<a href="https://parts.igem.org/Part:BBa_K3861017">BBa_K3861017</a> is an <i>E</i>. coli optimized version of the GFP coding sequence which is heavily used within iGEM projects throughout the years, highlighted by the high frequency of updates on the respective part registry. To increase the usability of this part for our model organism <i>Salmonella typhimurium</i>, we codon harmonized the original sequences towards Salmonella to increase the GFP expression in our host. For this, we ranked the frequency of all triplets coding for each amino acid based on global expression pattern studies in <i>E</i>. coli and <i>S</i>. typhimurium, respectively. Now, using the <a href="https://parts.igem.org/Part:BBa_K3861017">BBa_K3861017</a> is an <i>E</i> base sequence, the respective triplet of <i>S</i>. typhimurium that aligns to the same rank as the <i>E</i>. coli triplet was determined. For example, in E. coli the second most translated codon for Alanine was substituted for the second ranked <i>S</i>. typhimurium Alanine coding triplet. By this, we deliberately took into account slow and fast codons and transferred this information to our part sequence.
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<i>Salmonella</i> Typhimurium codon harmonized GFP expressed by the lactate-inducible PlldR promoter.
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In contrast to codon optimization, where independent of the source organism, simply the “best” (most frequently used) codon of an amino acid in the target organism is applied, we believe that codon harmonization increases the chances to generate stable and proper folded proteins in heterologous expression scenarios.
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Latest revision as of 22:02, 19 October 2021
PlldR-GFP(Harmonized for Salmonella Typhimurium)
Salmonella Typhimurium codon harmonized GFP expressed by the lactate-inducible PlldR promoter.
Sequence and Features
Assembly Compatibility:
10
INCOMPATIBLE WITH RFC[10]
Illegal prefix found in sequence at 7 Illegal suffix found in sequence at 1065
12
INCOMPATIBLE WITH RFC[12]
Illegal EcoRI site found at 7 Illegal NheI site found at 106 Illegal NheI site found at 129 Illegal SpeI site found at 1066 Illegal PstI site found at 1080 Illegal NotI site found at 13 Illegal NotI site found at 1073
21
INCOMPATIBLE WITH RFC[21]
Illegal EcoRI site found at 7
23
INCOMPATIBLE WITH RFC[23]
Illegal prefix found in sequence at 7 Illegal suffix found in sequence at 1066
25
INCOMPATIBLE WITH RFC[25]
Illegal prefix found in sequence at 7 Illegal suffix found in sequence at 1056 Illegal XbaI site found at 22
