Evolution in Regulatory Regions Rapidly Compensates the Cost of Nonoptimal Codon Usage

The redundant genetic code contains synonymous codons, whose relative frequencies vary among species. Nonoptimal codon usage lowers gene translation efficiency, potentially leading to a fitness cost. This is particularly relevant for horizontal gene transfer, common among bacteria and a key player in antibiotic resistance propagation. By mimicking the horizontal transfer of an antibiotic resistance gene, we established that a nonoptimal codon usage renders Escherichia coli 10-20 times more sensitive to the antibiotic. After 350 generations of experimental evolution under antibiotic selection pressure, this cost was compensated through both in cis changes in the gene promoter and in trans changes in the host bacterial genome, without introducing mutations in the coding sequence of the resistance gene. Further, we have found experimental evidence for convergent molecular adaptive evolution. The high fitness cost of nonoptimal codon usage remains a minor obstacle to gene fixation upon horizontal transfer. Our results highlight the importance of rapid evolution of regulatory mechanisms in the adaptation to new environmental and genetic situations.