Part:BBa_K3871001

Description

mCherry is a red fluorescent protein used as a reporter derived from the fluorophore DsRed, which was originally isolated from Discosoma sea anemones. It is commonly used due to its colour and photostability compared to other monomeric fluorophores.

This part is a variant of mCherry, the sequence of which was modified to optimize its expression in Bacillus subtilis against E. coli using the Communique tool developed by the 2021 TAU Israel team. This specific variant was optimized based on codon usage bias in highly expressed genes in B. subtilis. You may read more about the optimization model here.

For more information on this part, please consult the 2021 TAU Israel wiki results page found here. Information about experimental procedures can be found here and here.

Typical Decoding Rate (TDR) [8]:

Figure 3.7: TDR scores of E. Coli genes vs. their expression levels

This measurement is based on ribosome profiling data (Ribo-Seq), which provides a snapshot of a mid-translation ribosomal position on the mRNA molecules in a cell during certain conditions.

*This index is relatively complicated because the Ribo-Seq data is hard to produce and very noisy. Additionally, the sequences optimized according to this index underperformed in the POC experiment, thus we decided not to add this optimization to our final software.