Difference between revisions of "Part:BBa K3861019"

Latest revision as of 03:26, 22 October 2021

GFP harmonized for Salmonella Typhimurium

BBa_E0040 is 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 Salmonella Typhimurium, 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 E. coli and S. Typhimurium, respectively. Now, using the BBa_E0040 base sequence, the respective triplet of S. Typhimurium that aligns to the same rank as the E. coli triplet was determined. For example, in E. coli the second most translated codon for alanine was substituted for the second ranked S. Typhimurium alanine coding triplet. By this, we deliberately took into account slow and fast translated codons and transferred this information to our part sequence. In contrast to codon optimization, in which the every codon is replaced by the most frequently used codons of the target organism independent of the codon usage of the source organism, we believe that codon harmonization increases the chances to generate stable and proper folded proteins in heterologous expression scenarios.

Sequence and Features

Assembly Compatibility:

10
COMPATIBLE WITH RFC[10]
12
COMPATIBLE WITH RFC[12]
21
COMPATIBLE WITH RFC[21]
23
COMPATIBLE WITH RFC[23]
25
COMPATIBLE WITH RFC[25]
1000
INCOMPATIBLE WITH RFC[1000]
Illegal BsaI.rc site found at 665

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-<a href="https://parts.igem.org/Part:BBa_E0840">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</i> typhimurium (<i>S</i>. typhimurium), we codon harmonized the original sequences towards <i>Salmonella</i> 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 BBa_K3861017  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 <i>E</i>. 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.
+<a href="https://parts.igem.org/Part:BBa_E0040">BBa_E0040</a> is 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</i> Typhimurium, we codon harmonized the original sequences towards <i>Salmonella</i> 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. coli</I> and <i>S</i>. Typhimurium, respectively. Now, using the <a href="https://parts.igem.org/Part:BBa_E0040">BBa_E0040</a> base sequence, the respective triplet of <i>S</i>. Typhimurium that aligns to the same rank as the <I>E. coli</i> triplet was determined. For example, in <I>E. coli</i> 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 translated codons and transferred this information to our part sequence.
-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.
+In contrast to codon optimization, in which the every codon is replaced by the most frequently used codons of the target organism independent of the codon usage of the source organism, we believe that codon harmonization increases the chances to generate stable and proper folded proteins in heterologous expression scenarios.
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