Evolving lineages face a constant intracellular threat: most new coding sequence mutations destabilize the folding of the encoded protein. Misfolded proteins form insoluble aggregates and are hypothesized to be intrinsically cytotoxic. Here, we experimentally isolate a fitness cost caused by toxicity of misfolded proteins. We exclude other costs of protein misfolding, such as loss of functional protein or attenuation of growth-limiting protein synthesis resources, by comparing growth rates of budding yeast expressing folded or misfolded variants of a gratuitous protein, YFP, at equal levels. We quantify a fitness cost that increases with misfolded protein abundance, up to as much as a 3.2% growth rate reduction when misfolded YFP represents less than 0.1% of total cellular protein.Comparable experiments on variants of the yeast gene orotidine-5′-phosphate decarboxylase (URA3) produce similar results. Quantitative proteomic measurements reveal that, within the cell, misfolded YFP induces coordinated synthesis of interacting cytosolic chaperone proteins in the absence of a wider stress response, providing evidence for an evolved modular response to misfolded proteins in the cytosol. These results underscore the distinct and evolutionarily relevant molecular threat of protein misfolding, independent of protein function. Assuming that most misfolded proteins impose similar costs, yeast cells express almost all proteins at steady-state levels sufficient to expose their encoding genes to selection against misfolding, lending credibility to the recent suggestion that such selection imposes a global constraint on molecular evolution.proteomics | stability | heat shock | evolutionary rate M ost new genetic mutations arising in protein-coding sequences decrease the likelihood that the encoding protein will fold properly (1, 2). Misfolding reduces the concentration of functional proteins, squanders cellular time and energy on production of useless proteins (3), and generates misfolded proteins that may harm cells (4). Given the high probability and diverse effects of failed protein folding, isolating and quantifying the influences of misfolding on fitness are essential for the development of mechanistic answers to fundamental questions in evolutionary biology: the distribution of fitness effects of new mutations, the interpretation of varying rates of molecular evolution, and the significance of compensatory mutations. Understanding how misfolding affects cell fitness may also illuminate the molecular basis of human diseases, particularly neurological disorders linked to misfolded protein toxicity (4, 5).Patterns of coding sequence evolution across taxa depend strongly on gene expression, with apparently limited contribution from protein function (6, 7). This has led to the misfolding hypothesis: that within-genome variation in purifying selection on coding sequences is predominantly shaped by the fitness cost of misfolded proteins and therefore, correlates with gene expression and protein abundance (8,9). It predicts that...