Difference between revisions of "Part:BBa K4201008:Design"

 
 
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===Design Notes===
 
===Design Notes===
−
Design Considerations
+
Codon optimization for <i>Glycine max</i> (soybean) is a unique design consideration for all of CU Boulder’s coding sequences including our TAT. Codon optimization is the intentional use of specific codons for specific amino acids, dependent on what tRNAs are most abundant in the organism. While codon optimization is a common consideration for synthetic biologists, our sequences are unique for iGEM because they are intended for expression in soybeans.
  
 +
[[File:TAT paclitaxel.png|400px|thumb|right|A diagram of the metabolic pathway for the synthesis of paclitaxel. TAT converts taxadiene-5α-ol into taxadiene-5α-yl-acetate, outlined in red.]]
  
  
 
===Source===
 
===Source===
  
−
Source
+
This taxadiene acetyl transferase sequence originates from <i>Taxus cuspidata</i>, which is a species of Yew Tree<sup>3</sup>.  All of our DNA fragments are obtained via de novo synthesis by iGEM sponsors Twist Bioscience and Integrated DNA technologies. Codon Optimization was completed with their respective optimization programs.
  
 
===References===
 
===References===
 +
1. Wang, T. et al. Recent Research Progress in Taxol Biosynthetic Pathway and Acylation Reactions Mediated by Taxus Acyltransferases. Molecules 26, 2855 (2021).<br>
 +
2. Raeispour Shirazi, M., Rahpeyma, S. A., Rashidi Monfared, S., Zolala, J. & Lohrasbi-Nejad, A. Identification and in-silico characterization of taxadien-5α-ol-O-acetyltransferase (TDAT) gene in Corylus avellana L. PLoS ONE 16, e0256704 (2021).
 +
<br>3. TAT - Taxadien-5-alpha-ol O-acetyltransferase - Taxus cuspidata (Japanese yew) | UniProtKB | UniProt. https://www.uniprot.org/uniprotkb/Q9M6F0/entry.

Latest revision as of 00:27, 12 October 2022


TAT


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal EcoRI site found at 759
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal EcoRI site found at 759
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal EcoRI site found at 759
    Illegal BglII site found at 226
    Illegal BglII site found at 428
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal EcoRI site found at 759
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal EcoRI site found at 759
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI site found at 1
    Illegal BsaI.rc site found at 1337


Design Notes

Codon optimization for Glycine max (soybean) is a unique design consideration for all of CU Boulder’s coding sequences including our TAT. Codon optimization is the intentional use of specific codons for specific amino acids, dependent on what tRNAs are most abundant in the organism. While codon optimization is a common consideration for synthetic biologists, our sequences are unique for iGEM because they are intended for expression in soybeans.

A diagram of the metabolic pathway for the synthesis of paclitaxel. TAT converts taxadiene-5α-ol into taxadiene-5α-yl-acetate, outlined in red.


Source

This taxadiene acetyl transferase sequence originates from Taxus cuspidata, which is a species of Yew Tree3. All of our DNA fragments are obtained via de novo synthesis by iGEM sponsors Twist Bioscience and Integrated DNA technologies. Codon Optimization was completed with their respective optimization programs.

References

1. Wang, T. et al. Recent Research Progress in Taxol Biosynthetic Pathway and Acylation Reactions Mediated by Taxus Acyltransferases. Molecules 26, 2855 (2021).
2. Raeispour Shirazi, M., Rahpeyma, S. A., Rashidi Monfared, S., Zolala, J. & Lohrasbi-Nejad, A. Identification and in-silico characterization of taxadien-5α-ol-O-acetyltransferase (TDAT) gene in Corylus avellana L. PLoS ONE 16, e0256704 (2021).
3. TAT - Taxadien-5-alpha-ol O-acetyltransferase - Taxus cuspidata (Japanese yew) | UniProtKB | UniProt. https://www.uniprot.org/uniprotkb/Q9M6F0/entry.