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.

Genes acquired by horizontal gene transfer (HGT) may provide the recipient organism with potentially new functions, but proper expression level and integration of the transferred genes in the novel environment are not granted. Notably, transferred genes can differ from the receiving genome in codon usage preferences, leading to impaired translation and reduced functionality.Here, we characterize the genomic and proteomic changes undergone during experimental evolution of Escherichia coli after HGT of three synonymous versions, presenting very different codon usage preference, of an antibiotic resistance gene. The experimental evolution was conducted with and without the corresponding antibiotic and the mutational patterns and proteomic profiles after 1,000 generations largely depend on the experimental growth conditions (e.g., mutations in antibiotic off-target genes), and on the synonymous gene version transferred (e.g., mutations in genes responsive to translational stress). The transfer of an exogenous gene extensively modifies the whole proteome, and these proteomic changes are different for the different version of the transferred gene. Additionally, we identified conspicuous changes in global regulators and in intermediate metabolism, confirmed the evolutionary ratchet generated by mutations in DNA repair genes and highlighted the plasticity of bacterial genomes accumulating large and occasionally transient duplications.Our results support a central role of HGT in fuelling evolution as a powerful mechanism promoting rapid, often dramatic genotypic and phenotypic changes. The profound reshaping of the pre-existing geno/phenotype allows the recipient bacteria to explore new ways of functioning, far beyond the mere acquisition of a novel function.