FIGURE 2.

Conservation of antizyme mRNA sequences from Basidiomycota, and their encoded products. A, an alignment of 35 ORF1 antizyme mRNA sequences was used to generate the nucleotide and amino acid logos shown here. Of these sequences, 34 belong to Agaricomycetes, and 1 belongs to Dacrymycetes (supplemental Sequence List S1). Starting from the 3′ end of the nucleotide logo indicated are the ORF1 stop codon, the shift site, the sequence of module A, and the conserved peptide encoding region. Other conserved features more distal to the shift site, such as a conserved dipeptide and a conserved 5′ stem loop, are also indicated. The gaps in the logos indicate that each nucleotide or amino acid residue occurs with equal probability at the corresponding position. B, alignment of 54 Basidiomycotal antizyme mRNA sequences 3′ of the shift site. The region shown here contains the conserved 3′ RNA structure. The nucleotide variations in loop 2 are highlighted in green. The correct reading frame is indicated in the first sequence of the alignment. The absolutely conserved four nucleotide sequence abutting stem 1 are shown in magenta. Completely conserved nucleotides are indicated by an asterisk below the alignment. The four sequences of the Tremellomycetes class that lack the potential RNA structure were left uncolored and were not taken into account when analyzing the alignment. The underlined names are of the sequences used for the alignments in Fig. 2A. The scheme of the phylogenetic tree was adapted from the work of Floudas et al. (41) and is not intended to indicate precise evolutionary distances and scales. P.taeda* refers to an EST derived from a Pinus taeda library that is an Agaricomycetes contaminant of unknown identity. Dacryop.** stands for Dacryopinax sp. C, the predicted secondary structure of the putative RNA stimulator, inferred from the alignment, featuring the C. cinerea mRNA sequence; the coloring corresponds to that of the alignment.