1
|
Lizarrondo J, Wilfling F. Selective Autophagy of Macromolecular Complexes: What Does It Take to be Taken? J Mol Biol 2024; 436:168574. [PMID: 38636617 DOI: 10.1016/j.jmb.2024.168574] [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: 01/19/2024] [Revised: 04/08/2024] [Accepted: 04/11/2024] [Indexed: 04/20/2024]
Abstract
Proteins are known to perform an astonishing array of functions thanks to their ability to cooperate and modulate each other's properties. Inside cells, proteins can assemble into large multi-subunit complexes to carry out complex cellular functions. The correct assembly and maintenance of the functional state of macromolecular protein complexes is crucial for human health. Failure to do so leads to loss of function and potential accumulation of harmful materials, which is associated with a variety of human diseases such as neurodegeneration and cancer. Autophagy engulfs cytosolic material in autophagosomes, and therefore is best suited to eliminate intact macromolecular complexes without disassembling them, which could interfere with de novo assembly. In this review, we discuss the role of autophagy in the selective degradation of macromolecular complexes. We highlight the current state of knowledge for different macromolecular complexes and their selective autophagic degradation. We emphasize the gaps in our understanding of what it takes for these large macromolecular complexes to be degraded and point to future work that may shed light on the regulation of the selective degradation of macromolecular complexes by autophagy.
Collapse
Affiliation(s)
- Javier Lizarrondo
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt a.M. 60598, Germany; Mechanisms of Cellular Quality Control, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, Frankfurt a.M. 60438, Germany
| | - Florian Wilfling
- Mechanisms of Cellular Quality Control, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, Frankfurt a.M. 60438, Germany.
| |
Collapse
|
2
|
Lin WH, Opoc FG, Liao CW, Roy K, Steinmetz L, Leu JY. Histone deacetylase Hos2 regulates protein expression noise by potentially modulating the protein translation machinery. Nucleic Acids Res 2024; 52:7556-7571. [PMID: 38783136 PMCID: PMC11260488 DOI: 10.1093/nar/gkae432] [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: 02/02/2024] [Revised: 05/05/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024] Open
Abstract
Non-genetic variations derived from expression noise at transcript or protein levels can result in cell-to-cell heterogeneity within an isogenic population. Although cells have developed strategies to reduce noise in some cellular functions, this heterogeneity can also facilitate varying levels of regulation and provide evolutionary benefits in specific environments. Despite several general characteristics of cellular noise having been revealed, the detailed molecular pathways underlying noise regulation remain elusive. Here, we established a dual-fluorescent reporter system in Saccharomyces cerevisiae and performed experimental evolution to search for mutations that increase expression noise. By analyzing evolved cells using bulk segregant analysis coupled with whole-genome sequencing, we identified the histone deacetylase Hos2 as a negative noise regulator. A hos2 mutant down-regulated multiple ribosomal protein genes and exhibited partially compromised protein translation, indicating that Hos2 may regulate protein expression noise by modulating the translation machinery. Treating cells with translation inhibitors or introducing mutations into several Hos2-regulated ribosomal protein genes-RPS9A, RPS28B and RPL42A-enhanced protein expression noise. Our study provides an effective strategy for identifying noise regulators and also sheds light on how cells regulate non-genetic variation through protein translation.
Collapse
Affiliation(s)
- Wei-Han Lin
- Doctoral Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Florica J G Opoc
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Chia-Wei Liao
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Kevin R Roy
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lars M Steinmetz
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg 69117, Germany
| | - Jun-Yi Leu
- Doctoral Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| |
Collapse
|
3
|
Weber R, Chang CT. Human DDX6 regulates translation and decay of inefficiently translated mRNAs. eLife 2024; 13:RP92426. [PMID: 38989862 PMCID: PMC11239181 DOI: 10.7554/elife.92426] [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] [Indexed: 07/12/2024] Open
Abstract
Recent findings indicate that the translation elongation rate influences mRNA stability. One of the factors that has been implicated in this link between mRNA decay and translation speed is the yeast DEAD-box helicase Dhh1p. Here, we demonstrated that the human ortholog of Dhh1p, DDX6, triggers the deadenylation-dependent decay of inefficiently translated mRNAs in human cells. DDX6 interacts with the ribosome through the Phe-Asp-Phe (FDF) motif in its RecA2 domain. Furthermore, RecA2-mediated interactions and ATPase activity are both required for DDX6 to destabilize inefficiently translated mRNAs. Using ribosome profiling and RNA sequencing, we identified two classes of endogenous mRNAs that are regulated in a DDX6-dependent manner. The identified targets are either translationally regulated or regulated at the steady-state-level and either exhibit signatures of poor overall translation or of locally reduced ribosome translocation rates. Transferring the identified sequence stretches into a reporter mRNA caused translation- and DDX6-dependent degradation of the reporter mRNA. In summary, these results identify DDX6 as a crucial regulator of mRNA translation and decay triggered by slow ribosome movement and provide insights into the mechanism by which DDX6 destabilizes inefficiently translated mRNAs.
Collapse
Affiliation(s)
- Ramona Weber
- Department of Biochemistry, Max Planck Institute for Developmental BiologyTübingenGermany
- Institute for Regenerative Medicine (IREM), University of ZurichZurichSwitzerland
| | - Chung-Te Chang
- Department of Biochemistry, Max Planck Institute for Developmental BiologyTübingenGermany
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung UniversityTaipei CityTaiwan
| |
Collapse
|
4
|
Fu Y, Jiang F, Zhang X, Pan Y, Xu R, Liang X, Wu X, Li X, Lin K, Shi R, Zhang X, Ferrandon D, Liu J, Pei D, Wang J, Wang T. Perturbation of METTL1-mediated tRNA N 7- methylguanosine modification induces senescence and aging. Nat Commun 2024; 15:5713. [PMID: 38977661 PMCID: PMC11231295 DOI: 10.1038/s41467-024-49796-8] [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: 11/07/2023] [Accepted: 06/14/2024] [Indexed: 07/10/2024] Open
Abstract
Cellular senescence is characterized by a decrease in protein synthesis, although the underlying processes are mostly unclear. Chemical modifications to transfer RNAs (tRNAs) frequently influence tRNA activity, which is crucial for translation. We describe how tRNA N7-methylguanosine (m7G46) methylation, catalyzed by METTL1-WDR4, regulates translation and influences senescence phenotypes. Mettl1/Wdr4 and m7G gradually diminish with senescence and aging. A decrease in METTL1 causes a reduction in tRNAs, especially those with the m7G modification, via the rapid tRNA degradation (RTD) pathway. The decreases cause ribosomes to stall at certain codons, impeding the translation of mRNA that is essential in pathways such as Wnt signaling and ribosome biogenesis. Furthermore, chronic ribosome stalling stimulates the ribotoxic and integrative stress responses, which induce senescence-associated secretory phenotype. Moreover, restoring eEF1A protein mitigates senescence phenotypes caused by METTL1 deficiency by reducing RTD. Our findings demonstrate that tRNA m7G modification is essential for preventing premature senescence and aging by enabling efficient mRNA translation.
Collapse
Affiliation(s)
- Yudong Fu
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou, China
- GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fan Jiang
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou, China
- GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou, China
| | - Xiao Zhang
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou, China
- GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yingyi Pan
- Sino-French Hoffmann Institute, Guangzhou Medical University, Guangzhou, China
| | - Rui Xu
- Department of pediatrics, Foshan maternal and children's hospital affiliated to southern medical university, 528000, Foshan, Guangdong, China
| | - Xiu Liang
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou, China
- GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou, China
| | - Xiaofen Wu
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou, China
- GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou, China
| | | | - Kaixuan Lin
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou, China
- GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou, China
| | - Ruona Shi
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou, China
- GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou, China
| | - Xiaofei Zhang
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou, China
- GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dominique Ferrandon
- Sino-French Hoffmann Institute, Guangzhou Medical University, Guangzhou, China
- Université de Strasbourg, Strasbourg, France
- Modèles Insectes de l'Immunité Innée, UPR 9022 du CNRS, Strasbourg, France
| | - Jing Liu
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou, China
- GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou, China
- Joint School of Lifesciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China, Guangzhou Medical University, 511436, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Duanqing Pei
- School of Life Sciences, Westlake University, Hangzhou, China
| | - Jie Wang
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou, China.
- GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou, China.
- Joint School of Lifesciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China, Guangzhou Medical University, 511436, Guangzhou, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Tao Wang
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
- GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou, China.
- GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, Guangzhou, China.
- University of Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
McGirr T, Onar O, Jafarnejad SM. Dysregulated ribosome quality control in human diseases. FEBS J 2024. [PMID: 38949989 DOI: 10.1111/febs.17217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/31/2024] [Accepted: 06/20/2024] [Indexed: 07/03/2024]
Abstract
Precise regulation of mRNA translation is of fundamental importance for maintaining homeostasis. Conversely, dysregulated general or transcript-specific translation, as well as abnormal translation events, have been linked to a multitude of diseases. However, driven by the misconception that the transient nature of mRNAs renders their abnormalities inconsequential, the importance of mechanisms that monitor the quality and fidelity of the translation process has been largely overlooked. In recent years, there has been a dramatic shift in this paradigm, evidenced by several seminal discoveries on the role of a key mechanism in monitoring the quality of mRNA translation - namely, Ribosome Quality Control (RQC) - in the maintenance of homeostasis and the prevention of diseases. Here, we will review recent advances in the field and emphasize the biological significance of the RQC mechanism, particularly its implications in human diseases.
Collapse
Affiliation(s)
- Tom McGirr
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, UK
| | - Okan Onar
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, UK
- Department of Biology, Faculty of Science, Ankara University, Turkey
| | | |
Collapse
|
7
|
Meadow ME, Broas S, Hoare M, Alimohammadi F, Welle KA, Swovick K, Hryhorenko JR, Martinez JC, Biashad SA, Seluanov A, Gorbunova V, Buchwalter A, Ghaemmaghami S. Proteome Birthdating Reveals Age-Selectivity of Protein Ubiquitination. Mol Cell Proteomics 2024; 23:100791. [PMID: 38797438 PMCID: PMC11260378 DOI: 10.1016/j.mcpro.2024.100791] [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: 12/14/2023] [Revised: 03/27/2024] [Accepted: 05/15/2024] [Indexed: 05/29/2024] Open
Abstract
Within a cell, proteins have distinct and highly variable half-lives. As a result, the molecular ages of proteins can range from seconds to years. How the age of a protein influences its environmental interactions is a largely unexplored area of biology. To investigate the age-selectivity of cellular pathways, we developed a methodology termed "proteome birthdating" that barcodes proteins based on their time of synthesis. We demonstrate that this approach provides accurate measurements of protein turnover kinetics from a single biological sample encoding multiple labeling time-points. As a first application of the birthdated proteome, we investigated the age distribution of the human ubiquitinome. Our results indicate that the vast majority of ubiquitinated proteins in a cell consist of newly synthesized proteins and that these young proteins constitute the bulk of the degradative flux through the proteasome. Rapidly ubiquitinated nascent proteins are enriched in cytosolic subunits of large protein complexes. Conversely, proteins destined for the secretory pathway and vesicular transport have older ubiquitinated populations. Our data also identify a smaller subset of older ubiquitinated cellular proteins that do not appear to be targeted to the proteasome for rapid degradation. Together, our data provide an age census of the human ubiquitinome and establish proteome birthdating as a robust methodology for investigating the protein age-selectivity of diverse cellular pathways.
Collapse
Affiliation(s)
- Michael E Meadow
- Department of Biology, University of Rochester, New York, USA; Medical Scientist Training Program, University of Rochester, New York, USA
| | - Sarah Broas
- Department of Biology, University of Rochester, New York, USA
| | - Margaret Hoare
- Department of Biology, University of Rochester, New York, USA
| | - Fatemeh Alimohammadi
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, New York, USA
| | - Kevin A Welle
- University of Rochester Mass Spectrometry Resource Laboratory, New York, USA
| | - Kyle Swovick
- University of Rochester Mass Spectrometry Resource Laboratory, New York, USA
| | | | - John C Martinez
- Department of Biology, University of Rochester, New York, USA
| | | | - Andrei Seluanov
- Department of Biology, University of Rochester, New York, USA; Department of Medicine, University of Rochester Medical Center, Rochester, New York, USA
| | - Vera Gorbunova
- Department of Biology, University of Rochester, New York, USA; Department of Medicine, University of Rochester Medical Center, Rochester, New York, USA
| | - Abigail Buchwalter
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California, USA
| | - Sina Ghaemmaghami
- Department of Biology, University of Rochester, New York, USA; University of Rochester Mass Spectrometry Resource Laboratory, New York, USA.
| |
Collapse
|
8
|
Escalante LE, Hose J, Howe H, Paulsen N, Place M, Gasch AP. Premature aging in aneuploid yeast is caused in part by aneuploidy-induced defects in Ribosome Quality Control. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.22.600216. [PMID: 38948718 PMCID: PMC11213126 DOI: 10.1101/2024.06.22.600216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Premature aging is a hallmark of Down syndrome, caused by trisomy of human chromosome 21, but the reason is unclear and difficult to study in humans. We used an aneuploid model in wild yeast to show that chromosome amplification disrupts nutrient-induced cell-cycle arrest, quiescence entry, and healthy aging, across genetic backgrounds and amplified chromosomes. We discovered that these defects are due in part to aneuploidy-induced dysfunction in Ribosome Quality Control (RQC). Compared to euploids, aneuploids entering quiescence display aberrant ribosome profiles, accumulate RQC intermediates, and harbor an increased load of protein aggregates. Although they have normal proteasome capacity, aneuploids show signs of ubiquitin dysregulation, which impacts cyclin abundance to disrupt arrest. Remarkably, inducing ribosome stalling in euploids produces similar aberrations, while up-regulating limiting RQC subunits or proteins in ubiquitin metabolism alleviates many of the aneuploid defects. Our results provide implications for other aneuploidy disorders including Down syndrome.
Collapse
Affiliation(s)
- Leah E. Escalante
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, 53706
| | - James Hose
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, 53706
| | - Hollis Howe
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, 53706
| | - Norah Paulsen
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, 53706
| | - Michael Place
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, 53706
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53706
| | - Audrey P. Gasch
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, 53706
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53706
- Department of Medical Genetics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53706
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Jha MP, Kumar V, Ghosh A, Mapa K. Sse1, Hsp110 chaperone of yeast, controls the cellular fate during endoplasmic reticulum stress. G3 (BETHESDA, MD.) 2024; 14:jkae075. [PMID: 38577891 DOI: 10.1093/g3journal/jkae075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 02/20/2024] [Accepted: 03/21/2024] [Indexed: 04/06/2024]
Abstract
Sse1 is a cytosolic Hsp110 molecular chaperone of yeast, Saccharomyces cerevisiae. Its multifaceted roles in cellular protein homeostasis as a nucleotide exchange factor (NEF), as a protein-disaggregase and as a chaperone linked to protein synthesis (CLIPS) are well documented. In the current study, we show that SSE1 genetically interacts with IRE1 and HAC1, the endoplasmic reticulum-unfolded protein response (ER-UPR) sensors implicating its role in ER protein homeostasis. Interestingly, the absence of this chaperone imparts unusual resistance to tunicamycin-induced ER stress which depends on the intact Ire1-Hac1 mediated ER-UPR signaling. Furthermore, cells lacking SSE1 show inefficient ER-stress-responsive reorganization of translating ribosomes from polysomes to monosomes that drive uninterrupted protein translation during tunicamycin stress. In consequence, the sse1Δ strain shows prominently faster reversal from ER-UPR activated state indicating quicker restoration of homeostasis, in comparison to the wild-type (WT) cells. Importantly, Sse1 plays a critical role in controlling the ER-stress-mediated cell division arrest, which is escaped in sse1Δ strain during chronic tunicamycin stress. Accordingly, sse1Δ strain shows significantly higher cell viability in comparison to WT yeast imparting the stark fitness following short-term as well as long-term tunicamycin stress. These data, all together, suggest that cytosolic chaperone Sse1 is an important modulator of ER stress response in yeast and it controls stress-induced cell division arrest and cell death during overwhelming ER stress induced by tunicamycin.
Collapse
Affiliation(s)
- Mainak Pratim Jha
- Protein Homeostasis Laboratory, Department of Life Sciences, School of Natural Sciences, Shiv Nadar Institution of Eminence, Delhi-NCR, Gautam Buddha Nagar, Greater Noida, Uttar Pradesh 201314, India
| | - Vignesh Kumar
- Chemical and Systems Biology Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Asmita Ghosh
- Chemical and Systems Biology Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Koyeli Mapa
- Protein Homeostasis Laboratory, Department of Life Sciences, School of Natural Sciences, Shiv Nadar Institution of Eminence, Delhi-NCR, Gautam Buddha Nagar, Greater Noida, Uttar Pradesh 201314, India
| |
Collapse
|
11
|
Chen S, Collart MA. Membrane-associated mRNAs: A Post-transcriptional Pathway for Fine-turning Gene Expression. J Mol Biol 2024; 436:168579. [PMID: 38648968 DOI: 10.1016/j.jmb.2024.168579] [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: 10/30/2023] [Revised: 04/14/2024] [Accepted: 04/16/2024] [Indexed: 04/25/2024]
Abstract
Gene expression is a fundamental and highly regulated process involving a series of tightly coordinated steps, including transcription, post-transcriptional processing, translation, and post-translational modifications. A growing number of studies have revealed an additional layer of complexity in gene expression through the phenomenon of mRNA subcellular localization. mRNAs can be organized into membraneless subcellular structures within both the cytoplasm and the nucleus, but they can also targeted to membranes. In this review, we will summarize in particular our knowledge on localization of mRNAs to organelles, focusing on important regulators and available techniques for studying organellar localization, and significance of this localization in the broader context of gene expression regulation.
Collapse
Affiliation(s)
- Siyu Chen
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Institute of Genetics and Genomics of Geneva, Geneva, Switzerland.
| | - Martine A Collart
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Institute of Genetics and Genomics of Geneva, Geneva, Switzerland.
| |
Collapse
|
12
|
Cai T, Zhang B, Reddy E, Wu Y, Tang Y, Mondal I, Wang J, Ho WS, Lu RO, Wu Z. The mitochondrial stress-induced protein carboxyl-terminal alanine and threonine tailing (msiCAT-tailing) promotes glioblastoma tumorigenesis by modulating mitochondrial functions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.15.594447. [PMID: 38798583 PMCID: PMC11118334 DOI: 10.1101/2024.05.15.594447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
The rapid and sustained proliferation in cancer cells requires accelerated protein synthesis. Accelerated protein synthesis and disordered cell metabolism in cancer cells greatly increase the risk of translation errors. ribosome-associated quality control (RQC) is a recently discovered mechanism for resolving ribosome collisions caused by frequent translation stalls. The role of the RQC pathway in cancer initiation and progression remains controversial and confusing. In this study, we investigated the pathogenic role of mitochondrial stress-induced protein carboxyl-terminal terminal alanine and threonine tailing (msiCAT-tailing) in glioblastoma (GBM), which is a specific RQC response to translational arrest on the outer mitochondrial membrane. We found that msiCAT-tailed mitochondrial proteins frequently exist in glioblastoma stem cells (GSCs). Ectopically expressed msiCAT-tailed mitochondrial ATP synthase F1 subunit alpha (ATP5α) protein increases the mitochondrial membrane potential and blocks mitochondrial permeability transition pore (MPTP) formation/opening. These changes in mitochondrial properties confer resistance to staurosporine (STS)-induced apoptosis in GBM cells. Therefore, msiCAT-tailing can promote cell survival and migration, while genetic and pharmacological inhibition of msiCAT-tailing can prevent the overgrowth of GBM cells. Highlights The RQC pathway is disturbed in glioblastoma (GBM) cellsmsiCAT-tailing on ATP5α elevates mitochondrial membrane potential and inhibits MPTP openingmsiCAT-tailing on ATP5α inhibits drug-induced apoptosis in GBM cellsInhibition of msiCAT-tailing impedes overall growth of GBM cells.
Collapse
|
13
|
Buggiani J, Meinnel T, Giglione C, Frottin F. Advances in nuclear proteostasis of metazoans. Biochimie 2024:S0300-9084(24)00081-6. [PMID: 38642824 DOI: 10.1016/j.biochi.2024.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/12/2024] [Accepted: 04/16/2024] [Indexed: 04/22/2024]
Abstract
The proteostasis network and associated protein quality control (PQC) mechanisms ensure proteome functionality and are essential for cell survival. A distinctive feature of eukaryotic cells is their high degree of compartmentalization, requiring specific and adapted proteostasis networks for each compartment. The nucleus, essential for maintaining the integrity of genetic information and gene transcription, is one such compartment. While PQC mechanisms have been investigated for decades in the cytoplasm and the endoplasmic reticulum, our knowledge of nuclear PQC pathways is only emerging. Recent developments in the field have underscored the importance of spatially managing aberrant proteins within the nucleus. Upon proteotoxic stress, misfolded proteins and PQC effectors accumulate in various nuclear membrane-less organelles. Beyond bringing together effectors and substrates, the biophysical properties of these organelles allow novel PQC functions. In this review, we explore the specificity of the nuclear compartment, the effectors of the nuclear proteostasis network, and the PQC roles of nuclear membrane-less organelles in metazoans.
Collapse
Affiliation(s)
- Julia Buggiani
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Thierry Meinnel
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Carmela Giglione
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Frédéric Frottin
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France.
| |
Collapse
|
14
|
Xi H, Wang Y, Ni X, Zhang M, Luo Y. Patulin Biodegradation Mechanism Study in Pichia guilliermondii S15-8 Based on PgSDR-A5D9S1. Toxins (Basel) 2024; 16:177. [PMID: 38668602 PMCID: PMC11053455 DOI: 10.3390/toxins16040177] [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: 02/21/2024] [Revised: 03/24/2024] [Accepted: 03/29/2024] [Indexed: 04/29/2024] Open
Abstract
Patulin contamination has become a bottleneck problem in the safe production of fruit products, although biodegradation technology shows potential application value in patulin control. In the present study, the patulin biodegradation mechanism in a probiotic yeast, Pichia guilliermondii S15-8, was investigated. Firstly, the short-chain dehydrogenase PgSDR encoded by gene A5D9S1 was identified as a patulin degradation enzyme, through RNA sequencing and verification by qRT-PCR. Subsequently, the exogenous expression system of the degradation protein PgSDR-A5D9S1 in E. coli was successfully constructed and demonstrated a more significant patulin tolerance and degradation ability. Furthermore, the structure of PgSDR-A5D9S1 and its active binding sites with patulin were predicted via molecular docking analysis. In addition, the heat-excited protein HSF1 was predicted as the transcription factor regulating the patulin degradation protein PgSDR-A5D9S1, which may provide clues for the further analysis of the molecular regulation mechanism of patulin degradation. This study provides a theoretical basis and technical support for the industrial application of biodegradable functional strains.
Collapse
Affiliation(s)
- Huijuan Xi
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi’an 710119, China; (H.X.); (Y.W.); (X.N.); (M.Z.)
- School of Public Health, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China
| | - Yebo Wang
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi’an 710119, China; (H.X.); (Y.W.); (X.N.); (M.Z.)
| | - Xulei Ni
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi’an 710119, China; (H.X.); (Y.W.); (X.N.); (M.Z.)
| | - Minjie Zhang
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi’an 710119, China; (H.X.); (Y.W.); (X.N.); (M.Z.)
| | - Ying Luo
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi’an 710119, China; (H.X.); (Y.W.); (X.N.); (M.Z.)
- Department of Food Science and Technology, National University of Singapore, Science Drive 2, Singapore 117542, Singapore
| |
Collapse
|
15
|
Ju D, Wu S, Li L, Xie Y. Ubiquitylation-independent cotranslational degradation of dihydrofolate reductase and ubiquitin. Biochem Biophys Res Commun 2024; 702:149651. [PMID: 38350414 DOI: 10.1016/j.bbrc.2024.149651] [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: 01/29/2024] [Revised: 01/31/2024] [Accepted: 02/06/2024] [Indexed: 02/15/2024]
Abstract
Nascent proteins are degraded during or immediately after synthesis, a process called cotranslational protein degradation (CTPD). Although CTPD was observed decades ago, it has never been fully explored mechanistically and functionally. We show here that dihydrofolate reductase (DHFR) and ubiquitin (Ub), two stable proteins widely used in protein degradation studies, are actually subject to CTPD. Unlike canonical posttranslational protein degradation, CTPD of DHFR and Ub does not require prior ubiquitylation. Our data also suggest that protein expression level and N-terminal folding pattern may be two critical determinants for CTPD. Thus, this study reveals that CTPD plays a role in regulating the homeostasis of long-lived proteins and provides insights into the mechanism of CTPD.
Collapse
Affiliation(s)
- Donghong Ju
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, 48201, USA; Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, 48201, USA; Department of Internal Medicine, Wayne State University School of Medicine, Detroit, MI, 48201, USA; Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Shichao Wu
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Li Li
- Department of Internal Medicine, Wayne State University School of Medicine, Detroit, MI, 48201, USA; Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Youming Xie
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, 48201, USA; Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, 48201, USA.
| |
Collapse
|
16
|
Lv L, Mo J, Qing Y, Wang S, Chen L, Mei A, Xu R, Huang H, Tan J, Li Y, Liu J. NEMF-mediated Listerin-independent mitochondrial translational surveillance by E3 ligase Pirh2 and mitochondrial protease ClpXP. Cell Rep 2024; 43:113860. [PMID: 38412092 DOI: 10.1016/j.celrep.2024.113860] [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: 07/27/2023] [Revised: 12/13/2023] [Accepted: 02/08/2024] [Indexed: 02/29/2024] Open
Abstract
The ribosome-associated protein quality control (RQC) pathway acts as a translational surveillance mechanism to maintain proteostasis. In mammalian cells, the cytoplasmic RQC pathway involves nuclear export mediator factor (NEMF)-dependent recruitment of the E3 ligase Listerin to ubiquitinate ribosome-stalled nascent polypeptides on the lysine residue for degradation. However, the quality control of ribosome-stalled nuclear-encoded mitochondrial nascent polypeptides remains elusive, as these peptides can be partially imported into mitochondria through translocons, restricting accessibility to the lysine by Listerin. Here, we identify a Listerin-independent organelle-specific mitochondrial RQC pathway that acts on NEMF-mediated carboxy-terminal poly-alanine modification. In the pathway, mitochondrial proteins carrying C-end poly-Ala tails are recognized by the cytosolic E3 ligase Pirh2 and the ClpXP protease in the mitochondria, which coordinately clear ribosome-stalled mitochondrial nascent polypeptides. Defects in this elimination pathway result in NEMF-mediated aggregates and mitochondrial integrity failure, thus providing a potential molecular mechanism of the RQC pathway in mitochondrial-associated human diseases.
Collapse
Affiliation(s)
- Liang Lv
- Department of Gastroenterology, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Jinyou Mo
- Center for Medical Research, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Yumin Qing
- Department of Gastroenterology, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China; Center for Medical Research, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Shuchao Wang
- Center for Medical Research, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Leijie Chen
- Department of Gastroenterology, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China; Center for Medical Research, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Anna Mei
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Ru Xu
- Department of Obstetrics and Gynecology, Reproductive Medicine Center, The Second Xiangya Hospital, Changsha, Hunan, China
| | - Hualin Huang
- Department of Obstetrics and Gynecology, Reproductive Medicine Center, The Second Xiangya Hospital, Changsha, Hunan, China
| | - Jieqiong Tan
- Center for Medical Genetics, School of Life Science, Central South University, Changsha, Hunan 410078, China
| | - Yifu Li
- Center for Medical Research, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China
| | - Jia Liu
- Center for Medical Research, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, China.
| |
Collapse
|
17
|
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.
Collapse
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.
| |
Collapse
|
18
|
Li Y, Liu D, Zhang X, Rimal S, Lu B, Li S. RACK1 and IRE1 participate in the translational quality control of amyloid precursor protein in Drosophila models of Alzheimer's disease. J Biol Chem 2024; 300:105719. [PMID: 38311171 PMCID: PMC10907166 DOI: 10.1016/j.jbc.2024.105719] [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: 10/13/2023] [Revised: 01/17/2024] [Accepted: 01/29/2024] [Indexed: 02/10/2024] Open
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder characterized by dysregulation of the expression and processing of the amyloid precursor protein (APP). Protein quality control systems are dedicated to remove faulty and deleterious proteins to maintain cellular protein homeostasis (proteostasis). Identidying mechanisms underlying APP protein regulation is crucial for understanding AD pathogenesis. However, the factors and associated molecular mechanisms regulating APP protein quality control remain poorly defined. In this study, we show that mutant APP with its mitochondrial-targeting sequence ablated exhibited predominant endoplasmic reticulum (ER) distribution and led to aberrant ER morphology, deficits in locomotor activity, and shortened lifespan. We searched for regulators that could counteract the toxicity caused by the ectopic expression of this mutant APP. Genetic removal of the ribosome-associated quality control (RQC) factor RACK1 resulted in reduced levels of ectopically expressed mutant APP. By contrast, gain of RACK1 function increased mutant APP level. Additionally, overexpression of the ER stress regulator (IRE1) resulted in reduced levels of ectopically expressed mutant APP. Mechanistically, the RQC related ATPase VCP/p97 and the E3 ubiquitin ligase Hrd1 were required for the reduction of mutant APP level by IRE1. These factors also regulated the expression and toxicity of ectopically expressed wild type APP, supporting their relevance to APP biology. Our results reveal functions of RACK1 and IRE1 in regulating the quality control of APP homeostasis and mitigating its pathogenic effects, with implications for the understanding and treatment of AD.
Collapse
Affiliation(s)
- Yu Li
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
| | - Dongyue Liu
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
| | - Xuejing Zhang
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
| | - Suman Rimal
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Bingwei Lu
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Shuangxi Li
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China.
| |
Collapse
|
19
|
Peng G, Liu M, Luo Z, Deng S, Wang Q, Wang M, Chen H, Xiao Y, Zhang Y, Hong H, Zhu L, Liu Z, Zhou L, Wang Y, Zhuang C, Zhou H. An E3 ubiquitin ligase CSIT2 controls critical sterility-inducing temperature of thermo-sensitive genic male sterile rice. THE NEW PHYTOLOGIST 2024; 241:2059-2074. [PMID: 38197218 DOI: 10.1111/nph.19520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 12/08/2023] [Indexed: 01/11/2024]
Abstract
Thermo-sensitive genic male sterile (TGMS) lines are the core of two-line hybrid rice (Oryza sativa). However, elevated or unstable critical sterility-inducing temperatures (CSITs) of TGMS lines are bottlenecks that restrict the development of two-line hybrid rice. However, the genes and molecular mechanisms controlling CSIT remain unknown. Here, we report the CRITICAL STERILITY-INDUCING TEMPERATURE 2 (CSIT2) that encodes a really interesting new gene (RING) type E3 ligase, controlling the CSIT of thermo-sensitive male sterility 5 (tms5)-based TGMS lines through ribosome-associated protein quality control (RQC). CSIT2 binds to the large and small ribosomal subunits and ubiquitinates 80S ribosomes for dissociation, and may also ubiquitinate misfolded proteins for degradation. Mutation of CSIT2 inhibits the possible damage to ubiquitin system and protein translation, which allows more proteins such as catalases to accumulate for anther development and inhibits abnormal accumulation of reactive oxygen species (ROS) and premature programmed cell death (PCD) in anthers, partly rescuing male sterility and raised the CSIT of tms5-based TGMS lines. These findings reveal a mechanism controlling CSIT and provide a strategy for solving the elevated or unstable CSITs of tms5-based TGMS lines in two-line hybrid rice.
Collapse
Affiliation(s)
- Guoqing Peng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- College of Agriculture & Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Minglong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Ziliang Luo
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | - Shuangfan Deng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Qinghua Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Mumei Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Huiqiong Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yueping Xiao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yongjie Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Haona Hong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Liya Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Zhenlan Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Lingyan Zhou
- College of Agriculture & Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Yingxiang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Chuxiong Zhuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Hai Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| |
Collapse
|
20
|
Geng J, Li S, Li Y, Wu Z, Bhurtel S, Rimal S, Khan D, Ohja R, Brandman O, Lu B. Stalled translation by mitochondrial stress upregulates a CNOT4-ZNF598 ribosomal quality control pathway important for tissue homeostasis. Nat Commun 2024; 15:1637. [PMID: 38388640 PMCID: PMC10883933 DOI: 10.1038/s41467-024-45525-3] [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: 01/17/2023] [Accepted: 01/26/2024] [Indexed: 02/24/2024] Open
Abstract
Translational control exerts immediate effect on the composition, abundance, and integrity of the proteome. Ribosome-associated quality control (RQC) handles ribosomes stalled at the elongation and termination steps of translation, with ZNF598 in mammals and Hel2 in yeast serving as key sensors of translation stalling and coordinators of downstream resolution of collided ribosomes, termination of stalled translation, and removal of faulty translation products. The physiological regulation of RQC in general and ZNF598 in particular in multicellular settings is underexplored. Here we show that ZNF598 undergoes regulatory K63-linked ubiquitination in a CNOT4-dependent manner and is upregulated upon mitochondrial stresses in mammalian cells and Drosophila. ZNF598 promotes resolution of stalled ribosomes and protects against mitochondrial stress in a ubiquitination-dependent fashion. In Drosophila models of neurodegenerative diseases and patient cells, ZNF598 overexpression aborts stalled translation of mitochondrial outer membrane-associated mRNAs, removes faulty translation products causal of disease, and improves mitochondrial and tissue health. These results shed lights on the regulation of ZNF598 and its functional role in mitochondrial and tissue homeostasis.
Collapse
Affiliation(s)
- Ji Geng
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Shuangxi Li
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Yu Li
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Zhihao Wu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Sunil Bhurtel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Suman Rimal
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Danish Khan
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Rani Ohja
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Onn Brandman
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Bingwei Lu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| |
Collapse
|
21
|
Minoia M, Quintana-Cordero J, Jetzinger K, Kotan IE, Turnbull KJ, Ciccarelli M, Masser AE, Liebers D, Gouarin E, Czech M, Hauryliuk V, Bukau B, Kramer G, Andréasson C. Chp1 is a dedicated chaperone at the ribosome that safeguards eEF1A biogenesis. Nat Commun 2024; 15:1382. [PMID: 38360885 PMCID: PMC10869706 DOI: 10.1038/s41467-024-45645-w] [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: 06/02/2023] [Accepted: 01/29/2024] [Indexed: 02/17/2024] Open
Abstract
Cotranslational protein folding depends on general chaperones that engage highly diverse nascent chains at the ribosomes. Here we discover a dedicated ribosome-associated chaperone, Chp1, that rewires the cotranslational folding machinery to assist in the challenging biogenesis of abundantly expressed eukaryotic translation elongation factor 1A (eEF1A). Our results indicate that during eEF1A synthesis, Chp1 is recruited to the ribosome with the help of the nascent polypeptide-associated complex (NAC), where it safeguards eEF1A biogenesis. Aberrant eEF1A production in the absence of Chp1 triggers instant proteolysis, widespread protein aggregation, activation of Hsf1 stress transcription and compromises cellular fitness. The expression of pathogenic eEF1A2 variants linked to epileptic-dyskinetic encephalopathy is protected by Chp1. Thus, eEF1A is a difficult-to-fold protein that necessitates a biogenesis pathway starting with dedicated folding factor Chp1 at the ribosome to protect the eukaryotic cell from proteostasis collapse.
Collapse
Affiliation(s)
- Melania Minoia
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Jany Quintana-Cordero
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Katharina Jetzinger
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
- Center for Molecular Biology of the University of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Ilgin Eser Kotan
- Center for Molecular Biology of the University of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Kathryn Jane Turnbull
- Department of Clinical Microbiology, Rigshospitalet, 2200, Copenhagen, Denmark
- Department of Molecular Biology, Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, Science for Life Laboratory, Umeå University, Umeå, Sweden
| | - Michela Ciccarelli
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Anna E Masser
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Dorina Liebers
- Center for Molecular Biology of the University of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Eloïse Gouarin
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Marius Czech
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Vasili Hauryliuk
- Science for Life Laboratory, Department of Experimental Medical Science, Lund University, Lund, Sweden
- University of Tartu, Institute of Technology, 50411, Tartu, Estonia
| | - Bernd Bukau
- Center for Molecular Biology of the University of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Günter Kramer
- Center for Molecular Biology of the University of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Claes Andréasson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.
| |
Collapse
|
22
|
Svetlov MS, Dunand CF, Nakamoto JA, Atkinson GC, Safdari HA, Wilson DN, Vázquez-Laslop N, Mankin AS. Peptidyl-tRNA hydrolase is the nascent chain release factor in bacterial ribosome-associated quality control. Mol Cell 2024; 84:715-726.e5. [PMID: 38183984 DOI: 10.1016/j.molcel.2023.12.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/08/2023] [Accepted: 12/01/2023] [Indexed: 01/08/2024]
Abstract
Rescuing stalled ribosomes often involves their splitting into subunits. In many bacteria, the resultant large subunits bearing peptidyl-tRNAs are processed by the ribosome-associated quality control (RQC) apparatus that extends the C termini of the incomplete nascent polypeptides with polyalanine tails to facilitate their degradation. Although the tailing mechanism is well established, it is unclear how the nascent polypeptides are cleaved off the tRNAs. We show that peptidyl-tRNA hydrolase (Pth), the known role of which has been to hydrolyze ribosome-free peptidyl-tRNA, acts in concert with RQC factors to release nascent polypeptides from large ribosomal subunits. Dislodging from the ribosomal catalytic center is required for peptidyl-tRNA hydrolysis by Pth. Nascent protein folding may prevent peptidyl-tRNA retraction and interfere with the peptide release. However, oligoalanine tailing makes the peptidyl-tRNA ester bond accessible for Pth-catalyzed hydrolysis. Therefore, the oligoalanine tail serves not only as a degron but also as a facilitator of Pth-catalyzed peptidyl-tRNA hydrolysis.
Collapse
Affiliation(s)
- Maxim S Svetlov
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA; Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA.
| | - Clémence F Dunand
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA; Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Jose A Nakamoto
- Department of Experimental Medicine, University of Lund, 221 00 Lund, Sweden
| | - Gemma C Atkinson
- Department of Experimental Medicine, University of Lund, 221 00 Lund, Sweden
| | - Haaris A Safdari
- Institute for Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany
| | - Nora Vázquez-Laslop
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA; Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Alexander S Mankin
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA; Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA.
| |
Collapse
|
23
|
Monem PC, Arribere JA. A ubiquitin language communicates ribosomal distress. Semin Cell Dev Biol 2024; 154:131-137. [PMID: 36963992 PMCID: PMC10878831 DOI: 10.1016/j.semcdb.2023.03.009] [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: 04/15/2022] [Revised: 02/10/2023] [Accepted: 03/16/2023] [Indexed: 03/26/2023]
Abstract
Cells entrust ribosomes with the critical task of identifying problematic mRNAs and facilitating their degradation. Ribosomes must communicate when they encounter and stall on an aberrant mRNA, lest they expose the cell to toxic and disease-causing proteins, or they jeopardize ribosome homeostasis and cellular translation. In recent years, ribosomal ubiquitination has emerged as a central signaling step in this process, and proteomic studies across labs and experimental systems show a myriad of ubiquitination sites throughout the ribosome. Work from many labs zeroed in on ubiquitination in one region of the small ribosomal subunit as being functionally significant, with the balance and exact ubiquitination sites determined by stall type, E3 ubiquitin ligases, and deubiquitinases. This review discusses the current literature surrounding ribosomal ubiquitination during translational stress and considers its role in committing translational complexes to decay.
Collapse
Affiliation(s)
- Parissa C Monem
- Department of Molecular, Cell, and Developmental Biology, University of California at Santa Cruz, Santa Cruz, CA, USA
| | - Joshua A Arribere
- Department of Molecular, Cell, and Developmental Biology, University of California at Santa Cruz, Santa Cruz, CA, USA.
| |
Collapse
|
24
|
Yang EJN, Liao PC, Pon L. Mitochondrial protein and organelle quality control-Lessons from budding yeast. IUBMB Life 2024; 76:72-87. [PMID: 37731280 PMCID: PMC10842221 DOI: 10.1002/iub.2783] [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: 06/30/2023] [Accepted: 08/11/2023] [Indexed: 09/22/2023]
Abstract
Mitochondria are essential for normal cellular function and have emerged as key aging determinants. Indeed, defects in mitochondrial function have been linked to cardiovascular, skeletal muscle and neurodegenerative diseases, premature aging, and age-linked diseases. Here, we describe mechanisms for mitochondrial protein and organelle quality control. These surveillance mechanisms mediate repair or degradation of damaged or mistargeted mitochondrial proteins, segregate mitochondria based on their functional state during asymmetric cell division, and modulate cellular fitness, the response to stress, and lifespan control in yeast and other eukaryotes.
Collapse
Affiliation(s)
- Emily Jie-Ning Yang
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032
| | - Pin-Chao Liao
- Institute of Molecular Medicine & Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan 30013
| | - Liza Pon
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032
| |
Collapse
|
25
|
Dos Santos OAL, Carneiro RL, Requião RD, Ribeiro-Alves M, Domitrovic T, Palhano FL. Transcriptional profile of ribosome-associated quality control components and their associated phenotypes in mammalian cells. Sci Rep 2024; 14:1439. [PMID: 38228636 PMCID: PMC10792078 DOI: 10.1038/s41598-023-50811-z] [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: 08/30/2023] [Accepted: 12/26/2023] [Indexed: 01/18/2024] Open
Abstract
During protein synthesis, organisms detect translation defects that induce ribosome stalling and result in protein aggregation. The Ribosome-associated Quality Control (RQC) complex, comprising TCF25, LTN1, and NEMF, is responsible for identifying incomplete protein products from unproductive translation events, targeting them for degradation. Although RQC disruption causes adverse effects on vertebrate neurons, data regarding mRNA/protein expression and regulation across tissues are lacking. Employing high-throughput methods, we analyzed public datasets to explore RQC gene expression and phenotypes. Our findings revealed widespread expression of RQC components in human tissues; however, silencing of RQC yielded only mild negative effects on cell growth. Notably, TCF25 exhibited elevated mRNA levels that were not reflected in the protein content. We experimentally demonstrated that this disparity arose from post-translational protein degradation by the proteasome. Additionally, we observed that cellular aging marginally influenced RQC expression, leading to reduced mRNA levels in specific tissues. Our results suggest the necessity of RQC expression in all mammalian tissues. Nevertheless, when RQC falters, alternative mechanisms seem to compensate, ensuring cell survival under nonstress conditions.
Collapse
Affiliation(s)
- Otávio Augusto Leitão Dos Santos
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Rodolfo L Carneiro
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Rodrigo D Requião
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Marcelo Ribeiro-Alves
- Fundação Oswaldo Cruz, Instituto Nacional de Infectologia Evandro Chagas, Rio de Janeiro, 21040-900, Brazil
| | - Tatiana Domitrovic
- Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Fernando L Palhano
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil.
| |
Collapse
|
26
|
Garde R, Dea A, Herwig MF, Pincus D. Feedback control of the heat shock response by spatiotemporal regulation of Hsp70. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.574867. [PMID: 38260373 PMCID: PMC10802473 DOI: 10.1101/2024.01.09.574867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Cells maintain homeostasis via dynamic regulation of stress response pathways. Stress pathways transiently induce response regulons via negative feedback loops, but the extent to which individual genes provide feedback has not been comprehensively measured for any pathway. Here, we disrupted induction of each gene in the Saccharomyces cerevisiae heat shock response (HSR) and quantified cell growth and HSR dynamics following heat shock. The screen revealed a core feedback loop governing expression of the chaperone Hsp70 reinforced by an auxiliary feedback loop controlling Hsp70 subcellular localization. Mathematical modeling and live imaging demonstrated that multiple HSR targets converge to promote Hsp70 nuclear localization via its release from cytosolic condensates. Following ethanol stress, a distinct set of factors similarly converged on Hsp70, suggesting that nonredundant subsets of the HSR regulon confer feedback under different conditions. Flexible spatiotemporal feedback loops may broadly organize stress response regulons and expand their adaptive capacity.
Collapse
Affiliation(s)
- Rania Garde
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL
| | - Annisa Dea
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL
| | - Madeline F. Herwig
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL
| | - David Pincus
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL
- Center for Physics of Evolving Systems, University of Chicago, Chicago, IL
| |
Collapse
|
27
|
Liu J, Nagy N, Ayala-Torres C, Aguilar-Alonso F, Morais-Esteves F, Xu S, Masucci MG. Remodeling of the ribosomal quality control and integrated stress response by viral ubiquitin deconjugases. Nat Commun 2023; 14:8315. [PMID: 38097648 PMCID: PMC10721647 DOI: 10.1038/s41467-023-43946-0] [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: 03/02/2023] [Accepted: 11/23/2023] [Indexed: 12/17/2023] Open
Abstract
The strategies adopted by viruses to reprogram the translation and protein quality control machinery and promote infection are poorly understood. Here, we report that the viral ubiquitin deconjugase (vDUB)-encoded in the large tegument protein of Epstein-Barr virus (EBV BPLF1)-regulates the ribosomal quality control (RQC) and integrated stress responses (ISR). The vDUB participates in protein complexes that include the RQC ubiquitin ligases ZNF598 and LTN1. Upon ribosomal stalling, the vDUB counteracts the ubiquitination of the 40 S particle and inhibits the degradation of translation-stalled polypeptides by the proteasome. Impairment of the RQC correlates with the readthrough of stall-inducing mRNAs and with activation of a GCN2-dependent ISR that redirects translation towards upstream open reading frames (uORFs)- and internal ribosome entry sites (IRES)-containing transcripts. Physiological levels of active BPLF1 promote the translation of the EBV Nuclear Antigen (EBNA)1 mRNA in productively infected cells and enhance the release of progeny virus, pointing to a pivotal role of the vDUB in the translation reprogramming that enables efficient virus production.
Collapse
Affiliation(s)
- Jiangnan Liu
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Noemi Nagy
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Carlos Ayala-Torres
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Francisco Aguilar-Alonso
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- Unidad de Desarrollo e Investigación en Bioterapéuticos (UDIBI), Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Francisco Morais-Esteves
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Shanshan Xu
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Maria G Masucci
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
| |
Collapse
|
28
|
Kawan M, Körner M, Schlosser A, Buchberger A. p97/VCP Promotes the Recycling of Endocytic Cargo. Mol Biol Cell 2023; 34:ar126. [PMID: 37756124 PMCID: PMC10848945 DOI: 10.1091/mbc.e23-06-0237] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 09/11/2023] [Accepted: 09/20/2023] [Indexed: 09/29/2023] Open
Abstract
The endocytic pathway is of central importance for eukaryotic cells, as it enables uptake of extracellular materials, membrane protein quality control and recycling, as well as modulation of receptor signaling. While the ATPase p97 (VCP, Cdc48) has been found to be involved in the fusion of early endosomes and endolysosomal degradation, its role in endocytic trafficking is still incompletely characterized. Here, we identify myoferlin (MYOF), a ferlin family member with functions in membrane trafficking and repair, as a hitherto unknown p97 interactor. The interaction of MYOF with p97 depends on the cofactor PLAA previously linked to endosomal sorting. Besides PLAA, shared interactors of p97 and MYOF comprise several proteins involved in endosomal recycling pathways, including Rab11, Rab14, and the transferrin receptor CD71. Accordingly, a fraction of p97 and PLAA localizes to MYOF-, Rab11-, and Rab14-positive endosomal compartments. Pharmacological inhibition of p97 delays transferrin recycling, indicating that p97 promotes not only the lysosomal degradation, but also the recycling of endocytic cargo.
Collapse
Affiliation(s)
- Mona Kawan
- Chair of Biochemistry I, University of Würzburg, Biocenter, Am Hubland, 97074 Würzburg, Germany
| | - Maria Körner
- Chair of Biochemistry I, University of Würzburg, Biocenter, Am Hubland, 97074 Würzburg, Germany
| | - Andreas Schlosser
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Josef-Schneider-Straße 2, 97080 Würzburg, Germany
| | - Alexander Buchberger
- Chair of Biochemistry I, University of Würzburg, Biocenter, Am Hubland, 97074 Würzburg, Germany
| |
Collapse
|
29
|
Ugajin N, Imami K, Takada H, Ishihama Y, Chiba S, Mishima Y. Znf598-mediated Rps10/eS10 ubiquitination contributes to the ribosome ubiquitination dynamics during zebrafish development. RNA (NEW YORK, N.Y.) 2023; 29:1910-1927. [PMID: 37751929 PMCID: PMC10653392 DOI: 10.1261/rna.079633.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 09/05/2023] [Indexed: 09/28/2023]
Abstract
The ribosome is a translational apparatus that comprises about 80 ribosomal proteins and four rRNAs. Recent studies reported that ribosome ubiquitination is crucial for translational regulation and ribosome-associated quality control (RQC). However, little is known about the dynamics of ribosome ubiquitination under complex biological processes of multicellular organisms. To explore ribosome ubiquitination during animal development, we generated a zebrafish strain that expresses a FLAG-tagged ribosomal protein Rpl36/eL36 from its endogenous locus. We examined ribosome ubiquitination during zebrafish development by combining affinity purification of ribosomes from rpl36-FLAG zebrafish embryos with immunoblotting analysis. Our findings showed that the ubiquitination of ribosomal proteins dynamically changed as development proceeded. We also showed that during zebrafish development, the ribosome was ubiquitinated by Znf598, an E3 ubiquitin ligase that activates RQC. Ribosomal protein Rps10/eS10 was found to be a key ubiquitinated protein during development. Furthermore, we showed that Rps10/eS10 ubiquitination-site mutations reduced the overall ubiquitination pattern of the ribosome. These results demonstrate the complexity and dynamics of ribosome ubiquitination during zebrafish development.
Collapse
Affiliation(s)
- Nozomi Ugajin
- Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
| | - Koshi Imami
- RIKEN Center for Integrative Medical Sciences, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiraku Takada
- Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shinobu Chiba
- Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
| | - Yuichiro Mishima
- Department of Frontier Life Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
| |
Collapse
|
30
|
Lyons EF, Devanneaux LC, Muller RY, Freitas AV, Meacham ZA, McSharry MV, Trinh VN, Rogers AJ, Ingolia NT, Lareau LF. Codon optimality modulates protein output by tuning translation initiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.27.568910. [PMID: 38076849 PMCID: PMC10705293 DOI: 10.1101/2023.11.27.568910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
The impact of synonymous codon choice on protein output has important implications for understanding endogenous gene expression and design of synthetic mRNAs. Previously, we used a neural network model to design a series of synonymous fluorescent reporters whose protein output in yeast spanned a seven-fold range corresponding to their predicted translation speed. Here, we show that this effect is not due primarily to the established impact of slow elongation on mRNA stability, but rather, that an active mechanism further decreases the number of proteins made per mRNA. We combine simulations and careful experiments on fluorescent reporters to argue that translation initiation is limited on non-optimally encoded transcripts. Using a genome-wide CRISPRi screen to discover factors modulating the output from non-optimal transcripts, we identify a set of translation initiation factors including multiple subunits of eIF3 whose depletion restored protein output of a non-optimal reporter. Our results show that codon usage can directly limit protein production, across the full range of endogenous variability in codon usage, by limiting translation initiation.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Van N Trinh
- Department of Bioengineering, University of California, Berkeley
| | | | | | - Liana F Lareau
- Department of Molecular and Cell Biology
- California Institute for Quantitative Biosciences
- Department of Bioengineering, University of California, Berkeley
| |
Collapse
|
31
|
Meydan S, Barros GC, Simões V, Harley L, Cizubu BK, Guydosh NR, Silva GM. The ubiquitin conjugase Rad6 mediates ribosome pausing during oxidative stress. Cell Rep 2023; 42:113359. [PMID: 37917585 PMCID: PMC10755677 DOI: 10.1016/j.celrep.2023.113359] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 07/26/2023] [Accepted: 10/13/2023] [Indexed: 11/04/2023] Open
Abstract
Oxidative stress causes K63-linked ubiquitination of ribosomes by the E2 ubiquitin conjugase Rad6. How Rad6-mediated ubiquitination of ribosomes affects translation, however, is unclear. We therefore perform Ribo-seq and Disome-seq in Saccharomyces cerevisiae and show that oxidative stress causes ribosome pausing at specific amino acid motifs, which also leads to ribosome collisions. However, these redox-pausing signatures are lost in the absence of Rad6 and do not depend on the ribosome-associated quality control (RQC) pathway. We also show that Rad6 is needed to inhibit overall translation in response to oxidative stress and that its deletion leads to increased expression of antioxidant genes. Finally, we observe that the lack of Rad6 leads to changes during translation that affect activation of the integrated stress response (ISR) pathway. Our results provide a high-resolution picture of the gene expression changes during oxidative stress and unravel an additional stress response pathway affecting translation elongation.
Collapse
Affiliation(s)
- Sezen Meydan
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Postdoctoral Research Associate Training Fellowship, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, MD 20982, USA
| | | | - Vanessa Simões
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Lana Harley
- Department of Biology, Duke University, Durham, NC 27708, USA
| | | | - Nicholas R Guydosh
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Gustavo M Silva
- Department of Biology, Duke University, Durham, NC 27708, USA.
| |
Collapse
|
32
|
Li X, Mariappan M. Nascent Chain Ubiquitination is Uncoupled from Degradation to Enable Protein Maturation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.09.561585. [PMID: 37873109 PMCID: PMC10592752 DOI: 10.1101/2023.10.09.561585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
A significant proportion of nascent proteins undergo polyubiquitination on ribosomes in mammalian cells, yet the fate of these proteins remains elusive. The ribosome-associated quality control (RQC) is a mechanism that mediates the ubiquitination of nascent chains on stalled ribosomes. Here, we find that nascent proteins ubiquitinated on stalled ribosomes by the RQC E3 ligase LTN1 are insufficient for proteasomal degradation. Our biochemical reconstitution studies reveal that ubiquitinated nascent chains are promptly deubiquitinated in the cytosol upon release from stalled ribosomes, as they are no longer associated with LTN1 E3 ligase for continuous ubiquitination to compete with cytosolic deubiquitinases. These deubiquitinated nascent chains can mature into stable proteins. However, if they misfold and expose a degradation signal, the cytosolic quality control recognizes them for re-ubiquitination and subsequent proteasomal degradation. Thus, our findings suggest that cycles of ubiquitination and deubiquitination spare foldable nascent proteins while ensuring the degradation of terminally misfolded proteins.
Collapse
Affiliation(s)
- Xia Li
- Department of Cell Biology, Nanobiology Institute, Yale School of Medicine, Yale University West Campus, West Haven, CT 06516, USA
| | - Malaiyalam Mariappan
- Department of Cell Biology, Nanobiology Institute, Yale School of Medicine, Yale University West Campus, West Haven, CT 06516, USA
| |
Collapse
|
33
|
Braxton JR, Southworth DR. Structural insights of the p97/VCP AAA+ ATPase: How adapter interactions coordinate diverse cellular functionality. J Biol Chem 2023; 299:105182. [PMID: 37611827 PMCID: PMC10641518 DOI: 10.1016/j.jbc.2023.105182] [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: 05/30/2023] [Revised: 08/05/2023] [Accepted: 08/14/2023] [Indexed: 08/25/2023] Open
Abstract
p97/valosin-containing protein is an essential eukaryotic AAA+ ATPase with diverse functions including protein homeostasis, membrane remodeling, and chromatin regulation. Dysregulation of p97 function causes severe neurodegenerative disease and is associated with cancer, making this protein a significant therapeutic target. p97 extracts polypeptide substrates from macromolecular assemblies by hydrolysis-driven translocation through its central pore. Growing evidence indicates that this activity is highly coordinated by "adapter" partner proteins, of which more than 30 have been identified and are commonly described to facilitate translocation through substrate recruitment or modification. In so doing, these adapters enable critical p97-dependent functions such as extraction of misfolded proteins from the endoplasmic reticulum or mitochondria, and are likely the reason for the extreme functional diversity of p97 relative to other AAA+ translocases. Here, we review the known functions of adapter proteins and highlight recent structural and biochemical advances that have begun to reveal the diverse molecular bases for adapter-mediated regulation of p97 function. These studies suggest that the range of mechanisms by which p97 activity is controlled is vastly underexplored with significant advances possible for understanding p97 regulation by the most known adapters.
Collapse
Affiliation(s)
- Julian R Braxton
- Graduate Program in Chemistry and Chemical Biology, University of California, San Francisco, San Francisco, California, USA; Department of Biochemistry and Biophysics and Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, California, USA
| | - Daniel R Southworth
- Department of Biochemistry and Biophysics and Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, California, USA.
| |
Collapse
|
34
|
Alagar Boopathy LR, Beadle E, Garcia-Bueno Rico A, Vera M. Proteostasis regulation through ribosome quality control and no-go-decay. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1809. [PMID: 37488089 DOI: 10.1002/wrna.1809] [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: 11/25/2022] [Revised: 06/14/2023] [Accepted: 06/30/2023] [Indexed: 07/26/2023]
Abstract
Cell functionality relies on the existing pool of proteins and their folding into functional conformations. This is achieved through the regulation of protein synthesis, which requires error-free mRNAs and ribosomes. Ribosomes are quality control hubs for mRNAs and proteins. Problems during translation elongation slow down the decoding rate, leading to ribosome halting and the eventual collision with the next ribosome. Collided ribosomes form a specific disome structure recognized and solved by ribosome quality control (RQC) mechanisms. RQC pathways orchestrate the degradation of the problematic mRNA by no-go decay and the truncated nascent peptide, the repression of translation initiation, and the recycling of the stalled ribosomes. All these events maintain protein homeostasis and return valuable ribosomes to translation. As such, cell homeostasis and function are maintained at the mRNA level by preventing the production of aberrant or unnecessary proteins. It is becoming evident that the crosstalk between RQC and the protein homeostasis network is vital for cell function, as the absence of RQC components leads to the activation of stress response and neurodegenerative diseases. Here, we review the molecular events of RQC discovered through well-designed stalling reporters. Given the impact of RQC in proteostasis, we discuss the relevance of identifying endogenous mRNA regulated by RQC and their preservation in stress conditions. This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms Translation > Regulation.
Collapse
Affiliation(s)
| | - Emma Beadle
- Department of Biochemistry, McGill University, Montreal, Canada
| | | | - Maria Vera
- Department of Biochemistry, McGill University, Montreal, Canada
| |
Collapse
|
35
|
Meydan S, Guydosh NR. Is there a localized role for translational quality control? RNA (NEW YORK, N.Y.) 2023; 29:1623-1643. [PMID: 37582617 PMCID: PMC10578494 DOI: 10.1261/rna.079683.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 07/26/2023] [Indexed: 08/17/2023]
Abstract
It is known that mRNAs and the machinery that translates them are not uniformly distributed throughout the cytoplasm. As a result, the expression of some genes is localized to particular parts of the cell and this makes it possible to carry out important activities, such as growth and signaling, in three-dimensional space. However, the functions of localized gene expression are not fully understood, and the underlying mechanisms that enable localized expression have not been determined in many cases. One consideration that could help in addressing these challenges is the role of quality control (QC) mechanisms that monitor translating ribosomes. On a global level, QC pathways are critical for detecting aberrant translation events, such as a ribosome that stalls while translating, and responding by activating stress pathways and resolving problematic ribosomes and mRNAs at the molecular level. However, it is unclear how these pathways, even when uniformly active throughout the cell, affect local translation. Importantly, some QC pathways have themselves been reported to be enriched in the proximity of particular organelles, but the extent of such localized activity remains largely unknown. Here, we describe the major QC pathways and review studies that have begun to explore their roles in localized translation. Given the limited data in this area, we also pose broad questions about the possibilities and limitations for how QC pathways could facilitate localized gene expression in the cell with the goal of offering ideas for future experimentation.
Collapse
Affiliation(s)
- Sezen Meydan
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
- National Institute of General Medical Sciences, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Nicholas R Guydosh
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| |
Collapse
|
36
|
Zhang H, Murphy P, Yu J, Lee S, Tsai FTF, van Hoof A, Ling J. Coordination between aminoacylation and editing to protect against proteotoxicity. Nucleic Acids Res 2023; 51:10606-10618. [PMID: 37742077 PMCID: PMC10602869 DOI: 10.1093/nar/gkad778] [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: 06/16/2023] [Revised: 08/13/2023] [Accepted: 09/14/2023] [Indexed: 09/25/2023] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are essential enzymes that ligate amino acids to tRNAs, and often require editing to ensure accurate protein synthesis. Recessive mutations in aaRSs cause various neurological disorders in humans, yet the underlying mechanism remains poorly understood. Pathogenic aaRS mutations frequently cause protein destabilization and aminoacylation deficiency. In this study, we report that combined aminoacylation and editing defects cause severe proteotoxicity. We show that the ths1-C268A mutation in yeast threonyl-tRNA synthetase (ThrRS) abolishes editing and causes heat sensitivity. Surprisingly, experimental evolution of the mutant results in intragenic mutations that restore heat resistance but not editing. ths1-C268A destabilizes ThrRS and decreases overall Thr-tRNAThr synthesis, while the suppressor mutations in the evolved strains improve aminoacylation. We further show that deficiency in either ThrRS aminoacylation or editing is insufficient to cause heat sensitivity, and that ths1-C268A impairs ribosome-associated quality control. Our results suggest that aminoacylation deficiency predisposes cells to proteotoxic stress.
Collapse
Affiliation(s)
- Hong Zhang
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
| | - Parker Murphy
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
| | - Jason Yu
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
| | - Sukyeong Lee
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Advanced Technology Core for Macromolecular X-ray Crystallography, Baylor College of Medicine, Houston, TX 77030, USA
| | - Francis T F Tsai
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Advanced Technology Core for Macromolecular X-ray Crystallography, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ambro van Hoof
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Jiqiang Ling
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
| |
Collapse
|
37
|
Iyer KV, Müller M, Tittel LS, Winz ML. Molecular Highway Patrol for Ribosome Collisions. Chembiochem 2023; 24:e202300264. [PMID: 37382189 DOI: 10.1002/cbic.202300264] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 06/25/2023] [Accepted: 06/28/2023] [Indexed: 06/30/2023]
Abstract
During translation, messenger RNAs (mRNAs) are decoded by ribosomes which can stall for various reasons. These include chemical damage, codon composition, starvation, or translation inhibition. Trailing ribosomes can collide with stalled ribosomes, potentially leading to dysfunctional or toxic proteins. Such aberrant proteins can form aggregates and favor diseases, especially neurodegeneration. To prevent this, both eukaryotes and bacteria have evolved different pathways to remove faulty nascent peptides, mRNAs and defective ribosomes from the collided complex. In eukaryotes, ubiquitin ligases play central roles in triggering downstream responses and several complexes have been characterized that split affected ribosomes and facilitate degradation of the various components. As collided ribosomes signal translation stress to affected cells, in eukaryotes additional stress response pathways are triggered when collisions are sensed. These pathways inhibit translation and modulate cell survival and immune responses. Here, we summarize the current state of knowledge about rescue and stress response pathways triggered by ribosome collisions.
Collapse
Affiliation(s)
- Kaushik Viswanathan Iyer
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Max Müller
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Lena Sophie Tittel
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| | - Marie-Luise Winz
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128, Mainz, Germany
| |
Collapse
|
38
|
Peng G, Liu M, Zhu L, Luo W, Wang Q, Wang M, Chen H, Luo Z, Xiao Y, Zhang Y, Hong H, Liu Z, Zhou L, Guo G, Wang Y, Zhuang C, Zhou H. The E3 ubiquitin ligase CSIT1 regulates critical sterility-inducing temperature by ribosome-associated quality control to safeguard two-line hybrid breeding in rice. MOLECULAR PLANT 2023; 16:1695-1709. [PMID: 37743625 DOI: 10.1016/j.molp.2023.09.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 08/28/2023] [Accepted: 09/21/2023] [Indexed: 09/26/2023]
Abstract
Two-line hybrid breeding can fully utilize heterosis in crops. In thermo-sensitive genic male sterile (TGMS) lines, low critical sterility-inducing temperature (CSIT) is vital to safeguard the production of two-line hybrid seeds in rice (Oryza sativa), but the molecular mechanism determining CSIT is unclear. Here, we report the cloning of CSIT1, which encodes an E3 ubiquitin ligase, and show that CSIT1 modulates the CSIT of thermo-sensitive genic male sterility 5 (tms5)-based TGMS lines through ribosome-associated quality control (RQC). Biochemical assays demonstrated that CSIT1 binds to the 80S ribosomes and ubiquitinates abnormal nascent polypeptides for degradation in the RQC process. Loss of CSIT1 function inhibits the possible damage of tms5 to the ubiquitination system and protein translation, resulting in enhanced accumulation of anther-related proteins such as catalase to suppress abnormal accumulation of reactive oxygen species and premature programmed cell death in the tapetum, thereby leading to a much higher CSIT in the tms5-based TGMS lines. Taken together, our findings reveal a regulatory mechanism of CSIT, providing new insights into RQC and potential targets for future two-line hybrid breeding.
Collapse
Affiliation(s)
- Guoqing Peng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; College of Agriculture & Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Minglong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Liya Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Wenlong Luo
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Qinghua Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Mumei Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Huiqiong Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Ziliang Luo
- Agronomy Department, University of Florida, Gainesville, FL 32610, USA
| | - Yueping Xiao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Yongjie Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Haona Hong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Zhenlan Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Lingyan Zhou
- College of Agriculture & Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Guoqiang Guo
- Hengyang Academy of Agricultural Sciences, Hengyang 421101, China
| | - Yingxiang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Chuxiong Zhuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China.
| | - Hai Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China.
| |
Collapse
|
39
|
Peng R, Cao J, Zhang C, Zhou J, Su BB, Tu DY, Jiang GQ, Jin SJ, Xu YP, Bai DS. In vivo CRISPR screen identifies LTN1 as a novel tumor suppressor ubiquitinating insulin-like growth factor 2 mRNA-binding protein 1 in hepatocellular carcinoma. Hepatol Commun 2023; 7:e0256. [PMID: 37708447 PMCID: PMC10503668 DOI: 10.1097/hc9.0000000000000256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 07/15/2023] [Indexed: 09/16/2023] Open
Abstract
BACKGROUND AND AIMS Hepatocellular carcinoma (HCC) is a frequent and aggressive kind of cancer. Although E3 ligases play important roles in HCC development, several E3 ligases remain unknown. APPROACH AND RESULTS Through in vivo CRISPR knockout (KO) screens targeting related E3 ligase genes in HCC nude mice models, we discovered LTN1 as a novel tumor suppressor in HCC. Co-IP paired with 2D-LC-MS/MS and subsequent western blotting in HCC cells were used to identify the interactome of LTN1. Compared to matched normal tissues, the expression of LTN1 was decreased in human HCC tissues (ANT) (157/209). Clinically, patients with HCC who expressed low levels of LTN1 had a poor prognosis. Forced expression of LTN1 decreased cell growth in vitro and in vivo, whereas knockdown of LTN1 increased cell growth. Mechanistically, elevated LTN1 expression inhibited HCC cell growth by ubiquitinating and destabilizing the IGF2BP1 protein, which inhibited the c-Myc and IGF-1R signaling pathways. There was a negative correlation between the LTN1 protein expression and the IGF2BP1 protein expression in HCC tissues (R2=0.2799, P=0.0165). CONCLUSIONS LTN1 may be a crucial tumor suppressor for determining the prognosis and a possible therapeutic target since it inhibits the proliferation of HCC cells by ubiquitinating IGF2BP1.
Collapse
Affiliation(s)
- Rui Peng
- Department of Hepatobiliary Surgery, Clinical Medical College, Yangzhou University, Yangzhou, China
| | - Jun Cao
- Department of Hepatobiliary Surgery, Clinical Medical College, Yangzhou University, Yangzhou, China
| | - Chi Zhang
- Department of Hepatobiliary Surgery, Clinical Medical College, Yangzhou University, Yangzhou, China
| | - Jie Zhou
- Department of Hepatobiliary Surgery, Clinical Medical College, Yangzhou University, Yangzhou, China
| | - Bing-Bing Su
- Department of Hepatobiliary Surgery, Clinical Medical College, Yangzhou University, Yangzhou, China
| | - Dao-Yuan Tu
- Department of Hepatobiliary Surgery, Clinical Medical College, Yangzhou University, Yangzhou, China
| | - Guo-Qing Jiang
- Department of Hepatobiliary Surgery, Clinical Medical College, Yangzhou University, Yangzhou, China
| | - Sheng-Jie Jin
- Department of Hepatobiliary Surgery, Clinical Medical College, Yangzhou University, Yangzhou, China
| | - Ya-Ping Xu
- Department of Gastroenterology, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, China
| | - Dou-Sheng Bai
- Department of Hepatobiliary Surgery, Clinical Medical College, Yangzhou University, Yangzhou, China
| |
Collapse
|
40
|
Rödl S, Herrmann JM. The role of the proteasome in mitochondrial protein quality control. IUBMB Life 2023; 75:868-879. [PMID: 37178401 DOI: 10.1002/iub.2734] [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: 02/21/2023] [Accepted: 04/15/2023] [Indexed: 05/15/2023]
Abstract
The abundance of each cellular protein is dynamically adjusted to the prevailing metabolic and stress conditions by modulation of their synthesis and degradation rates. The proteasome represents the major machinery for the degradation of proteins in eukaryotic cells. How the ubiquitin-proteasome system (UPS) controls protein levels and removes superfluous and damaged proteins from the cytosol and the nucleus is well characterized. However, recent studies showed that the proteasome also plays a crucial role in mitochondrial protein quality control. This mitochondria-associated degradation (MAD) thereby acts on two layers: first, the proteasome removes mature, functionally compromised or mis-localized proteins from the mitochondrial surface; and second, the proteasome cleanses the mitochondrial import pore of import intermediates of nascent proteins that are stalled during translocation. In this review, we provide an overview about the components and their specific functions that facilitate proteasomal degradation of mitochondrial proteins in the yeast Saccharomyces cerevisiae. Thereby we explain how the proteasome, in conjunction with a set of intramitochondrial proteases, maintains mitochondrial protein homeostasis and dynamically adapts the levels of mitochondrial proteins to specific conditions.
Collapse
Affiliation(s)
- Saskia Rödl
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | | |
Collapse
|
41
|
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.
Collapse
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
| |
Collapse
|
42
|
Patil PR, Burroughs AM, Misra M, Cerullo F, Costas-Insua C, Hung HC, Dikic I, Aravind L, Joazeiro CAP. Mechanism and evolutionary origins of alanine-tail C-degron recognition by E3 ligases Pirh2 and CRL2-KLHDC10. Cell Rep 2023; 42:113100. [PMID: 37676773 PMCID: PMC10591846 DOI: 10.1016/j.celrep.2023.113100] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 07/11/2023] [Accepted: 08/22/2023] [Indexed: 09/09/2023] Open
Abstract
In ribosome-associated quality control (RQC), nascent polypeptides produced by interrupted translation are modified with C-terminal polyalanine tails ("Ala-tails") that function outside ribosomes to induce ubiquitylation by E3 ligases Pirh2 (p53-induced RING-H2 domain-containing) or CRL2 (Cullin-2 RING ligase2)-KLHDC10. Here, we investigate the molecular basis of Ala-tail function using biochemical and in silico approaches. We show that Pirh2 and KLHDC10 directly bind to Ala-tails and that structural predictions identify candidate Ala-tail-binding sites, which we experimentally validate. The degron-binding pockets and specific pocket residues implicated in Ala-tail recognition are conserved among Pirh2 and KLHDC10 homologs, suggesting that an important function of these ligases across eukaryotes is in targeting Ala-tailed substrates. Moreover, we establish that the two Ala-tail-binding pockets have convergently evolved, either from an ancient module of bacterial provenance (Pirh2) or via tinkering of a widespread C-degron-recognition element (KLHDC10). These results shed light on the recognition of a simple degron sequence and the evolution of Ala-tail proteolytic signaling.
Collapse
Affiliation(s)
- Pratik Rajendra Patil
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH-Alliance, 69120 Heidelberg, Germany
| | - A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Mohit Misra
- Institute of Biochemistry II, Goethe University Faculty of Medicine, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main, Germany
| | - Federico Cerullo
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH-Alliance, 69120 Heidelberg, Germany
| | - Carlos Costas-Insua
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH-Alliance, 69120 Heidelberg, Germany
| | - Hao-Chih Hung
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH-Alliance, 69120 Heidelberg, Germany
| | - Ivan Dikic
- Institute of Biochemistry II, Goethe University Faculty of Medicine, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main, Germany
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Claudio A P Joazeiro
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH-Alliance, 69120 Heidelberg, Germany; Department of Molecular Medicine, UF Scripps Biomedical Research, Jupiter, FL 33458, USA.
| |
Collapse
|
43
|
Sako H, Youssef M, Elisseeva O, Akimoto T, Suzuki K, Ushida T, Yamamoto T. microRNAs slow translating ribosomes to prevent protein misfolding in eukaryotes. EMBO J 2023; 42:e112469. [PMID: 37492926 PMCID: PMC10505912 DOI: 10.15252/embj.2022112469] [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: 08/25/2022] [Revised: 03/20/2023] [Accepted: 06/18/2023] [Indexed: 07/27/2023] Open
Abstract
Slower translation rates reduce protein misfolding. Such reductions in speed can be mediated by the presence of non-optimal codons, which allow time for proper folding to occur. Although this phenomenon is conserved from bacteria to humans, it is not known whether there are additional eukaryote-specific mechanisms which act in the same way. MicroRNAs (miRNAs), not present in prokaryotes, target both coding sequences (CDS) and 3' untranslated regions (UTR). Given their low suppressive efficiency, it has been unclear why miRNAs are equally likely to bind to a CDS. Here, we show that miRNAs transiently stall translating ribosomes, preventing protein misfolding with little negative effect on protein abundance. We first analyzed ribosome profiles and miRNA binding sites to examine whether miRNAs stall ribosomes. Furthermore, either global or specific miRNA deficiency accelerated ribosomes and induced aggregation of a misfolding-prone polypeptide reporter. These defects were rescued by slowing ribosomes using non-cleaving shRNAs as miRNA mimics. We finally show that proinsulin misfolding, associated with type II diabetes, was resolved by non-cleaving shRNAs. Our findings provide a eukaryote-specific mechanism of co-translational protein folding and a previously unknown mechanism of action to target protein misfolding diseases.
Collapse
Affiliation(s)
- Hiroaki Sako
- Cell Signal UnitOkinawa Institute of Science and Technology Graduate University (OIST)OkinawaJapan
| | - Mohieldin Youssef
- Cell Signal UnitOkinawa Institute of Science and Technology Graduate University (OIST)OkinawaJapan
| | - Olga Elisseeva
- Cell Signal UnitOkinawa Institute of Science and Technology Graduate University (OIST)OkinawaJapan
| | | | | | - Takashi Ushida
- Department of Mechanical EngineeringThe University of TokyoTokyoJapan
| | - Tadashi Yamamoto
- Cell Signal UnitOkinawa Institute of Science and Technology Graduate University (OIST)OkinawaJapan
| |
Collapse
|
44
|
Körner M, Meyer SR, Marincola G, Kern MJ, Grimm C, Schuelein-Voelk C, Fischer U, Hofmann K, Buchberger A. The FAM104 proteins VCF1/2 promote the nuclear localization of p97/VCP. eLife 2023; 12:e92409. [PMID: 37713320 PMCID: PMC10541173 DOI: 10.7554/elife.92409] [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: 09/03/2023] [Accepted: 09/10/2023] [Indexed: 09/17/2023] Open
Abstract
The ATPase p97 (also known as VCP, Cdc48) has crucial functions in a variety of important cellular processes such as protein quality control, organellar homeostasis, and DNA damage repair, and its de-regulation is linked to neuromuscular diseases and cancer. p97 is tightly controlled by numerous regulatory cofactors, but the full range and function of the p97-cofactor network is unknown. Here, we identify the hitherto uncharacterized FAM104 proteins as a conserved family of p97 interactors. The two human family members VCP nuclear cofactor family member 1 and 2 (VCF1/2) bind p97 directly via a novel, alpha-helical motif and associate with p97-UFD1-NPL4 and p97-UBXN2B complexes in cells. VCF1/2 localize to the nucleus and promote the nuclear import of p97. Loss of VCF1/2 results in reduced nuclear p97 levels, slow growth, and hypersensitivity to chemical inhibition of p97 in the absence and presence of DNA damage, suggesting that FAM104 proteins are critical regulators of nuclear p97 functions.
Collapse
Affiliation(s)
- Maria Körner
- University of Würzburg, Biocenter, Chair of Biochemistry IWürzburgGermany
| | - Susanne R Meyer
- University of Würzburg, Biocenter, Chair of Biochemistry IWürzburgGermany
| | | | - Maximilian J Kern
- Department of Molecular Cell Biology, Max Planck Institute of BiochemistryMartinsriedGermany
| | - Clemens Grimm
- University of Würzburg, Biocenter, Chair of Biochemistry IWürzburgGermany
| | | | - Utz Fischer
- University of Würzburg, Biocenter, Chair of Biochemistry IWürzburgGermany
| | - Kay Hofmann
- Institute of Genetics, University of CologneCologneGermany
| | | |
Collapse
|
45
|
Latallo MJ, Wang S, Dong D, Nelson B, Livingston NM, Wu R, Zhao N, Stasevich TJ, Bassik MC, Sun S, Wu B. Single-molecule imaging reveals distinct elongation and frameshifting dynamics between frames of expanded RNA repeats in C9ORF72-ALS/FTD. Nat Commun 2023; 14:5581. [PMID: 37696852 PMCID: PMC10495369 DOI: 10.1038/s41467-023-41339-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 08/30/2023] [Indexed: 09/13/2023] Open
Abstract
C9ORF72 hexanucleotide repeat expansion is the most common genetic cause of both amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). One pathogenic mechanism is the accumulation of toxic dipeptide repeat (DPR) proteins like poly-GA, GP and GR, produced by the noncanonical translation of the expanded RNA repeats. However, how different DPRs are synthesized remains elusive. Here, we use single-molecule imaging techniques to directly measure the translation dynamics of different DPRs. Besides initiation, translation elongation rates vary drastically between different frames, with GP slower than GA and GR the slowest. We directly visualize frameshift events using a two-color single-molecule translation assay. The repeat expansion enhances frameshifting, but the overall frequency is low. There is a higher chance of GR-to-GA shift than in the reversed direction. Finally, the ribosome-associated protein quality control (RQC) factors ZNF598 and Pelota modulate the translation dynamics, and the repeat RNA sequence is important for invoking the RQC pathway. This study reveals that multiple translation steps modulate the final DPR production. Understanding repeat RNA translation is critically important to decipher the DPR-mediated pathogenesis and identify potential therapeutic targets in C9ORF72-ALS/FTD.
Collapse
Affiliation(s)
- Malgorzata J Latallo
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Shaopeng Wang
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Daoyuan Dong
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Blake Nelson
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Nathan M Livingston
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Rong Wu
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Ning Zhao
- Department of Biochemistry and Molecular Genetics, University of Colorado-Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Timothy J Stasevich
- Department of Biochemistry and Molecular Genetics, University of Colorado-Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Michael C Bassik
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Shuying Sun
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
| | - Bin Wu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
| |
Collapse
|
46
|
McQuown AJ, Nelliat AR, Reif D, Sabbarini IM, Membreno BS, Wu CCC, Denic V. A Zpr1 co-chaperone mediates folding of eukaryotic translation elongation factor 1A via a GTPase cycle. Mol Cell 2023; 83:3108-3122.e13. [PMID: 37597513 PMCID: PMC10528422 DOI: 10.1016/j.molcel.2023.07.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/23/2023] [Accepted: 07/27/2023] [Indexed: 08/21/2023]
Abstract
General protein folding is mediated by chaperones that utilize ATP hydrolysis to regulate client binding and release. Zinc-finger protein 1 (Zpr1) is an essential ATP-independent chaperone dedicated to the biogenesis of eukaryotic translation elongation factor 1A (eEF1A), a highly abundant GTP-binding protein. How Zpr1-mediated folding is regulated to ensure rapid Zpr1 recycling remains an unanswered question. Here, we use yeast genetics and microscopy analysis, biochemical reconstitution, and structural modeling to reveal that folding of eEF1A by Zpr1 requires GTP hydrolysis. Furthermore, we identify the highly conserved altered inheritance of mitochondria 29 (Aim29) protein as a Zpr1 co-chaperone that recognizes eEF1A in the GTP-bound, pre-hydrolysis conformation. This interaction dampens Zpr1⋅eEF1A GTPase activity and facilitates client exit from the folding cycle. Our work reveals that a bespoke ATP-independent chaperone system has mechanistic similarity to ATPase chaperones but unexpectedly relies on client GTP hydrolysis to regulate the chaperone-client interaction.
Collapse
Affiliation(s)
- Alexander J McQuown
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Anjali R Nelliat
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Dvir Reif
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Ibrahim M Sabbarini
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Britnie Santiago Membreno
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Colin Chih-Chien Wu
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Vladimir Denic
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
| |
Collapse
|
47
|
Chu S, Xie X, Payan C, Stochaj U. Valosin containing protein (VCP): initiator, modifier, and potential drug target for neurodegenerative diseases. Mol Neurodegener 2023; 18:52. [PMID: 37545006 PMCID: PMC10405438 DOI: 10.1186/s13024-023-00639-y] [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: 02/20/2023] [Accepted: 06/27/2023] [Indexed: 08/08/2023] Open
Abstract
The AAA+ ATPase valosin containing protein (VCP) is essential for cell and organ homeostasis, especially in cells of the nervous system. As part of a large network, VCP collaborates with many cofactors to ensure proteostasis under normal, stress, and disease conditions. A large number of mutations have revealed the importance of VCP for human health. In particular, VCP facilitates the dismantling of protein aggregates and the removal of dysfunctional organelles. These are critical events to prevent malfunction of the brain and other parts of the nervous system. In line with this idea, VCP mutants are linked to the onset and progression of neurodegeneration and other diseases. The intricate molecular mechanisms that connect VCP mutations to distinct brain pathologies continue to be uncovered. Emerging evidence supports the model that VCP controls cellular functions on multiple levels and in a cell type specific fashion. Accordingly, VCP mutants derail cellular homeostasis through several mechanisms that can instigate disease. Our review focuses on the association between VCP malfunction and neurodegeneration. We discuss the latest insights in the field, emphasize open questions, and speculate on the potential of VCP as a drug target for some of the most devastating forms of neurodegeneration.
Collapse
Affiliation(s)
- Siwei Chu
- Department of Physiology, McGill University, Montreal, HG3 1Y6, Canada
| | - Xinyi Xie
- Department of Physiology, McGill University, Montreal, HG3 1Y6, Canada
| | - Carla Payan
- Department of Physiology, McGill University, Montreal, HG3 1Y6, Canada
| | - Ursula Stochaj
- Department of Physiology, McGill University, Montreal, HG3 1Y6, Canada.
- Quantitative Life Sciences Program, McGill University, Montreal, Canada.
| |
Collapse
|
48
|
Ju D, Li L, Xie Y. Homeostatic regulation of ribosomal proteins by ubiquitin-independent cotranslational degradation. Proc Natl Acad Sci U S A 2023; 120:e2306152120. [PMID: 37459537 PMCID: PMC10372694 DOI: 10.1073/pnas.2306152120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 06/14/2023] [Indexed: 07/20/2023] Open
Abstract
Ribosomes are the workplace for protein biosynthesis. Protein production required for normal cell function is tightly linked to ribosome abundance. It is well known that ribosomal genes are actively transcribed and ribosomal messenger RNAs (mRNAs) are rapidly translated, and yet ribosomal proteins have relatively long half-lives. These observations raise questions as to how homeostasis of ribosomal proteins is controlled. Here, we show that ribosomal proteins, while posttranslationally stable, are subject to high-level cotranslational protein degradation (CTPD) except for those synthesized as ubiquitin (Ub) fusion precursors. The N-terminal Ub moiety protects fused ribosomal proteins from CTPD. We further demonstrate that cotranslational folding efficiency and expression level are two critical factors determining CTPD of ribosomal proteins. Different from canonical posttranslational degradation, we found that CTPD of all the ribosomal proteins tested in this study does not require prior ubiquitylation. This work provides insights into the regulation of ribosomal protein homeostasis and furthers our understanding of the mechanism and biological significance of CTPD.
Collapse
Affiliation(s)
- Donghong Ju
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI48201
- Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI48201
- Department of Internal Medicine, Wayne State University School of Medicine, Detroit, MI48201
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI48201
| | - Li Li
- Department of Internal Medicine, Wayne State University School of Medicine, Detroit, MI48201
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI48201
| | - Youming Xie
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI48201
- Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI48201
| |
Collapse
|
49
|
Alagar Boopathy L, Beadle E, Xiao A, Garcia-Bueno Rico A, Alecki C, Garcia de-Andres I, Edelmeier K, Lazzari L, Amiri M, Vera M. The ribosome quality control factor Asc1 determines the fate of HSP70 mRNA on and off the ribosome. Nucleic Acids Res 2023; 51:6370-6388. [PMID: 37158240 PMCID: PMC10325905 DOI: 10.1093/nar/gkad338] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 04/16/2023] [Accepted: 04/20/2023] [Indexed: 05/10/2023] Open
Abstract
Cells survive harsh environmental conditions by potently upregulating molecular chaperones such as heat shock proteins (HSPs), particularly the inducible members of the HSP70 family. The life cycle of HSP70 mRNA in the cytoplasm is unique-it is translated during stress when most cellular mRNA translation is repressed and rapidly degraded upon recovery. Contrary to its 5' untranslated region's role in maximizing translation, we discovered that the HSP70 coding sequence (CDS) suppresses its translation via the ribosome quality control (RQC) mechanism. The CDS of the most inducible Saccharomyces cerevisiae HSP70 gene, SSA4, is uniquely enriched with low-frequency codons that promote ribosome stalling during heat stress. Stalled ribosomes are recognized by the RQC components Asc1p and Hel2p and two novel RQC components, the ribosomal proteins Rps28Ap and Rps19Bp. Surprisingly, RQC does not signal SSA4 mRNA degradation via No-Go-Decay. Instead, Asc1p destabilizes SSA4 mRNA during recovery from heat stress by a mechanism independent of ribosome binding and SSA4 codon optimality. Therefore, Asc1p operates in two pathways that converge to regulate the SSA4 mRNA life cycle during stress and recovery. Our research identifies Asc1p as a critical regulator of the stress response and RQC as the mechanism tuning HSP70 synthesis.
Collapse
Affiliation(s)
| | - Emma Beadle
- Department of Biochemistry. McGill University, Montreal, QuebecH3G 1Y6, Canada
| | - Alan RuoChen Xiao
- Department of Biochemistry. McGill University, Montreal, QuebecH3G 1Y6, Canada
| | | | - Celia Alecki
- Department of Biochemistry. McGill University, Montreal, QuebecH3G 1Y6, Canada
| | | | - Kyla Edelmeier
- Department of Biochemistry. McGill University, Montreal, QuebecH3G 1Y6, Canada
| | - Luca Lazzari
- Department of Biochemistry. McGill University, Montreal, QuebecH3G 1Y6, Canada
| | - Mehdi Amiri
- Department of Biochemistry. McGill University, Montreal, QuebecH3G 1Y6, Canada
| | - Maria Vera
- Department of Biochemistry. McGill University, Montreal, QuebecH3G 1Y6, Canada
| |
Collapse
|
50
|
Kito Y, Matsumoto A, Ichihara K, Shiraishi C, Tang R, Hatano A, Matsumoto M, Han P, Iwasaki S, Nakayama KI. The ASC-1 complex promotes translation initiation by scanning ribosomes. EMBO J 2023; 42:e112869. [PMID: 37092320 PMCID: PMC10267693 DOI: 10.15252/embj.2022112869] [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: 10/19/2022] [Revised: 03/18/2023] [Accepted: 03/27/2023] [Indexed: 04/25/2023] Open
Abstract
Translation initiates when the eIF4F complex binds the 5' mRNA cap, followed by 5' untranslated region scanning for the start codon by scanning ribosomes. Here, we demonstrate that the ASC-1 complex (ASCC), which was previously shown to promote the dissociation of colliding 80S ribosomes, associates with scanning ribosomes to regulate translation initiation. Selective translation complex profiling (TCP-seq) analysis revealed that ASCC3, a helicase domain-containing subunit of ASCC, localizes predominantly to the 5' untranslated region of mRNAs. Ribo-seq, TCP-seq, and luciferase reporter analyses showed that ASCC3 knockdown impairs 43S preinitiation complex loading and scanning dynamics, thereby reducing translation efficiency. Whereas eIF4A, an RNA helicase in the eIF4F complex, is important for global translation, ASCC was found to regulate the scanning process for a specific subset of transcripts. Our results have thus revealed that ASCC is required not only for dissociation of colliding 80S ribosomes but also for efficient translation initiation by scanning ribosomes at a subset of transcripts.
Collapse
Affiliation(s)
- Yuki Kito
- Division of Cell Biology, Medical Institute of BioregulationKyushu UniversityFukuokaJapan
| | - Akinobu Matsumoto
- Division of Cell Biology, Medical Institute of BioregulationKyushu UniversityFukuokaJapan
| | - Kazuya Ichihara
- Division of Cell Biology, Medical Institute of BioregulationKyushu UniversityFukuokaJapan
| | - Chisa Shiraishi
- Division of Cell Biology, Medical Institute of BioregulationKyushu UniversityFukuokaJapan
| | - Ronghao Tang
- Division of Cell Biology, Medical Institute of BioregulationKyushu UniversityFukuokaJapan
| | - Atsushi Hatano
- Department of Omics and Systems BiologyGraduate School of Medical and Dental Sciences, Niigata UniversityNiigataJapan
| | - Masaki Matsumoto
- Department of Omics and Systems BiologyGraduate School of Medical and Dental Sciences, Niigata UniversityNiigataJapan
| | - Peixun Han
- RNA Systems Biochemistry LaboratoryRIKEN Cluster for Pioneering ResearchWakoJapan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier SciencesThe University of TokyoKashiwaJapan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry LaboratoryRIKEN Cluster for Pioneering ResearchWakoJapan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier SciencesThe University of TokyoKashiwaJapan
| | - Keiichi I Nakayama
- Division of Cell Biology, Medical Institute of BioregulationKyushu UniversityFukuokaJapan
| |
Collapse
|