Difference between revisions of "Team:USP-EEL-Brazil/Design"
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| − | <h4 class="grey-text heading-weight" align = "left" style="font-size:40px; font-family:Broadway;"> | + | <h4 class="grey-text heading-weight" align = "left" style="font-size:40px; font-family:Broadway;">Step by Step</h4> |
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• <a href="https://www.ncbi.nlm.nih.gov/nuccore/166812030">Laccase from <i>Phoma sp.</i> UHH 5-1-03 (DSM 2245):</a>3073 pb - 607 aa </p> | • <a href="https://www.ncbi.nlm.nih.gov/nuccore/166812030">Laccase from <i>Phoma sp.</i> UHH 5-1-03 (DSM 2245):</a>3073 pb - 607 aa </p> | ||
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<p style=" margin-bottom: 50px; text-align: justify; text-indent: 5%; ">To analyze and remove the introns, we used the <a href="http://www.softberry.com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfind">FGENESH tool</a> from Softberry. After that, to verify if the gene sequence expressed a functional protein we used the <a href="https://web.expasy.org/translate/ ">Translate tool</a>from Expazy. There we confirmed our sequences as correct. | <p style=" margin-bottom: 50px; text-align: justify; text-indent: 5%; ">To analyze and remove the introns, we used the <a href="http://www.softberry.com/berry.phtml?topic=fgenesh&group=programs&subgroup=gfind">FGENESH tool</a> from Softberry. After that, to verify if the gene sequence expressed a functional protein we used the <a href="https://web.expasy.org/translate/ ">Translate tool</a>from Expazy. There we confirmed our sequences as correct. | ||
Once our laccases are from fungi and we plan to express them into a bacterial chassis, we had to remove the signal peptide. To do so, we used the <a href="http://www.cbs.dtu.dk/services/SignalP/">SignalP 4.1 tool</a> from DTU Bioinformatics .</p> | Once our laccases are from fungi and we plan to express them into a bacterial chassis, we had to remove the signal peptide. To do so, we used the <a href="http://www.cbs.dtu.dk/services/SignalP/">SignalP 4.1 tool</a> from DTU Bioinformatics .</p> | ||
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| − | <p><center>Laccase <i>Phoma sp.</i>(Lac PH):</center></p> | + | <p></br></br></br><center>Laccase <i>Phoma sp.</i>(Lac PH):</center></p> |
<img style="text-align:center; margin-bottom: 5%;" src="https://static.igem.org/mediawiki/2018/f/f7/T--USP-EEL-Brazil--Phoma.jpeg" width=100%> | <img style="text-align:center; margin-bottom: 5%;" src="https://static.igem.org/mediawiki/2018/f/f7/T--USP-EEL-Brazil--Phoma.jpeg" width=100%> | ||
<p><center>Laccase <i>Pleurotus ostreatus</i> (Lac PL):</center></p> | <p><center>Laccase <i>Pleurotus ostreatus</i> (Lac PL):</center></p> | ||
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<p style=" margin-bottom: 50px; text-align: justify; text-indent: 5%; "> | <p style=" margin-bottom: 50px; text-align: justify; text-indent: 5%; "> | ||
| − | Also, our instructor Evandro Mulinari provided for us a laccase from <a href="https://www.ncbi.nlm.nih.gov/protein/XP_003656170"> | + | Also, our instructor Evandro Mulinari provided for us a laccase from <a href="https://www.ncbi.nlm.nih.gov/protein/XP_003656170"><i>Thielavia terrestris </i>NRRL 8126</a> of his own design. |
<p style=" margin-bottom: 50px; text-align: justify; text-indent: 5%; ">The gene was designed in such a way that, when expressed, the protein contains peptides with cleavage sites for TEV followed by thioredoxin and 6 histidines at the N-terminus, to make the protein purification easier.</p> | <p style=" margin-bottom: 50px; text-align: justify; text-indent: 5%; ">The gene was designed in such a way that, when expressed, the protein contains peptides with cleavage sites for TEV followed by thioredoxin and 6 histidines at the N-terminus, to make the protein purification easier.</p> | ||
<p><center>Laccase <i>Thielava terrestris </i>(Lac TT):</center></p> | <p><center>Laccase <i>Thielava terrestris </i>(Lac TT):</center></p> | ||
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Latest revision as of 02:50, 18 October 2018
Step by Step
The sequences of our target genes were found in the CAZy data bank, where laccases are identified as enzymes from the Auxiliary Activity Family 1 (AA1):
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• Laccase from Pleurotus ostreatus NRRL0366:3471 pb - 533 aa
• Laccase from Phoma sp. UHH 5-1-03 (DSM 2245):3073 pb - 607 aa
To analyze and remove the introns, we used the FGENESH tool from Softberry. After that, to verify if the gene sequence expressed a functional protein we used the Translate toolfrom Expazy. There we confirmed our sequences as correct. Once our laccases are from fungi and we plan to express them into a bacterial chassis, we had to remove the signal peptide. To do so, we used the SignalP 4.1 tool from DTU Bioinformatics .
Completed this process we removed any restriction sites for EcoRI, NotI, PstI and SpeI from the gene. For the synthesis, we inserted an RBS sequence and the biobrick prefix and suffix, obtaining the following gene features:
Our final biobrick construct for the laccase expression constituted on the following desing:
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Obtained from the iGEM Registry: BBa_R0010 and found on the 2018 DNA Distribution Kit (kit plate 3, well 4G). |
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| Sequence obtained from iGEM Registry: BBa_B0030 and synthesized with the gene. |
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Laccase gene from Pleurotus ostreatus NRRL0366:3471 (Lac PL), was designed and synthesized by the team. |
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Laccase gene from Phoma sp. UHH 5-1-03 (DSM 2245) (Lac PH), was designed and synthesized by the team. |
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Found on the pSBIC3 backbone. |
Also, our instructor Evandro Mulinari provided for us a laccase from Thielavia terrestris NRRL 8126 of his own design.
The gene was designed in such a way that, when expressed, the protein contains peptides with cleavage sites for TEV followed by thioredoxin and 6 histidines at the N-terminus, to make the protein purification easier.
This laccase (Lac TT) was inserted into the pETTrx-1a / LIC vector, witch contains resistance to kanamycin and has the expression regulated by the Lac operon. The transformation was done into E. coli Rosetta Gami 2 (DE3).