FIG. 3.

Deep functional divergence between Puf3p and Puf4p. (A) The phylogenetic tree of the PUM-HD domains from the Puf3p and Puf4p orthologs (bootstrap scores are presented in Supplementary fig. 3, Supplementary Material online). Glam-Puf protein is used as the out-group. The branches to Puf3p and Puf4p in each species were coded in red and blue, respectively. (B) Functional conservation of Puf3p and Puf4p orthologs in fungi. The conserved amino acids for the repeat #3 and #5 of the PUM-HD domain are displayed using ClustalX (Thompson et al. 1997). The red (C ↔ T) and blue (R ↔ C) arrows denote the conserved amino acids in Puf3p and Puf4p that are critical for different motif recognition between these two proteins. (C) Little functional overlapping between Puf3p and Puf4p. The y axis denotes the ratio of genes having both P3E and P4E over the total number of genes with P3E and/or P4E in each species (x axis).