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

As viruses must utilize their hosts' cellular machinery, there is an expectation that virus genomes are enriched for host-preferred codons. This appears to be only partially true. Many viral genomes contain more host-preferred codons than expected by chance, especially in highly expressed genes encoding viral structural proteins (41) . However, many viral genes are not enriched in host-preferred codons. Sometimes unpreferred codons are used to regulate viral gene expression (42) . Other virus genomes appear to have little preference for codons abundant in the host genome. For instance, Lucks et al. found that the majority of 74 bacteriophage genomes show no significant preference for host-preferred codons (41) . Similar discordance between host and viral codon usage patterns are observed in other studies (43) (44) (45) . This discordance could be caused by insufficient selection on codon usage, porcine reproductive and respiratory syndrome, echovirus 7, tick-borne encephalitis, vesicular stomatitis, dengue, T7, Lassa, adeno, and swine fever viruses (reviewed in (60) ). The most common method for synonymously deoptimizing viruses is recoding wildtype genes with increased proportions of non preferred codons (58, (61) (62) (63) (64) (65) (65) (66) (67) (68) (69) although other methods of recoding have been successful as well. For example, viral fitness was decreased when synonymous substitutions were randomly introduced (70-72) , when codons were replaced by those infrequently used in viral (not host) genes (57, 66, 73) , when the proportion of optimal codons was increased (64, 74, 75) , or when the number of codons one substitution away from a translational termination codon was increased (76) .