Grant: Discovery Grants Program - Individual

Proteins are molecular machines that do almost everything in our cells, from digesting food to moving our limbs and allowing electrical impulses to run down our nerves. The instructions for making proteins are stored in our DNA. Oddly, these instructions are interrupted by regions called introns, which need to be removed in a process called pre-mRNA splicing. Introns have traditionally been thought of as junk, bits of genetic material that need to be removed so the important protein instructions can be followed. But that raises a question: if introns are useless, why are there almost no examples of organisms that have eliminated them from their genomes? Humans have many introns, on average ~10 per gene, but most species alive today have lost introns, many to an extreme extent. For example, the parasite T. brucei has only two introns left in its genome. Yet with few exceptions, even organisms that have lost almost all of their introns still have a few left. I propose a new hypothesis about introns, namely that they play a universally conserved role in helping organisms adapt to stress. In other words, they are not simply junk that needs to be removed, rather they have an indispensable biological function. My trainees and I study C. merolae, a microscopic red alga found in acidic hot springs. The ancestral red alga had ~2000 introns, but C. merolae has only 38 left. We are therefore working to figure out whether the remaining introns have an important biological function, or whether they have simply not yet disappeared. OBJECTIVES: My long-term objective is to test the hypothesis that introns are almost universally retained due to their role in adapting to stress, specifically by regulating ribosome creation. My short-term objective is to exploit the power of our genetically tractable algal system to test specific hypotheses about the possible functions of introns. APPROACH: Using powerful RNA sequencing technologies, we will assess splicing under a variety of stress conditions (heat, starvation, etc.) to determine whether introns play an important role in adaptation. We will purify introns to examine their associated proteins, remove introns to test whether the resulting algae are impaired in recovery from stress, and use single-molecule microscopy to see where they are in the cell. FEASIBILITY: The experiments I propose here aim to discover new biology, but employ techniques we have used extensively with collaborators around the world. NOVELTY and SIGNIFICANCE: With C. merolae, my lab has developed the first new model system in years for studying splicing, a model that is unique in its simplicity and evolutionary implications. With this proposal, I aim to overturn the received wisdom about introns and leverage the deep conservation of intron function to argue for a new view of what introns do. Notably, C. merolae also has tremendous potential in biotechnology, and by streamlining its genome this work will facilitate its use.