1
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Xu F, Suyama R, Inada T, Kawaguchi S, Kai T. HemK2 functions for sufficient protein synthesis and RNA stability through eRF1 methylation during Drosophila oogenesis. Development 2024; 151:dev202795. [PMID: 38881530 DOI: 10.1242/dev.202795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 06/07/2024] [Indexed: 06/18/2024]
Abstract
HemK2 is a highly conserved methyltransferase, but the identification of its genuine substrates has been controversial, and its biological importance in higher organisms remains unclear. We elucidate the role of HemK2 in the methylation of eukaryotic Release Factor 1 (eRF1), a process that is essential for female germline development in Drosophila melanogaster. Knockdown of hemK2 in the germline cells (hemK2-GLKD) induces apoptosis, accompanied by a pronounced decrease in both eRF1 methylation and protein synthesis. Overexpression of a methylation-deficient eRF1 variant recapitulates the defects observed in hemK2-GLKD, suggesting that eRF1 is a primary methylation target of HemK2. Furthermore, hemK2-GLKD leads to a significant reduction in mRNA levels in germline cell. These defects in oogenesis and protein synthesis can be partially restored by inhibiting the No-Go Decay pathway. In addition, hemK2 knockdown is associated with increased disome formation, suggesting that disruptions in eRF1 methylation may provoke ribosomal stalling, which subsequently activates translation-coupled mRNA surveillance mechanisms that degrade actively translated mRNAs. We propose that HemK2-mediated methylation of eRF1 is crucial for ensuring efficient protein production and mRNA stability, which are vital for the generation of high-quality eggs.
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Affiliation(s)
- Fengmei Xu
- Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
| | - Ritsuko Suyama
- Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
| | - Toshifumi Inada
- Division of RNA and Gene regulation, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Shinichi Kawaguchi
- Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
| | - Toshie Kai
- Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
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2
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Zafar H, Hassan AH, Demo G. Translation machinery captured in motion. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1792. [PMID: 37132456 DOI: 10.1002/wrna.1792] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 03/14/2023] [Accepted: 04/17/2023] [Indexed: 05/04/2023]
Abstract
Translation accuracy is one of the most critical factors for protein synthesis. It is regulated by the ribosome and its dynamic behavior, along with translation factors that direct ribosome rearrangements to make translation a uniform process. Earlier structural studies of the ribosome complex with arrested translation factors laid the foundation for an understanding of ribosome dynamics and the translation process as such. Recent technological advances in time-resolved and ensemble cryo-EM have made it possible to study translation in real time at high resolution. These methods provided a detailed view of translation in bacteria for all three phases: initiation, elongation, and termination. In this review, we focus on translation factors (in some cases GTP activation) and their ability to monitor and respond to ribosome organization to enable efficient and accurate translation. This article is categorized under: Translation > Ribosome Structure/Function Translation > Mechanisms.
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Affiliation(s)
- Hassan Zafar
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Ahmed H Hassan
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Gabriel Demo
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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3
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Seely SM, Parajuli NP, De Tarafder A, Ge X, Sanyal S, Gagnon MG. Molecular basis of the pleiotropic effects by the antibiotic amikacin on the ribosome. Nat Commun 2023; 14:4666. [PMID: 37537169 PMCID: PMC10400623 DOI: 10.1038/s41467-023-40416-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 07/26/2023] [Indexed: 08/05/2023] Open
Abstract
Aminoglycosides are a class of antibiotics that bind to ribosomal RNA and exert pleiotropic effects on ribosome function. Amikacin, the semisynthetic derivative of kanamycin, is commonly used for treating severe infections with multidrug-resistant, aerobic Gram-negative bacteria. Amikacin carries the 4-amino-2-hydroxy butyrate (AHB) moiety at the N1 amino group of the central 2-deoxystreptamine (2-DOS) ring, which may confer amikacin a unique ribosome inhibition profile. Here we use in vitro fast kinetics combined with X-ray crystallography and cryo-EM to dissect the mechanisms of ribosome inhibition by amikacin and the parent compound, kanamycin. Amikacin interferes with tRNA translocation, release factor-mediated peptidyl-tRNA hydrolysis, and ribosome recycling, traits attributed to the additional interactions amikacin makes with the decoding center. The binding site in the large ribosomal subunit proximal to the 3'-end of tRNA in the peptidyl (P) site lays the groundwork for rational design of amikacin derivatives with improved antibacterial properties.
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Affiliation(s)
- Savannah M Seely
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Narayan P Parajuli
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, SE-75124, Uppsala, Sweden
| | - Arindam De Tarafder
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, SE-75124, Uppsala, Sweden
| | - Xueliang Ge
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, SE-75124, Uppsala, Sweden
| | - Suparna Sanyal
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, SE-75124, Uppsala, Sweden.
| | - Matthieu G Gagnon
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA.
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77555, USA.
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, 77555, USA.
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, 77555, USA.
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4
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Loveland AB, Svidritskiy E, Susorov D, Lee S, Park A, Zvornicanin S, Demo G, Gao FB, Korostelev AA. Ribosome inhibition by C9ORF72-ALS/FTD-associated poly-PR and poly-GR proteins revealed by cryo-EM. Nat Commun 2022; 13:2776. [PMID: 35589706 PMCID: PMC9120013 DOI: 10.1038/s41467-022-30418-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 04/29/2022] [Indexed: 12/15/2022] Open
Abstract
Toxic dipeptide-repeat (DPR) proteins are produced from expanded G4C2 repeats in the C9ORF72 gene, the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Two DPR proteins, poly-PR and poly-GR, repress cellular translation but the molecular mechanism remains unknown. Here we show that poly-PR and poly-GR of ≥20 repeats inhibit the ribosome's peptidyl-transferase activity at nanomolar concentrations, comparable to specific translation inhibitors. High-resolution cryogenic electron microscopy (cryo-EM) reveals that poly-PR and poly-GR block the polypeptide tunnel of the ribosome, extending into the peptidyl-transferase center (PTC). Consistent with these findings, the macrolide erythromycin, which binds in the tunnel, competes with poly-PR and restores peptidyl-transferase activity. Our results demonstrate that strong and specific binding of poly-PR and poly-GR in the ribosomal tunnel blocks translation, revealing the structural basis of their toxicity in C9ORF72-ALS/FTD.
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Affiliation(s)
- Anna B Loveland
- RNA Therapeutics Institute, UMass Chan Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Egor Svidritskiy
- RNA Therapeutics Institute, UMass Chan Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Denis Susorov
- RNA Therapeutics Institute, UMass Chan Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Soojin Lee
- Department of Neurology, UMass Chan Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Alexander Park
- RNA Therapeutics Institute, UMass Chan Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Sarah Zvornicanin
- RNA Therapeutics Institute, UMass Chan Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Gabriel Demo
- RNA Therapeutics Institute, UMass Chan Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
- Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Fen-Biao Gao
- Department of Neurology, UMass Chan Medical School, 368 Plantation Street, Worcester, MA, 01605, USA.
| | - Andrei A Korostelev
- RNA Therapeutics Institute, UMass Chan Medical School, 368 Plantation Street, Worcester, MA, 01605, USA.
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5
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Abstract
Accurate protein synthesis (translation) relies on translation factors that rectify ribosome fluctuations into a unidirectional process. Understanding this process requires structural characterization of the ribosome and translation-factor dynamics. In the 2000s, crystallographic studies determined high-resolution structures of ribosomes stalled with translation factors, providing a starting point for visualizing translation. Recent progress in single-particle cryogenic electron microscopy (cryo-EM) has enabled near-atomic resolution of numerous structures sampled in heterogeneous complexes (ensembles). Ensemble and time-resolved cryo-EM have now revealed unprecedented views of ribosome transitions in the three principal stages of translation: initiation, elongation, and termination. This review focuses on how translation factors help achieve high accuracy and efficiency of translation by monitoring distinct ribosome conformations and by differentially shifting the equilibria of ribosome rearrangements for cognate and near-cognate substrates. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Andrei A Korostelev
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA;
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6
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Korostelev AA. Diversity and Similarity of Termination and Ribosome Rescue in Bacterial, Mitochondrial, and Cytoplasmic Translation. BIOCHEMISTRY (MOSCOW) 2021; 86:1107-1121. [PMID: 34565314 DOI: 10.1134/s0006297921090066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
When a ribosome encounters the stop codon of an mRNA, it terminates translation, releases the newly made protein, and is recycled to initiate translation on a new mRNA. Termination is a highly dynamic process in which release factors (RF1 and RF2 in bacteria; eRF1•eRF3•GTP in eukaryotes) coordinate peptide release with large-scale molecular rearrangements of the ribosome. Ribosomes stalled on aberrant mRNAs are rescued and recycled by diverse bacterial, mitochondrial, or cytoplasmic quality control mechanisms. These are catalyzed by rescue factors with peptidyl-tRNA hydrolase activity (bacterial ArfA•RF2 and ArfB, mitochondrial ICT1 and mtRF-R, and cytoplasmic Vms1), that are distinct from each other and from release factors. Nevertheless, recent structural studies demonstrate a remarkable similarity between translation termination and ribosome rescue mechanisms. This review describes how these pathways rely on inherent ribosome dynamics, emphasizing the active role of the ribosome in all translation steps.
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Affiliation(s)
- Andrei A Korostelev
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, MA, USA.
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7
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Powers KT, Stevenson-Jones F, Yadav SKN, Amthor B, Bufton JC, Borucu U, Shen D, Becker JP, Lavysh D, Hentze MW, Kulozik AE, Neu-Yilik G, Schaffitzel C. Blasticidin S inhibits mammalian translation and enhances production of protein encoded by nonsense mRNA. Nucleic Acids Res 2021; 49:7665-7679. [PMID: 34157102 PMCID: PMC8287960 DOI: 10.1093/nar/gkab532] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 05/16/2021] [Accepted: 06/08/2021] [Indexed: 12/14/2022] Open
Abstract
Deciphering translation is of paramount importance for the understanding of many diseases, and antibiotics played a pivotal role in this endeavour. Blasticidin S (BlaS) targets translation by binding to the peptidyl transferase center of the large ribosomal subunit. Using biochemical, structural and cellular approaches, we show here that BlaS inhibits both translation elongation and termination in Mammalia. Bound to mammalian terminating ribosomes, BlaS distorts the 3′CCA tail of the P-site tRNA to a larger extent than previously reported for bacterial ribosomes, thus delaying both, peptide bond formation and peptidyl-tRNA hydrolysis. While BlaS does not inhibit stop codon recognition by the eukaryotic release factor 1 (eRF1), it interferes with eRF1’s accommodation into the peptidyl transferase center and subsequent peptide release. In human cells, BlaS inhibits nonsense-mediated mRNA decay and, at subinhibitory concentrations, modulates translation dynamics at premature termination codons leading to enhanced protein production.
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Affiliation(s)
- Kyle T Powers
- University of Bristol, School of Biochemistry, University Walk, Bristol BS8 1TD, UK
| | | | - Sathish K N Yadav
- University of Bristol, School of Biochemistry, University Walk, Bristol BS8 1TD, UK
| | - Beate Amthor
- Department of Pediatric Oncology, Hematology and Immunology, Hopp Children's Cancer Research Center Heidelberg (KiTZ), University of Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU) European Molecular Biology Laboratory (EMBL) and University of Heidelberg, Heidelberg, Germany
| | - Joshua C Bufton
- University of Bristol, School of Biochemistry, University Walk, Bristol BS8 1TD, UK
| | - Ufuk Borucu
- University of Bristol, School of Biochemistry, University Walk, Bristol BS8 1TD, UK
| | - Dakang Shen
- University of Bristol, School of Biochemistry, University Walk, Bristol BS8 1TD, UK
| | - Jonas P Becker
- Department of Pediatric Oncology, Hematology and Immunology, Hopp Children's Cancer Research Center Heidelberg (KiTZ), University of Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU) European Molecular Biology Laboratory (EMBL) and University of Heidelberg, Heidelberg, Germany
| | - Daria Lavysh
- Department of Pediatric Oncology, Hematology and Immunology, Hopp Children's Cancer Research Center Heidelberg (KiTZ), University of Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU) European Molecular Biology Laboratory (EMBL) and University of Heidelberg, Heidelberg, Germany
| | - Matthias W Hentze
- Molecular Medicine Partnership Unit (MMPU) European Molecular Biology Laboratory (EMBL) and University of Heidelberg, Heidelberg, Germany.,European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Andreas E Kulozik
- Department of Pediatric Oncology, Hematology and Immunology, Hopp Children's Cancer Research Center Heidelberg (KiTZ), University of Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU) European Molecular Biology Laboratory (EMBL) and University of Heidelberg, Heidelberg, Germany
| | - Gabriele Neu-Yilik
- Department of Pediatric Oncology, Hematology and Immunology, Hopp Children's Cancer Research Center Heidelberg (KiTZ), University of Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit (MMPU) European Molecular Biology Laboratory (EMBL) and University of Heidelberg, Heidelberg, Germany
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8
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Demo G, Gamper HB, Loveland AB, Masuda I, Carbone CE, Svidritskiy E, Hou YM, Korostelev AA. Structural basis for +1 ribosomal frameshifting during EF-G-catalyzed translocation. Nat Commun 2021; 12:4644. [PMID: 34330903 PMCID: PMC8324841 DOI: 10.1038/s41467-021-24911-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 07/12/2021] [Indexed: 12/25/2022] Open
Abstract
Frameshifting of mRNA during translation provides a strategy to expand the coding repertoire of cells and viruses. How and where in the elongation cycle +1-frameshifting occurs remains poorly understood. We describe seven ~3.5-Å-resolution cryo-EM structures of 70S ribosome complexes, allowing visualization of elongation and translocation by the GTPase elongation factor G (EF-G). Four structures with a + 1-frameshifting-prone mRNA reveal that frameshifting takes place during translocation of tRNA and mRNA. Prior to EF-G binding, the pre-translocation complex features an in-frame tRNA-mRNA pairing in the A site. In the partially translocated structure with EF-G•GDPCP, the tRNA shifts to the +1-frame near the P site, rendering the freed mRNA base to bulge between the P and E sites and to stack on the 16S rRNA nucleotide G926. The ribosome remains frameshifted in the nearly post-translocation state. Our findings demonstrate that the ribosome and EF-G cooperate to induce +1 frameshifting during tRNA-mRNA translocation.
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MESH Headings
- Biocatalysis
- Cryoelectron Microscopy
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Escherichia coli Proteins/chemistry
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/metabolism
- Frameshifting, Ribosomal/genetics
- Models, Molecular
- Nucleic Acid Conformation
- Peptide Chain Elongation, Translational/genetics
- Peptide Elongation Factor G/chemistry
- Peptide Elongation Factor G/genetics
- Peptide Elongation Factor G/metabolism
- Protein Conformation
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Ribosomes/genetics
- Ribosomes/metabolism
- Ribosomes/ultrastructure
- tRNA Methyltransferases/genetics
- tRNA Methyltransferases/metabolism
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Affiliation(s)
- Gabriel Demo
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, MA, USA
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Howard B Gamper
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Anna B Loveland
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, MA, USA
| | - Isao Masuda
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Christine E Carbone
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, MA, USA
| | - Egor Svidritskiy
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, MA, USA
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA.
| | - Andrei A Korostelev
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, UMass Medical School, Worcester, MA, USA.
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9
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Parajuli NP, Mandava CS, Pavlov MY, Sanyal S. Mechanistic insights into translation inhibition by aminoglycoside antibiotic arbekacin. Nucleic Acids Res 2021; 49:6880-6892. [PMID: 34125898 PMCID: PMC8266624 DOI: 10.1093/nar/gkab495] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/17/2021] [Accepted: 05/26/2021] [Indexed: 11/13/2022] Open
Abstract
How aminoglycoside antibiotics limit bacterial growth and viability is not clearly understood. Here we employ fast kinetics to reveal the molecular mechanism of action of a clinically used, new-generation, semisynthetic aminoglycoside Arbekacin (ABK), which is designed to avoid enzyme-mediated deactivation common to other aminoglycosides. Our results portray complete picture of ABK inhibition of bacterial translation with precise quantitative characterizations. We find that ABK inhibits different steps of translation in nanomolar to micromolar concentrations by imparting pleotropic effects. ABK binding stalls elongating ribosomes to a state, which is unfavorable for EF-G binding. This prolongs individual translocation step from ∼50 ms to at least 2 s; the mean time of translocation increases inversely with EF-G concentration. ABK also inhibits translation termination by obstructing RF1/RF2 binding to the ribosome. Furthermore, ABK decreases accuracy of mRNA decoding (UUC vs. CUC) by ∼80 000 fold, causing aberrant protein production. Importantly, translocation and termination events cannot be completely stopped even with high ABK concentration. Extrapolating our kinetic model of ABK action, we postulate that aminoglycosides impose bacteriostatic effect mainly by inhibiting translocation, while they become bactericidal in combination with decoding errors.
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Affiliation(s)
- Narayan Prasad Parajuli
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, SE-75124 Uppsala, Sweden
| | - Chandra Sekhar Mandava
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, SE-75124 Uppsala, Sweden
| | - Michael Y Pavlov
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, SE-75124 Uppsala, Sweden
| | - Suparna Sanyal
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, SE-75124 Uppsala, Sweden
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10
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Pundir S, Ge X, Sanyal S. GGQ methylation enhances both speed and accuracy of stop codon recognition by bacterial class-I release factors. J Biol Chem 2021; 296:100681. [PMID: 33887323 PMCID: PMC8131318 DOI: 10.1016/j.jbc.2021.100681] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/13/2021] [Accepted: 04/16/2021] [Indexed: 10/28/2022] Open
Abstract
Accurate translation termination in bacteria requires correct recognition of the stop codons by the class-I release factors (RFs) RF1 and RF2, which release the nascent peptide from the peptidyl tRNA after undergoing a "compact to open" conformational transition. These RFs possess a conserved Gly-Gly-Gln (GGQ) peptide release motif, of which the Q residue is posttranslationally methylated. GGQ-methylated RFs have been shown to be faster in peptide release than the unmethylated ones, but it was unknown whether this modification had additional roles. Using a fluorescence-based real-time in vitro translation termination assay in a stopped-flow instrument, we demonstrate that methylated RF1 and RF2 are two- to four-fold more accurate in the cognate stop codon recognition than their unmethylated variants. Using pH titration, we show that the lack of GGQ methylation facilitates the "compact to open" transition, which results in compromised accuracy of the unmethylated RFs. Furthermore, thermal melting studies using circular dichroism and SYPRO-orange fluorescence demonstrate that GGQ methylation increases overall stability of the RF proteins. This increased stability, we suspect, is the basis for the more controlled conformational change of the methylated RFs upon codon recognition, which enhances both their speed and accuracy. This GGQ methylation-based modulation of the accuracy of RFs can be a tool for regulating translational termination in vivo.
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Affiliation(s)
- Shreya Pundir
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Xueliang Ge
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Suparna Sanyal
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden.
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11
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Kummer E, Schubert KN, Schoenhut T, Scaiola A, Ban N. Structural basis of translation termination, rescue, and recycling in mammalian mitochondria. Mol Cell 2021; 81:2566-2582.e6. [PMID: 33878294 DOI: 10.1016/j.molcel.2021.03.042] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/12/2021] [Accepted: 03/24/2021] [Indexed: 12/26/2022]
Abstract
The mitochondrial translation system originates from a bacterial ancestor but has substantially diverged in the course of evolution. Here, we use single-particle cryo-electron microscopy (cryo-EM) as a screening tool to identify mitochondrial translation termination mechanisms and to describe them in molecular detail. We show how mitochondrial release factor 1a releases the nascent chain from the ribosome when it encounters the canonical stop codons UAA and UAG. Furthermore, we define how the peptidyl-tRNA hydrolase ICT1 acts as a rescue factor on mitoribosomes that have stalled on truncated messages to recover them for protein synthesis. Finally, we present structural models detailing the process of mitochondrial ribosome recycling to explain how a dedicated elongation factor, mitochondrial EFG2 (mtEFG2), has specialized for cooperation with the mitochondrial ribosome recycling factor to dissociate the mitoribosomal subunits at the end of the translation process.
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Affiliation(s)
- Eva Kummer
- Swiss Federal Institute of Technology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, 8093 Zurich, Switzerland.
| | - Katharina Noel Schubert
- Swiss Federal Institute of Technology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, 8093 Zurich, Switzerland
| | - Tanja Schoenhut
- Swiss Federal Institute of Technology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, 8093 Zurich, Switzerland
| | - Alain Scaiola
- Swiss Federal Institute of Technology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, 8093 Zurich, Switzerland
| | - Nenad Ban
- Swiss Federal Institute of Technology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, 8093 Zurich, Switzerland.
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12
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Müller C, Crowe-McAuliffe C, Wilson DN. Ribosome Rescue Pathways in Bacteria. Front Microbiol 2021; 12:652980. [PMID: 33815344 PMCID: PMC8012679 DOI: 10.3389/fmicb.2021.652980] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 02/23/2021] [Indexed: 12/18/2022] Open
Abstract
Ribosomes that become stalled on truncated or damaged mRNAs during protein synthesis must be rescued for the cell to survive. Bacteria have evolved a diverse array of rescue pathways to remove the stalled ribosomes from the aberrant mRNA and return them to the free pool of actively translating ribosomes. In addition, some of these pathways target the damaged mRNA and the incomplete nascent polypeptide chain for degradation. This review highlights the recent developments in our mechanistic understanding of bacterial ribosomal rescue systems, including drop-off, trans-translation mediated by transfer-messenger RNA and small protein B, ribosome rescue by the alternative rescue factors ArfA and ArfB, as well as Bacillus ribosome rescue factor A, an additional rescue system found in some Gram-positive bacteria, such as Bacillus subtilis. Finally, we discuss the recent findings of ribosome-associated quality control in particular bacterial lineages mediated by RqcH and RqcP. The importance of rescue pathways for bacterial survival suggests they may represent novel targets for the development of new antimicrobial agents against multi-drug resistant pathogenic bacteria.
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Affiliation(s)
| | | | - Daniel N. Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
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13
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Kurita D, Abo T, Himeno H. Molecular determinants of release factor 2 for ArfA-mediated ribosome rescue. J Biol Chem 2020; 295:13326-13337. [PMID: 32727848 DOI: 10.1074/jbc.ra120.014664] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/27/2020] [Indexed: 02/01/2023] Open
Abstract
Translation termination in bacteria requires that the stop codon be recognized by release factor RF1 or RF2, leading to hydrolysis of the ester bond between the peptide and tRNA on the ribosome. As a consequence, normal termination cannot proceed if the translated mRNA lacks a stop codon. In Escherichia coli, the ribosome rescue factor ArfA releases the nascent polypeptide from the stalled ribosome with the help of RF2 in a stop codon-independent manner. Interestingly, the reaction does not proceed if RF1 is instead provided, even though the structures of RF1 and RF2 are very similar. Here, we identified the regions of RF2 required for the ArfA-dependent ribosome rescue system. Introduction of hydrophobic residues from RF2 found at the interface between RF2 and ArfA into RF1 allowed RF1 to associate with the ArfA-ribosome complex to a certain extent but failed to promote peptidyl-tRNA hydrolysis, whereas WT RF1 did not associate with the complex. We also identified the key residues required for the process after ribosome binding. Our findings provide a basis for understanding how the ArfA-ribosome complex is specifically recognized by RF2 and how RF2 undergoes a conformational change upon binding to the ArfA-ribosome complex.
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Affiliation(s)
- Daisuke Kurita
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Japan.
| | - Tatsuhiko Abo
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Hyouta Himeno
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Japan.
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14
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Loveland AB, Demo G, Korostelev AA. Cryo-EM of elongating ribosome with EF-Tu•GTP elucidates tRNA proofreading. Nature 2020; 584:640-645. [PMID: 32612237 PMCID: PMC7483604 DOI: 10.1038/s41586-020-2447-x] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 04/10/2020] [Indexed: 11/13/2022]
Abstract
Ribosomes accurately decode mRNA by proofreading each aminoacyl-tRNA delivered by elongation factor EF-Tu1. Understanding the molecular mechanism of proofreading requires visualizing GTP-catalyzed elongation, which has remained a challenge2–4. Here, time-resolved cryo-EM revealed 33 states following aminoacyl-tRNA delivery by EF-Tu•GTP. Instead of locking cognate tRNA upon initial recognition, the ribosomal decoding center (DC) dynamically monitors codon-anticodon interactions before and after GTP hydrolysis. GTP hydrolysis allows EF-Tu’s GTPase domain to extend away, releasing EF-Tu from tRNA. Then, the 30S subunit locks cognate tRNA in the DC, and rotates, enabling the tRNA to bypass 50S protrusions during accommodation into the peptidyl transferase center. By contrast, the DC fails to lock near-cognate tRNA, allowing dissociation of near-cognate tRNA during both initial selection (before GTP hydrolysis) and proofreading (after GTP hydrolysis). These findings reveal structural similarity between initial selection5,6 and the previously unseen proofreading, which together govern efficient rejection of incorrect tRNA.
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Affiliation(s)
- Anna B Loveland
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Gabriel Demo
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.,Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Andrei A Korostelev
- RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.
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15
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Emmanuel JS, Sengupta A, Gordon ER, Noble JT, Cruz-Vera LR. The regulatory TnaC nascent peptide preferentially inhibits release factor 2-mediated hydrolysis of peptidyl-tRNA. J Biol Chem 2019; 294:19224-19235. [PMID: 31712310 DOI: 10.1074/jbc.ra119.011313] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/01/2019] [Indexed: 01/29/2023] Open
Abstract
The tnaC regulatory gene from the tna operon of Escherichia coli controls the transcription of its own operon through an attenuation mechanism relying on the accumulation of arrested ribosomes during inhibition of its own translation termination. This free l-Trp-dependent mechanism of inhibition of translation termination remains unclear. Here, we analyzed the inhibitory effects of l-Trp on the function of two known E. coli translation termination factors, RF1 and RF2. Using a series of reporter genes, we found that the in vivo l-Trp sensitivity of tnaC gene expression is influenced by the identity of its stop codon, with the UGA stop codon producing higher expression efficiency of the tnaA-lacZ gene construct than the UAG stop codon. In vitro TnaC-peptidyl-tRNA accumulation and toe-printing assays confirmed that in the presence of l-Trp, the UGA stop codon generates higher accumulation of both TnaC-peptidyl-tRNA and arrested ribosomes than does the UAG stop codon. RF-mediated hydrolysis assays corroborated that l-Trp blocks RF2 function more than that of RF1. Mutational analyses disclosed that amino acids substitutions at the 246 and 256 residue positions surrounding the RF2-GGQ functional motif reduce l-Trp-dependent expression of the tnaC(UGA) tnaA-lacZ construct and the ability of l-Trp to inhibit RF2-mediated cleavage of the TnaC-peptidyl-tRNA. Altogether, our results indicate that l-Trp preferentially blocks RF2 activity during translation termination of the tnaC gene. This inhibition depends on the identities of amino acid residues surrounding the RF2-GGQ functional motif.
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Affiliation(s)
| | - Arnab Sengupta
- University of Alabama in Huntsville, Huntsville, Alabama 35899
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16
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Svidritskiy E, Demo G, Loveland AB, Xu C, Korostelev AA. Extensive ribosome and RF2 rearrangements during translation termination. eLife 2019; 8:46850. [PMID: 31513010 PMCID: PMC6742477 DOI: 10.7554/elife.46850] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 08/28/2019] [Indexed: 12/31/2022] Open
Abstract
Protein synthesis ends when a ribosome reaches an mRNA stop codon. Release factors (RFs) decode the stop codon, hydrolyze peptidyl-tRNA to release the nascent protein, and then dissociate to allow ribosome recycling. To visualize termination by RF2, we resolved a cryo-EM ensemble of E. coli 70S•RF2 structures at up to 3.3 Å in a single sample. Five structures suggest a highly dynamic termination pathway. Upon peptidyl-tRNA hydrolysis, the CCA end of deacyl-tRNA departs from the peptidyl transferase center. The catalytic GGQ loop of RF2 is rearranged into a long β-hairpin that plugs the peptide tunnel, biasing a nascent protein toward the ribosome exit. Ribosomal intersubunit rotation destabilizes the catalytic RF2 domain on the 50S subunit and disassembles the central intersubunit bridge B2a, resulting in RF2 departure. Our structures visualize how local rearrangements and spontaneous inter-subunit rotation poise the newly-made protein and RF2 to dissociate in preparation for ribosome recycling.
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Affiliation(s)
- Egor Svidritskiy
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States
| | - Gabriel Demo
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States
| | - Anna B Loveland
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States
| | - Chen Xu
- Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Andrei A Korostelev
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States.,Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
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17
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The structural basis for release-factor activation during translation termination revealed by time-resolved cryogenic electron microscopy. Nat Commun 2019; 10:2579. [PMID: 31189921 PMCID: PMC6561943 DOI: 10.1038/s41467-019-10608-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 05/14/2019] [Indexed: 11/08/2022] Open
Abstract
When the ribosome encounters a stop codon, it recruits a release factor (RF) to hydrolyze the ester bond between the peptide chain and tRNA. RFs have structural motifs that recognize stop codons in the decoding center and a GGQ motif for induction of hydrolysis in the peptidyl transfer center 70 Å away. Surprisingly, free RF2 is compact, with only 20 Å between its codon-reading and GGQ motifs. Cryo-EM showed that ribosome-bound RFs have extended structures, suggesting that RFs are compact when entering the ribosome and then extend their structures upon stop codon recognition. Here we use time-resolved cryo-EM to visualize transient compact forms of RF1 and RF2 at 3.5 and 4 Å resolution, respectively, in the codon-recognizing ribosome complex on the native pathway. About 25% of complexes have RFs in the compact state at 24 ms reaction time, and within 60 ms virtually all ribosome-bound RFs are transformed to their extended forms. Translation termination is under strong selection pressure for high speed and accuracy. Here the authors provide a 3D view of the dynamics of a translating bacterial ribosome as it recruits a class-1 release factor (RF1 or RF2) upon encountering a stop codon, and propose a structure-based kinetic model for the early steps in bacterial translation termination.
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18
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Abstract
Ribosomes are biological nanomachine that synthesise all proteins within a cell. It took decades to reveal the architecture of this essential cellular component. To understand the structure -function relationship of this nanomachine needed the utilisisation of different biochemical, biophysical and structural techniques. Structural studies combined with mutagenesis of the different ribosomal complexes comprising various RNAs and proteins enabled us to understand how this machine works inside a cell. Nowadays quite a number of ribosomal structures were published that confirmed biochemical studies on particular steps of protein synthesis by the ribosome . Four major steps were identified: initiation , elongation, termination and recycling. These steps lead us to the important question how the ribosome function can be regulated. Advances in technology for cryo electron microscopy: sample preparations, image recording, developments in algorithms for image analysis and processing significantly helped in revelation of structural details of the ribosome . We now have a library of ribosome structures from prokaryotes to eukaryotes that enable us to understand the complex mechanics of this nanomachine. As this structural library continues to grow, we gradually improve our understanding of this process and how it can be regulated and how the specific ribosomes can be stalled or activated, or completely disabled. This article provides a comprehensive overview of ribosomal structures that represent structural snapshots of the ribosome at its different functional states. Better understanding rises more particular questions that have to be addressed by determination structures of more complexes.Synopsis: Structural biology of the ribosome.
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Affiliation(s)
- Abid Javed
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, Malet Street, London, WC1E 7HX, UK
| | - Elena V Orlova
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, Malet Street, London, WC1E 7HX, UK.
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19
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Control of mRNA Translation by Versatile ATP-Driven Machines. Trends Biochem Sci 2018; 44:167-180. [PMID: 30527974 DOI: 10.1016/j.tibs.2018.11.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 10/29/2018] [Accepted: 11/01/2018] [Indexed: 12/13/2022]
Abstract
Translation is organized in a cycle that requires ribosomal subunits, mRNA, aminoacylated transfer RNAs, and myriad regulatory factors. As soon as translation reaches a stop codon or stall, a termination or surveillance process is launched via the release factors eRF1 or Pelota, respectively. The ATP-binding cassette (ABC) protein ABCE1 interacts with release factors and coordinates the recycling process in Eukarya and Archaea. After splitting, ABCE1 stays with the small ribosomal subunit and emerges as an integral part of translation initiation complexes. In addition, eEF3 and ABCF proteins control translation by binding at the E-site. In this review, we highlight advances in the fundamental role of ABC systems in mRNA translation in view of their collective inner mechanics.
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Svidritskiy E, Demo G, Korostelev AA. Mechanism of premature translation termination on a sense codon. J Biol Chem 2018; 293:12472-12479. [PMID: 29941456 DOI: 10.1074/jbc.aw118.003232] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Accurate translation termination by release factors (RFs) is critical for the integrity of cellular proteomes. Premature termination on sense codons, for example, results in truncated proteins, whose accumulation could be detrimental to the cell. Nevertheless, some sense codons are prone to triggering premature termination, but the structural basis for this is unclear. To investigate premature termination, we determined a cryo-EM structure of the Escherichia coli 70S ribosome bound with RF1 in response to a UAU (Tyr) sense codon. The structure reveals that RF1 recognizes a UAU codon similarly to a UAG stop codon, suggesting that sense codons induce premature termination because they structurally mimic a stop codon. Hydrophobic interaction between the nucleobase of U3 (the third position of the UAU codon) and conserved Ile-196 in RF1 is important for misreading the UAU codon. Analyses of RNA binding in ribonucleoprotein complexes or by amino acids reveal that Ile-U packing is a frequent protein-RNA-binding motif with key functional implications. We discuss parallels with eukaryotic translation termination by the release factor eRF1.
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Affiliation(s)
- Egor Svidritskiy
- From the RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Gabriel Demo
- From the RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Andrei A Korostelev
- From the RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605
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