Fig. 2: Phylogeny of the Met4 and Met28 paralogs in budding yeasts.

A Protein sequences retrieved from YGOB⁵², CGOB⁵³ or the indicated accession numbers were aligned using ClustalO implemented in Seaview⁵⁴. Trees were inferred using PhyML restricted to conserved regions selected using Gblocks. WGD = Whole Genome Duplication; KLE = Kluyveromyces/Lachancea/Eremothecium. B Met4 and Met28 sequences of S. cerevisiae (Sc), C. parapsilosis (Cp) and O. parapolymorpha (Op) are drawn to scale. The A. nidulans duplicated protein pair MetR/MetZ is also included. Met4-like sequences in yeast species from the CUG-Ser1 clade, the Pichiaceae, and clades within the Saccharomycetaceae share a common domain organisation. Starting from the N-terminal end of the protein: Activation Domains (AD) encompassing Ubiquitin Interaction Motifs (UIM, which protects ubiquitinated Met4 from degradation), a conserved Lysine (K) that is the target of poly-ubiquitination, Inhibitory Region (IR, required for Met30-mediated inhibition of activity in the presence of a high concentration of methionine), Auxiliary domain (AUX, required to fully relieve IR-mediated repression), Interaction domain (INT, required for binding of Met31/Met32), and the bZIP DNA binding domain. The degenerated basic region of the bZIP domain in S. cerevisiae Met4 is indicated by the pink vertical stripes. Met28-like sequences are shorter and lack the N-terminal domain organisation observed in Met4, but they have a bZIP binding domain at the C-terminal end.