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

ABSTRACT: Protein methylation occurs predominantly on lysine and arginine residues, but histidine also serves as a substrate for the modification. However, a limited number of enzymes responsible for this modification have been reported. Moreover, the biological role of histidine methylation has remained poorly understood. Here, we report that human METTL18 is a histidine methyltransferase for the ribosomal protein RPL3 and that the modification specifically slows ribosome traverse on tyrosine 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 tuning. Indeed, genome-wide ribosome profiling revealed suppressed ribosomal translocation at tyrosine codons 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 code” that ensures proteome integrity in cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE200172 | GEO | 2022/06/15

REPOSITORIES: GEO

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

Project description:In addition to predominant protein methylation on lysine and arginine residues, histidine also serves as a substrate for the modification. However, a limited number of enzymes responsible for this modification has been reported. Moreover, the biological mission of the histidine methylation has remained poorly understood. Here, we reported that human METTL18 is a histidine methyltransferase for ribosomal protein RPL3 and that the modification specifically slows ribosome traverse on tyrosine codons, allowing proper folding of synthesized proteins. Harnessing in vitro methylation assay with methyl-donor analogue and quantitative mass spectrometry, we identified that His245 of RPL3 is methylated at τ-N position by METTL18. Structural comparison of the modified and unmodified ribosomes showed the stoichiometric modification and suggested its role in translation tuning. Indeed, genome-wide ribosome profiling revealed the suppressed ribosomal translocation at tyrosine codons by RPL3 methylation. Because the slower elongation provides enough time for nascent protein folding, RPL3 methylation protects cells from cellular aggregation of Tyr-rich proteins. Our results reveal histidine methylation as an example of “ribosome code”, which ensures proteome integrity in cells.

2022-06-15 | GSE179854 | GEO

Human METTL18 is a histidine-specific methyltransferase that targets RPL3 and affects ribosome biogenesis and function

Project description:Methylation is a common post-translational modification that occurs primarily on lysine and arginine, but also on some other residues, such as histidine. METTL18 is the last uncharacterized member of a group of human methyltransferases (MTases) that mainly exert lysine methylation, and here we set out to elucidate its function. We found METTL18 to be a nuclear protein that contains a functional nuclear localization signal and accumulates in nucleoli. Recombinant METTL18 methylated a single protein in nuclear extracts and in isolated ribosomes from METTL18 knock-out (KO) cells. This protein was identified as 60S ribosomal protein L3 (RPL3), and we also performed an RPL3 interactomics screen and identified METTL18 as the most significantly enriched MTase. Protein mass spectrometry and amino acid analyses revealed that His-245 in RPL3 carries a 3-methylhistidine (3MH; also referred to as t-methylhistidine) modification, which was absent in METTL18 KO cells. In addition, both recombinant and endogenous METTL18 were found to be monomethylated at His-154, likely resulting from auto-methylation, and further corroborating METTL18 as a histidine-specific MTase. Finally, METTL18 KO cells displayed altered pre-rRNA processing, decreased polysomes formation and codon-specific changes in mRNA translation, indicating that METTL18-mediated methylation of RPL3 is important for optimal ribosome biogenesis and function. In conclusion, we have here established METTL18 as the second human histidine-specific protein MTase, and demonstrated its functional relevance.

2021-02-28 | GSE146364 | GEO

Study of ribosome dynamics of rpl3[W255C] and its interactions with ribosome-associated chaperones

Project description:Proteostasis is a fundamental network of cellular pathways that ensures the optimal concentration and composition of correctly folded proteins within cells in normal and stress conditions. Among key components of this network are the molecular chaperones, which mediate protein folding but also act as modulators of protein synthesis. We have reported on a functional link between translation and de novo folding of proteins in the yeast Saccharomyces cerevisiae by uncovering a specific synthetic-lethal interaction between apparent unrelated mutant variants, the uL3[W255C] variant of the ribosomal protein uL3 and the null mutants of Zuo1 and Ssz1. Zuo1 and Ssz1 are components of the chaperone system named as ribosome-associated complex. Here, we performed a genome-wide analysis of ribosome dynamics by 5PSeq (Pelechano et al. 2015 PMID 26046441) in strains harbouring either wild-type uL3 or mutant uL3[W255C] in the presence or absence of Zuo1 or Ssz1. This method allows the study of ribosome dynamics, by sequencing 5’ phosphorylated mRNA co-translational degradation intermediates. Our results indicate that the rpl3[W255C] mutant is slightly impaired in translation elongation, defect that is significantly enhanced when combined with the deprivation of either Zuo1 or Ssz1.

2020-11-25 | GSE114899 | GEO

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

Project description:METTL18-mediated histidine methylation on RPL3 modulates translation elongation for proteostasis maintenance.

| PRJNA823531 | ENA

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

Project description:METTL18-mediated histidine methylation on RPL3 modulates translation elongation for proteostasis maintenance

| PRJNA745343 | ENA

Rbp95 binds 25S rRNA helix H95 and cooperates with the Npa1 complex during early pre-60S particle maturation

Project description:Eukaryotic ribosome synthesis involves more than 200 assembly factors, which promote ribosomal RNA (rRNA) processing, modification and folding, and assembly of ribosomal proteins. The formation and maturation of the earliest pre-60S particles requires structural remodeling by the Npa1 complex, but is otherwise still poorly understood. Here we introduce Rbp95, a constituent of early pre-60S particles, as a novel ribosome assembly factor that likely already binds before the 90S to pre-60S transition. We show that Rbp95 is both genetically and physically linked to most Npa1 complex members, and to ribosomal protein Rpl3. Notably, the RNA-binding protein Rbp95 associates with helix H95 in the 3’ region of the 25S rRNA, in close proximity to the binding sites of Npa1 and Rpl3. Additionally, Rbp95 interacts with several snoRNAs. In the absence of Rbp95, proteins binding in proximity to helix H95 are less efficiently recruited to early pre-60S particles. Moreover, combined mutation of Rbp95 and Npa1 complex members leads to a delay in the formation of early pre-60S particles. We propose that Rbp95 acts together with the Npa1 complex in the 90S to pre-60S transition and in promoting pre-rRNA folding events within pre-60S particles that facilitate the recruitment of subsequent assembly factors.

2022-10-13 | PXD030106 | Pride

Human METTL18 is a histidine-specific methyltransferase that targets RPL3 and affects ribosome biogenesis and function

Project description:Human METTL18 is a histidine-specific methyltransferase that targets RPL3 and affects ribosome biogenesis and function

| PRJNA610254 | ENA

Novel roles for ribosomal histidine methylation revealed by proteomics and large-scale cross-linking mass spectrometry

Project description:The methylation of histidine residues is increasingly found to be both prevalent throughout the proteome, and also relevant to human disease. Hpm1p mono-methylates H243 in the ribosomal protein Rpl3 and represents the only histidine methyltransferase in Saccharomyces cerevisiae. Interestingly, the hpm1 deletion strain is highly pleiotropic, with many extra-ribosomal phenotypes including improved growth rates in alternative carbon sources. Here we aimed to understand how methylation of one histidine in one ribosomal protein could result in such diverse phenotypes by combining targeted mass spectrometry, growth assays, quantitative proteomics and cross-linking mass spectrometry. We confirmed the localisation and stoichiometry of the H243 site, found unreported sensitivities of Δhpm1 yeast to non-ribosomal stressors, and identified thirty differentially-abundant proteins upon hpm1 knockout, most with clear links to the coordination of sugar metabolism. We adapted the emerging technique of quantitative large scale cross-linking mass spectrometry for use in budding yeast, which resulted in the identification of 1,267 unique in vivo lysine-lysine pairs. By reproducibly monitoring over 350, we detected changes to membrane protein structure, chromatin compaction, and mitochondrial protein-protein interactions, independently of changes in protein abundance themselves. Taken together, these studies reveal a clear role for Hpm1p in the coordination of sugar metabolism, contextualise the deletion strain’s pleiotropy and illustrate how cross-linking mass spectrometry can generate mechanistic insights into complex cellular processes.

2022-08-12 | PXD027953 | Pride

Role of eEF2 diphthamide modification in translational fidelity

Project description:Diphthamide (DPH) is a conserved amino acid modification on eukaryotic translation elongation factor eEF2. We show that loss of DPH increases -1 ribosomal frameshifting at both programmed, including in SARS-CoV-2, and non-programmed sites. Ribosome profiling of yeast and mammalian cells lacking DPH reveals increased ribosomal drop-off during elongation. The drop-off defect on the long yeast MDN1 gene was suppressed by eliminating out-of-frame stop codons. Our data reveal that loss of DPH impairs the fidelity of translocation during translation elongation resulting in increased rates of ribosomal frameshifting and premature termination at out-of-frame stop codons.

2023-01-10 | GSE176169 | GEO

Optimization of codon translation rates via tRNA modifications maintains proteome integrity

Project description:Proteins begin to fold as they emerge from translating ribosomes. The kinetics of ribosome transit along a given mRNA can influence nascent chain folding, but the extent to which individual codon translation rates impact proteome integrity remains unknown. Here, we show that slower decoding of discrete codons elicits widespread protein aggregation in vivo. Using ribosome profiling, we find that loss of anticodon wobble uridine (U34) modifications in a subset of tRNAs leads to ribosome pausing at their cognate codons in S. cerevisiae and C. elegans. Yeast cells lacking U34 modifications exhibit gene expression hallmarks of proteotoxic stress and accumulate aggregates of endogenous proteins with key cellular functions. Moreover, these cells are severely compromised in clearing stress-induced protein aggregates. Overexpression of hypomodified tRNAs alleviates ribosome pausing, concomitantly restoring protein homeostasis. Our findings demonstrate that modified U34 is an evolutionarily conserved accelerator of decoding and reveal an unanticipated role for tRNA anticodon modifications in maintaining proteome integrity. Ribosome profiling of wild-type and tRNA modification-deficient yeast and nematodes. Yeast samples were generated in various growth conditions (rich medium versus stress induced by treatment with diamide or rapamycin) and paired mRNA-Seq was performed on a subset of samples. Dataset contains three biological replicates for yeast samples and two biological replicates for nematode samples.

2015-06-04 | E-GEOD-67387 | biostudies-arrayexpress

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