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Evolution of the isoelectric point of mammalian proteins as a consequence of indels and adaptive evolution

Authors

  • Nicolas Alendé,

    1. UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine and Medical Sciences, University College Dublin, Dublin 4, Republic of Ireland
    2. UCD Complex and Adaptive Systems Laboratory, University College Dublin, Dublin 4, Republic of Ireland
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  • Jens E. Nielsen,

    1. School of Biomolecular and Biomedical Science, Centre for Synthesis and Chemical Biology, UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
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  • Denis C. Shields,

    1. UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine and Medical Sciences, University College Dublin, Dublin 4, Republic of Ireland
    2. UCD Complex and Adaptive Systems Laboratory, University College Dublin, Dublin 4, Republic of Ireland
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  • Nora Khaldi

    Corresponding author
    1. UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine and Medical Sciences, University College Dublin, Dublin 4, Republic of Ireland
    2. UCD Complex and Adaptive Systems Laboratory, University College Dublin, Dublin 4, Republic of Ireland
    • UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine and Medical Sciences, University College Dublin, Dublin 4, Republic of Ireland
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  • Authors' contributions: NA and NK, carried out the analysis; DS and NK supervised, NK conceived the overall idea and strategy, and wrote the paper. DS, NA, and JN contributed to the writing of the paper.

Abstract

Although important shifts in the isoelectric point of prokaryotic proteins, mainly due to adaptation to environmental pH, have been widely reported, such studies have not covered mammalian proteins, where pH changes may relate to changes in subcellular or tissue compartmentalization. We explored the isoelectric point of the proteome of 13 mammalian species. We detected proteins that have shifted their pI the most among 13 mammalian species, and investigated if these differences reflect adaptations of the orthologous proteins to different conditions. We find that proteins exhibiting a high isoelectric point change are enriched in certain GO terms, including immune defense, and mitochondrial proteins. We show that the shift in pI between orthologous proteins is not strongly associated with the overall rate of protein evolution, nor with protein length. Our results reveal that insertions/deletions are the main reason behind the shift of pI. However, for some proteins we find evidence of selection shifting the pI of the protein through amino acid replacement. Finally, we argue that shifts in pI might relate to the gain of additional activities, such as new interacting partners, in one ortholog as opposed to the other, and may potentially relate to functional differences between mammals. Proteins 2011. © 2011 Wiley-Liss, Inc.

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