FX174 Attenuation by Whole Genome Codon Deoptimization

James T. Van Leuven; Martina M. Ederer; Katelyn Burleigh; LuAnn Scott; Randall A. Hughes; Vlad Codrea; Andrew D. Ellington; Holly Wichman; Craig Miller

A good predictor of translational throughput is mRNA secondary structure (21) . Tightly folded mRNAs are traversed by the ribosome more slowly than unfolded mRNAs, although 16 . CC-BY-NC 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02.10.942847 doi: bioRxiv preprint faster translation is not necessarily beneficial. mRNA structure is used to slow translation where pausing is needed, most notably before protein structures that require co-translational folding (32, 33) and at the 5' end of a transcript, where proper loading of a mRNA onto a ribosome foreshadows correct and efficient translation (29) . Our data support the importance of mRNA folding stability for organismal fitness, as the stability of recoded ΦX174 genes is correlated with ΦX174 fitness (fig. 6b) . Interestingly, the optimized ΦX174 strains almost always have increased mRNA folding stabilities and decreased fitness values, suggesting the folding stability of each mRNA may be near optimal in the wild-type virus. While it is unclear to us why the optimized strains have increased mRNA folding stabilities, departure from wild-type-either more or less stable-results in fitness declines. This suggests that wild-type ΦX174 sits at a peak in its fitness landscape.