title: Emergence and evolution of yeast prion and prion-like proteins.
abstract: BACKGROUND
  Prions are transmissible, propagating alternative states of proteins, and are usually made from the fibrillar, beta-sheet-rich assemblies termed amyloid. Prions in the budding yeast Saccharomyces cerevisiae propagate heritable phenotypes, uncover hidden genetic variation, function in large-scale gene regulation, and can act like diseases. Almost all these amyloid prions have asparagine/glutamine-rich (N/Q-rich) domains. Other proteins, that we term here 'prionogenic amyloid formers' (PAFs), have been shown to form amyloid in vivo, and to have N/Q-rich domains that can propagate heritable states in yeast cells. Also, there are >200 other S.cerevisiae proteins with prion-like N/Q-rich sequence composition. Furthermore, human proteins with such N/Q-rich composition have been linked to the pathomechanisms of neurodegenerative amyloid diseases.
  
  
  RESULTS
  Here, we exploit the increasing abundance of complete fungal genomes to examine the ancestry of prions/PAFs and other N/Q-rich proteins across the fungal kingdom. We find distinct evolutionary behavior for Q-rich and N-rich prions/PAFs; those of ancient ancestry (outside the budding yeasts, Saccharomycetes) are Q-rich, whereas N-rich cases arose early in Saccharomycetes evolution. This emergence of N-rich prion/PAFs is linked to a large-scale emergence of N-rich proteins during Saccharomycetes evolution, with Saccharomycetes showing a distinctive trend for population sizes of prion-like proteins that sets them apart from all the other fungi. Conversely, some clades, e.g. Eurotiales, have much fewer N/Q-rich proteins, and in some cases likely lose them en masse, perhaps due to greater amyloid intolerance, although they contain relatively more non-N/Q-rich predicted prions. We find that recent mutational tendencies arising during Saccharomycetes evolution (i.e., increased numbers of N residues and a tendency to form more poly-N tracts), contributed to the expansion/development of the prion phenomenon. Variation in these mutational tendencies in Saccharomycetes is correlated with the population sizes of prion-like proteins, thus implying that selection pressures on N/Q-rich protein sequences against amyloidogenesis are not generally maintained in budding yeasts.
  
  
  CONCLUSIONS
  These results help to delineate further the limits and origins of N/Q-rich prions, and provide insight as a case study of the evolution of compositionally-defined protein domains.
authors.affiliation: Department of Biology, McGill University, Montreal, QC, Canada.
authors.forename: Lu
authors.initials: L
authors.lastname: An
authors.affiliation: Bioinformatics and Molecular Evolution Unit, NUI Maynooth, Maynooth, Ireland.
authors.forename: David
authors.initials: D
authors.lastname: Fitzpatrick
authors.affiliation: Department of Biology, McGill University, Montreal, QC, Canada. paul.harrison@mcgill.ca.
authors.forename: Paul M
authors.initials: PM
authors.lastname: Harrison
mesh_terms: D020816:Amino Acid Motifs; D000682:Amyloid / Q000737:chemistry / Q000235:genetics; D001203:Ascomycota / Q000145:classification / Q000235:genetics*; D019143:Evolution, Molecular; D005656:Fungal Proteins / Q000737:chemistry / Q000235:genetics*; D016681:Genome, Fungal; D011328:Prions / Q000737:chemistry / Q000235:genetics*; D017434:Protein Structure, Tertiary; D015003:Yeasts / Q000235:genetics*
chemical_list: D000682:Amyloid; D005656:Fungal Proteins; D011328:Prions
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