Drummond:Research

Key Questions

 * 1) What proportion of newly synthesized proteins fail to fold, and why?
 * 2) How do cells decide when a misfolded should be degraded rather than given another chance to fold?
 * 3) What is the cost of producing a protein that misfolds, compared to the cost if that protein folds properly?
 * 4) Why are misfolded proteins costly?
 * 5) How does inaccuracy in the translational apparatus (ribosomes, aa-tRNA synthetases, etc.) shape the evolution of coding sequences and proteins?

Fitness costs and cellular consequences of misfolding
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.

Supporting website here.

Mistranslation-induced misfolding and gene evolution
Strikingly consistent correlations between rates of coding-sequence evolution and gene expression levels are apparent across taxa, but the biological causes behind the selective pressures on coding-sequence evolution remain controversial. Here we demonstrate conserved patterns of simple covariation between sequence evolution, codon usage, and mRNA level in E. coli, yeast, worm, fly, mouse, and human that suggest that all observed trends stem largely from a unified underlying selective pressure. In metazoans, these trends are strongest in tissues composed of neurons, whose structure and lifetime confer extreme sensitivity to protein misfolding. We propose, and demonstrate using a molecular-level evolutionary simulation, that selection against toxicity of misfolded proteins generated by ribosome errors suffices to create all the observed covariation. The mechanistic model of molecular evolution which emerges yields testable biochemical predictions, calls into question use of nonsynonymous-to-synonymous substitution ratios (Ka/Ks) to detect functional selection, and suggests how mistranslation may contribute to neurodegenerative disease.

Citation

 * 1) Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Drummond DA, Wilke CO. Cell. 2008 Jul 25;134(2):341-52. Faculty of 1000 rated Preview by Powers and Balch. Download [[Media:Drummond08-MisfoldingPreprint.pdf|preprint PDF]], [[Media:Drummond08-MisfoldingPreprintSuppl.pdf|supplementary materials]], data.

Evolution and expression data
These tab-delimited files include gene and ortholog identifiers, dN, dS, ts/tv ratio, expression level, Fop, and (for the multicellular organisms) intronic guanine/cytosine (GC) content.
 * [[Media:DrummondWilkeCell2008Data.zip|Evolution and expression data]] [ZIP archive, ~800K]

Coding sequence alignments
Alignments are in FASTA format, ZIP-compressed.
 * [[Media:Ecoli-styphimurium-alignments.zip|E. coli vs. S. typhimurium]] (~1.8MB)
 * [[Media:Scer-spar-alignments.zip|S. cerevisiae vs. S. paradoxus]] (~3.8MB)
 * [[Media:Cele-cbri-alignments.zip|C. elegans vs. C. briggsae]] (~4.7MB)
 * [[Media:Dmel-dyak-alignments.zip|D. melanogaster vs. D. yakuba]] (~5.3MB)
 * [[Media:Mouse-rat-alignments.zip|M. musculus vs. R. norvegicus]] (~8.7MB)
 * [[Media:Human-dog-alignments.zip|H. sapiens vs. C. familiaris]] (~8.3MB)