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Do Amino Acid Biosynthetic Costs Constrain Protein Evolution in Saccharomyces cerevisiae?

Abstract

Prokaryotic organisms preferentially utilize less energetically costly amino acids in highly expressed genes. Studies have shown that the proteome of Saccharomyces cerevisiae also exhibits this behavior, but only in broad terms. This study examines the question of metabolic efficiency as a proteome-shaping force at a finer scale, examining whether trends consistent with cost minimization as an evolutionary force are present independent of protein function and amino acid physicochemical property, and consistently with respect to amino acid biosynthetic costs. Inverse correlations between the average amino acid biosynthetic cost of the protein product and the levels of gene expression in S. cerevisiae are consistent with natural selection to minimize costs. There are, however, patterns of amino acid usage that raise questions about the strength (and possibly the universality) of this selective force in shaping S. cerevisiae’s proteome.

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Acknowledgments

This study was supported in part by Grant MBC-0132097 to R.V.M. and by NSF Grant DEB-0521964 to H.A. We also thank an anonymous reviewer for numerous helpful comments and suggestions regarding an early version of the manuscript.

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Correspondence to Dan E. Krane.

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Raiford, D.W., Heizer, E.M., Miller, R.V. et al. Do Amino Acid Biosynthetic Costs Constrain Protein Evolution in Saccharomyces cerevisiae?. J Mol Evol 67, 621–630 (2008). https://doi.org/10.1007/s00239-008-9162-9

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Keywords

  • Saccharomyces cerevisiae
  • Biosynthetic cost
  • Metabolic efficiency
  • Expressivity
  • Amino acid