Team:Humboldt Berlin/Improve


Optimization of BBa_K3861017 to BBa_K3861020 via Codon Harmonization

BBa_K3861017 is an Escherichia coli (E. coli) optimized version of the green fluorescent protein (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 (S. typhimurium), we codon harmonized the original sequences towards S. typhimurium 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_K3861017 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 codons and transferred this information to our part sequence. The resulting part can be viewed here: BBa_K3861020.

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.