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Repeat-Modulated Population Genetic Effects in Fungal Proteins

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Abstract

A number of fungal lineages, notably N. crassa, have evolved a novel mechanism of processing genomic duplication events known as repeat-induced point (RIP) mutation. This mechanism appears, on the one hand, to act as a conservative genomic safeguard, by introducing stop codons into duplicated nucleotide sequences, thereby preempting consequences such as dosage effects. However, it also typically performs further nonsynonymous (i.e., amino acid-changing) nucleotide substitutions, the significance of which is unclear. We explore here the possibility that RIP-mutated genes which evade silencing may have some microevolutionary impact on functional sequences. Our approach focuses on structurally important hydrophobic/polar (HP) amino-acid substitutions effected by RIP. We exploit a simple generic protein folding model to predict the associated emergence of increased protein-structural stability and variance within a large population.

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Acknowledgments

Funding for this work was provided by the Swedish Foundation for Strategic Research. We also acknowledge the reviewers of this paper for some valuable comments.

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Authors and Affiliations

  1. Department of Biochemistry and Biophysics, and Stockholm Bioinformatics Center, Stockholm University, 10691, Stockholm, Sweden

    F. N. Braun & D. A. Liberles

  2. Computational Biology Unit, BCCS, University of Bergen, 5020, Bergen, Norway

    D. A. Liberles

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  1. F. N. Braun
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  2. D. A. Liberles
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Braun, F.N., Liberles, D.A. Repeat-Modulated Population Genetic Effects in Fungal Proteins. J Mol Evol 59, 97–102 (2004). https://doi.org/10.1007/s00239-004-2608-9

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  • DOI: https://doi.org/10.1007/s00239-004-2608-9

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