Final Report Summary - FITNESS & EVOLUTION (Intracellular protein aggregation: fitness and evolution)
The synergy between experimental and computational studies has provided important insights in the understanding of protein aggregation process. The aggregation propensity of a polypeptide is just below the limit that allows proteins to remain soluble at the concentrations required for life20. Because of this tight equilibrium, aggregation event can result from even minor changes in the sequence or in the expression levels of otherwise harmless proteins21-23. Recent computational studies have reported the existence of a selective pressure to escape protein aggregation exerted on both the protein sequence and the gene expression levels. In addition, this pressure seems to differ based on protein structure, biological function, localization and abundance21-23. However, a direct experimental evidence demonstrating how natural selection shapes protein sequence and concentration in a live cell is still missing, principally due to the difficulties in reproducing evolutionary constraints and time-scales in the laboratory.
Against this backdrop, the present project has analyzed how protein aggregation is selected in a biological context employing yeast as a cellular model. The specific questions that we have answered are:
Q1. How protein aggregation affects cell fitness?
Q2. How protein aggregation is selected in a population?
Q3. How can this selection be modulated?
To answer these questions we have exploited a population genetics approach to infer the costs and benefits of protein aggregation on cell fitness. We have created a novel in vivo system that involves two main elements: an aggregation-prone tag and a functional protein. The functional protein is an enzyme that can catalyze two different reactions depending on the substrate provided. The Substrate1 can be transformed into a product essential for cell growth (Product1). The Substrate2 is transformed into a product that kills the cell (Product2). When the medium contains Product1 the cell can incorporate it and the enzymatic activity is not longer essential. As a result, in this model the protein aggregation could be (A) deleterious, (B) neutral or (C) beneficial for the cell fitness. By competing different strains in the same culture, we can simulate how protein aggregation is selected in a population. The data obtained from the competition experiments allows quantifying the selection coefficient associated to the protein aggregation. Due to the special properties of this model we can separately calculate three different fitness effects associated to protein aggregation. Accordingly, when the enzyme is not-essential we just measure misfolding stress, when the enzyme is essential we also measure a loss of function, and when the enzyme is toxic we measure a gain of a beneficial function.
Our results show that aggregation has a neutral effect on fitness and are the associated gain or loss of function that determined the final cell fitness. Our work also reveals that protein aggregation could increase population variability and survival expectancy of cells exposed to variable environments. These data suggest a tolerable and common protein aggregation process for which the cell has developed quality control mechanisms. Protein aggregation may not always entail a gain or loss of function and, in case of a non-essential protein could have low impact in cell fitness. Moreover, within the same genomic background, changes in the environment can modify the protein aggregation effects; enabling situations were aggregation is beneficial and others were is toxic. Overall, the present work supports that during evolution protein aggregation has been selected both for and against.