Phylogenetic comparison of the URE2 minimal IRES element in seven Saccharomyces genera. (A) ClustalW comparison of the nucleotide sequences of the prion-forming domain and the minimal URE2 IRES element in the seven genera listed. The minimal URE2 IRES element is underlined. Identical nucleotides are illustrated as color dots, while variable nucleotides are indicated by colored letters. Wobble nucleotides are highlighted with bold dots (●) above the Saccharomyces cerevisiae sequence with the nucleotide numbers. The internal AUG codon is highlighted with a bracket and star. (B) The sequence comparison in A is mapped onto the previously determined secondary structure of the Saccharomyces cerevisiae minimal URE2 IRES element (Reineke et al. 2008). The variation in each genus at each nucleotide is indicated by colored letters that correspond to the genus (red, Saccharomyces douglassi and paradoxus; blue, Saccharomyces bayanus; green, Saccharomyces mikatae; fuchsia, Saccharomyces pastorianus; orange, Saccharomyces kudriavzevii). Bold arrows indicate nucleotide positions that vary without perturbing the base-pairing status. The internal AUG codon is highlighted in yellow, and numbers correspond to nucleotide numbers listed in A. Domains 1–3 of the minimal URE2 IRES element are indicated in brackets, and base-pair X and bulge Y are indicated with boxes.
