TY - JOUR T1 - Experimental evolution of modern <em>Escherichia coli</em> harboring an ancient Elongation Factor gene JF - bioRxiv DO - 10.1101/040626 SP - 040626 AU - Betül Kaçar AU - Lily I. Tran AU - Xueliang Ge AU - Suparna Sanyal AU - Eric A. Gaucher Y1 - 2016/01/01 UR - http://biorxiv.org/content/early/2016/02/22/040626.abstract N2 - Species achieve evolutionary innovations through two major genetic mechanisms, namely regulatory- and structural-level mutations. The ability of populations to evolve involves a balance between selection, genetic drift, epistasis, biochemical and biophysical requirements, thermodynamic properties and other factors. This adaptive diversity begs the question as to whether a restricted pathway governs adaptations or whether multiple pathways are possible to achieve an adaptive response. By combining a unique set of tools drawn from synthetic biology, evolutionary biology and genomics, we experimentally evolved and then characterized the adaptive properties of a modern E. coli strain containing a 700 million-year-old reconstructed ancestral Elongation Factor Tu (EF-Tu) gene inserted into its genome for the first time. We then tracked the evolutionary steps taken by the ancient-modern hybrid microorganism through laboratory evolution by monitoring genomic mutations. This study reveals that lineages respond to the ancient gene by increasing the expression levels of the maladapted protein, rather than through direct accumulation of mutations in the open reading frame. In particular, these findings show that the general strategy for the bacteria to adapt to the ancient protein is to accumulate mutations in the cis-regulatory region; gene-coding mutations appear to preclude rapid adaptation upon integration of the ancient gene for our system.Author Summary Understanding the historical forces that have shaped the evolution of past organisms over time mainly relies on analyzing the behavior of organisms that exist today. This reconciliation requires an evolutionary framework that includes explicit functional links between genomes, natural selection, molecular innovation, phenotypic diversity and adaptation; yet, creating a framework that synthesizes all of these components remains a challenge. Here we make a novel attempt at such a synthesis by combining synthetic biology with natural selection to explore the historical constraints at work in evolutionary processes. In order to study historical pathways and the mechanisms of protein evolution in a complex cellular environment, we directly engineered a synthetic gene representing a 700 million-year-old ancestor of the contemporary elongation factor protein inside a modern E. coli strain. We then traced the evolutionary steps of the microorganism harboring this ancient gene by subjecting it to laboratory evolution, directly monitoring any resulting changes within the integrated ancient gene and the rest of the host genome through whole-genome sequencing. Our results demonstrate that an ancient gene can interact with modern cellular machinery, albeit with a cost of decreased fitness, and that lineages respond to the ancient gene by increasing the transcription levels of the maladapted protein. Further development of ancient-modern hybrid model systems has the potential to provide information about fundamental evolutionary processes at work in modern microbes. ER -