Difference between revisions of "Team:British Columbia/Part Collection"

 
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    <h1>Parts Collection!</h1>
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<p> Our collection of parts contains genes required for modification of imidacloprid and degradation of 6-chloronicotinic acid (6-CNA). Final parts were assembled in pSB1C3 backbone harboring the chloramphenicol resistance gene and designed to have a LacI repressor, ribosome binding site, pTAC promoter, our degradation genes of interest, and double terminator. </p>
 
<p> Our collection of parts contains genes required for modification of imidacloprid and degradation of 6-chloronicotinic acid (6-CNA). Final parts were assembled in pSB1C3 backbone harboring the chloramphenicol resistance gene and designed to have a LacI repressor, ribosome binding site, pTAC promoter, our degradation genes of interest, and double terminator. </p>
  
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<p> The three composite parts each containing a cytochrome P450 (CYP) were designed to include an N-terminal pelB signal sequence to target expression to the periplasm and a cytochrome P450 reductase (CPR) for functionality of the CYP. The CPR was also made with it’s own designated rbs, promoter, <i>pelB</i> signal sequence, and terminator. </p>
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<p> The three composite parts each containing a cytochrome P450 (CYP) were designed to include an N-terminal <i>pelB</i> signal sequence to target expression to the periplasm and a cytochrome P450 reductase (CPR) for functionality of the CYP. The CPR was also made with it’s own designated rbs, promoter, <i>pelB</i> signal sequence, and terminator. </p>
  
 
<p> Composite parts with multiple degradation genes were designed so that each gene in the construct had a dedicated rbs, promoter, and double terminator. </p>
 
<p> Composite parts with multiple degradation genes were designed so that each gene in the construct had a dedicated rbs, promoter, and double terminator. </p>
  
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<center><h3> Favourite Parts: </h3></center>
  
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    <p><center><h3><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1813026">BBa_K1813026</a></center></h3>
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Cch2 is a novel chlorohydrolase that was identified in a soil bacterium, Bradyrhizobiaceae strain SG-6C, that is capable of dechlorinating 6-chloronicotinic acid (6-CNA) to 6-hydroxynicotinic acid (6-HNA). 6-CNA has been found to accumulate in soils and plant material following application of imidacloprid. Due to the associated toxicity of 6-CNA to bees, demonstrating that this part can be used to degrade 6-CNA to 6-HNA, a less toxic metabolite, was a big accomplishment. </p>
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    <p><center><h3><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1813064">BBa_K1813064</a></center></h3>
  
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This composite part consists of CYP6G1 is a cytochrome P450 (CYP) from <i>Drosophila melanogaster</i> that can modify imidacloprid to 4- and 5-hydroxyimidacloprid. These degradation products have been demonstrated to be less toxic to bees. Previous work by Middle East Technical University (METU) had worked on this part (<a href="http://parts.igem.org/Part:BBa_K1197013">BBa_K1197013</a>); however, it is not available from the registry. In attempts to make an improvement to this part, we included a <i>pelB</i> signal sequence immediately upstream of the gene to target CYP6G1 to the periplasm. Though we were not able to validate that this improved the part, previous literature on expression of CYP’s suggests that inclusion of a signal sequence greatly improves heterologous protein expression.
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<center><h3><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1813067">BBa_K1813067</a></center></h3>
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The objective of our probeeotic project was to genetically modify a native bee gut microbe to be capable of degrading imidacloprid and 6-CNA. A step towards that goal included generating a construct that consisted of multiple imidacloprid modification genes and genes for complete mineralization of 6-CNA to fumarate. Unfortunately, we were unable to generate any data on this composite part as <i>E. coli</i> harboring this plasmid did not grow well in liquid media.
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<center><h3>Composite parts: Imidacloprid modification</center></h3>
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<a href="http://parts.igem.org/Part:BBa_K1813064">BBa_K1813064</a> CYP6G1 from <i>D. melanogaster</i> with N-terminal PelB signal sequence and <i>Anopheles gambiae</i> cytochrome P450 reductase. CYP6G1 can convert imidacloprid to 4- and 5-hydroxy imidacloprid.</p>
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<p><a href="http://parts.igem.org/Part:BBa_K1813065">BBa_K1813065</a> CYP6CM1 from <i>Bemisia tabaci</i> with N-terminal PelB signal sequence and <i>Anopheles gambiae</i> cytochrome P450 reductase. CYP6CM1 can convert imidacloprid to 5-hydroxy imidacloprid.</p>
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<p><a href="http://parts.igem.org/Part:BBa_K1813066">BBa_K1813066</a> CYP2D6 from human with N-terminal PelB signal sequence and <i>Anopheles gambiae</i>  cytochrome P450 reductase. CYP6G1 can convert imidacloprid to nitrosoimine derivative.
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<center><h3>Composite parts: 6-CNA Degradation</center></h3>
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<a href="http://parts.igem.org/Part:BBa_K1813020">BBa_K1813026</a> Cch2 is from Bradyrhizobiaceae strain SG-6C for conversion of 6-CNA to 6-HNA.</p>
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<p><a href="http://parts.igem.org/Part:BBa_K1813020">BBa_K1813020</a> NicC is from <i>Pseudmonas putida</i> KT2240 for conversion of 6-HNA to 2,5-dihydroxypyridine</p>
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<p><a href="http://parts.igem.org/Part:BBa_K1813031">BBa_K1813031</a> NicX is from <i>Pseudmonas putida</i> KT2240 for conversion of 2,5-dihydroxypyridine to N-formylmaleamic acid</p>
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<p><a href="http://parts.igem.org/Part:BBa_K1813021">BBa_K1813021</a> NicD is from <i>Pseudmonas putida</i> KT2240 for conversion of  N-formylmaleamic acid to maleamic acid</p>
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<p><a href="http://parts.igem.org/Part:BBa_K1813022">BBa_K1813022</a> NicE is from <i>Pseudmonas putida</i> KT2240 for conversion of maleamic acid to maleic acid</p>
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<p><a href="http://parts.igem.org/Part:BBa_K1813023">BBa_K1813023</a> NicF is from <i>Pseudmonas putida</i> KT2240 for conversion of maleic acid to fumarate
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<a href="http://parts.igem.org/Part:BBa_K1813035">BBa_K1813035</a> Consists of the genes required for degradation of 6-CNA to fumarate. These include genes coding for Cch2, to convert 6-CNA to 6-HNA, and NicCXDEF, the five enzymes required for degradation of 6-HNA to fumarate. The end-product, fumarate can be funneled into central metabolism. </p>
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<p><a href="http://parts.igem.org/Part:BBa_K1813067">BBa_K1813067</a> Contains one of the three CYPs investigated, CYP6G1, cytochrome P450 reductase, <i>cch2</i>, and the <i>nicCXDEF</i> cluster. This construct would allow for modification of imidacloprid to a less toxic form by CYP6G1, conversion of 6-CNA to 6-HNA by Cch2, and degradation of 6-HNA to fumarate by NicCXDEF pathway.</p>
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<p><a href="http://parts.igem.org/Part:BBa_K1813066">BBa_K1813066</a> As above, but with CYP6CM1 in place of CYP6G1.</p>
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<p><a href="http://parts.igem.org/Part:BBa_K1813072">BBa_K1813072</a> Also as above, but with CYP2D6 in place of CYP6G1.
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<p>Refer to the British Columbia 2015 iGEM team list of parts in the Standard Registry of Standard Biological Parts <a href="http://parts.igem.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2015&group=British_Columbia">(link here)</a> for all intermediate composite parts and coding sequences used in the design of our composite parts.</p>
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<p>Did your team make a lot of great parts? Is there a theme that ties all your parts together? Do you have more than 10 parts in this collection? Did you make a CRISPR collection, a MoClo collection, or a collection of awesome pigment parts? Describe your parts collection on this page, so the judges can evaluate you for the Best Part Collection award.</p>
 
<p>Did your team make a lot of great parts? Is there a theme that ties all your parts together? Do you have more than 10 parts in this collection? Did you make a CRISPR collection, a MoClo collection, or a collection of awesome pigment parts? Describe your parts collection on this page, so the judges can evaluate you for the Best Part Collection award.</p>
  
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Latest revision as of 03:44, 19 September 2015

UBC iGEM 2015

 

Part Collection

 

Parts Collection!

Our collection of parts contains genes required for modification of imidacloprid and degradation of 6-chloronicotinic acid (6-CNA). Final parts were assembled in pSB1C3 backbone harboring the chloramphenicol resistance gene and designed to have a LacI repressor, ribosome binding site, pTAC promoter, our degradation genes of interest, and double terminator.

The three composite parts each containing a cytochrome P450 (CYP) were designed to include an N-terminal pelB signal sequence to target expression to the periplasm and a cytochrome P450 reductase (CPR) for functionality of the CYP. The CPR was also made with it’s own designated rbs, promoter, pelB signal sequence, and terminator.

Composite parts with multiple degradation genes were designed so that each gene in the construct had a dedicated rbs, promoter, and double terminator.

Favourite Parts:


BBa_K1813026

Cch2 is a novel chlorohydrolase that was identified in a soil bacterium, Bradyrhizobiaceae strain SG-6C, that is capable of dechlorinating 6-chloronicotinic acid (6-CNA) to 6-hydroxynicotinic acid (6-HNA). 6-CNA has been found to accumulate in soils and plant material following application of imidacloprid. Due to the associated toxicity of 6-CNA to bees, demonstrating that this part can be used to degrade 6-CNA to 6-HNA, a less toxic metabolite, was a big accomplishment.

BBa_K1813064

This composite part consists of CYP6G1 is a cytochrome P450 (CYP) from Drosophila melanogaster that can modify imidacloprid to 4- and 5-hydroxyimidacloprid. These degradation products have been demonstrated to be less toxic to bees. Previous work by Middle East Technical University (METU) had worked on this part (BBa_K1197013); however, it is not available from the registry. In attempts to make an improvement to this part, we included a pelB signal sequence immediately upstream of the gene to target CYP6G1 to the periplasm. Though we were not able to validate that this improved the part, previous literature on expression of CYP’s suggests that inclusion of a signal sequence greatly improves heterologous protein expression.

BBa_K1813067

The objective of our probeeotic project was to genetically modify a native bee gut microbe to be capable of degrading imidacloprid and 6-CNA. A step towards that goal included generating a construct that consisted of multiple imidacloprid modification genes and genes for complete mineralization of 6-CNA to fumarate. Unfortunately, we were unable to generate any data on this composite part as E. coli harboring this plasmid did not grow well in liquid media.

Composite parts: Imidacloprid modification

BBa_K1813064 CYP6G1 from D. melanogaster with N-terminal PelB signal sequence and Anopheles gambiae cytochrome P450 reductase. CYP6G1 can convert imidacloprid to 4- and 5-hydroxy imidacloprid.

BBa_K1813065 CYP6CM1 from Bemisia tabaci with N-terminal PelB signal sequence and Anopheles gambiae cytochrome P450 reductase. CYP6CM1 can convert imidacloprid to 5-hydroxy imidacloprid.

BBa_K1813066 CYP2D6 from human with N-terminal PelB signal sequence and Anopheles gambiae cytochrome P450 reductase. CYP6G1 can convert imidacloprid to nitrosoimine derivative.

Composite parts: 6-CNA Degradation

BBa_K1813026 Cch2 is from Bradyrhizobiaceae strain SG-6C for conversion of 6-CNA to 6-HNA.

BBa_K1813020 NicC is from Pseudmonas putida KT2240 for conversion of 6-HNA to 2,5-dihydroxypyridine

BBa_K1813031 NicX is from Pseudmonas putida KT2240 for conversion of 2,5-dihydroxypyridine to N-formylmaleamic acid

BBa_K1813021 NicD is from Pseudmonas putida KT2240 for conversion of N-formylmaleamic acid to maleamic acid

BBa_K1813022 NicE is from Pseudmonas putida KT2240 for conversion of maleamic acid to maleic acid

BBa_K1813023 NicF is from Pseudmonas putida KT2240 for conversion of maleic acid to fumarate

Composite parts: Multi-gene Pesticide Degradation

BBa_K1813035 Consists of the genes required for degradation of 6-CNA to fumarate. These include genes coding for Cch2, to convert 6-CNA to 6-HNA, and NicCXDEF, the five enzymes required for degradation of 6-HNA to fumarate. The end-product, fumarate can be funneled into central metabolism.

BBa_K1813067 Contains one of the three CYPs investigated, CYP6G1, cytochrome P450 reductase, cch2, and the nicCXDEF cluster. This construct would allow for modification of imidacloprid to a less toxic form by CYP6G1, conversion of 6-CNA to 6-HNA by Cch2, and degradation of 6-HNA to fumarate by NicCXDEF pathway.

BBa_K1813066 As above, but with CYP6CM1 in place of CYP6G1.

BBa_K1813072 Also as above, but with CYP2D6 in place of CYP6G1.


Refer to the British Columbia 2015 iGEM team list of parts in the Standard Registry of Standard Biological Parts (link here) for all intermediate composite parts and coding sequences used in the design of our composite parts.