title: Differences in the number of intrinsically disordered regions between yeast duplicated proteins, and their relationship with functional divergence.
abstract: BACKGROUND
  Intrinsically disordered regions are enriched in short interaction motifs that play a critical role in many protein-protein interactions. Since new short interaction motifs may easily evolve, they have the potential to rapidly change protein interactions and cellular signaling. In this work we examined the dynamics of gain and loss of intrinsically disordered regions in duplicated proteins to inspect if changes after genome duplication can create functional divergence. For this purpose we used Saccharomyces cerevisiae and the outgroup species Lachancea kluyveri.
  
  
  RESULTS
  We find that genes duplicated as part of a genome duplication (ohnologs) are significantly more intrinsically disordered than singletons (p<2.2(e)-16, Wilcoxon), reflecting a preference for retaining intrinsically disordered proteins in duplicate. In addition, there have been marked changes in the extent of intrinsic disorder following duplication. A large number of duplicated genes have more intrinsic disorder than their L. kluyveri ortholog (29% for duplicates versus 25% for singletons) and an even greater number have less intrinsic disorder than the L. kluyveri ortholog (37% for duplicates versus 25% for singletons). Finally, we show that the number of physical interactions is significantly greater in the more intrinsically disordered ohnolog of a pair (p = 0.003, Wilcoxon).
  
  
  CONCLUSIONS
  This work shows that intrinsic disorder gain and loss in a protein is a mechanism by which a genome can also diverge and innovate. The higher number of interactors for proteins that have gained intrinsic disorder compared with their duplicates may reflect the acquisition of new interaction partners or new functional roles.
authors.affiliation: UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine and Medical Sciences, and UCD Complex and Adaptive Systems Laboratory, University College Dublin, Dublin, Republic of Ireland.
authors.forename: Floriane
authors.initials: F
authors.lastname: Montanari
authors.forename: Denis C
authors.initials: DC
authors.lastname: Shields
authors.forename: Nora
authors.initials: N
authors.lastname: Khaldi
mesh_terms: D000595:Amino Acid Sequence; D019295:Computational Biology; D019143:Evolution, Molecular; D020440:Gene Duplication; D020131:Genes, Duplicate; D014644:Genetic Variation; D016681:Genome, Fungal; D008969:Molecular Sequence Data; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics*; D017386:Sequence Homology, Amino Acid
chemical_list: D029701:Saccharomyces cerevisiae Proteins