Synthetic Cross-Phyla Gene Replacement and Evolutionary Assimilation of Major Enzymes

The ability of DNA to produce a functional protein even after transfer to a foreign host is of fundamental importance in both evolutionary biology and biotechnology, enabling horizontal gene transfer in the wild and heterologous expression in the lab. However, the influence of genetic particulars on DNA’s functionality in a new host remains poorly understood, as do the evolutionary mechanisms of assimilation and refinement. Here, we describe an automation-enabled large-scale experiment wherein Escherichia coli strains were evolved in parallel after replacement of genes pgi or tpiA with orthologous DNA from donor species spanning all domains of life, from humans to hyperthermophilic archaea. We show via analysis of hundreds of clones evolved for 50,000+ cumulative generations across dozens of independent lineages that orthogene-upregulating mutations can completely mitigate fitness defects resulting from initial nonfunctionality, with coding sequence changes unnecessary. Gene target, donor species, and genomic location of the swap all influenced outcomes – both the nature of adaptive mutations (often synonymous) and the frequency with which strains successfully evolved to assimilate the foreign DNA. Additionally, time series DNA sequencing and replay evolution experiments revealed transient copy number expansions, the contingency of lineage outcome on first-step mutations, and the ability for strains to escape from sub-optimal local fitness maxima. Overall, this study establishes the influence of various DNA and protein features on cross-species genetic interchangeability and evolutionary outcomes, with implications for both horizontal gene transfer and rational strain design.