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The yeast [ PSI  + ] prion, formed by the Sup35 (eRF3) protein, has multiple structural variants differing in the strength of nonsense suppressor phenotype. Structure of [ PSI  + ] and its variation are characterized poorly. Here, we mapped Sup35 amyloid cores of 26 [ PSI  + ] ex vivo prions of different origin using proteinase K digestion and mass spectrometric identification of resistant peptides. In all [ PSI  + ] variants the Sup35 amino acid residues 2-32 were fully resistant and the region up to residue 72 was partially resistant. Proteinase K-resistant structures were also found within regions 73-124, 125-153, and 154-221, but their presence differed between [ PSI  + ] isolates. Two distinct digestion patterns were observed for region 2-72, which always correlated with the "strong" and "weak" [ PSI  + ] nonsense suppressor phenotypes. Also, all [ PSI  + ] with a weak pattern were eliminated by multicopy HSP104 gene and were not toxic when combined with multicopy SUP35 . [ PSI  + ] with a strong pattern showed opposite properties, being resistant to multicopy HSP104 and lethal with multicopy SUP35 . Thus, Sup35 prion cores can be composed of up to four elements. [ PSI  + ] variants can be divided into two classes reliably distinguishable basing on structure of the first element and the described assays.

Yeast Sup35 Prion Structure: Two Types, Four Parts, Many Variants