Parallel evolution of chimeric genes in microbial evolution experiments

Recombination can generate new or improved proteins by merging pieces of pre-existing genes into a new whole. Here, when we reanalysed genomic data from several laboratory evolution experiments with Escherichia coli, evidence for the convergent evolution of chimeric genes became apparent. In these experiments, a pair of paralogous genes was recombined into a single hybrid copy by large genomic deletions. In one case, the excision of a cryptic e14 prophage occurred in 6 out of 8 replicates of a 22-day fluoroquinolone-resistance evolution experiment. These parallel prophage excisions recombined an icd isocitrate dehydrogenase gene with a homologous icdC C-terminal fragment pseudogene. In the other case, convergent 23 kbp deletions recombined cpsG paralogs across replicate populations of the Lenski long-term evolution experiment with E. coli, generating a chimeric phosphomannomutase. Together, these results indicate that chimeric genes evolve rapidly in bacteria and are more common than previously believed because they are easily missed by standard genomic analyses. Experiments are needed to determine whether these chimeric proteins are adaptive or are merely by-products of their associated genomic deletions.