1
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Guo W, Russo S, Tuorto F. Lost in translation: How neurons cope with tRNA decoding. Bioessays 2024; 46:e2400107. [PMID: 38990077 DOI: 10.1002/bies.202400107] [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: 04/30/2024] [Revised: 06/20/2024] [Accepted: 06/24/2024] [Indexed: 07/12/2024]
Abstract
Post-transcriptional tRNA modifications contribute to the decoding efficiency of tRNAs by supporting codon recognition and tRNA stability. Recent work shows that the molecular and cellular functions of tRNA modifications and tRNA-modifying-enzymes are linked to brain development and neurological disorders. Lack of these modifications affects codon recognition and decoding rate, promoting protein aggregation and translational stress response pathways with toxic consequences to the cell. In this review, we discuss the peculiarity of local translation in neurons, suggesting a role for fine-tuning of translation performed by tRNA modifications. We provide several examples of tRNA modifications involved in physiology and pathology of the nervous system, highlighting their effects on protein translation and discussing underlying mechanisms, like the unfolded protein response (UPR), ribosome quality control (RQC), and no-go mRNA decay (NGD), which could affect neuronal functions. We aim to deepen the understanding of the roles of tRNA modifications and the coordination of these modifications with the protein translation machinery in the nervous system.
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Affiliation(s)
- Wei Guo
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Mannheim Cancer Center (MCC), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Stefano Russo
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Mannheim Cancer Center (MCC), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Francesca Tuorto
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Mannheim Cancer Center (MCC), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
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2
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Ennis A, Wang L, Wang X, Yu C, Saidi L, Xu Y, Yun S, Huang L, Ye Y. NEMF-mediated CAT-tailing defines distinct branches of translocation-associated quality control. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.27.610005. [PMID: 39253483 PMCID: PMC11383284 DOI: 10.1101/2024.08.27.610005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Ribosome stalling during co-translational translocation at the endoplasmic reticulum (ER) causes translocon clogging and impairs ER protein biogenesis. Mammalian cells resolve translocon clogging vial a poorly characterized translocation-associated quality control (TAQC) process. Here, we combine genome-wide CRISPR screen with live cell imaging to dissect the molecular linchpin of TAQC. We show that substrates translated from mRNAs bearing a ribosome stalling poly(A) sequence are degraded by lysosomes and the proteasome, while substrates encoded by non-stop mRNAs are degraded by an unconventional ER-associated degradation (ERAD) mechanism involving ER-to-Golgi trafficking and KDEL-dependent substrate retrieval. The triaging diversity appears to result from the heterogeneity of NEMF-mediated CATylation, because a systematic characterization of representative CAT-tail mimetics establishes an AT-rich tail as a "degron" for ERAD, whereas an AG-rich tail can direct a secretory protein to the lysosome. Our study reveals an unexpected protein sorting function for CAT-tailing that safeguards ER protein biogenesis.
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Affiliation(s)
- Amanda Ennis
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lihui Wang
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- Current affiliation: Innovent USA, 319 N Bernardo Avenue, Mountain View, CA, 94043
| | - Xiaorong Wang
- Department of Physiology and Biophysics, University of California Irvine, Irvine, CA 92687, USA
| | - Clinton Yu
- Department of Physiology and Biophysics, University of California Irvine, Irvine, CA 92687, USA
| | - Layla Saidi
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yue Xu
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sijung Yun
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- Current affiliation: Yottabiomed, LLC. 8908 Ewing Dr., Bethesda, MD 20817
| | - Lan Huang
- Department of Physiology and Biophysics, University of California Irvine, Irvine, CA 92687, USA
| | - Yihong Ye
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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3
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Chen KY, Park H, Subramaniam AR. Massively parallel identification of sequence motifs triggering ribosome-associated mRNA quality control. Nucleic Acids Res 2024; 52:7171-7187. [PMID: 38647082 PMCID: PMC11229359 DOI: 10.1093/nar/gkae285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 02/28/2024] [Accepted: 04/04/2024] [Indexed: 04/25/2024] Open
Abstract
Decay of mRNAs can be triggered by ribosome slowdown at stretches of rare codons or positively charged amino acids. However, the full diversity of sequences that trigger co-translational mRNA decay is poorly understood. To comprehensively identify sequence motifs that trigger mRNA decay, we use a massively parallel reporter assay to measure the effect of all possible combinations of codon pairs on mRNA levels in S. cerevisiae. In addition to known mRNA-destabilizing sequences, we identify several dipeptide repeats whose translation reduces mRNA levels. These include combinations of positively charged and bulky residues, as well as proline-glycine and proline-aspartate dipeptide repeats. Genetic deletion of the ribosome collision sensor Hel2 rescues the mRNA effects of these motifs, suggesting that they trigger ribosome slowdown and activate the ribosome-associated quality control (RQC) pathway. Deep mutational scanning of an mRNA-destabilizing dipeptide repeat reveals a complex interplay between the charge, bulkiness, and location of amino acid residues in conferring mRNA instability. Finally, we show that the mRNA effects of codon pairs are predictive of the effects of endogenous sequences. Our work highlights the complexity of sequence motifs driving co-translational mRNA decay in eukaryotes, and presents a high throughput approach to dissect their requirements at the codon level.
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Affiliation(s)
- Katharine Y Chen
- Basic Sciences Division and Computational Biology Section of the Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Heungwon Park
- Basic Sciences Division and Computational Biology Section of the Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Arvind Rasi Subramaniam
- Basic Sciences Division and Computational Biology Section of the Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
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4
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Tseng YJ, Krans A, Malik I, Deng X, Yildirim E, Ovunc S, Tank EH, Jansen-West K, Kaufhold R, Gomez N, Sher R, Petrucelli L, Barmada S, Todd P. Ribosomal quality control factors inhibit repeat-associated non-AUG translation from GC-rich repeats. Nucleic Acids Res 2024; 52:5928-5949. [PMID: 38412259 PMCID: PMC11162809 DOI: 10.1093/nar/gkae137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 02/05/2024] [Accepted: 02/19/2024] [Indexed: 02/29/2024] Open
Abstract
A GGGGCC (G4C2) hexanucleotide repeat expansion in C9ORF72 causes amyotrophic lateral sclerosis and frontotemporal dementia (C9ALS/FTD), while a CGG trinucleotide repeat expansion in FMR1 leads to the neurodegenerative disorder Fragile X-associated tremor/ataxia syndrome (FXTAS). These GC-rich repeats form RNA secondary structures that support repeat-associated non-AUG (RAN) translation of toxic proteins that contribute to disease pathogenesis. Here we assessed whether these same repeats might trigger stalling and interfere with translational elongation. We find that depletion of ribosome-associated quality control (RQC) factors NEMF, LTN1 and ANKZF1 markedly boost RAN translation product accumulation from both G4C2 and CGG repeats while overexpression of these factors reduces RAN production in both reporter assays and C9ALS/FTD patient iPSC-derived neurons. We also detected partially made products from both G4C2 and CGG repeats whose abundance increased with RQC factor depletion. Repeat RNA sequence, rather than amino acid content, is central to the impact of RQC factor depletion on RAN translation-suggesting a role for RNA secondary structure in these processes. Together, these findings suggest that ribosomal stalling and RQC pathway activation during RAN translation inhibits the generation of toxic RAN products. We propose augmenting RQC activity as a therapeutic strategy in GC-rich repeat expansion disorders.
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Affiliation(s)
- Yi-Ju Tseng
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Amy Krans
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
- Ann Arbor Veterans Administration Healthcare, Ann Arbor, MI 48109, USA
| | - Indranil Malik
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, 502284 Telangana, India
| | - Xiexiong Deng
- Department of Molecular, Cellular and Developmental Biology, Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Evrim Yildirim
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sinem Ovunc
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Elizabeth M H Tank
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Karen Jansen-West
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Ross Kaufhold
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
- Medical Scientist Training Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nicolas B Gomez
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
- Medical Scientist Training Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Roger Sher
- Department of Neurobiology and Behavior & Center for Nervous System Disorders, Stony Brook University, Stony Brook, NY 11794, USA
| | | | - Sami J Barmada
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter K Todd
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
- Ann Arbor Veterans Administration Healthcare, Ann Arbor, MI 48109, USA
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5
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Inada T, Beckmann R. Mechanisms of Translation-coupled Quality Control. J Mol Biol 2024; 436:168496. [PMID: 38365086 DOI: 10.1016/j.jmb.2024.168496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/05/2024] [Accepted: 02/12/2024] [Indexed: 02/18/2024]
Abstract
Stalling of ribosomes engaged in protein synthesis can lead to significant defects in the function of newly synthesized proteins and thereby impair protein homeostasis. Consequently, partially synthesized polypeptides resulting from translation stalling are recognized and eliminated by several quality control mechanisms. First, if translation elongation reactions are halted prematurely, a quality control mechanism called ribosome-associated quality control (RQC) initiates the ubiquitination of the nascent polypeptide chain and subsequent proteasomal degradation. Additionally, when ribosomes with defective codon recognition or peptide-bond formation stall during translation, a quality control mechanism known as non-functional ribosomal RNA decay (NRD) leads to the degradation of malfunctioning ribosomes. In both of these quality control mechanisms, E3 ubiquitin ligases selectively recognize ribosomes in distinct translation-stalling states and ubiquitinate specific ribosomal proteins. Significant efforts have been devoted to characterize E3 ubiquitin ligase sensing of ribosome 'collision' or 'stalling' and subsequent ribosome is rescued. This article provides an overview of our current understanding of the molecular mechanisms and physiological functions of ribosome dynamics control and quality control of abnormal translation.
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Affiliation(s)
- Toshifumi Inada
- Division of RNA and Gene Regulation, Institute of Medical Science, The University of Tokyo, Minato-Ku, Tokyo 108-8639, Japan.
| | - Roland Beckmann
- Gene Center and Department of Biochemistry, Feodor-Lynen-Str. 25, University of Munich, 81377 Munich, Germany.
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6
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Chen KY, Park H, Subramaniam AR. Massively parallel identification of sequence motifs triggering ribosome-associated mRNA quality control. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.27.559793. [PMID: 37808677 PMCID: PMC10557687 DOI: 10.1101/2023.09.27.559793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Decay of mRNAs can be triggered by ribosome slowdown at stretches of rare codons or positively charged amino acids. However, the full diversity of sequences that trigger co-translational mRNA decay is poorly understood. To comprehensively identify sequence motifs that trigger mRNA decay, we use a massively parallel reporter assay to measure the effect of all possible combinations of codon pairs on mRNA levels in S. cerevisiae. In addition to known mRNA-destabilizing sequences, we identify several dipeptide repeats whose translation reduces mRNA levels. These include combinations of positively charged and bulky residues, as well as proline-glycine and proline-aspartate dipeptide repeats. Genetic deletion of the ribosome collision sensor Hel2 rescues the mRNA effects of these motifs, suggesting that they trigger ribosome slowdown and activate the ribosome-associated quality control (RQC) pathway. Deep mutational scanning of an mRNA-destabilizing dipeptide repeat reveals a complex interplay between the charge, bulkiness, and location of amino acid residues in conferring mRNA instability. Finally, we show that the mRNA effects of codon pairs are predictive of the effects of endogenous sequences. Our work highlights the complexity of sequence motifs driving co-translational mRNA decay in eukaryotes, and presents a high throughput approach to dissect their requirements at the codon level.
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Affiliation(s)
- Katharine Y. Chen
- Basic Sciences Division and Computational Biology Section of the Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Heungwon Park
- Basic Sciences Division and Computational Biology Section of the Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Arvind Rasi Subramaniam
- Basic Sciences Division and Computational Biology Section of the Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
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7
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Tseng YJ, Malik I, Deng X, Krans A, Jansen-West K, Tank EM, Gomez NB, Sher R, Petrucelli L, Barmada SJ, Todd PK. Ribosomal quality control factors inhibit repeat-associated non-AUG translation from GC-rich repeats. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.07.544135. [PMID: 37333274 PMCID: PMC10274811 DOI: 10.1101/2023.06.07.544135] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
A GGGGCC (G4C2) hexanucleotide repeat expansion in C9ORF72 causes amyotrophic lateral sclerosis and frontotemporal dementia (C9ALS/FTD), while a CGG trinucleotide repeat expansion in FMR1 leads to the neurodegenerative disorder Fragile X-associated tremor/ataxia syndrome (FXTAS). These GC-rich repeats form RNA secondary structures that support repeat-associated non-AUG (RAN) translation of toxic proteins that contribute to disease pathogenesis. Here we assessed whether these same repeats might trigger stalling and interfere with translational elongation. We find that depletion of ribosome-associated quality control (RQC) factors NEMF, LTN1, and ANKZF1 markedly boost RAN translation product accumulation from both G4C2 and CGG repeats while overexpression of these factors reduces RAN production in both reporter cell lines and C9ALS/FTD patient iPSC-derived neurons. We also detected partially made products from both G4C2 and CGG repeats whose abundance increased with RQC factor depletion. Repeat RNA sequence, rather than amino acid content, is central to the impact of RQC factor depletion on RAN translation - suggesting a role for RNA secondary structure in these processes. Together, these findings suggest that ribosomal stalling and RQC pathway activation during RAN translation elongation inhibits the generation of toxic RAN products. We propose augmenting RQC activity as a therapeutic strategy in GC-rich repeat expansion disorders.
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Affiliation(s)
- Yi-Ju Tseng
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Indranil Malik
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Xiexiong Deng
- Department of Molecular, Cellular and Developmental Biology, Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Amy Krans
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109, USA
- Ann Arbor Veterans Administration Healthcare, Ann Arbor, MI, 48109, USA
| | - Karen Jansen-West
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | | | - Nicolas B. Gomez
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, MI, 48109, USA
- Medical Scientist Training Program, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Roger Sher
- Department of Neurobiology and Behavior & Center for Nervous System Disorders, Stony Brook University, Stony Brook, NY, 11794, USA
| | | | - Sami J. Barmada
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Peter K. Todd
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109, USA
- Ann Arbor Veterans Administration Healthcare, Ann Arbor, MI, 48109, USA
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8
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Tesina P, Ebine S, Buschauer R, Thoms M, Matsuo Y, Inada T, Beckmann R. Molecular basis of eIF5A-dependent CAT tailing in eukaryotic ribosome-associated quality control. Mol Cell 2023; 83:607-621.e4. [PMID: 36804914 DOI: 10.1016/j.molcel.2023.01.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/29/2022] [Accepted: 01/23/2023] [Indexed: 02/18/2023]
Abstract
Ribosome-associated quality control (RQC) is a conserved process degrading potentially toxic truncated nascent peptides whose malfunction underlies neurodegeneration and proteostasis decline in aging. During RQC, dissociation of stalled ribosomes is followed by elongation of the nascent peptide with alanine and threonine residues, driven by Rqc2 independently of mRNA, the small ribosomal subunit and guanosine triphosphate (GTP)-hydrolyzing factors. The resulting CAT tails (carboxy-terminal tails) and ubiquitination by Ltn1 mark nascent peptides for proteasomal degradation. Here we present ten cryogenic electron microscopy (cryo-EM) structures, revealing the mechanistic basis of individual steps of the CAT tailing cycle covering initiation, decoding, peptidyl transfer, and tRNA translocation. We discovered eIF5A as a crucial eukaryotic RQC factor enabling peptidyl transfer. Moreover, we observed dynamic behavior of RQC factors and tRNAs allowing for processivity of the CAT tailing cycle without additional energy input. Together, these results elucidate key differences as well as common principles between CAT tailing and canonical translation.
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Affiliation(s)
- Petr Tesina
- Gene Center and Department of Biochemistry, Feodor-Lynen-Str. 25, University of Munich, 81377 Munich, Germany.
| | - Shuhei Ebine
- Division of RNA and gene regulation, Institute of Medical Science, The University of Tokyo, Minato-Ku 108-8639, Japan
| | - Robert Buschauer
- Gene Center and Department of Biochemistry, Feodor-Lynen-Str. 25, University of Munich, 81377 Munich, Germany
| | - Matthias Thoms
- Gene Center and Department of Biochemistry, Feodor-Lynen-Str. 25, University of Munich, 81377 Munich, Germany
| | - Yoshitaka Matsuo
- Division of RNA and gene regulation, Institute of Medical Science, The University of Tokyo, Minato-Ku 108-8639, Japan
| | - Toshifumi Inada
- Division of RNA and gene regulation, Institute of Medical Science, The University of Tokyo, Minato-Ku 108-8639, Japan.
| | - Roland Beckmann
- Gene Center and Department of Biochemistry, Feodor-Lynen-Str. 25, University of Munich, 81377 Munich, Germany.
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9
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Tomomatsu S, Watanabe A, Tesina P, Hashimoto S, Ikeuchi K, Li S, Matsuo Y, Beckmann R, Inada T. Two modes of Cue2-mediated mRNA cleavage with distinct substrate recognition initiate no-go decay. Nucleic Acids Res 2023; 51:253-270. [PMID: 36583309 PMCID: PMC9841427 DOI: 10.1093/nar/gkac1172] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/17/2022] [Accepted: 11/25/2022] [Indexed: 12/31/2022] Open
Abstract
Ribosome collisions are recognized by E3 ubiquitin ligase Hel2/ZNF598, leading to RQC (ribosome-associated quality control) and to endonucleolytic cleavage and degradation of the mRNA termed NGD (no-go decay). NGD in yeast requires the Cue2 endonuclease and occurs in two modes, either coupled to RQC (NGDRQC+) or RQC uncoupled (NGDRQC-). This is mediated by an unknown mechanism of substrate recognition by Cue2. Here, we show that the ubiquitin binding activity of Cue2 is required for NGDRQC- but not for NGDRQC+, and that it involves the first two N-terminal Cue domains. In contrast, Trp122 of Cue2 is crucial for NGDRQC+. Moreover, Mbf1 is required for quality controls by preventing +1 ribosome frameshifting induced by a rare codon staller. We propose that in Cue2-dependent cleavage upstream of the collided ribosomes (NGDRQC-), polyubiquitination of eS7 is recognized by two N-terminal Cue domains of Cue2. In contrast, for the cleavage within collided ribosomes (NGDRQC+), the UBA domain, Trp122 and the interaction between Mbf1 and uS3 are critical.
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Affiliation(s)
- Shota Tomomatsu
- Division of RNA and Gene Regulation, Institute of Medical Science, The University of Tokyo, Minato-Ku 108-8639, Japan
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-Ku, Tokyo, Japan
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Atsuya Watanabe
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Petr Tesina
- Gene Center and Department of Biochemistry, Feodor-Lynen-Strasse 25, University of Munich, D-81377 Munich, Germany
| | - Satoshi Hashimoto
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Ken Ikeuchi
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
- Gene Center and Department of Biochemistry, Feodor-Lynen-Strasse 25, University of Munich, D-81377 Munich, Germany
| | - Sihan Li
- Division of RNA and Gene Regulation, Institute of Medical Science, The University of Tokyo, Minato-Ku 108-8639, Japan
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Yoshitaka Matsuo
- Division of RNA and Gene Regulation, Institute of Medical Science, The University of Tokyo, Minato-Ku 108-8639, Japan
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Roland Beckmann
- Gene Center and Department of Biochemistry, Feodor-Lynen-Strasse 25, University of Munich, D-81377 Munich, Germany
| | - Toshifumi Inada
- Division of RNA and Gene Regulation, Institute of Medical Science, The University of Tokyo, Minato-Ku 108-8639, Japan
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
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10
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Burke PC, Park H, Subramaniam AR. A nascent peptide code for translational control of mRNA stability in human cells. Nat Commun 2022; 13:6829. [PMID: 36369503 PMCID: PMC9652226 DOI: 10.1038/s41467-022-34664-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 11/02/2022] [Indexed: 11/13/2022] Open
Abstract
Stability of eukaryotic mRNAs is associated with their codon, amino acid, and GC content. Yet, coding sequence motifs that predictably alter mRNA stability in human cells remain poorly defined. Here, we develop a massively parallel assay to measure mRNA effects of thousands of synthetic and endogenous coding sequence motifs in human cells. We identify several families of simple dipeptide repeats whose translation triggers mRNA destabilization. Rather than individual amino acids, specific combinations of bulky and positively charged amino acids are critical for the destabilizing effects of dipeptide repeats. Remarkably, dipeptide sequences that form extended β strands in silico and in vitro slowdown ribosomes and reduce mRNA levels in vivo. The resulting nascent peptide code underlies the mRNA effects of hundreds of endogenous peptide sequences in the human proteome. Our work suggests an intrinsic role for the ribosome as a selectivity filter against the synthesis of bulky and aggregation-prone peptides.
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Affiliation(s)
- Phillip C Burke
- Basic Sciences Division and Computational Biology Section of the Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
- Department of Microbiology, University of Washington, Seattle, WA, 98195, USA
| | - Heungwon Park
- Basic Sciences Division and Computational Biology Section of the Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Arvind Rasi Subramaniam
- Basic Sciences Division and Computational Biology Section of the Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA.
- Department of Microbiology, University of Washington, Seattle, WA, 98195, USA.
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11
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Zheng AJL, Thermou A, Daskalogianni C, Malbert-Colas L, Karakostis K, Le Sénéchal R, Trang Dinh V, Tovar Fernandez MC, Apcher S, Chen S, Blondel M, Fahraeus R. The nascent polypeptide-associated complex (NAC) controls translation initiation in cis by recruiting nucleolin to the encoding mRNA. Nucleic Acids Res 2022; 50:10110-10122. [PMID: 36107769 PMCID: PMC9508830 DOI: 10.1093/nar/gkac751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/10/2022] [Indexed: 11/20/2022] Open
Abstract
Protein aggregates and abnormal proteins are toxic and associated with neurodegenerative diseases. There are several mechanisms to help cells get rid of aggregates but little is known on how cells prevent aggregate-prone proteins from being synthesised. The EBNA1 of the Epstein-Barr virus (EBV) evades the immune system by suppressing its own mRNA translation initiation in order to minimize the production of antigenic peptides for the major histocompatibility (MHC) class I pathway. Here we show that the emerging peptide of the disordered glycine–alanine repeat (GAr) within EBNA1 dislodges the nascent polypeptide-associated complex (NAC) from the ribosome. This results in the recruitment of nucleolin to the GAr-encoding mRNA and suppression of mRNA translation initiation in cis. Suppressing NAC alpha (NACA) expression prevents nucleolin from binding to the GAr mRNA and overcomes GAr-mediated translation inhibition. Taken together, these observations suggest that EBNA1 exploits a nascent protein quality control pathway to regulate its own rate of synthesis that is based on sensing the nascent GAr peptide by NAC followed by the recruitment of nucleolin to the GAr-encoding RNA sequence.
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Affiliation(s)
- Alice J L Zheng
- Inserm UMRS 1131, Institut de Génétique Moléculaire, Université de Paris, Hôpital St. Louis , F-75010 Paris , France
| | - Aikaterini Thermou
- Inserm UMRS 1131, Institut de Génétique Moléculaire, Université de Paris, Hôpital St. Louis , F-75010 Paris , France
- ICCVS, University of Gdańsk , Science, ul. Wita Stwosza 63 , 80-308 Gdańsk , Poland
| | - Chrysoula Daskalogianni
- Inserm UMRS 1131, Institut de Génétique Moléculaire, Université de Paris, Hôpital St. Louis , F-75010 Paris , France
- ICCVS, University of Gdańsk , Science, ul. Wita Stwosza 63 , 80-308 Gdańsk , Poland
| | - Laurence Malbert-Colas
- Inserm UMRS 1131, Institut de Génétique Moléculaire, Université de Paris, Hôpital St. Louis , F-75010 Paris , France
| | - Konstantinos Karakostis
- Inserm UMRS 1131, Institut de Génétique Moléculaire, Université de Paris, Hôpital St. Louis , F-75010 Paris , France
| | - Ronan Le Sénéchal
- Inserm UMR 1078, Université de Bretagne Occidentale (UBO), Etablissement Français du Sang (EFS) Bretagne, CHRU Brest , 29200 , Brest , France
| | - Van Trang Dinh
- Inserm UMR 1078, Université de Bretagne Occidentale (UBO), Etablissement Français du Sang (EFS) Bretagne, CHRU Brest , 29200 , Brest , France
| | - Maria C Tovar Fernandez
- Inserm UMRS 1131, Institut de Génétique Moléculaire, Université de Paris, Hôpital St. Louis , F-75010 Paris , France
- ICCVS, University of Gdańsk , Science, ul. Wita Stwosza 63 , 80-308 Gdańsk , Poland
| | - Sébastien Apcher
- Institut Gustave Roussy, Université Paris Sud, Unité 1015 département d’immunologie , 114, rue Edouard Vaillant , 94805 Villejuif , France
| | - Sa Chen
- Department of Medical Biosciences, Building 6M, Umeå University , 901 85 Umeå , Sweden
| | - Marc Blondel
- Inserm UMR 1078, Université de Bretagne Occidentale (UBO), Etablissement Français du Sang (EFS) Bretagne, CHRU Brest , 29200 , Brest , France
| | - Robin Fahraeus
- Inserm UMRS 1131, Institut de Génétique Moléculaire, Université de Paris, Hôpital St. Louis , F-75010 Paris , France
- Department of Medical Biosciences, Building 6M, Umeå University , 901 85 Umeå , Sweden
- RECAMO, Masaryk Memorial Cancer Institute , Zluty kopec 7 , 65653 Brno , Czech Republic
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Mishima Y, Han P, Ishibashi K, Kimura S, Iwasaki S. Ribosome slowdown triggers codon-mediated mRNA decay independently of ribosome quality control. EMBO J 2022; 41:e109256. [PMID: 35040509 PMCID: PMC8886528 DOI: 10.15252/embj.2021109256] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 12/06/2021] [Accepted: 12/09/2021] [Indexed: 12/11/2022] Open
Abstract
The control of mRNA stability plays a central role in regulating gene expression patterns. Recent studies have revealed that codon composition in the open reading frame determines mRNA stability in multiple organisms. Based on genome-wide correlation approaches, this previously unrecognized role for the genetic code is attributable to the kinetics of the codon-decoding process by the ribosome. However, complementary experimental analyses are required to clarify the codon effects on mRNA stability and the related cotranslational mRNA decay pathways, for example, those triggered by aberrant ribosome stalling. In the current study, we performed a set of reporter-based analyses to define codon-mediated mRNA decay and ribosome stall-dependent mRNA decay in zebrafish embryos. Our analysis showed that the effect of codons on mRNA stability stems from the decoding process, independent of the ribosome quality control factor Znf598 and stalling-dependent mRNA decay. We propose that codon-mediated mRNA decay is rather triggered by transiently slowed ribosomes engaging in a productive translation cycle in zebrafish embryos.
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Affiliation(s)
- Yuichiro Mishima
- Department of Frontier Life SciencesFaculty of Life SciencesKyoto Sangyo UniversityKyotoJapan,RNA Systems Biochemistry LaboratoryRIKEN Cluster for Pioneering ResearchSaitamaJapan
| | - Peixun Han
- RNA Systems Biochemistry LaboratoryRIKEN Cluster for Pioneering ResearchSaitamaJapan,Department of Computational Biology and Medical SciencesGraduate School of Frontier SciencesThe University of TokyoChibaJapan
| | - Kota Ishibashi
- Department of Frontier Life SciencesFaculty of Life SciencesKyoto Sangyo UniversityKyotoJapan
| | - Seisuke Kimura
- Department of Industrial Life SciencesFaculty of Life SciencesKyoto Sangyo UniversityKyotoJapan,Center for Plant SciencesKyoto Sangyo UniversityKyotoJapan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry LaboratoryRIKEN Cluster for Pioneering ResearchSaitamaJapan,Department of Computational Biology and Medical SciencesGraduate School of Frontier SciencesThe University of TokyoChibaJapan
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