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Proteome-wide evidence for enhanced positive Darwinian selection within intrinsically disordered regions in proteins

Johan Nilsson1, Mats Grahn1 and Anthony PH Wright12*

Author affiliations

1 School of Life Sciences, Södertörn University, SE-141 89 Huddinge, Sweden

2 Clinical Research Center, Novum Level 5, Department of Laboratory Medicine and Center for Biosciences, Karolinska Institutet, SE-141 86 Huddinge, Sweden

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Citation and License

Genome Biology 2011, 12:R65  doi:10.1186/gb-2011-12-7-r65

Published: 19 July 2011

Abstract

Background

Understanding the adaptive changes that alter the function of proteins during evolution is an important question for biology and medicine. The increasing number of completely sequenced genomes from closely related organisms, as well as individuals within species, facilitates systematic detection of recent selection events by means of comparative genomics.

Results

We have used genome-wide strain-specific single nucleotide polymorphism data from 64 strains of budding yeast (Saccharomyces cerevisiae or Saccharomyces paradoxus) to determine whether adaptive positive selection is correlated with protein regions showing propensity for different classes of structure conformation. Data from phylogenetic and population genetic analysis of 3,746 gene alignments consistently shows a significantly higher degree of positive Darwinian selection in intrinsically disordered regions of proteins compared to regions of alpha helix, beta sheet or tertiary structure. Evidence of positive selection is significantly enriched in classes of proteins whose functions and molecular mechanisms can be coupled to adaptive processes and these classes tend to have a higher average content of intrinsically unstructured protein regions.

Conclusions

We suggest that intrinsically disordered protein regions may be important for the production and maintenance of genetic variation with adaptive potential and that they may thus be of central significance for the evolvability of the organism or cell in which they occur.