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Independent effects of protein core size and expression on residue-level structure-evolution relationships.

ABSTRACT: Recently, we demonstrated that yeast protein evolutionary rate at the level of individual amino acid residues scales linearly with degree of solvent accessibility. This residue-level structure-evolution relationship is sensitive to protein core size: surface residues from large-core proteins evolve much faster than those from small-core proteins, while buried residues are equally constrained independent of protein core size. In this work, we investigate the joint effects of protein core size and expression on the residue-level structure-evolution relationship. At the whole-protein level, protein expression is a much more dominant determinant of protein evolutionary rate than protein core size. In contrast, at the residue level, protein core size and expression both have major impacts on protein structure-evolution relationships. In addition, protein core size and expression influence residue-level structure-evolution relationships in qualitatively different ways. Protein core size preferentially affects the non-synonymous substitution rates of surface residues compared to buried residues, and has little influence on synonymous substitution rates. In comparison, protein expression uniformly affects all residues independent of degree of solvent accessibility, and affects both non-synonymous and synonymous substitution rates. Protein core size and expression exert largely independent effects on protein evolution at the residue level, and can combine to produce dramatic changes in the slope of the linear relationship between residue evolutionary rate and solvent accessibility. Our residue-level findings demonstrate that protein core size and expression are both important, yet qualitatively different, determinants of protein evolution. These results underscore the complementary nature of residue-level and whole-protein analysis of protein evolution.

SUBMITTER: Franzosa EA

PROVIDER: S-EPMC3463513 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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Independent effects of protein core size and expression on residue-level structure-evolution relationships.

Franzosa Eric A EA Xia Yu Y

PloS one 20121003 10

Recently, we demonstrated that yeast protein evolutionary rate at the level of individual amino acid residues scales linearly with degree of solvent accessibility. This residue-level structure-evolution relationship is sensitive to protein core size: surface residues from large-core proteins evolve much faster than those from small-core proteins, while buried residues are equally constrained independent of protein core size. In this work, we investigate the joint effects of protein core size and ...[more]

PMID: 23056364

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Project description:Abstract Brain size, brain architecture, and eye size vary extensively in vertebrates. However, the extent to which the evolution of these components is intricately connected remains unclear. Trinidadian killifish, Anablepsoides hartii, are found in sites that differ in the presence and absence of large predatory fish. Decreased rates of predation are associated with evolutionary shifts in brain size; males from sites without predators have evolved a relatively larger brain and eye size than males from sites with predators. Here, we evaluated the extent to which the evolution of brain size, brain structure, and eye size covary in male killifish. We utilized wild?caught and common garden?reared specimens to determine whether specific components of the brain have evolved in response to differences in predation and to determine if there is covariation between the evolution of brain size, brain structure, and eye size. We observed consistent shifts in brain architecture in second generation common garden reared, but not wild caught preserved fish. Male killifish from sites that lack predators exhibited a significantly larger telencephalon, optic tectum, cerebellum, and dorsal medulla when compared with fish from sites with predators. We also found positive connections between the evolution of brain structure and eye size but not between overall brain size and eye size. These results provide evidence for evolutionary covariation between the components of the brain and eye size. Such results suggest that selection, directly or indirectly, acts upon specific regions of the brain, rather than overall brain size, to enhance visual capabilities. We evaluated the extent to which the evolution of brain size, brain structure, and eye size covary in male killifish from sites that vary in predation. We found positive connections between the evolution of brain structure and eye size but not between brain size and eye size. We also found that male killifish from sites that lack predators exhibited significantly larger brain structures than those from sites with predators. These results provide evidence for evolutionary covariation between the components of the brain and eye size and that selection, directly or indirectly, acts upon specific regions of the brain, rather than overall brain size, to enhance visual capabilities.

Dataset Information

Independent effects of protein core size and expression on residue-level structure-evolution relationships.

Publications

Independent effects of protein core size and expression on residue-level structure-evolution relationships.

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