Deciphering the mechanisms and dynamics of proto-gene evolution

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The phenomenon of de novo gene birth may underlie what makes each species unique, yet it remains poorly understood. We have recently found evidence that regions of the genome thought to be junk DNA can be translated, providing an evolutionary reservoir of “proto-genes” that promote de novo gene birth. This proposal aims at characterizing the mechanisms and dynamics of proto-gene evolution by investigating three complementary angles: 1) How do proto-genes promote adaptation? To answer this question, we will overexpress proto-genes and assorted control sequences in yeast and dissect their impact on cellular fitness across multiple environmental conditions. 2) Is the proto-gene model universal? To answer this question, we will perform a computational reconstruction of the natural history of de novo gene birth in mammals, insects, malaria and fungi though the design and implementation of novel dating algorithms. This will enable us to evaluate which features that characterize these distinct lineages, such as genome size for example, influence the frequency of proto-gene evolution. 2) How do genomic sequences exit the non-genic state? It is unclear whether a proto-gene is more likely to emerge from a non-genic sequence following mutations emulating a novel promoter structure, or an open reading frame. To assess the feasibility of these competing mechanisms, we will construct yeast mutants where a gene has been synthetically killed by destroying either is open reading frame or its promoter. We will then evolve these mutants under a variety of selective pressures and observe if one mechanism is more successful than the other.