Pervasive convergent evolution and extreme phenotypes define chaperone requirements of protein homeostasis

Maintaining protein homeostasis is an essential requirement for cell and organismal viability. An elaborate regulatory system within cells, the protein homeostasis network, safeguards that proteins are correctly folded and functional. At the heart of this regulatory system lies a class of specialized protein quality control enzymes called chaperones that are tasked with assisting proteins in their folding, avoiding aggregation, and degradation. Failure and decline of protein homeostasis are directly associated with conditions of aging and aging-related neurodegenerative diseases such as Alzheimers and Parkinsons. However, it is not clear what tips the balance of protein homeostasis and leads to onset of aging and diseases. Here, we present a comparative genomics analysis of protein homeostasis in eukaryotes and report general principles of maintaining protein homeostasis across the eukaryotic tree of life. Expanding a previous analysis of 16 eukaryotes to 216 eukaryotic genomes, we find a strong correlation between the size of eukaryotic chaperone networks and size of the genomes that is distinct for different species kingdoms. Importantly, organisms with pronounced phenotypes clearly buck this trend. Northobranchius furzeri, the shortest-lived vertebrate and widely used model for fragile protein homeostasis is found to be chaperone limited. Heterocephalus glaber as the longest-lived rodent thus especially robust organism is characterized by above average numbers of chaperones. Our work thus indicates that the balance in protein homeostasis may be a key variable in explaining organismal robustness. Finally, our work provides an elegant example of harnessing the power of evolution and comparative genomics to address fundamental open questions in biology with direct relevance to human diseases.