Abstract
Due to the redundancy of the genetic code most amino acids are encoded by multiple synonymous codons. It has been proposed that a biased frequency of synonymous codons can affect the function of proteins by modulating distinct steps in transcription, translation and folding. Here, we use two similar prototype K+ channels as model systems to examine whether codon choice has an impact on protein sorting. By monitoring transient expression of GFP-tagged channels in mammalian cells, we find that one of the two channels is sorted in a codon and cell cycle-dependent manner either to mitochondria or the secretory pathway. The data establish that a gene with either rare or frequent codons serves, together with a cell-state-dependent decoding mechanism, as a secondary code for sorting intracellular membrane proteins.
Highlights
Carmen Valenzuela Miranda, Each amino acid in a protein is on average encoded by about three synonymous codons
To examine the influence of codon bias on Kesv sorting, we compared its location in HEK293 cells after expressing the GFP-tagged protein from a wild type (Kesvwt ) gene, a gene that was codon-optimized for expression in mammalian cells (Kesvop ) and a gene with a randomized sequence of favorable/unfavorable codons (Kesvran ) (Figure S1 and Figure S2A)
Cells transfected with the wt gene can be grouped into three distinct populations: (i) a majority of cells with the GFP-tagged protein being targeted to the mitochondria in a background of GFP fluorescence in the cytosol (Figure 1A,C), (ii) a small number of cells with the channel in the secretory pathway (SP) (Figure S3A and Figure 1C), and (iii) cells with a strong GFP signal throughout the cell (Figure S3B, Figure 1C)
Summary
Carmen Valenzuela Miranda, Each amino acid in a protein is on average encoded by about three synonymous codons. This provides a quasi-infinite sequence space of mRNA molecules and the potential of transmitting much more information than required for only coding the primary amino acid sequence In this context it is well established that synonymous codons are used with distinct frequencies in different genomes [1] and that mRNAs encoding the same polypeptide with a codon bias can dramatically alter the amount of protein expression [2] including membrane proteins [3]. This phenomenon is already successfully used in biotechnology to increase protein production; similar codon-optimization strategies have been proposed as therapeutic tools for tuning the cellular production of recombinant protein drugs, in mRNA therapies as well as in the production of DNA/RNA vaccines [4,5]. There are isolated reports in which codon changes resulted in altered functional properties of proteins [13,14] and in some cases synonymous mutations have even been linked to diseases [4]
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