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

While it is clear that synonymous recoding causes attenuation and the strategy holds promise for vaccine development, we lack a predictive understanding of the process. Part of this results from the biological complexity and variation in the systems involved. In many cases, the fitness impact of recoding is cell-line dependent (62, 66, (68) (69) (70) (77) (78) (79) , is inconsistent between in vivo and in vitro experiments (63, 69, 79, 79) , or is temporally variable (73) . Another obstacle is the nature of the genetic code itself: it is generally challenging to manipulate one compositional feature of the genome and hold all the others fixed. For example, when codons are shuffled to change codon pair frequency, mRNA stability may be affected. Or when codons are deoptimized, codon pair frequencies also change. This makes it difficult to attribute the cause of fitness decreases to one factor ( e.g. codon usage adaptation), especially when the features are correlated. As we do here, most studies have focused on manipulating a single compositional feature of the genome and measuring its impact on fitness. Standardizing recoding methodologies and features measured across studies would greatly improve our understanding of the factors that drive fitness decreases and other phenotypic effects caused by synonymous deoptimization.