METTL18-mediated histidine methylation of RPL3 modulates translation elongation for proteostasis maintenance

Abstract

Protein methylation occurs predominantly on lysine and arginine residues, but histidine also serves as a methylation substrate. However, a limited number of enzymes responsible for this modification have been reported. Moreover, the biological role of histidine methylation has remained poorly understood to date. Here, we report that human METTL18 is a histidine methyltransferase for the ribosomal protein RPL3 and that the modification specifically slows ribosome traversal on Tyr codons, allowing the proper folding of synthesized proteins. By performing an in vitro methylation assay with a methyl donor analog and quantitative mass spectrometry, we found that His245 of RPL3 is methylated at the τ-N position by METTL18. Structural comparison of the modified and unmodified ribosomes showed stoichiometric modification and suggested a role in translation reactions. Indeed, genome-wide ribosome profiling and an in vitro translation assay revealed that translation elongation at Tyr codons was suppressed by RPL3 methylation. Because the slower elongation provides enough time for nascent protein folding, RPL3 methylation protects cells from the cellular aggregation of Tyr-rich proteins. Our results reveal histidine methylation as an example of a ribosome modification that ensures proteome integrity in cells.

Histidine N1-position-specific methyltransferase CARNMT1 targets C3H zinc finger proteins and modulates RNA metabolism

“…His methylation plays an important role in the regulation of actin function and muscle contractility. METTL18, the mammalian homolog of HPM1, also catalyzes N3-position-specific His methylation of RPL3 ( Małecki et al 2021 ; Matsuura-Suzuki et al 2022 ). METTL9 is a protein N1-position-specific His MTase that targets alternating His residues, resulting in the regulation of metal ion binding ( Davydova et al 2021 ).…”

“…Since the consensus motif is likely their sum, N1-position-specific His methylation by METTL9 and CARNMT1 may occur across mammalian proteomes. Indeed, both METTL9 ( Davydova et al 2021 ) and CARNMT1 have diverse protein substrates in mammals, whereas the N3-position-specific His MTases SETD3 and METTL18 specifically target β-actin ( Kwiatkowski et al 2018 ; Wilkinson et al 2019 ) and RPL3 ( Małecki et al 2021 ; Matsuura-Suzuki et al 2022 ), respectively. Notably, the Cx(F/Y)xH motif is not sufficient for methylation by CARNMT1.…”

“…Recombinant METTL9 ( Davydova et al 2021 ) and METTL18 ( Matsuura-Suzuki et al 2022 ) were described previously. To obtain GST-CARNMT1, 9xHis-CARNMT1, or salmonella MTAN recombinant protein (a gift from Vern Schramm; Addgene plasmid 64041, , RRID: Addgene_64041), BL21 (pLysS) strains were transformed with the pGEX4T plasmids or pET19 plasmids, and the bacteria were cultured in 2× YT medium with 100 µg/mL ampicillin and 0.2 mM isopropyl β-D-1-thiogalactopyranoside (IPTG) for 18 h at 18°C.…”

“…In 2010, histidine protein methyltransferase 1 (HPM1) was discovered as the first His MTase methylating the N3 position of yeast ribosomal protein L3 (RPL3) ( Webb et al 2010 ). Methyltransferase-like 18 (METTL18), the mammalian homolog of HPM1, methylates the His of RPL3 and regulates ribosomal function ( Małecki et al 2021 ; Matsuura-Suzuki et al 2022 ). In addition to HPM1/METTL18, SET domain-containing 3 (SETD3) was discovered as another N3-position-specific His MTase that targets β-actin ( Kwiatkowski et al 2018 ; Wilkinson et al 2019 ).…”

“…For example, SETD3-mediated β-actin methylation plays a role in muscle contractility, and loss of SETD3 causes primary dystocia ( Wilkinson et al 2019 ). His methylation of RPL3 regulates translation elongation ( Matsuura-Suzuki et al 2022 ) and translation dynamics ( Małecki et al 2021 ) in mammals and ribosome assembly in yeast ( Al-Hadid et al 2014 ). His methylation by METTL9 regulates zinc ion binding and transport ( Davydova et al 2021 ; Lv et al 2021 ) and oxidative phosphorylation ( Davydova et al 2021 ).…”