Difference between revisions of "Team:DTU-Denmark/Parts"
Helenautzon (Talk | contribs) |
Helenautzon (Talk | contribs) |
||
| (4 intermediate revisions by 2 users not shown) | |||
| Line 26: | Line 26: | ||
| − | <div class=" topimg pull-right sm-no-float col-md- | + | <div class=" topimg pull-right sm-no-float col-md-7 "> |
| Line 38: | Line 38: | ||
| − | <div class="pull-left col-md- | + | <div class="pull-left col-md-5 sm-text-center com-sm-12 "> |
| − | <div class="team-overview"> | + | <div class="team-overview" style="font-size:1em";> |
<h2>Parts overview</h2> | <h2>Parts overview</h2> | ||
| Line 356: | Line 356: | ||
<div class="sizemargins"> | <div class="sizemargins"> | ||
| − | <p> | + | <p>This is a device for testing promoters by expressing mCherry.</p> |
| Line 549: | Line 549: | ||
<div class="sizemargins"> | <div class="sizemargins"> | ||
| − | <p> | + | <p>This part is the bacterial promoter <a href="http://parts.igem.org/Part:BBa_R0010" target="_blank">BBa_R0010</a> with MoClo level 0 compatible overhangs.</p> |
| − | <p style="text-align:center;"> <img src="https://static.igem.org/mediawiki/2019/5/59/T--DTU-Denmark--moclo.jpg" alt="The figure shows the 238 basepair long MoClo promoter | + | <p style="text-align:center;"> <img src="https://static.igem.org/mediawiki/2019/5/59/T--DTU-Denmark--moclo.jpg" alt="The figure shows the 238 basepair long MoClo promoter stand-in" style="max-width: 721px;"> |
</p> | </p> | ||
| Line 581: | Line 581: | ||
<div class="sizemargins"> | <div class="sizemargins"> | ||
| − | <p> | + | <p>Transcriptional terminator from <i>Aspergillus nidulans</i>. Domesticated to be in compliance with RFC[1000]</p> |
| Line 613: | Line 613: | ||
<div class="sizemargins"> | <div class="sizemargins"> | ||
| − | <p> | + | <p>Protein secretion tag from the GlaA enzyme from <i>Aspergillus niger</i>.</p> |
| Line 646: | Line 646: | ||
<div class="sizemargins"> | <div class="sizemargins"> | ||
| − | <p> | + | <p>This part is a superfolded, monomeric, stable green fluorescent protein.</p> |
| Line 678: | Line 678: | ||
<div class="sizemargins"> | <div class="sizemargins"> | ||
| − | <p> | + | <p>This plasmid is designed as a shuttle vector to test different fungal promoters</p> |
| Line 805: | Line 805: | ||
<div class="sizemargins"> | <div class="sizemargins"> | ||
| − | <p> | + | <p>CThis coding sequence from <i>Aspergillus fumigatus</i> is encoding Orotidine 5'-phosphate decarboxylase.</p> |
| Line 991: | Line 991: | ||
| − | + | ||
| − | + | ||
| − | + | ||
</div> | </div> | ||
Latest revision as of 02:21, 22 October 2019
Parts overview
Through this project we have created a library of Aspergillus promoters and other fungal parts, which will make it easier for future iGEM-teams to work with filamentous fungi. These, along with other parts we have created or characterized, are described below.
Type: Regulatory
Size: 683 bp
This is a strong promoter for Aspergillus niger that has high activity in the exponential phase. This is a synthetic exponential phase promoter, created as part of the LEAP (Library of Engineered Aspergillus Promoters) project. It is based on the glaA promoter from different Aspergillus spp., and the gene was chosen based on RNA-seq data from Aspergillus niger. The consensus promoter was expected to have really high expression. This version has “noise” added to the sequence to support a hypothesis that it was possible to turn down expression of the promoter.
Assembly Compatibility:
Type: Regulatory
Size: 842 bp
This is a medium strength constitutive promoter for Aspergillus niger. This is a synthetic constitutive promoter, created as part of the LEAP (Library of Engineered Aspergillus Promoters) project. It is based on the sonB promoter from different Aspergillus spp., and the gene was chosen based on RNA-seq data from Aspergillus niger. [1] This version is a consensus sequence of the sonB promoters in Aspergillus and is expected to have a medium strength expression.
Assembly Compatibility:
Type: Regulatory
Size: 926 bp
This is a strong constitutive promoter for Aspergillus niger that has especially high activity in the lag phase. This is a synthetic constitutive promoter, created as part of the LEAP (Library of Engineered Aspergillus Promoters) project. It is based on the gpdA promoter from different Aspergillus spp., and the gene was chosen based on RNA-seq data from Aspergillus niger. This version is a consensus sequence of the promoters in Aspergillus and is expected to have a high expression.
Assembly Compatibility:
Type: Regulatory
Size: 926 bp
This is a medium strength constitutive promoter for Aspergillus niger. This is a synthetic constitutive promoter, created as part of the LEAP (Library of Engineered Aspergillus Promoters) project. It is based on the gpdA promoter from different Aspergillus spp., and the gene was chosen based on RNA-seq data from Aspergillus niger. The consensus promoter was expected to have high expression. This version has “noise” added to the sequence to support a hypothesis that it was possible to turn down expression of the promoter.
Assembly Compatibility:
Type: Regulatory
Size: 986 bp
This is a very strong constitutive promoter for Aspergillus niger that has especially high activity in the exponential growth phase. This is a synthetic constitutive promoter, created as part of the LEAP (Library of Engineered Aspergillus Promoters) project. It is based on the mstA promoter from different Aspergillus spp., and the gene was chosen based on RNA-seq data from Aspergillus niger. This version is a consensus sequence of the mstA promoters in Aspergillus and is expected to have a high constitutive expression.
Assembly Compatibility:
Type: Regulatory
Size: 933 bp
This is a weak constitutive promoter for Aspergillus niger. This is a synthetic constitutive promoter, created as part of the LEAP (Library of Engineered Aspergillus Promoters) project. It is based on an unknown promoter from different Aspergillus spp., and the gene was chosen based on RNA-seq data from Aspergillus niger. This version is a consensus sequence of the An07g08210 promoters in Aspergillus and is expected to have a weak constitutive expression.
Assembly Compatibility:
Type: Regulatory
Size: 973 bp
This is a strong promoter for Aspergillus niger that has high activity in the late exponential phase and stationary phase. This is a synthetic constitutive promoter, created as part of the LEAP (Library of Engineered Aspergillus Promoters) project. It is based on the gfaA promoter from different Aspergillus spp., and the gene was chosen based on RNA-seq data from Aspergillus niger. This version is a consensus sequence of the promoters in Aspergillus and is expected to have a high expression.
Assembly Compatibility:
Type: Regulatory
Size: 1014 bp
This is a strong promoter for Aspergillus niger that has high activity in the stationary growth phase. This is a synthetic stationary phase promoter, created as part of the LEAP (Library of Engineered Aspergillus Promoters) project. It is based on the hfbD promoter from different Aspergillus spp., and the gene was chosen based on RNA-seq data from Aspergillus niger. This is a consensus promoter and are expected to have high expression in the stationary phase.
Assembly Compatibility:
Type: Measurement
Size: 1505 bp
This is a device for testing promoters by expressing mCherry.
Assembly Compatibility:
Type: Regulatory
Size: 683 bp
This is a promoter for Aspergillus niger of unknown strength that is expected to have high expression in the exponential growth phase. This is a synthetic exponential phase promoter, created as part of the LEAP (Library of Engineered Aspergillus Promoters) project. It is based on the glaA promoter from different Aspergillus spp., and the gene was chosen based on RNA-seq data from Aspergillus niger. The consensus promoter was expected to have really high expression. This version has “noise” added to the sequence to support a hypothesis that it was possible to turn down expression of the promoter.
Assembly Compatibility:
Type: Regulatory
Size: 842 bp
This is a promoter for Aspergillus niger of unknown strength that is expected to have constitutive expression. This is a synthetic constitutive promoter, created as part of the LEAP (Library of Engineered Aspergillus Promoters) project. It is based on the sonB promoter from different Aspergillus spp., and the gene was chosen based on RNA-seq data from Aspergillus niger. This version is a consensus sequence of the sonB promoters in Aspergillus and is expected to have a medium strength expression
Assembly Compatibility:
Type: Regulatory
Size: 986 bp
This is a very strong constitutive promoter for Aspergillus niger that has especially high activity in the exponential growth phase. This is a synthetic constitutive promoter, created as part of the LEAP (Library of Engineered Aspergillus Promoters) project. It is based on the gfaA promoter from different Aspergillus spp., and the gene was chosen based on RNA-seq data from Aspergillus niger. This version has introduced stokastic noise compared to the consensus sequence of the promoters in Aspergillus and is therefore expected to have a lower expression.
Assembly Compatibility:
Type: Regulatory
Size: 724 bp
This is a promoter for Aspergillus niger of unknown strength that should be active in the stationary phase. This is a synthetic constitutive promoter, created as part of the LEAP (Library of Engineered Aspergillus Promoters) project. It is based on the sonB promoter from different Aspergillus spp., and the gene was chosen based on RNA-seq data from Aspergillus niger. [1] This version is a consensus sequence of an unknown gene's promoters in Aspergillus.
Assembly Compatibility:
Type: Regulatory
Size: 973 bp
This is a promoter on unknown for Aspergillus niger that is expected to have high activity in the late exponential phase and stationary phase. This is a synthetic constitutive promoter, created as part of the LEAP (Library of Engineered Aspergillus Promoters) project. It is based on the gfaA promoter from different Aspergillus spp., and the gene was chosen based on RNA-seq data from Aspergillus niger. This version has introduced stokastic noise compared to the consensus sequence of the promoters in Aspergillus and is therefore expected to have a lower expression.
Assembly Compatibility:
Type: Regulatory
Size: 238 bp
This part is the bacterial promoter BBa_R0010 with MoClo level 0 compatible overhangs.
Assembly Compatibility:
Type: Terminator
Size: 485 bp
Transcriptional terminator from Aspergillus nidulans. Domesticated to be in compliance with RFC[1000]
Assembly Compatibility:
Type: Tag
Size: 63 bp
Protein secretion tag from the GlaA enzyme from Aspergillus niger.
Assembly Compatibility:
Type: Coding
Size: 720 bp
This part is a superfolded, monomeric, stable green fluorescent protein.
Assembly Compatibility:
Type: Measurement
Size: 10725 bp
This plasmid is designed as a shuttle vector to test different fungal promoters
Assembly Compatibility:
Type: Composite
Size: 1324 bp
This PyrG transcriptional unit can be used as a marker gene to select for succesful transformants of Pyr- mutants.
Assembly Compatibility:
Type: Plasmid Backbone
Size: 7896 bp
This is a plasmid containing an E.coli ORI, an ampicillin selection marker, and the AMA1 sequence. Inserts can be integrated into the plasmid by using a PacI/Nt.BbvCI USER assembly casette.
Assembly Compatibility:
Type: Coding
Size: 5721 bp
This sequence is used for creating autonomously replicating plasmids to use for Aspergillus spp.
Assembly Compatibility:
Type: Coding
Size: 906 bp
CThis coding sequence from Aspergillus fumigatus is encoding Orotidine 5'-phosphate decarboxylase.
Assembly Compatibility:
Type: Regulatory
Size: 418 bp
Promoter from the PyrG selection marker gene from Aspergillus fumigatus
Assembly Compatibility:
Type: Composite
Size: 5546 bp
This part is designed to be inserted into pSB1C3 by Gibson cloning to make an integration plasmid for Aspergillus niger. The part is meant to be linearised by PCR prior to protoplast-mediated transformation, where the IS2 sites will lead to genomic integration of the insert (in this case just PyrG part BBa_K3046022) into the albA conidial pigment gene. Correct gene integration will, therefore, yield white/yellow conidia instead of the black conidia seen for the wildtype A. niger.
Assembly Compatibility:
Type: Measurement
Size: 7139 bp
This part is designed to be inserted into pSB1C3 by Gibson cloning to make an integration plasmid for Aspergillus niger. The part is meant to be linearised by PCR prior to protoplast-mediated transformation, where the IS2 sites will lead to genomic integration of the insert (in this case just PyrG part BBa_K3046022) into the albA conidial pigment gene. Correct gene integration will therefore yield white/yellow conidia instead of the black conidia seen for the wildtype A. niger.
Assembly Compatibility:
Type: DNA
Size: 2096 bp
This part is a long sequence of DNA that are homologous to a part of the albA conidial pigment gene. This homology can be used for homologous recombination of genomic constructs flanked by this IS2 sequence (along with the downstream sequence BBa_K3046033).
Assembly Compatibility:
Type: DNA
Size: 2112 bp
This part is a long sequence of DNA that are homologous to a part of the albA conidial pigment gene. This homology can be used for homologous recombination of genomic constructs flanked by this IS2 sequence (along with the upstream sequence BBa_K3046032).
Assembly Compatibility:
