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

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

PROVIDER: PRJNA745343 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15096303.fastq.gz	Fastqsanger.gz
	SRR15096304.fastq.gz	Fastqsanger.gz
	SRR15096305.fastq.gz	Fastqsanger.gz
	SRR15096306.fastq.gz	Fastqsanger.gz
	SRR15096307.fastq.gz	Fastqsanger.gz

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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: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

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

Project description: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.

2022-06-15 | GSE200172 | GEO

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

Project description: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.

| S-EPMC9177149 | biostudies-literature

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

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

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

Proteomics exploration of the human RPL3 interactome

Project description:Exploring the interactome of human RPL3 by MS-based proteomics.

2021-09-08 | PXD016055 | Pride

RPL3L-containing ribosomes determine translation elongation dynamics required for cardiac function

Project description:Although several ribosomal protein (RP) paralogs are expressed in a tissue-specific manner, how these proteins affect translation and why they are required only in certain tissues have remained unclear. Here we show that RPL3L, a paralog of RPL3 specifically expressed in heart and skeletal muscle, influences translation elongation dynamics. Deficiency of RPL3L-containing ribosomes (RPL3L-ribosomes) in RPL3L knockout male mice resulted in impaired cardiac contractility. Ribosome occupancy at mRNA codons was found to be altered in the RPL3L-deficient heart, and the changes were negatively correlated with those observed in myoblasts overexpressing RPL3L. RPL3L-ribosomes were less prone to collisions compared with RPL3-containing canonical ribosomes. Although the loss of RPL3L-ribosomes altered translation elongation dynamics for the entire transcriptome, its effects were most pronounced for transcripts related to cardiac muscle contraction and dilated cardiomyopathy, with the abundance of the encoded proteins being correspondingly decreased. Our results provide new insight into the mechanisms and physiological relevance of tissue-specific translational regulation.

2023-03-15 | GSE203072 | GEO

WGS histidine overproducers

Project description:Whole genomes sequencing to determine mutations in histidine overproducers generated with a toxic histidine analog

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