Identification of Protein N-Terminal Methyltransferases in Yeast and Humans

Protein modification by methylation is important in cellular function. We show here that the Saccharomyces cerevisiae YBR261C/TAEI gene encodes an N-terminal protein methyltransferase catalyzing the modification of two ribosomal protein substrates, Rpll2ab and Rps25a/Rps25b. The YBR261C/Tael protein is conserved across eukaryotes; all of these proteins share sequence similarity with known seven beta-strand class I methyltransferases. Wild-type yeast cytosol and mouse heart cytosol catalyze the methylation of a synthetic peptide (PPKQQLSKY) that contains the first eight amino acids of the processed N-terminus of Rps25a/Rps25b. However, no methylation of this peptide is seen in yeast cytosol from a Delta YBR261C/tael deletion strain. Yeast YBR261C/TAEI and the human orthologue METTLIIA genes were expressed as fusion proteins in Escherichia call and were shown to be capable of stoichiometrically dimethylating the N-terminus of the synthetic peptide. Furthermore, the YBR261C/Tael and METTLIIA recombinant proteins methylate variants of the synthetic peptide containing N-terminal alanine and serine residues. However, methyltransferase activity is lamely abolished when the proline residue in position 2 or the lysine residue in position 3 is substituted. Thus, the methyltransferases described here specifically recognize the N-terminal X-Pro-Lys sequence motif, and we suggest designating the yeast enzyme Ntml and the human enzyme NTMTI. These enzymes may account for nearly all previously described eukaryotic protein N-terminal methylation reactions. A number of other yeast and human proteins also share the recognition motif and may be similarly modified. We conclude that protein X-Pro-Lys N-terminal methylation reactions catalyzed by the enzymes described here may be widespread in nature.