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A shift in aggregation avoidance strategy marks a long-term direction to protein evolution

S.G. Foy, View ORCID ProfileB.A. Wilson, J. Bertram, M.H.J. Cordes, View ORCID ProfileJ. Masel
doi: https://doi.org/10.1101/176867
S.G. Foy
1Department of Ecology and Evolutionary Biology, University of Arizona, 1041 E Lowell St Tucson AZ 85721 USA
2St. Jude Children’s Research Hospital, Memphis, Tennessee
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B.A. Wilson
1Department of Ecology and Evolutionary Biology, University of Arizona, 1041 E Lowell St Tucson AZ 85721 USA
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  • ORCID record for B.A. Wilson
J. Bertram
1Department of Ecology and Evolutionary Biology, University of Arizona, 1041 E Lowell St Tucson AZ 85721 USA
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M.H.J. Cordes
3Department of Chemistry & Biochemistry, University of Arizona
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J. Masel
1Department of Ecology and Evolutionary Biology, University of Arizona, 1041 E Lowell St Tucson AZ 85721 USA
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  • For correspondence: masel@email.arizona.edu
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Abstract

To detect a direction to evolution, without the pitfalls of reconstructing ancestral states, we need to compare “more evolved” to “less evolved” entities. But because all extant species have the same common ancestor, none are chronologically more evolved than any other. However, different gene families were born at different times, allowing us to compare young protein-coding genes to those that are older and hence have been evolving for longer. To be retained during evolution, a protein must not only have a function, but must also avoid toxic dysfunction such as protein aggregation. There is conflict between the two requirements; hydrophobic amino acids form the cores of protein folds, but also promote aggregation. Young genes avoid strongly hydrophobic amino acids, which is presumably the simplest solution to the aggregation problem. Here we show that young genes’ few hydrophobic residues are clustered near one another along the primary sequence, presumably to assist folding. The higher aggregation risk created by the higher hydrophobicity of older genes is counteracted by more subtle effects in the ordering of the amino acids, including a reduction in the clustering of hydrophobic residues until they eventually become more interspersed than if distributed randomly. This interspersion has previously been reported to be a general property of proteins, but here we find that it is restricted to old genes. Quantitatively, the index of dispersion delineates a gradual trend, i.e. a decrease in the clustering of hydrophobic amino acids over billions of years.

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Posted October 23, 2018.
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A shift in aggregation avoidance strategy marks a long-term direction to protein evolution
S.G. Foy, B.A. Wilson, J. Bertram, M.H.J. Cordes, J. Masel
bioRxiv 176867; doi: https://doi.org/10.1101/176867
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A shift in aggregation avoidance strategy marks a long-term direction to protein evolution
S.G. Foy, B.A. Wilson, J. Bertram, M.H.J. Cordes, J. Masel
bioRxiv 176867; doi: https://doi.org/10.1101/176867

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