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.