This page supports "Misfolded proteins impose a dosage-dependent fitness cost and trigger a cytosolic unfolded protein response in yeast," K. Geiler-Samerotte et al., Proceedings of the National Academy of Sciences 2010 (paper, Supporting Information, Appendix PDF/.docx).
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, yellow fluorescent 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 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 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.
All procedures are described in the paper and, in detail, in the Appendix (PDF,.docx) and Supporting Information.
Data used to generate the figures in the paper (Excel format) including cell counts for fitness experiments, fluorescence and cell counts for YFPm3 titration experiment, KG079/KG071 protein ratios for induced and uninduced conditions (.xls, zipped, ~700k).
Protein database (FASTA format, zipped) for protein identification and quantification of strains KG071 (harboring YFPwt) and KG079 (harboring YFPm3) (text, zipped, ~2.4M).