Mutations to Less-Preferred Synonymous Codons in a Highly Expressed Gene of XXXX : Fitness and Epistatic Interactions.

@entity4857 @entity376 @entity526 @entity368
UNASSIGNED: Codon-tRNA coevolution to maximize protein production has been, until recently, the dominant hypothesis to explain codon-usage bias in highly expressed bacterial genes. Two predictions of this hypothesis are 1) selection is weak; and 2) similar silent replacements at different codons should have similar fitness consequence. We used an allele-replacement strategy to change five specific 3rd-codon-position (silent) sites in the highly expressed @entity526 ribosomal protein gene rplQ from the wild type to a less-preferred alternative. We introduced the five mutations within a 10-codon region. Four of the silent sites were chosen to test the second prediction, with a CTG to CTA mutation being introduced at two closely linked @entity368 codons and an AAA to AAG mutation being introduced at two closely linked @entity376 codons. We also introduced a fifth silent mutation, a GTG to GTA mutation at a @entity4857 codon in the same genic region. We measured the fitness effect of the individual mutations by competing each single-mutant strain against the parental wild-type strain, using a disrupted form of the araA gene as a selectively neutral phenotypic marker to distinguish between strains in direct competition experiments. Three of the silent mutations had a fitness effect of  s  > 0.02, which is contradictory to the prediction that selection will be weak. The two @entity368 mutations had significantly different fitness effects, as did the two @entity376 mutations, contradictory to the prediction that similar mutations at different codons should have similar fitness effects. We also constructed a strain carrying all five silent mutations in combination. Its fitness effect was greater than that predicted from the individual fitness values, suggesting that negative synergistic epistasis acts on the combination allele.
