoxylate shunt. Uppercase characters hybridize to the template, while the lowercase characters contain the BioBrick prefix or suffix.</figcaption>
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            <table>
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                <tr>
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                  <th>Primers</th> <th>Sequence (5’ → 3’)</th>
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                </tr>
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                <tr>
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                    <td>glyox op FW (prefix)</td> <td>gaattcgcggccgcttctagaGAAAAATATGAACAAGCTATGAATAAAAAG</td>
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                </tr>
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                <tr>
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                    <td>glyox op RV (suffix)</td> <td>ctgcagcggccgctactagtaAACAAACAACAGGAATCATCAGAC</td>
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                </tr>
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            </table>
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          </figure>
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<h3 class="sidetitle">ahrC knock-out</h3>
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<p class="text">The second modification to <i>B. subtilis</i> was to make it overproduce arginine needed by the cyanobacteria in the co-culture. This was done by deleting the gene ahrC, which codes for a repressor of arginine biosynthesis [8]. Furthermore, the reporter gene GFP was inserted to be able to quantify the abundance of <i>B. subtilis</i> relative the cyanobacteria in the co-culture. The final construct can be seen in Figure X.</p>
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<figure>
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<img src="https://static.igem.org/mediawiki/2016/f/f7/T--Chalmers_Gothenburg--ahrC.png" width="700px">
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<div><b>Figure X</b> Construct for inserting GFP and knocking out the arginine repressor ahrC in <i>B. subtilis</i>.</div>
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</figure>
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<p class="text">The fragments were amplified with the primers in Table X. The homology regions up- and downstream of ahrC was amplified from genomic DNA extracted from <i>B. subtilis</i>. The reporter gene was assembled by ligation of the BioBricks BBa_E0840 and BBa_K823003, which was then amplified with primers containing overhangs for Gibson assembly. The chloramphenicol and ampicillin resistance gene were amplified from the pBs1C plasmid. </p>
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          <figure>
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            <figcaption class="table-caption"><b>Table X.</b> Primers used for generating the fragments for knock-out of ahrC and the overexpression of GFP. Uppercase characters hybridize to the template, while the lowercase characters contain the overlapping overhang to the fragment within the parenthesis in the primer name.</figcaption>
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            <table>
 +
                <tr>
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                  <th>Primers</th> <th>Sequence (5’ → 3’)</th>
 +
                </tr>
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                <tr>
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                    <td>Dw ahrC FW (amp+Ori)</td> <td>aaccattattatcCCGATTCGATTTCTTCGAG</td>
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                </tr>
 +
                <tr>
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                    <td>Dw ahrC RV</td> <td>CAGAAAATCTAACAAAGATAAGAGGTG</td>
 +
                </tr>
 +
                <tr>
 +
                    <td>cat FW (Dw ahrC)</td> <td>cctcttatctttgttagattttctgTGTCAATTCTCATGTTTGACAGC</td>
 +
                </tr>
 +
                <tr>
 +
                    <td>cat RV (pVeg+GFP)</td> <td>tcgggtgggcctttctgcgtttataCTCCTGCATTAGGAAGCAGC</td>
 +
                </tr>
 +
                <tr>
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                    <td>pVeg+GFP FW</td> <td>TATAAACGCAGAAAGGCCC</td>
 +
                </tr>
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                <tr>
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                    <td>pVeg+GFP RV (Up ahrC)</td> <td>ttggaaatagaggtgcttacGGAGTTCTGAGAATTGGTATGC</td>
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                </tr>
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                <tr>
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                    <td>Up ahrC FW (pVeg+GFP)</td> <td>aactccGTAAGCACCTCTATTTCCAAGC</td>
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                </tr>
 +
                <tr>
 +
                    <td>Up ahrC RV (ori+ampR)</td> <td>gagctggatacttCTCTGTCAAAGATAAAATTATGATTG</td>
 +
                </tr>
 +
                <tr>
 +
                    <td>amp+Ori FW (Up ahrC)</td> <td>atctttgacagagAAGTATCCAGCTCGAGGTCG</td>
 +
                </tr>
 +
                <tr>
 +
                    <td>amp+Ori RV (Dw ahrC)</td> <td>gaaatcgaatcggGATAATAATGGTTTCTTAGACGTCAGG</td>
 +
                </tr>
 +
            </table>
 +
          </figure>
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</div>
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<div class="target" id="yar">
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Revision as of 16:44, 17 October 2016

Chalmers Gothenburg iGEM 2016

PROJECT
Constructs

All the constructs used in our project are summarized on this page. The DNA fragments of each construct were assembled with Gibson assembly after addition of overlapping sequences through PCR with primers containing overhangs to the adjacent DNA fragment (20-25 base pairs). Design of constructs and primers were performed in Snapgene with the aid of the web tools NEBuilder and Tm calculator. DNA sequences were obtained using Genbank, KEGG, and Addgene.

Synechocystis sp. PCC 6803

The constructs for Synechocystis are based on three different knock-outs: argininosuccinate lyase (ArgH), glutamine synthetase (GlnA) and acetyl-CoA synthetase (Acs). ArgH is knocked out when Synechocystis is going to be used in a consortia with E. coli or B. subtilis, while GlnA is knocked out when Y. lipolytica or S. cerevisiae is the producing organisms. Furthermore, AckA and pta are overexpressed in Synechocystis, along with knock-out of Acs, to increase the metabolic flux towards acetate through the pta-AckA pathway [1]. As a starting point, the mutant JA06 received by the Paul Hudson group at KTH was used as it already excreted some amounts of acetate [2].

Figure 1. The plasmid pNF

The homology regions for the knock-out constructs are designed to be around 1000 base pairs each. All Synechocystis constructs are modified versions of the pNF plasmid, shown in Figure 1, which contains the E. coli origin of replication pBR322, an ampicillin resistance marker and a kanamycin resistance marker (KmR). This plasmid was linearized with the primers in Table 1, which only amplified the origin of replication and amp marker, before Gibson assembly.

One important thing to keep in mind when knocking out genes in Synechocystis is the fact that it has several copies of its genome [3]. To make sure that all of the copies of the specific amino acid synthesising gene is knocked out, transformants should be restreaked several times and checked through colony PCR [4].

Table 1. Primers used for linearizing pNF
Primers Sequence (5’ → 3’)
pNF FW GTTCACTGGCCGTCGTTTTAC
pNF RV CATGCAAGCTTGGCGTAATC

Constructs for simultaneous knock-out and insertion

1. Knock-out ArgH + insert AckA

This construct consists of five parts: upstream homology region of ArgH, KmR cassette, pTrc promoter, AckA and the downstream homology region, Figure 2. This construct knocks out the ArgH gene when transformed into Synechocystis, making it an arginine auxotroph which is needed to make the cyanobacteria dependent on the producing organism. Furthermore, the endogenous AckA is inserted under the control of the strong consecutive promoter pTrc, for increased acetate production. By combining these two modifications into one construct, the number of constructs were reduced and thus the number of different markers needed.

Figure 2. Construct for simultaneous knock-out of ArgH and insertion of AckA

All the primers used for this construct are shown in Table 2. AckA and the flanking sequences of ArgH are amplified from genomic DNA of Synechocystis. The KmR cassette is amplified from the pNF plasmid and the pTrc promoter is amplified from the pCyJ2 plasmid.

Table 2. Primers used for generating the fragments for the ArgH knock-out and AckA insertion. Uppercase characters hybridize to the template, while the lowercase characters contain the overlapping overhang to the fragment within the parenthesis in the primer name. The numbering of the primers indicates which constructs it can be used for.
Primers Sequence (5’ → 3’)
1,5 ArgH Up FW (pNF) accatgattacgccaagcttgcatgCGCCTGTTATAACACCCC
1,5 ArgH Up RV (KmR) gctctagagtgatagaattcGGGATTTCGTTGTGATAGTTAG
1 Kmr FW (argH) ttgctaactatcacaacgaaatcccGAATTCTATCACTCTAGAGCCAGG
1 Kmr RV (pTrc) attctgcctcgtgatacgcctaggtCGCTACTAGTACAACAAAGCCA
1,2, pTrc FW (KmR) gctttgttgtactagtagcgACCTAGGCGTATCACGAGG
1,2, pTrc RV (AckA) ttgagaatcaggaatttcatTCTAGATTTCTCCTCTTTTGTGTG
1 AckA FW (pTrc) tcacacaaaagaggagaaatctagaATGAAATTCCTGATTCTCAATGC
1 AckA RV (argH) aacctgggcatatctccacaccaatAGCCTAATTCAACATTTATCTTCAC
1 ArgH Dw FW (AckA) gataaatgttgaattaggctATTGGTGTGGAGATATGCC
1,5 ArgH Dw RV (pNF) cgttgtaaaacgacggccagtgaacCACCTTTTAAAAGAATGGCG

2. Knock-out GlnA + insert AckA

The purpose of this five-piece construct (Figure 3) is to make synechocystis glutamine auxotroph, while also overexpressing AckA for increased acetate production.

Figure 3.Construct for simultaneous knock-out of GlnA and insertion of AckA

All the primers used for this construct are shown in Table 3. AckA and the flanking sequences of GlnA are amplified from genomic DNA of synechocystis. The KmR cassette is amplified from the pNF plasmid and the pTrc promoter is amplified from the pCyJ2 plasmid.

Table 3. Primers used for generating the fragments for the GlnA knock-out and AckA insertion. Uppercase characters hybridize to the template, while the lowercase characters contain the overlapping overhang to the fragment within the parenthesis in the primer name. The numbering of the primers indicates which constructs it can be used for.
Primers Sequence (5’ → 3’)
2,6 glnA Up FW (pNF) accatgattacgccaagcttgcatgAAAACGTCATGGCGATC
2,6 glnA Up RV (KmR) gctctagagtgatagaattcTTTTTCTCCTTAGTGCAGTCAG
2 KmR FW (glnA) tatctgactgcactaaggagaaaaaGAATTCTATCACTCTAGAGCCAGG
2 KmR RV (pTrc) attctgcctcgtgatacgcctaggtCGCTACTAGTACAACAAAGCCA
1,2 pTrc FW (KmR) gctttgttgtactagtagcgACCTAGGCGTATCACGAGG
1,2 pTrc RV (AckA) ttgagaatcaggaatttcatTCTAGATTTCTCCTCTTTTGTGTG
2 AckA FW (pTrc) tcacacaaaagaggagaaatctagaATGAAATTCCTGATTCTCAATGC
2 AckA RV (glnA) ctaaaactgggtgagatggactggtAGCCTAATTCAACATTTATCTTCAC
2 glnA Dw FW (AckA) gataaatgttgaattaggctACCAGTCCATCTCACCCA
2,6 glnA Dw RV (pNF) cgttgtaaaacgacggccagtgaacGAGTGGATTTTAAAAACTCTTCGAC

3. Knock-out Acs + insert RFP

This construct (Figure 4) knocks out Acs to increase the acetate production [1], while also expressing mRFP1 to be able to quantify the levels of Synechocystis compared to the producing organism in the microbial consortia.

Figure 4. Construct for simultaneous knock-out of Acs and insertion of mRFP1

All the primers used for this construct are shown in Table 4. The flanking sequences of Acs are amplified from genomic DNA of Synechocystis and mRFP1 is amplified from a plasmid supplied by the last year iGEM team of Chalmers Gothenburg. The SpR cassette and the pTrc promoter are amplified from the pCyJ2 plasmid. The terminator tB0015 is amplified from the pNF plasmid.

Table 4. Primers used for generating the fragments for the Acs knock-out and mRFP1 insertion. Uppercase characters hybridize to the template, while the lowercase characters contain the overlapping overhang to the fragment within the parenthesis in the primer name. The numbering of the primers indicates which constructs it can be used for.
Primers Sequence (5’ → 3’)
3,4,7 acs Up FW (pNF) accatgattacgccaagcttgcatgCAAATTAGCCAAACCCACG
3,4,7 acs Up RV (SpR) ccaccaattttctcttcagcTAGCGTGTTGGACAAATTACG
3,4 SpR FW (acs) ctcccgtaatttgtccaacacgctaGCTGAAGAGAAAATTGGTGG
3,4 SpR RV (pTrc) attctgcctcgtgatacgcctaggtTAAGAGGTTCCAACTTTCACC
3,4 pTrc FW (SpR) gtgaaagttggaacctcttaACCTAGGCGTATCACGAGGC
3 pTrc RV (RFP1) acgtcctcggaggaggCCATTCTAGATTTCTCCTCTTTTGTGTG
3 RFP FW (pTrc) tcacacaaaagaggagaaatctagaATGGCCTCCTCCGAGG
3 RFP RV (tB0015) tcgggtgggcctttctgcgtttataTTAGGCGCCGGTGGA
3 B0015 FW (RFP1) gccactccaccggcgcctaaTATAAACGCAGAAAGGCCC
3 B0015 RV (acs Dw) aaagactttgacggagaaccCCAGGCATCAAATAAAACG
3 acs Dw FW (tB0015) gcctttcgttttatttgatgcctggGGTTCTCCGTCAAAGTCTTT
3,4,7 acs Dw RV (pNF) cgttgtaaaacgacggccagtgaacTTTCCACTTCACTTGGTTTGT

4. Knock-out Acs + insert Pta

The purpose of the final knock-out and insertion construct (Figure 5) is to increase the acetate production in Synechocystis by knocking out Acs and overexpressing Pta [1].

Figure 5. Construct for simultaneous knock-out of Acs and insertion of Pta.

All the primers used for this construct are shown in Table 5. The fragments are almost the same as in construct 3, expect the overhangs of the fragments and the Pta gene (amplified from genomic DNA of synechocystis) which replaced the mRFP1.

Table 5. Primers used for generating the fragments for the Acs knock-out and pta insertion. Uppercase characters hybridize to the template, while the lowercase characters contain the overlapping overhang to the fragment within the parenthesis in the primer name. The numbering of the primers indicates which constructs it can be used for.
Primers Sequence (5’ → 3’)
3,4,7 acs Up FW (pNF) accatgattacgccaagcttgcatgCAAATTAGCCAAACCCACG
3,4,7 acs Up RV (SpR) ccaccaattttctcttcagcTAGCGTGTTGGACAAATTACG
3,4 SpR FW (acs) ctcccgtaatttgtccaacacgctaGCTGAAGAGAAAATTGGTGG
3,4 SpR RV (pTrc) attctgcctcgtgatacgcctaggtTAAGAGGTTCCAACTTTCACC
3,4 pTrc FW (SpR) gtgaaagttggaacctcttaACCTAGGCGTATCACGAGGC
4 pTrc RV (pta) aaataaagggaactcgtcatTCTAGATTTCTCCTCTTTTGTGTG
4 pta FW (pTrc) tcacacaaaagaggagaaatctagaATGACGAGTTCCCTTTATTTAAGC
4 pta RV (acs Dw) aaagactttgacggagaaccTTTGGAGGGCAAAATCAAG
4 acs Dw FW (pta) aattaccttgattttgccctccaaaGGTTCTCCGTCAAAGTCTTT
3,4,7 acs Dw RV (pNF) cgttgtaaaacgacggccagtgaacTTTCCACTTCACTTGGTTTGT

Constructs for knock-out only

The following constructs are simplified variants of the previous ones by limiting the modification to a knock-out, without inserting additional genes except the marker.

5. Knock-out Argh

In this construct (Figure 6), ArgH is knocked out in Synechocystis by selection with kanamycin.

Figure 6. Construct for knock-out of ArgH.

All the primers used for this construct are shown in Table 6. The only difference in the fragments of this construct compared to construct 1 is the overlapping overhangs.

Table 6. Primers used for generating the fragments for the ArgH knock-out. Uppercase characters hybridize to the template, while the lowercase characters contain the overlapping overhang to the fragment within the parenthesis in the primer name. The numbering of the primers indicates which constructs it can be used for.
Primers Sequence (5’ → 3’)
1,5 ArgH Up FW (pNF) accatgattacgccaagcttgcatgCGCCTGTTATAACACCCC
1,5 ArgH Up RV (KmR) gctctagagtgatagaattcGGGATTTCGTTGTGATAGTTAG
5,6 KmR FW GAATTCTATCACTCTAGAGCCAGG
5,6 KmR RV CGCTACTAGTACAACAAAGCCA
5 ArgH Dw FW (KmR) acgtggctttgttgtactagtagcgATTGGTGTGGAGATATGC
1,5 ArgH Dw RV (pNF) cgttgtaaaacgacggccagtgaacCACCTTTTAAAAGAATGGCG

6. Knock-out GlnA

In this construct (Figure 7), ArgH is knocked out in Synechocystis by selection with kanamycin.

Figure 7. Construct for knock-out of GlnA.

All the primers used for this construct are shown in Table 7. The only difference in the fragments of this construct compared to construct 2 is the overlapping overhangs.

Table 7. Primers used for generating the fragments for the GlnA knock-out. Uppercase characters hybridize to the template, while the lowercase characters contain the overlapping overhang to the fragment within the parenthesis in the primer name. The numbering of the primers indicates which constructs it can be used for.
Primers Sequence (5’ → 3’)
2,6 glnA Up FW (pNF) accatgattacgccaagcttgcatgAAAACGTCATGGCGATC
2,6 glnA Up RV (KmR) gctctagagtgatagaattcTTTTTCTCCTTAGTGCAGTCAG
5,6 KmR FW GAATTCTATCACTCTAGAGCCAGG
5,6 KmR RV CGCTACTAGTACAACAAAGCCA
6 glnA Dw FW (KmR) gctttgttgtactagtagcgACCAGTCCATCTCACCCA
2,6 glnA Dw RV (pNF) cgttgtaaaacgacggccagtgaacGAGTGGATTTTAAAAACTCTTCGAC

7. Knock-out of Acs

In this construct (Figure 8), Acs is knocked out in Synechocystis by selection with spectinomycin.

Figure 8. Construct for knock-out of Acs

All the primers used for this construct are shown in Table 8. The only difference in the fragments of this construct compared to construct 3 and 4 is the overlapping overhangs.

Table 8. Primers used for generating the fragments for the Acs knock-out. Uppercase characters hybridize to the template, while the lowercase characters contain the overlapping overhang to the fragment within the parenthesis in the primer name. The numbering of the primers indicates which constructs it can be used for.
Primers Sequence (5’ → 3’)
3,4,7 acs Up FW (pNF) accatgattacgccaagcttgcatgCAAATTAGCCAAACCCACG
3,4,7 acs Up RV (SpR) ccaccaattttctcttcagcTAGCGTGTTGGACAAATTACG
7 SpR FW GCTGAAGAGAAAATTGGTGG
7 SpR RV TAAGAGGTTCCAACTTTCACC
7 acs Dw F (SpR) gtgaaagttggaacctcttaGGTTCTCCGTCAAAGTCTTT
3,4,7 acs Dw RV (pNF) cgttgtaaaacgacggccagtgaacTTTCCACTTCACTTGGTTTGT

Bacillus subtilis

The purpose of the constructs in B. subtilis is to enable it to grow on acetate and overproduce arginine. Both constructs are based on the vectors from the bacillus box made by the 2012 LMU-Munich iGEM-team [6].

1. Glyoxylate shunt

B. subtilis cannot utilize acetate as a carbon source, which can be solved by inserting the glyoxylate shunt from Bacillus licheniformis into B. subtilis, see Figure X. The shunt consists of two enzymes in an operon, aceA and aceB, under the control of a native B. licheniformis promoter, which have been shown to be active in B. subtilis as well [7].

Figure XConstruct for the glyoxylate shunt

The glyoxylate shunt was amplified from extracted genomic DNA from with the primers in Table X. Both the product and the vector pBs4S were cut with Xba1 and Spe1 before ligation and transformation into E. coli. This was not optimal as there is a risk of vector-only clones due to overlaps of Xba1 and Spe1 sticky ends, but had to be done anyway because the shunt contained both EcoR1 and Pst1 sites. They could have been removed through mutagenic PCR, but this was not done due to time limitations.

Table X. Primers used for generating the fragments glyoxylate shunt. Uppercase characters hybridize to the template, while the lowercase characters contain the BioBrick prefix or suffix.
Primers Sequence (5’ → 3’)
glyox op FW (prefix) gaattcgcggccgcttctagaGAAAAATATGAACAAGCTATGAATAAAAAG
glyox op RV (suffix) ctgcagcggccgctactagtaAACAAACAACAGGAATCATCAGAC

ahrC knock-out

The second modification to B. subtilis was to make it overproduce arginine needed by the cyanobacteria in the co-culture. This was done by deleting the gene ahrC, which codes for a repressor of arginine biosynthesis [8]. Furthermore, the reporter gene GFP was inserted to be able to quantify the abundance of B. subtilis relative the cyanobacteria in the co-culture. The final construct can be seen in Figure X.

Figure X Construct for inserting GFP and knocking out the arginine repressor ahrC in B. subtilis.

The fragments were amplified with the primers in Table X. The homology regions up- and downstream of ahrC was amplified from genomic DNA extracted from B. subtilis. The reporter gene was assembled by ligation of the BioBricks BBa_E0840 and BBa_K823003, which was then amplified with primers containing overhangs for Gibson assembly. The chloramphenicol and ampicillin resistance gene were amplified from the pBs1C plasmid.

Table X. Primers used for generating the fragments for knock-out of ahrC and the overexpression of GFP. Uppercase characters hybridize to the template, while the lowercase characters contain the overlapping overhang to the fragment within the parenthesis in the primer name.
Primers Sequence (5’ → 3’)
Dw ahrC FW (amp+Ori) aaccattattatcCCGATTCGATTTCTTCGAG
Dw ahrC RV CAGAAAATCTAACAAAGATAAGAGGTG
cat FW (Dw ahrC) cctcttatctttgttagattttctgTGTCAATTCTCATGTTTGACAGC
cat RV (pVeg+GFP) tcgggtgggcctttctgcgtttataCTCCTGCATTAGGAAGCAGC
pVeg+GFP FW TATAAACGCAGAAAGGCCC
pVeg+GFP RV (Up ahrC) ttggaaatagaggtgcttacGGAGTTCTGAGAATTGGTATGC
Up ahrC FW (pVeg+GFP) aactccGTAAGCACCTCTATTTCCAAGC
Up ahrC RV (ori+ampR) gagctggatacttCTCTGTCAAAGATAAAATTATGATTG
amp+Ori FW (Up ahrC) atctttgacagagAAGTATCCAGCTCGAGGTCG
amp+Ori RV (Dw ahrC) gaaatcgaatcggGATAATAATGGTTTCTTAGACGTCAGG