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 reanalyzed 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 were 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 kB deletions recombined cpsG paralogs across replicate populations of the Lenski long-term evolution experiment with Escherichia coli (LTEE), 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, are by-products of adaptive genomic deletions, or both. Data SummaryAll data used in this study are publicly available. All data, code, and results for this study are available on Zenodo (DOI: 10.5281/zenodo.20692138). Genomic data published by Mohiuddin et al. are available in the European Nucleotide Archive (Study ERP166963 with Study Accession PRJEB83321), and genomic data published by Tenaillon et al. are available from the NCBI BioProject database under accession number PRJNA294072. Impact StatementGenomic deletions can generate chimeric proteins by splicing together parts of existing genes. However, the extent to which chimeric proteins form, and the extent to which they are adaptive are not well-understood. Complex structural variants (such as chimeric protein formation) are often missed or incompletely annotated by standard genomic pipelines. Furthermore, there is an ongoing need for new methods to detect selection on complex structural variants. In this work, we report evidence of chimeric gene formation in laboratory evolution experiments with Escherichia coli. In both experiments, chimeric genes evolved in parallel across independent replicate populations, which is an unambiguous signal of positive selection (although it remains unclear whether selection is operating on the chimeric gene, the genomic deletion creating the chimeric gene, or both). The observation of chimeric gene formation in laboratory experiments indicate that chimeric genes evolve rapidly in bacteria and are more common than previously believed. Therefore, this work points to an important new direction for microbial genomics research: what is the extent of chimeric gene formation in natural bacterial populations, and what consequences might chimeric genes have for bacterial adaptation?