Fig. 3.

Phylogenetic relationships for proteasome subunits from zebrafish and additional vertebrates. Multimeric proteasomes have interchangeable catalytic subunits in most jawed vertebrates. Constitutive proteasome, immunoproteasome, and intermediate proteasome forms each degrade intracellular proteins into the peptide fragments that are presented by MHC molecules at the cell surface. The three ancestral PSMB subunits with distinct catalytic activities (Psmb5, Psmb6, and Psmb7) segregate into three major branches in the phylogenetic tree. These three constitutive proteasome subunits Psmb5 (LMPX), Psmb6 (LMPY), and Psmb7 (LMPZ) are replaced by IFN-inducible immunoproteasome subunits Psmb8 (LMP7), Psmb9 (LMP2), and Psmb10 (MECL-1), respectively, during an immune response. In addition, the thymoproteasome subunit Psmb11 replaces Psmb5 and Psmb8 specifically in the thymus. These more specialized, nonconstitutive, proteasome subunits seem to be specific to jawed vertebrates (87). Deduced amino acid sequences were used to construct maximum likelihood trees. For clarity only, the subunit encoded by the Zv9 reference genome is shown for three constitutive proteasome (Psmb5, Psmb6, and Psmb7) and two thymoproteasome (Psmb11a and Psmb11b) subunits. Chromosome locations for zebrafish subunits are provided in parentheses, including haplotype associations when applicable. Additional phylogenetic trees with bootstrap values and other species are provided in SI Appendix, Figs. S5–S7. Sequences are provided in Dataset S1.