Difference between revisions of "Part:BBa K1937008:Design"

 
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<b>Part: BBa_K1937008 (AF-A)</b><br>
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(Chassis <i>Bacillus subtilis</i>, carrier plasmid pSBBS0K-mini)<br>
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Length: 6558 bp<br>
  
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__NOTOC__
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<b>Background:</b>
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<partinfo>BBa_K1937008 short</partinfo>
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AF-A is a part designed to be combined with AF-B to form an operon of 5 antifungal peptides. The interest of using several antifungals is to have a broad spectrum of fungi target, because each antifungal has its own characteristics. The peptides were designed to be expressed and secreted by <i>Bacillus subtilis</i>. This operon was also initially designed to be expressed under the control of the pNagA or pNagP promoter (BBa_K1937003 and BBa_K1937005 respectively). In spite of several cloning strategies, the AF-B construction was not obtained, likely due to the toxicity of one of the peptides for <i>Bacillus subtilis</i>.
 +
This BioBrick is a part developed by the Toulouse 2016 iGEM team (http://2016.igem.org/Team:Toulouse_France).
  
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<partinfo>BBa_K1937008 SequenceAndFeatures</partinfo>
 
  
 +
<b>This part:</b>
 +
This part encodes two genes encoding antifungal peptides: a cutted Metchnikowin and the D4E1. We created it with the end of the Metchnikowin gene because we found out that only this part of the gene had the antifungal property (http://www.ebi.ac.uk/interpro/entry/IPR012513). The beginning of the gene translates for a propeptide. This gene comes from drosophila and translates a proline-rich peptide whose expression is immune-inducible. The peptide is active against fungi. The D4E1 gene is synthetic and translates a peptide that complexes with cholesterol, current in non-germinated conidia. This synthetic peptide is more resistant than the natural peptide CecroprineA because proteases from fungi have difficulties to degrade the synthetic one.(http://www.nrcresearchpress.com/doi/abs/10.1139/w98-032?journalCode=cjm#.V_pRgJOLT6Y). <br>
 +
So that each antifungal can be secreted out of the cell, it was necessary to add a sequence called AmyE that enables the transport of molecules outside of the cell. As AmyE is used twice in this Biobrick, we modified the AmyE sequences to avoid homologous recombination while keeping the same protein sequence. The NheI restriction site was added after the RBS to allow promoter swapping with biobrick Ba_K1937003 and BBa_K1937005). SacII and SalI restriction site were added to built the full 5 peptides operon. To create this biobrick, the part was inserted on the pSBBS0K-mini plasmid (BBa_K1937001).
  
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===Design Notes===
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<br>
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This part encodes two genes encoding antifungal peptides, issued from part BBa_K1937007, carried on the replicative Bacillus plasmid pSBBS0K: a cut Metchnikowin and the D4E1. We created it with the end of the Metchnikowin gene because we found out that only this part of the gene had the antifungal property (http://www.ebi.ac.uk/interpro/entry/IPR012513). The beginning of the gene translates for a propeptide.
+
[[File:BBa_K1937007-map1.png]]
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So that each antifungal can be secreted out of the cell, it was necessary to add a sequence called AmyE that enables the transport of molecules outside of the cell. As AmyE is used twice in this Biobrick, we modified the AmyE sequences to avoid homologous recombination while keeping the same protein sequence. The NheI restriction site was added after the RBS to allow promoter swapping with biobrick BBa_K1937003 or BBa_K1937005. SacII and SalI restriction site were added to built the full 5 peptides operon.
+
  
 +
<b>Validation:</b>
 +
The antifungal property was tested against <i>Talaromyces funiculosus</i>. Briefly, plates were evenly inoculated with the fungus and paper patches were added with either copper sulfate (positive control), water (negative control), <i>Bacillus subtilis</i> with pSBBS0K-mini (negative control, BBa_K1937001) or <i>Bacillus subtilis</i> with pSBBS0K-mini-AF-A. <br>
  
 +
[[File:Igemtoulouse2016af.jpg]]
  
 +
<br>
 +
Light but reproducible inhibition halo were observed after 3 days and still present after 8 days only when the <i>Bacillus subtilis</i> strain carry the antifungal plasmid.<br>
  
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===Source===
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<br>
  
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=<b>Sequence:</b>=<br><br>
 +
<b>Map</b>
 +
<br>
 +
[[File:BBa_K1937008-genemap.png]]
 +
<br>
 +
<html>
  
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This gene comes from drosophila and translates a proline-rich peptide whose expression is immune-inducible. The peptide is active against fungi. The D4E1 gene is synthetic and translates a peptide that complexes with cholesterol, current in non-germinated conidia. This synthetic peptide is more resistant than the natural peptide CecroprineA because proteases from fungi have difficulties to degrade the synthetic one (http://www.nrcresearchpress.com/doi/abs/10.1139/w98-032?journalCode=cjm#.V_pRgJOLT6Y).
+
<style>
  
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===References===
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/*LAYOUT */
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.column  {
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padding: 10px 0px;
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float:left;
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background-color:white;
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}
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.full_size {
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width:100%;
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word-wrap: break-word;
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}
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 +
 
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</style>
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<div class="column full_size" style="font-size:10px;">
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gAATTCGCGGCCGCTTCTAGAGggagttctgagaattggtatgccttataagtccaattaacagttgaaaacctgcataggagagctatgcgggttttttattttacataatgatacataatttaccgaaacttgcggaacataattgaggaatcatagaattttgtcaaaataattttattgacaacgtcttattaacgttgatataatttaaattttatttgacaaaaatgggctcgtgttgtacaataaatgtagtaaaggtggtgaaGCTAGCATGTTTGCTAAGAGATTCAAAACATCCTTACTCCCTTTGTTCGCGGGATTTTTGCTGCTGTTTCACCTCGTACTGGCCGGTCCGGCAGCAGCCAGTGCAGAAACCGCGAATAAGTCTAATGAGCATAGACATCAAGGCCCGATTTTTGATACAAGACCGTCACCGTTTAATCCGAATCAACCGAGACCGGGCCCGATTTATaaaggtggtgaaATGTTCGCTAAAAGATTCAAAACCAGCCTGCTGCCTTTATTTGCCGGATTCCTCCTTCTGTTCCACTTAGTGCTCGCGGGTCCGGCAGCAGCAAGCGCCGAAACGGCAAATAAGTCAAATGAGTCAAGTTACGGGCGAAAATCAAAGTACGGCTGCGGGCGAAGATCAAGCTATGACCAGGCACCGCGGGTCGACtgTTATCCGGCTATATTGCAGGAGCGATTATGAAACAAGAAGTTATCCTGGTACTCGACTGTGGCGCGACCAATGTCAGGGCCATCGCGGTTAATCGGCAGGGCAAAATTGTTGCCCGCGCCTCAACGCCTAATGCCAGCGATATCGCGATGGAAAACAACACCTGGCACCAGTGGTCTTTAGACGCCATTTTGCAACGCTTTGCTGATTGCTGTCGGCAAATCAATAGTGAACTGACTGAATGCCACATCCGaGGTATCGCCGTCACCACCTTTGGTGTGGATGGCGCTCTGGTAGATATACTAGTAGCGGCCGCTGCAG<br><br>
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</div>
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</html>
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<b>Annotation:</b><br>
 +
Pveg: 23-259 (Forward)<br>
 +
RBS D4E1: 479-490 (forward)<br>
 +
RBS Metch: 260-271 (forward)<br>
 +
Terminator: 1203-1282 (forward)<br>
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D4E1 : 614-673 (forward)<br>
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amyE for D4E1 : 491-613 (forward)<br>
 +
Cutted Metchnikowin : 401-478 (forward)<br>
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amyE for cutted Metchnikowin: 278-400 (forward)<br>
 +
Prefix: 1-22 (forward)<br>
 +
Suffixe: 986-1006 (forward)<br>
 +
 
 +
<br><br>

Revision as of 17:51, 17 October 2016

Part: BBa_K1937008 (AF-A)
(Chassis Bacillus subtilis, carrier plasmid pSBBS0K-mini)
Length: 6558 bp

Background: AF-A is a part designed to be combined with AF-B to form an operon of 5 antifungal peptides. The interest of using several antifungals is to have a broad spectrum of fungi target, because each antifungal has its own characteristics. The peptides were designed to be expressed and secreted by Bacillus subtilis. This operon was also initially designed to be expressed under the control of the pNagA or pNagP promoter (BBa_K1937003 and BBa_K1937005 respectively). In spite of several cloning strategies, the AF-B construction was not obtained, likely due to the toxicity of one of the peptides for Bacillus subtilis. This BioBrick is a part developed by the Toulouse 2016 iGEM team (http://2016.igem.org/Team:Toulouse_France).


This part: This part encodes two genes encoding antifungal peptides: a cutted Metchnikowin and the D4E1. We created it with the end of the Metchnikowin gene because we found out that only this part of the gene had the antifungal property (http://www.ebi.ac.uk/interpro/entry/IPR012513). The beginning of the gene translates for a propeptide. This gene comes from drosophila and translates a proline-rich peptide whose expression is immune-inducible. The peptide is active against fungi. The D4E1 gene is synthetic and translates a peptide that complexes with cholesterol, current in non-germinated conidia. This synthetic peptide is more resistant than the natural peptide CecroprineA because proteases from fungi have difficulties to degrade the synthetic one.(http://www.nrcresearchpress.com/doi/abs/10.1139/w98-032?journalCode=cjm#.V_pRgJOLT6Y).
So that each antifungal can be secreted out of the cell, it was necessary to add a sequence called AmyE that enables the transport of molecules outside of the cell. As AmyE is used twice in this Biobrick, we modified the AmyE sequences to avoid homologous recombination while keeping the same protein sequence. The NheI restriction site was added after the RBS to allow promoter swapping with biobrick Ba_K1937003 and BBa_K1937005). SacII and SalI restriction site were added to built the full 5 peptides operon. To create this biobrick, the part was inserted on the pSBBS0K-mini plasmid (BBa_K1937001).


BBa K1937007-map1.png

Validation: The antifungal property was tested against Talaromyces funiculosus. Briefly, plates were evenly inoculated with the fungus and paper patches were added with either copper sulfate (positive control), water (negative control), Bacillus subtilis with pSBBS0K-mini (negative control, BBa_K1937001) or Bacillus subtilis with pSBBS0K-mini-AF-A.

Igemtoulouse2016af.jpg


Light but reproducible inhibition halo were observed after 3 days and still present after 8 days only when the Bacillus subtilis strain carry the antifungal plasmid.


=Sequence:=

Map
BBa K1937008-genemap.png

gAATTCGCGGCCGCTTCTAGAGggagttctgagaattggtatgccttataagtccaattaacagttgaaaacctgcataggagagctatgcgggttttttattttacataatgatacataatttaccgaaacttgcggaacataattgaggaatcatagaattttgtcaaaataattttattgacaacgtcttattaacgttgatataatttaaattttatttgacaaaaatgggctcgtgttgtacaataaatgtagtaaaggtggtgaaGCTAGCATGTTTGCTAAGAGATTCAAAACATCCTTACTCCCTTTGTTCGCGGGATTTTTGCTGCTGTTTCACCTCGTACTGGCCGGTCCGGCAGCAGCCAGTGCAGAAACCGCGAATAAGTCTAATGAGCATAGACATCAAGGCCCGATTTTTGATACAAGACCGTCACCGTTTAATCCGAATCAACCGAGACCGGGCCCGATTTATaaaggtggtgaaATGTTCGCTAAAAGATTCAAAACCAGCCTGCTGCCTTTATTTGCCGGATTCCTCCTTCTGTTCCACTTAGTGCTCGCGGGTCCGGCAGCAGCAAGCGCCGAAACGGCAAATAAGTCAAATGAGTCAAGTTACGGGCGAAAATCAAAGTACGGCTGCGGGCGAAGATCAAGCTATGACCAGGCACCGCGGGTCGACtgTTATCCGGCTATATTGCAGGAGCGATTATGAAACAAGAAGTTATCCTGGTACTCGACTGTGGCGCGACCAATGTCAGGGCCATCGCGGTTAATCGGCAGGGCAAAATTGTTGCCCGCGCCTCAACGCCTAATGCCAGCGATATCGCGATGGAAAACAACACCTGGCACCAGTGGTCTTTAGACGCCATTTTGCAACGCTTTGCTGATTGCTGTCGGCAAATCAATAGTGAACTGACTGAATGCCACATCCGaGGTATCGCCGTCACCACCTTTGGTGTGGATGGCGCTCTGGTAGATATACTAGTAGCGGCCGCTGCAG

Annotation:
Pveg: 23-259 (Forward)
RBS D4E1: 479-490 (forward)
RBS Metch: 260-271 (forward)
Terminator: 1203-1282 (forward)
D4E1 : 614-673 (forward)
amyE for D4E1 : 491-613 (forward)
Cutted Metchnikowin : 401-478 (forward)
amyE for cutted Metchnikowin: 278-400 (forward)
Prefix: 1-22 (forward)
Suffixe: 986-1006 (forward)