A Novel 3-Methylhistidine Modification of Yeast Ribosomal Protein Rpl3 Is Dependent upon the YIL110W Methyltransferase

• Published in: The Journal of biological chemistry Vol. 285; no. 48; pp. 37598 - 37606
• Main Authors: Webb, Kristofor J., Zurita-Lopez, Cecilia I., Al-Hadid, Qais, Laganowsky, Arthur, Young, Brian D., Lipson, Rebecca S., Souda, Puneet, Faull, Kym F., Whitelegge, Julian P., Clarke, Steven G.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 26.11.2010; American Society for Biochemistry and Molecular Biology
• Subjects: Actin; Amino Acid Sequence; Covalent Regulation; Mass Spectrometry (MS); Methylhistidines - metabolism; Methyltransferase; Methyltransferases - chemistry; Methyltransferases - genetics; Methyltransferases - metabolism; Molecular Sequence Data; Post-translational Modification; Protein Methylation; Protein Synthesis and Degradation; Ribosomal Proteins - genetics; Ribosomal Proteins - metabolism; Ribosomes; S-adenosylmethionine (SAM); Saccharomyces cerevisiae; Saccharomyces cerevisiae - chemistry; Saccharomyces cerevisiae - enzymology; Saccharomyces cerevisiae - genetics; Saccharomyces cerevisiae - metabolism; Saccharomyces cerevisiae Proteins - genetics; Saccharomyces cerevisiae Proteins - metabolism; Sequence Alignment; Translation; Yeast; Protein Methylation; S-adenosylmethionine (SAM); Translation; Yeast; Actin; Post-translational Modification; Ribosomes; Methyltransferase; Mass Spectrometry (MS); Covalent Regulation
• ISSN: 0021-9258; 1083-351X
• DOI: 10.1074/jbc.M110.170787

We have shown that Rpl3, a protein of the large ribosomal subunit from baker's yeast (Saccharomyces cerevisiae), is stoichiometrically monomethylated at position 243, producing a 3-methylhistidine residue. This conclusion is supported by top-down and bottom-up mass spectrometry of Rpl3, as well as by biochemical analysis of Rpl3 radiolabeled in vivo with S-adenosyl-l-[methyl-3H]methionine. The results show that a +14-Da modification occurs within the GTKKLPRKTHRGLRKVAC sequence of Rpl3. Using high-resolution cation-exchange chromatography and thin layer chromatography, we demonstrate that neither lysine nor arginine residues are methylated and that a 3-methylhistidine residue is present. Analysis of 37 deletion strains of known and putative methyltransferases revealed that only the deletion of the YIL110W gene, encoding a seven β-strand methyltransferase, results in the loss of the +14-Da modification of Rpl3. We suggest that YIL110W encodes a protein histidine methyltransferase responsible for the modification of Rpl3 and potentially other yeast proteins, and now designate it Hpm1 (Histidine protein methyltransferase 1). Deletion of the YIL110W/HPM1 gene results in numerous phenotypes including some that may result from abnormal interactions between Rpl3 and the 25 S ribosomal RNA. This is the first report of a methylated histidine residue in yeast cells, and the first example of a gene required for protein histidine methylation in nature.