Understanding nuclear compensation to mitochondrial variation, dysfunction, and disease in a new evolutionary mutant model

PROJECT SUMMARY/ABSTRACT Mitochondria (mt) are responsible for the regulation of essential cellular processes including energy production, lipid biosynthesis, calcium homeostasis, the cell cycle, cell death, and immunity. Mt regulate these processes in part using their own genomes (mitogenomes). The mitogenome is small - encoding only 13 proteins – but the mt proteome is very large including upwards of 2,000 proteins, meaning proper mt function relies heavily on homeostasis between mito- and nuclear-encoded elements. However, maintaining mito-nuclear compatibility can be difficult. The mito- and nuclear genomes are inherited largely independently and the mitogenome evolves approximately 5-10 times faster than the nuclear genome creating many opportunities for divergent evolution and incompatibility leading to dysfunction. Mt-dysfunction is common and underlies many prevalent diseases including neuromuscular degenerative disorders, cancers, and metabolic diseases, yet we have struggled to understand mito- nuclear dynamics and their impacts on organismal health. This is in part because genomic variation – in both the nuclear and mitogenomes – can impact severity of mitochondrial dysfunction. Family members with the same causative mutation, often respond differently to treatments or have differences in symptoms because of genetic and life history variation. What is needed are studies focused on the role of genetic variation impacting mito-nuclear dynamics in multiple environments. Accounting for mitogenomic variation has been a major challenge for two main reasons. First, we are limited in our ability to edit the mitogenome. Some have been successful editing the mitogenome at low frequency, but we are not able to ubiquitously edit the mitogenome. Second, most animal models are limited in their mitogenomic variation. This is often by design in inbred lines, but even outbred models often have minimal mitogenomic variation. Here we propose the use of specific populations of threespine stickleback fish that will allow us to fill these gaps. Threespine stickleback are a well-known model for studying genetic variants underlying complex traits. We have recently characterized the mitogenomic variation across populations of these fish and have identified mitogenomic divergence that exceeds that of modern vs ancient humans. Despite this exceptional level of mt variation, there are many populations of fish with extreme mitogenomic divergence in admixture, generating natural experiments, and unique opportunities to understand how the nuclear genome is evolving and adapting to maintain mitogenomic variation. Importantly, the existence of dual marine/freshwater populations of stickleback with mitogenomic admixture allow us to ask questions about how mt are acting in these different environments and identify environmentally context-dependent nuclear compensations. This proposal largely leverages publicly available sequencing data and preserved specimens to fill existing gaps.