A molecular clamp ensures allosteric coordination of peptidyltransfer and ligand binding to the ribosomal A-site

Meškauskas, Arturas; Dinman, Jonathan D.

doi:10.1093/nar/gkq641

Cited by 35 publications

(55 citation statements)

References 64 publications

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“…H243 lies in a functionally important region of Rpl3 called the "basic thumb" that is proposed to synchronize the steps of translation elongation (Meskauskas and Dinman 2010). This basic thumb is a positively charged region, perpendicular to the tryptophan finger, proposed to function as a molecular clamp, linking functionally relevant rRNA domains through noncovalent interactions.…”

Section: Resultsmentioning

confidence: 99%

Methylation of yeast ribosomal protein Rpl3 promotes translational elongation fidelity

Al-Hadid

Roy

Chanfreau

et al. 2016

RNA

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Rpl3, a highly conserved ribosomal protein, is methylated at histidine 243 by the Hpm1 methyltransferase in Saccharomyces cerevisiae. Histidine 243 lies close to the peptidyl transferase center in a functionally important region of Rpl3 designated as the basic thumb that coordinates the decoding, peptidyl transfer, and translocation steps of translation elongation. Hpm1 was recently implicated in ribosome biogenesis and translation. However, the biological role of methylation of its Rpl3 substrate has not been identified. Here we interrogate the role of Rpl3 methylation at H243 by investigating the functional impact of mutating this histidine residue to alanine (rpl3-H243A). Akin to Hpm1-deficient cells, rpl3-H243A cells accumulate 35S and 23S pre-rRNA precursors to a similar extent, confirming an important role for histidine methylation in pre-rRNA processing. In contrast, Hpm1-deficient cells but not rpl3-H243A mutants show perturbed levels of ribosomal subunits. We show that Hpm1 has multiple substrates in different subcellular fractions, suggesting that methylation of proteins other than Rpl3 may be important for controlling ribosomal subunit levels. Finally, translational fidelity assays demonstrate that like Hpm1-deficient cells, rpl3-H243A mutants have defects in translation elongation resulting in decreased translational accuracy. These data suggest that Rpl3 methylation at H243 is playing a significant role in translation elongation, likely via the basic thumb, but has little impact on ribosomal subunit levels. Hpm1 is therefore a multifunctional methyltransferase with independent roles in ribosome biogenesis and translation.

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Section: Resultsmentioning

confidence: 99%

Methylation of yeast ribosomal protein Rpl3 promotes translational elongation fidelity

Al-Hadid

Roy

Chanfreau

et al. 2016

RNA

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“…His-243 of Rpl3 is buried deep within the 25S RNA near the A-site and peptidyltransferase center (73); the methylated N-3 atom contacts guanine-878 and adenine-876 of the 25S rRNA (7,74). Yeast hpm1 null cells have a pronounced deficiency of 60S subunits reflecting a significant defect in early rRNA processing with the accumulation of 35S and 23S intermediate RNA species (74).…”

Section: Protein Histidine Methyltransferasesmentioning

confidence: 99%

The ribosome: A hot spot for the identification of new types of protein methyltransferases

Clarke¹

2018

Journal of Biological Chemistry

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Cellular physiology depends on the alteration of protein structures by covalent modification reactions. Using a combination of bioinformatic, genetic, biochemical, and mass spectrometric approaches, it has been possible to probe ribosomal proteins from the yeast Saccharomyces cerevisiae for posttranslationally methylated amino acid residues and for the enzymes that catalyze these modifications. These efforts have resulted in the identification and characterization of the first protein histidine methyltransferase, the first N-terminal protein methyltransferase, two unusual types of protein arginine methyltransferases, and a new type of cysteine methylation. Two of these enzymes may modify their substrates during ribosomal assembly because the final methylated histidine and arginine residues are buried deep within the ribosome with contacts only with RNA. Two of these modifications occur broadly in eukaryotes, including humans, while the others demonstrate a more limited phylogenetic range. Analysis of strains where the methyltransferase genes are deleted has given insight into the physiological roles of these modifications. These reactions described here add diversity to the modifications that generate the typical methylated lysine and arginine residues previously described in histones and other proteins. Regulation of biological function by protein methylation reactionsIt is more and more apparent just how much of biological function is dependent upon posttranslational modifications (1). The human genome encodes some 900 enzymes catalyzing just protein phosphorylation or ubiquitination (2,3). However, it is now clear that methyl groups can stand beside phosphate groups and ubiquitin as major players in controlling the physiological functions of proteins. We are beginning to understand how the much greater diversity of protein methylation reactions can give rise to a greater diversity of function (1,4-8). We are also learning the importance of crosstalk between protein and DNA methylation reactions (9) and among protein methylation, phosphorylation, acetylation, and ubiquitination reactions (10-12). Finally, we are discovering how alterations in protein methylation pathways can lead to human pathology, particularly in cancer (13-15).The collection of over sixty human protein arginine and lysine methyltransferases that leave histone "marks" recognized by reader proteins to guide gene expression are perhaps the poster children for the importance of protein methyltransferases (16-17). However, recent work has emphasized the importance of methylating non-histone substrates at these residues, particularly ribosomal proteins, translation factors, and transcription factors in a wide variety of organisms (7,8,15,18,19). Furthermore, the methylation of lysine and arginine residues represents just the tip of the iceberg in protein methylation -modifications have also been established at histidine, modified histidine (diphthamide), glutamate, glutamine, asparagine, Lisoaspartate, D-aspartate, cysteine, isoprenylcysteine, me...

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“…H243 lies in the tryptophan finger domain of Rpl3p at the core of the 25S rRNA, more specifically, in a positively charged "basic thumb" that protrudes perpendicularly to the finger (54). The basic thumb has recently been shown to play a role in coordinating the processes occurring in the PTC, the aminoacyl-tRNA binding region, and the elongation factor binding site to promote unidirectional translation (54).…”

Section: Fig 7 Cells Deficient In Hpm1p Have Increased Amino Acid Mismentioning

confidence: 99%

Histidine Methylation of Yeast Ribosomal Protein Rpl3p Is Required for Proper 60S Subunit Assembly

Al-Hadid¹,

Roy²,

Munroe³

et al. 2014

Molecular and Cellular Biology

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Histidine protein methylation is an unusual posttranslational modification. In the yeast Saccharomyces cerevisiae, the large ribosomal subunit protein Rpl3p is methylated at histidine 243, a residue that contacts the 25S rRNA near the P site. Rpl3p methylation is dependent upon the presence of Hpm1p, a candidate seven-beta-strand methyltransferase. In this study, we elucidated the biological activities of Hpm1p in vitro and in vivo. Amino acid analyses reveal that Hpm1p is responsible for all of the detectable protein histidine methylation in yeast. The modification is found on a polypeptide corresponding to the size of Rpl3p in ribosomes and in a nucleus-containing organelle fraction but was not detected in proteins of the ribosome-free cytosol fraction. In vitro assays demonstrate that Hpm1p has methyltransferase activity on ribosome-associated but not free Rpl3p, suggesting that its activity depends on interactions with ribosomal components. hpm1 null cells are defective in early rRNA processing, resulting in a deficiency of 60S subunits and translation initiation defects that are exacerbated in minimal medium. Cells lacking Hpm1p are resistant to cycloheximide and verrucarin A and have decreased translational fidelity. We propose that Hpm1p plays a role in the orchestration of the early assembly of the large ribosomal subunit and in faithful protein production.

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A molecular clamp ensures allosteric coordination of peptidyltransfer and ligand binding to the ribosomal A-site

Cited by 35 publications

References 64 publications

Methylation of yeast ribosomal protein Rpl3 promotes translational elongation fidelity

Methylation of yeast ribosomal protein Rpl3 promotes translational elongation fidelity

The ribosome: A hot spot for the identification of new types of protein methyltransferases

Histidine Methylation of Yeast Ribosomal Protein Rpl3p Is Required for Proper 60S Subunit Assembly

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