Author: James T. Van Leuven; Martina M. Ederer; Katelyn Burleigh; LuAnn Scott; Randall A. Hughes; Vlad Codrea; Andrew D. Ellington; Holly Wichman; Craig Miller
Title: FX174 Attenuation by Whole Genome Codon Deoptimization Document date: 2020_2_11
ID: mpb4fy16_22
Snippet: For example, in some backgrounds, adding deoptimized H1 reduced fitness by only~1 doublings/hr. In other backgrounds, H1 reduced fitness by~8 doublings per hour. Despite this variation, there is a good correlation between change in CAI and change in fitness (R 2 =0.58, p=4.8E-10, fig. 5 and supplementary table S4 ). Applying this background correction indicates that only a portion of the fitness changes can be explained by changes in codon usage .....
Document: For example, in some backgrounds, adding deoptimized H1 reduced fitness by only~1 doublings/hr. In other backgrounds, H1 reduced fitness by~8 doublings per hour. Despite this variation, there is a good correlation between change in CAI and change in fitness (R 2 =0.58, p=4.8E-10, fig. 5 and supplementary table S4 ). Applying this background correction indicates that only a portion of the fitness changes can be explained by changes in codon usage bias. This is particularly true for genes A and H. Fragments in gene F seem to have more consistent effects ( fig. 5b) .
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