Why highly expressed proteins evolve slowly

doi:10.1073/pnas.0504070102

Why highly expressed proteins evolve slowly

^*Program in Computation and Neural Systems and ^‡Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125-4100; and ^§Keck Graduate Institute, Claremont, CA 91711

Edited by Francisco J. Ayala, University of California, Irvine, CA, and approved August 11, 2005 (received for review May 16, 2005)

Abstract

Much recent work has explored molecular and population-genetic constraints on the rate of protein sequence evolution. The best predictor of evolutionary rate is expression level, for reasons that have remained unexplained. Here, we hypothesize that selection to reduce the burden of protein misfolding will favor protein sequences with increased robustness to translational missense errors. Pressure for translational robustness increases with expression level and constrains sequence evolution. Using several sequenced yeast genomes, global expression and protein abundance data, and sets of paralogs traceable to an ancient whole-genome duplication in yeast, we rule out several confounding effects and show that expression level explains roughly half the variation in Saccharomyces cerevisiae protein evolutionary rates. We examine causes for expression's dominant role and find that genome-wide tests favor the translational robustness explanation over existing hypotheses that invoke constraints on function or translational efficiency. Our results suggest that proteins evolve at rates largely unrelated to their functions and can explain why highly expressed proteins evolve slowly across the tree of life.

Footnotes

↵ † To whom correspondence should be addressed. E-mail: drummond{at}alumni.princeton.edu.
Author contributions: D.A.D. designed and performed research; D.A.D., J.D.B., C.A., C.O.W., and F.H.A. contributed new reagents/analytic tools; D.A.D. analyzed data; and D.A.D., J.D.B., C.A., C.O.W., and F.H.A. wrote the paper.
This paper was submitted directly (Track II) to the PNAS office.
Abbreviations: dN, number of nonsynonymous substitutions per site; dS, number of synonymous substitutions per site; CAI, codon adaptation index; WGD, whole-genome duplication.