101
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Mechanism for recycling tRNAs on stalled ribosomes. Nat Struct Mol Biol 2019; 26:343-349. [PMID: 31011209 DOI: 10.1038/s41594-019-0211-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 03/06/2019] [Indexed: 11/08/2022]
Abstract
Aberrantly stalled ribosomes initiate the ribosome-associated quality control (RQC) and mRNA surveillance pathways for the degradation of potentially toxic peptides and faulty mRNAs. During RQC, ANKZF1 (yeast Vms1p) releases ubiquitinated nascent proteins from 60S ribosomal subunits for proteasomal degradation. Here, we use a cell-free system to show that ANKZF1 and Vms1p sever polypeptidyl-tRNAs on RQC complexes by precisely cleaving off the terminal 3'CCA nucleotides universal to all tRNAs. This produces a tRNA fragment that cannot be aminoacylated until its 3'CCA end is restored. The recycling of ANKZF1-cleaved tRNAs is intact in the mammalian cytosol via a two-step process that requires the removal of a 2',3'-cyclic phosphate and TRNT1, the sole CCA-adding enzyme that mediates tRNA biogenesis in eukaryotes. TRNT1 also discriminates between properly folded tRNA substrates and aberrant tRNA substrates, selectively tagging the latter for degradation. Thus, ANKZF1 liberates peptidyl-tRNAs from stalled ribosomes such that the tRNA is checked in an obligate way for integrity before reentry into the translation cycle.
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102
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Brody MJ, Vanhoutte D, Bakshi CV, Liu R, Correll RN, Sargent MA, Molkentin JD. Disruption of valosin-containing protein activity causes cardiomyopathy and reveals pleiotropic functions in cardiac homeostasis. J Biol Chem 2019; 294:8918-8929. [PMID: 31006653 DOI: 10.1074/jbc.ra119.007585] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 04/08/2019] [Indexed: 01/14/2023] Open
Abstract
Valosin-containing protein (VCP), also known as p97, is an ATPase with diverse cellular functions, although the most highly characterized is targeting of misfolded or aggregated proteins to degradation pathways, including the endoplasmic reticulum-associated degradation (ERAD) pathway. However, how VCP functions in the heart has not been carefully examined despite the fact that human mutations in VCP cause Paget disease of bone and frontotemporal dementia, an autosomal dominant multisystem proteinopathy that includes disease in the heart, skeletal muscle, brain, and bone. Here we generated heart-specific transgenic mice overexpressing WT VCP or a VCPK524A mutant with deficient ATPase activity. Transgenic mice overexpressing WT VCP exhibit normal cardiac structure and function, whereas mutant VCP-overexpressing mice develop cardiomyopathy. Mechanistically, mutant VCP-overexpressing hearts up-regulate ERAD complex components and have elevated levels of ubiquitinated proteins prior to manifestation of cardiomyopathy, suggesting dysregulation of ERAD and inefficient clearance of proteins targeted for proteasomal degradation. The hearts of mutant VCP transgenic mice also exhibit profound defects in cardiomyocyte nuclear morphology with increased nuclear envelope proteins and nuclear lamins. Proteomics revealed overwhelming interactions of endogenous VCP with ribosomal, ribosome-associated, and RNA-binding proteins in the heart, and impairment of cardiac VCP activity resulted in aggregation of large ribosomal subunit proteins. These data identify multifactorial functions and diverse mechanisms whereby VCP regulates cardiomyocyte protein and RNA quality control that are critical for cardiac homeostasis, suggesting how human VCP mutations negatively affect the heart.
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Affiliation(s)
- Matthew J Brody
- From the Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio 45229-3039
| | - Davy Vanhoutte
- From the Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio 45229-3039
| | - Chinmay V Bakshi
- From the Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio 45229-3039
| | - Ruije Liu
- From the Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio 45229-3039.,the Department of Biomedical Sciences, Grand Valley State University, Allendale, Michigan 49401, and
| | - Robert N Correll
- From the Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio 45229-3039.,the Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama 35487-0344
| | - Michelle A Sargent
- From the Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio 45229-3039
| | - Jeffery D Molkentin
- From the Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio 45229-3039, .,the Howard Hughes Medical Institute, Cincinnati, Ohio 45229-3039
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103
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Parzych K, Saavedra-García P, Valbuena GN, Al-Sadah HA, Robinson ME, Penfold L, Kuzeva DM, Ruiz-Tellez A, Loaiza S, Holzmann V, Caputo V, Johnson DC, Kaiser MF, Karadimitris A, Lam EWF, Chevet E, Feldhahn N, Keun HC, Auner HW. The coordinated action of VCP/p97 and GCN2 regulates cancer cell metabolism and proteostasis during nutrient limitation. Oncogene 2019; 38:3216-3231. [PMID: 30626938 PMCID: PMC6756015 DOI: 10.1038/s41388-018-0651-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 12/05/2018] [Accepted: 12/07/2018] [Indexed: 12/30/2022]
Abstract
VCP/p97 regulates numerous cellular functions by mediating protein degradation through its segregase activity. Its key role in governing protein homoeostasis has made VCP/p97 an appealing anticancer drug target. Here, we provide evidence that VCP/p97 acts as a regulator of cellular metabolism. We found that VCP/p97 was tied to multiple metabolic processes on the gene expression level in a diverse range of cancer cell lines and in patient-derived multiple myeloma cells. Cellular VCP/p97 dependency to maintain proteostasis was increased under conditions of glucose and glutamine limitation in a range of cancer cell lines from different tissues. Moreover, glutamine depletion led to increased VCP/p97 expression, whereas VCP/p97 inhibition perturbed metabolic processes and intracellular amino acid turnover. GCN2, an amino acid-sensing kinase, attenuated stress signalling and cell death triggered by VCP/p97 inhibition and nutrient shortages and modulated ERK activation, autophagy, and glycolytic metabolite turnover. Together, our data point to an interconnected role of VCP/p97 and GCN2 in maintaining cancer cell metabolic and protein homoeostasis.
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Affiliation(s)
- Katarzyna Parzych
- Cancer Cell Protein Metabolism Group, Centre for Haematology, Department of Medicine, Imperial College London, London, UK
| | - Paula Saavedra-García
- Cancer Cell Protein Metabolism Group, Centre for Haematology, Department of Medicine, Imperial College London, London, UK
| | - Gabriel N Valbuena
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, London, UK
| | - Hibah A Al-Sadah
- Cancer Cell Protein Metabolism Group, Centre for Haematology, Department of Medicine, Imperial College London, London, UK
| | - Mark E Robinson
- Centre for Haematology, Department of Medicine, Imperial College London, London, UK
| | - Lucy Penfold
- Cancer Cell Protein Metabolism Group, Centre for Haematology, Department of Medicine, Imperial College London, London, UK
| | - Desislava M Kuzeva
- Cancer Cell Protein Metabolism Group, Centre for Haematology, Department of Medicine, Imperial College London, London, UK
| | - Angie Ruiz-Tellez
- Cancer Cell Protein Metabolism Group, Centre for Haematology, Department of Medicine, Imperial College London, London, UK
| | - Sandra Loaiza
- Cancer Cell Protein Metabolism Group, Centre for Haematology, Department of Medicine, Imperial College London, London, UK
| | - Viktoria Holzmann
- Cancer Cell Protein Metabolism Group, Centre for Haematology, Department of Medicine, Imperial College London, London, UK
| | - Valentina Caputo
- Centre for Haematology, Department of Medicine, Imperial College London, London, UK
| | - David C Johnson
- Division of Molecular Pathfology, Institute of Cancer Research, Sutton, UK
| | - Martin F Kaiser
- Division of Molecular Pathfology, Institute of Cancer Research, Sutton, UK
| | | | - Eric W-F Lam
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, London, UK
| | - Eric Chevet
- INSERM U1242, Chemistry, Oncogenesis, Stress, Signaling, Université de Rennes 1, Rennes, France
- Centre de Lutte Contre le Cancer Eugène Marquis Rennes, Rennes, France
| | - Niklas Feldhahn
- Centre for Haematology, Department of Medicine, Imperial College London, London, UK
| | - Hector C Keun
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, London, UK
| | - Holger W Auner
- Cancer Cell Protein Metabolism Group, Centre for Haematology, Department of Medicine, Imperial College London, London, UK.
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104
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Ikeuchi K, Izawa T, Inada T. Recent Progress on the Molecular Mechanism of Quality Controls Induced by Ribosome Stalling. Front Genet 2019; 9:743. [PMID: 30705686 PMCID: PMC6344382 DOI: 10.3389/fgene.2018.00743] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 12/22/2018] [Indexed: 11/21/2022] Open
Abstract
Accurate gene expression is a prerequisite for all cellular processes. Cells actively promote correct protein folding, which prevents the accumulation of abnormal and non-functional proteins. Translation elongation is the fundamental step in gene expression to ensure cellular functions, and abnormal translation arrest is recognized and removed by the quality controls. Recent studies demonstrated that ribosome plays crucial roles as a hub for gene regulation and quality controls. Ribosome-interacting factors are critical for the quality control mechanisms responding to abnormal translation arrest by targeting its products for degradation. Aberrant mRNAs are produced by errors in mRNA maturation steps and cause aberrant translation and are eliminated by the quality control system. In this review, we focus on recent progress on two quality controls, Ribosome-associated Quality Control (RQC) and No-Go Decay (NGD), for abnormal translational elongation. These quality controls recognize aberrant ribosome stalling and induce rapid degradation of aberrant polypeptides and mRNAs thereby maintaining protein homeostasis and preventing the protein aggregation.
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Affiliation(s)
- Ken Ikeuchi
- Gene Regulation Laboratory, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Toshiaki Izawa
- Gene Regulation Laboratory, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Toshifumi Inada
- Gene Regulation Laboratory, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
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105
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Ikeuchi K, Tesina P, Matsuo Y, Sugiyama T, Cheng J, Saeki Y, Tanaka K, Becker T, Beckmann R, Inada T. Collided ribosomes form a unique structural interface to induce Hel2-driven quality control pathways. EMBO J 2019; 38:embj.2018100276. [PMID: 30609991 DOI: 10.15252/embj.2018100276] [Citation(s) in RCA: 190] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 11/19/2018] [Accepted: 12/10/2018] [Indexed: 01/17/2023] Open
Abstract
Ribosome stalling triggers quality control pathways targeting the mRNA (NGD: no-go decay) and the nascent polypeptide (RQC: ribosome-associated quality control). RQC requires Hel2-dependent uS10 ubiquitination and the RQT complex in yeast. Here, we report that Hel2-dependent uS10 ubiquitination and Slh1/Rqt2 are crucial for RQC and NGD induction within a di-ribosome (disome) unit, which consists of the leading stalled ribosome and the following colliding ribosome. Hel2 preferentially ubiquitinated a disome over a monosome on a quality control inducing reporter mRNA in an in vitro translation reaction. Cryo-EM analysis of the disome unit revealed a distinct structural arrangement suitable for recognition and modification by Hel2. The absence of the RQT complex or uS10 ubiquitination resulted in the elimination of NGD within the disome unit. Instead, we observed Hel2-mediated cleavages upstream of the disome, governed by initial Not4-mediated monoubiquitination of eS7 and followed by Hel2-mediated K63-linked polyubiquitination. We propose that Hel2-mediated ribosome ubiquitination is required both for canonical NGD (NGDRQC +) and RQC coupled to the disome and that RQC-uncoupled NGD outside the disome (NGDRQC -) can occur in a Not4-dependent manner.
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Affiliation(s)
- Ken Ikeuchi
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Petr Tesina
- Department of Biochemistry, Gene Center and Center for Integrated Protein Science Munich, University of Munich, Munich, Germany
| | - Yoshitaka Matsuo
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Takato Sugiyama
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Jingdong Cheng
- Department of Biochemistry, Gene Center and Center for Integrated Protein Science Munich, University of Munich, Munich, Germany
| | - Yasushi Saeki
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, Japan
| | - Keiji Tanaka
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, Japan
| | - Thomas Becker
- Department of Biochemistry, Gene Center and Center for Integrated Protein Science Munich, University of Munich, Munich, Germany
| | - Roland Beckmann
- Department of Biochemistry, Gene Center and Center for Integrated Protein Science Munich, University of Munich, Munich, Germany
| | - Toshifumi Inada
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
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106
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Knorr AG, Schmidt C, Tesina P, Berninghausen O, Becker T, Beatrix B, Beckmann R. Ribosome-NatA architecture reveals that rRNA expansion segments coordinate N-terminal acetylation. Nat Struct Mol Biol 2018; 26:35-39. [PMID: 30559462 DOI: 10.1038/s41594-018-0165-y] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 11/09/2018] [Indexed: 12/11/2022]
Abstract
The majority of eukaryotic proteins are N-terminally α-acetylated by N-terminal acetyltransferases (NATs). Acetylation usually occurs co-translationally and defects have severe consequences. Nevertheless, it is unclear how these enzymes act in concert with the translating ribosome. Here, we report the structure of a native ribosome-NatA complex from Saccharomyces cerevisiae. NatA (comprising Naa10, Naa15 and Naa50) displays a unique mode of ribosome interaction by contacting eukaryotic-specific ribosomal RNA expansion segments in three out of four binding patches. Thereby, NatA is dynamically positioned directly underneath the ribosomal exit tunnel to facilitate modification of the emerging nascent peptide chain. Methionine amino peptidases, but not chaperones or signal recognition particle, would be able to bind concomitantly. This work assigns a function to the hitherto enigmatic ribosomal RNA expansion segments and provides mechanistic insights into co-translational protein maturation by N-terminal acetylation.
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Affiliation(s)
- Alexandra G Knorr
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Christian Schmidt
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Petr Tesina
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Otto Berninghausen
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Thomas Becker
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany.
| | - Birgitta Beatrix
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany.
| | - Roland Beckmann
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany.
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107
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Simms CL, Kim KQ, Yan LL, Qiu J, Zaher HS. Interactions between the mRNA and Rps3/uS3 at the entry tunnel of the ribosomal small subunit are important for no-go decay. PLoS Genet 2018; 14:e1007818. [PMID: 30475795 PMCID: PMC6283612 DOI: 10.1371/journal.pgen.1007818] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 12/06/2018] [Accepted: 11/07/2018] [Indexed: 11/25/2022] Open
Abstract
No-go Decay (NGD) is a process that has evolved to deal with stalled ribosomes resulting from structural blocks or aberrant mRNAs. The process is distinguished by an endonucleolytic cleavage prior to degradation of the transcript. While many of the details of the pathway have been described, the identity of the endonuclease remains unknown. Here we identify residues of the small subunit ribosomal protein Rps3 that are important for NGD by affecting the cleavage reaction. Mutation of residues within the ribosomal entry tunnel that contact the incoming mRNA leads to significantly reduced accumulation of cleavage products, independent of the type of stall sequence, and renders cells sensitive to damaging agents thought to trigger NGD. These phenotypes are distinct from those seen in combination with other NGD factors, suggesting a separate role for Rps3 in NGD. Conversely, ribosomal proteins ubiquitination is not affected by rps3 mutations, indicating that upstream ribosome quality control (RQC) events are not dependent on these residues. Together, these results suggest that Rps3 is important for quality control on the ribosome and strongly supports the notion that the ribosome itself plays a central role in the endonucleolytic cleavage reaction during NGD. In all organisms, optimum cellular fitness depends on the ability of cells to recognize and degrade aberrant molecules. Messenger RNA is subject to alterations and, as a result, often presents roadblocks for the translating ribosomes. It is not surprising, then, that organisms evolved pathways to resolve these valuable stuck ribosomes. In eukaryotes, this process is called no-go decay (NGD) because it is coupled with decay of mRNAs that are associated with ribosomes that do not ‘go’. This decay process initiates with cleavage of the mRNA near the stall site, but some important details about this reaction are lacking. Here, we show that the ribosome itself is very central to the cleavage reaction. In particular, we identified a pair of residues of a ribosomal protein to be important for cleavage efficiency. These observations are consistent with prior structural studies showing that the residues make intimate contacts with the incoming mRNA in the entry tunnel. Altogether our data provide important clues about this quality-control pathway and suggest that the endonuclease not only recognizes stalled ribosomes but may have coevolved with the translation machinery to take advantage of certain residues of the ribosome to fulfill its function.
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MESH Headings
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/metabolism
- Amino Acid Sequence
- Amino Acid Substitution
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Endoribonucleases/genetics
- Endoribonucleases/metabolism
- GTP-Binding Proteins/genetics
- GTP-Binding Proteins/metabolism
- Genes, Fungal
- Models, Molecular
- Mutagenesis, Site-Directed
- Mutation
- Peptide Chain Elongation, Translational
- Protein Conformation
- RNA Stability
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Ribosomal Proteins/chemistry
- Ribosomal Proteins/genetics
- Ribosomal Proteins/metabolism
- Ribosome Subunits, Small/genetics
- Ribosome Subunits, Small/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/chemistry
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Sequence Homology, Amino Acid
- Ubiquitination
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Affiliation(s)
- Carrie L. Simms
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Kyusik Q. Kim
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Liewei L. Yan
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Jessica Qiu
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Hani S. Zaher
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
- * E-mail:
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108
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Wang J, Zhou J, Yang Q, Grayhack EJ. Multi-protein bridging factor 1(Mbf1), Rps3 and Asc1 prevent stalled ribosomes from frameshifting. eLife 2018; 7:39637. [PMID: 30465652 PMCID: PMC6301793 DOI: 10.7554/elife.39637] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 11/21/2018] [Indexed: 12/17/2022] Open
Abstract
Reading frame maintenance is critical for accurate translation. We show that the conserved eukaryotic/archaeal protein Mbf1 acts with ribosomal proteins Rps3/uS3 and eukaryotic Asc1/RACK1 to prevent frameshifting at inhibitory CGA-CGA codon pairs in the yeast Saccharomyces cerevisiae. Mutations in RPS3 that allow frameshifting implicate eukaryotic conserved residues near the mRNA entry site. Mbf1 and Rps3 cooperate to maintain the reading frame of stalled ribosomes, while Asc1 also mediates distinct events that result in recruitment of the ribosome quality control complex and mRNA decay. Frameshifting occurs through a +1 shift with a CGA codon in the P site and involves competition between codons entering the A site, implying that the wobble interaction of the P site codon destabilizes translation elongation. Thus, eukaryotes have evolved unique mechanisms involving both a universally conserved ribosome component and two eukaryotic-specific proteins to maintain the reading frame at ribosome stalls. Proteins perform all the chemical reactions needed to keep a cell alive; thus, it is essential to assemble them correctly. They are made by molecular machines called ribosomes, which follow a sequence of instructions written in genetic code in molecules known as mRNAs. Ribosomes essentially read the genetic code three letters at a time; each triplet either codes for the insertion of one of 20 building blocks into the emerging protein, or serves as a signal to stop the process. It is critical that, after reading one triplet, the ribosome moves precisely three letters to read the next triplet. If, for example, the ribosome shifted just two letters instead of three – a phenomenon known as “frameshifting” – it would completely change the building blocks that were used to make the protein. This could lead to atypical or aberrant proteins that either do not work or are even toxic to the cell. For a variety of reasons, ribosomes will often stall before they have finished building a protein. When this happens, the ribosome is more likely to frameshift. Cells commonly respond to stalled ribosomes by recruiting other molecules that work as quality control systems, some of which can disassemble the ribosome and break down the mRNA. In budding yeast, one part of the ribosome – named Asc1 – plays a key role in recruiting these quality control systems and in mRNA breakdown. If this component is removed, stalled ribosomes frameshift more frequently and, as a result, aberrant proteins accumulate in the cell. Since the Asc1 recruiter protein sits on the outside of the ribosome, it seemed likely that it might act through other factors to stop the ribosome from frameshifting when it stalls. However, it was unknown if such factors exist, what they are, or how they might work. Now, Wang et al. have identified two additional yeast proteins, named Mbf1 and Rps3, which cooperate to stop the ribosome from frameshifting after it stalls. Rps3, like Asc1, is a component of the ribosome, while Mbf1 is not. It appears that Rps3 likely stops frameshifting via an interaction with the incoming mRNA, because a region of Rps3 near the mRNA entry site to the ribosome is important for its activity. Further experiments then showed that the known Asc1-mediated breakdown of mRNAs did not depend on Mbf1 and Rps3, but also assists in stopping frameshifting. Thus, frameshifting of stalled ribosomes is prevented via two distinct ways: one that directly involves Mbf1 and Rps3 and one that is promoted by Asc1, which reduces the amounts of mRNAs on which ribosomes frameshift. These newly identified factors may provide insights into the precisely controlled protein-production machinery in the cell and into roles of the quality control systems. An improved understanding of mechanisms that prevent frameshifting could eventually lead to better treatments for some human diseases that result when these processes go awry, which include certain neurological conditions.
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Affiliation(s)
- Jiyu Wang
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York.,Center for RNA Biology, University of Rochester, Rochester, New York
| | - Jie Zhou
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York
| | - Qidi Yang
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York
| | - Elizabeth J Grayhack
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York.,Center for RNA Biology, University of Rochester, Rochester, New York
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109
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Cesaratto F, Sasset L, Myers MP, Re A, Petris G, Burrone OR. BiP/GRP78 Mediates ERAD Targeting of Proteins Produced by Membrane-Bound Ribosomes Stalled at the STOP-Codon. J Mol Biol 2018; 431:123-141. [PMID: 30367842 PMCID: PMC7094721 DOI: 10.1016/j.jmb.2018.10.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 10/15/2018] [Accepted: 10/16/2018] [Indexed: 11/29/2022]
Abstract
Translational stalling of ribosome bound to endoplasmic reticulum (ER) membrane requires an accurate clearance of the associated polypeptides, which is not completely understood in mammals. We characterized in mammalian cells the model of ribosomal stalling at the STOP-codon based on proteins tagged at the C-terminus with the picornavirus 2A peptide followed by a termination codon instead of the Proline (2A*). We exploited the 2A* stalling model to characterize the pathway of degradation of ER-targeted polypeptides. We report that the ER chaperone BiP/GRP78 is a new main factor involved. Moreover, degradation of the ER-stalled polypeptides required the activities of the AAA-ATPase VCP/p97, its associated deubiquitinylase YOD1, the ribosome-associated ubiquitin ligase Listerin and the proteasome. In human proteome, we found two human C-terminal amino acid sequences that cause similar stalling at the STOP-codon. Our data suggest that translational stalling at the ER membrane activates protein degradation at the interface of ribosomal- and ER-associated quality control systems. Ribosomal stalling at the STOP-codon causes degradation of the translated protein. Picornavirus 2A peptide and related sequences cause ribosome stalling at STOP-codon. BiP/GRP78 recognizes polypeptides produced by membrane-bound stalled ribosomes. ER-stalled polypeptides are disposed of through the ERAD pathway. BIP/GRP78 is a novel key player for ERAD targeting of stalled ribosomal peptides.
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Affiliation(s)
- Francesca Cesaratto
- Laboratory of Molecular Immunology, International Centre for Genetic Engineering and Biotechnology, ICGEB, Padriciano 99, 34149 Trieste, Italy
| | - Linda Sasset
- Laboratory of Molecular Immunology, International Centre for Genetic Engineering and Biotechnology, ICGEB, Padriciano 99, 34149 Trieste, Italy
| | - Michael P Myers
- Laboratory of Protein Networks, International Centre for Genetic Engineering and Biotechnology, ICGEB, Padriciano 99, 34149 Trieste, Italy
| | - Angela Re
- Centre for Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento, Italy; Center for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, C.so Trento 21, 10129 Torino, Italy; Center for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, C.so Trento 21, 10129 Torino, Italy
| | - Gianluca Petris
- Centre for Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento, Italy.
| | - Oscar R Burrone
- Laboratory of Molecular Immunology, International Centre for Genetic Engineering and Biotechnology, ICGEB, Padriciano 99, 34149 Trieste, Italy.
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110
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Karamyshev AL, Karamysheva ZN. Lost in Translation: Ribosome-Associated mRNA and Protein Quality Controls. Front Genet 2018; 9:431. [PMID: 30337940 PMCID: PMC6180196 DOI: 10.3389/fgene.2018.00431] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 09/11/2018] [Indexed: 12/15/2022] Open
Abstract
Aberrant, misfolded, and mislocalized proteins are often toxic to cells and result in many human diseases. All proteins and their mRNA templates are subject to quality control. There are several distinct mechanisms that control the quality of mRNAs and proteins during translation at the ribosome. mRNA quality control systems, nonsense-mediated decay, non-stop decay, and no-go decay detect premature stop codons, the absence of a natural stop codon, and stalled ribosomes in translation, respectively, and degrade their mRNAs. Defective truncated polypeptide nascent chains generated from faulty mRNAs are degraded by ribosome-associated protein quality control pathways. Regulation of aberrant protein production, a novel pathway, senses aberrant proteins by monitoring the status of nascent chain interactions during translation and triggers degradation of their mRNA. Here, we review the current progress in understanding of the molecular mechanisms of mRNA and protein quality controls at the ribosome during translation.
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Affiliation(s)
- Andrey L Karamyshev
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | - Zemfira N Karamysheva
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
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111
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Kuroha K, Zinoviev A, Hellen CUT, Pestova TV. Release of Ubiquitinated and Non-ubiquitinated Nascent Chains from Stalled Mammalian Ribosomal Complexes by ANKZF1 and Ptrh1. Mol Cell 2018; 72:286-302.e8. [PMID: 30244831 DOI: 10.1016/j.molcel.2018.08.022] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/24/2018] [Accepted: 08/15/2018] [Indexed: 01/08/2023]
Abstract
The ribosome-associated quality control (RQC) pathway degrades nascent chains (NCs) arising from interrupted translation. First, recycling factors split stalled ribosomes, yielding NC-tRNA/60S ribosome-nascent chain complexes (60S RNCs). 60S RNCs associate with NEMF, which recruits the E3 ubiquitin ligase Listerin that ubiquitinates NCs. The mechanism of subsequent ribosomal release of Ub-NCs remains obscure. We found that, in non-ubiquitinated 60S RNCs and 80S RNCs formed on non-stop mRNAs, tRNA is not firmly fixed in the P site, which allows peptidyl-tRNA hydrolase Ptrh1 to cleave NC-tRNA, suggesting the existence of a pathway involving release of non-ubiquitinated NCs. Association with NEMF and Listerin and ubiquitination of NCs results in accommodation of NC-tRNA, rendering 60S RNCs resistant to Ptrh1 but susceptible to ANKZF1, which induces specific cleavage in the tRNA acceptor arm, releasing proteasome-degradable Ub-NCs linked to four 3'-terminal tRNA nucleotides. We also found that TCF25, a poorly characterized RQC component, ensures preferential formation of the K48-ubiquitin linkage.
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Affiliation(s)
- Kazushige Kuroha
- Department of Cell Biology, SUNY Downstate Medical Center, Brooklyn, NY 11203, USA.
| | - Alexandra Zinoviev
- Department of Cell Biology, SUNY Downstate Medical Center, Brooklyn, NY 11203, USA
| | | | - Tatyana V Pestova
- Department of Cell Biology, SUNY Downstate Medical Center, Brooklyn, NY 11203, USA.
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112
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Arthur LL, Djuranovic S. PolyA tracks, polybasic peptides, poly-translational hurdles. WILEY INTERDISCIPLINARY REVIEWS. RNA 2018; 9:e1486. [PMID: 29869837 PMCID: PMC6281860 DOI: 10.1002/wrna.1486] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 04/25/2018] [Accepted: 04/26/2018] [Indexed: 12/26/2022]
Abstract
The abundance of messenger RNA (mRNA) is one of the major determinants of protein synthesis. As such, factors that influence mRNA stability often contribute to gene regulation. Polyadenylation of the 3' end of mRNA transcripts, the poly(A) tail, has long been recognized as one of these regulatory elements given its influence on translation efficiency and mRNA stability. Unwanted translation of the poly(A) tail signals to the cell an aberrant polyadenylation event or the lack of stop codons, which makes this sequence an important element in translation fidelity and mRNA surveillance response. Consequently, investigations into the effects of the poly(A) tail lead to the discoveries that poly-lysine as well as other polybasic peptide sequences and, to a much greater extent, polyA mRNA sequences within the open reading frame influence mRNA stability and translational efficiency. Conservation and evolutionary selection of codon usage in polyA track sequences across multiple organisms suggests a biological significance for coding polyA tracks in the regulation of gene expression. Here, we discuss the cellular responses and consequences of coding polyA track translation and synthesis of polybasic peptides. This article is categorized under: Translation > Translation Mechanisms Translation > Translation Regulation RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms.
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Affiliation(s)
- Laura L Arthur
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri
| | - Sergej Djuranovic
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri
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113
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Conservation of mRNA quality control factor Ski7 and its diversification through changes in alternative splicing and gene duplication. Proc Natl Acad Sci U S A 2018; 115:E6808-E6816. [PMID: 29967155 DOI: 10.1073/pnas.1801997115] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Eukaryotes maintain fidelity of gene expression by preferential degradation of aberrant mRNAs that arise by errors in RNA processing reactions. In Saccharomyces cerevisiae, Ski7 plays an important role in this mRNA quality control by mediating mRNA degradation by the RNA exosome. Ski7 was initially thought to be restricted to Saccharomyces cerevisiae and close relatives because the SKI7 gene and its paralog HBS1 arose by whole genome duplication (WGD) in a recent ancestor. We have recently shown that the preduplication gene was alternatively spliced and that Ski7 function predates WGD. Here, we use transcriptome analysis of diverse eukaryotes to show that diverse eukaryotes use alternative splicing of SKI7/HBS1 to encode two proteins. Although alternative splicing affects the same intrinsically disordered region of the protein, the pattern of splice site usage varies. This alternative splicing event arose in an early eukaryote that is a common ancestor of plants, animals, and fungi. Remarkably, through changes in alternative splicing and gene duplication, the Ski7 protein has diversified such that different species express one of four distinct Ski7-like proteins. We also show experimentally that the Saccharomyces cerevisiae SKI7 gene has undergone multiple changes that are incompatible with the Hbs1 function and may also have undergone additional changes to optimize mRNA quality control. The combination of transcriptome analysis in diverse eukaryotes and genetic analysis in yeast clarifies the mechanism by which a Ski7-like protein is expressed across eukaryotes and provides a unique view of changes in alternative splicing patterns of one gene over long evolutionary time.
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114
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Zurita Rendón O, Fredrickson EK, Howard CJ, Van Vranken J, Fogarty S, Tolley ND, Kalia R, Osuna BA, Shen PS, Hill CP, Frost A, Rutter J. Vms1p is a release factor for the ribosome-associated quality control complex. Nat Commun 2018; 9:2197. [PMID: 29875445 PMCID: PMC5989216 DOI: 10.1038/s41467-018-04564-3] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 05/03/2018] [Indexed: 12/02/2022] Open
Abstract
Eukaryotic cells employ the ribosome-associated quality control complex (RQC) to maintain homeostasis despite defects that cause ribosomes to stall. The RQC comprises the E3 ubiquitin ligase Ltn1p, the ATPase Cdc48p, Rqc1p, and Rqc2p. Upon ribosome stalling and splitting, the RQC assembles on the 60S species containing unreleased peptidyl-tRNA (60S:peptidyl–tRNA). Ltn1p and Rqc1p facilitate ubiquitination of the incomplete nascent chain, marking it for degradation. Rqc2p stabilizes Ltn1p on the 60S and recruits charged tRNAs to the 60S to catalyze elongation of the nascent protein with carboxy-terminal alanine and threonine extensions (CAT tails). By mobilizing the nascent chain, CAT tailing can expose lysine residues that are hidden in the exit tunnel, thereby supporting efficient ubiquitination. If the ubiquitin–proteasome system is overwhelmed or unavailable, CAT-tailed nascent chains can aggregate in the cytosol or within organelles like mitochondria. Here we identify Vms1p as a tRNA hydrolase that releases stalled polypeptides engaged by the RQC. The ribosome-associated quality control complex (RQC) functions to disassemble stalled ribosomes. Here the authors find that the tRNA hydrolase Vms1 is involved in the release of nascent peptide from stalled ribosomes.
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Affiliation(s)
- Olga Zurita Rendón
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815-6789, USA.,Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA
| | - Eric K Fredrickson
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA
| | - Conor J Howard
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, 94158, USA.,California Institute for Quantitative Biomedical Research, San Francisco, CA, 94158, USA
| | - Jonathan Van Vranken
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA
| | - Sarah Fogarty
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815-6789, USA.,Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA
| | - Neal D Tolley
- Molecular Medicine Program, University of Utah, Salt Lake City, UT, 84112, USA
| | - Raghav Kalia
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA.,Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, 94158, USA.,California Institute for Quantitative Biomedical Research, San Francisco, CA, 94158, USA
| | - Beatriz A Osuna
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, 94158, USA.,Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Peter S Shen
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA
| | - Christopher P Hill
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA
| | - Adam Frost
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA. .,Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, 94158, USA. .,California Institute for Quantitative Biomedical Research, San Francisco, CA, 94158, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
| | - Jared Rutter
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815-6789, USA. .,Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA.
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115
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Alberti S, Carra S. Quality Control of Membraneless Organelles. J Mol Biol 2018; 430:4711-4729. [PMID: 29758260 DOI: 10.1016/j.jmb.2018.05.013] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 05/04/2018] [Accepted: 05/04/2018] [Indexed: 02/06/2023]
Abstract
The formation of membraneless organelles (MLOs) by phase separation has emerged as a new way of organizing the cytoplasm and nucleoplasm of cells. Examples of MLOs forming via phase separation are nucleoli in the nucleus and stress granules in the cytoplasm. The main components of these MLOs are macromolecules such as RNAs and proteins. In order to assemble by phase separation, these proteins and RNAs have to undergo many cooperative interactions. These cooperative interactions are supported by specific molecular features within phase-separating proteins, such as multivalency and the presence of disordered domains that promote weak and transient interactions. However, these features also predispose phase-separating proteins to aberrant behavior. Indeed, evidence is emerging for a strong link between phase-separating proteins, MLOs, and age-related diseases. In this review, we discuss recent progress in understanding the formation, properties, and functions of MLOs. We pay special attention to the emerging link between MLOs and age-related diseases, and we explain how changes in the composition and physical properties of MLOs promote their conversion into an aberrant state. Furthermore, we discuss the key role of the protein quality control machinery in regulating the properties and functions of MLOs and thus in preventing age-related diseases.
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Affiliation(s)
- Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.
| | - Serena Carra
- Department of Biomedical, Metabolic and Neural Science, University of Modena and Reggio Emilia, Center for Neuroscience and Neurotechnology, 41125 Modena, Italy.
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116
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Multilayered Reprogramming in Response to Persistent DNA Damage in C. elegans. Cell Rep 2018; 20:2026-2043. [PMID: 28854356 PMCID: PMC5583510 DOI: 10.1016/j.celrep.2017.08.028] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 06/30/2017] [Accepted: 08/04/2017] [Indexed: 11/23/2022] Open
Abstract
DNA damage causally contributes to aging and age-related diseases. Mutations in nucleotide excision repair (NER) genes cause highly complex congenital syndromes characterized by growth retardation, cancer susceptibility, and accelerated aging in humans. Orthologous mutations in Caenorhabditis elegans lead to growth delay, genome instability, and accelerated functional decline, thus allowing investigation of the consequences of persistent DNA damage during development and aging in a simple metazoan model. Here, we conducted proteome, lipidome, and phosphoproteome analysis of NER-deficient animals in response to UV treatment to gain comprehensive insights into the full range of physiological adaptations to unrepaired DNA damage. We derive metabolic changes indicative of a tissue maintenance program and implicate an autophagy-mediated proteostatic response. We assign central roles for the insulin-, EGF-, and AMPK-like signaling pathways in orchestrating the adaptive response to DNA damage. Our results provide insights into the DNA damage responses in the organismal context.
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117
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Abstract
C-terminal polylysine (PL) can be synthesized from the polyadenine tail of prematurely cleaved mRNAs or when a read-though of a stop codon happens. Due to the highly positive charge, PL stalls in the electrostatically negative ribosomal exit channel. The stalled polypeptide recruits the Ribosome-associated quality control (RQC) complex which processes and extracts the nascent chain. Dysfunction of the RQC leads to the accumulation of PL-tagged proteins, induction of a stress response, and cellular toxicity. Not much is known about the PL-specific aspect of protein quality control. Using quantitative mass spectrometry, we uncovered the post-ribosomal PL-processing machinery in human cytosol. It encompasses key cytosolic complexes of the proteostasis network, such as chaperonin TCP-1 ring complexes (TRiC) and half-capped 19S-20S proteasomes. Furthermore, we found that the nuclear transport machinery associates with PL, which suggests a novel mechanism by which faulty proteins can be compartmentalized in the cell. The enhanced nuclear import of a PL-tagged polypeptide confirmed this implication, which leads to questions regarding the biological rationale behind it.
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118
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Verma R, Reichermeier KM, Burroughs AM, Oania RS, Reitsma JM, Aravind L, Deshaies RJ. Vms1 and ANKZF1 peptidyl-tRNA hydrolases release nascent chains from stalled ribosomes. Nature 2018; 557:446-451. [PMID: 29632312 PMCID: PMC6226276 DOI: 10.1038/s41586-018-0022-5] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 02/08/2018] [Indexed: 11/30/2022]
Affiliation(s)
- Rati Verma
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA.,Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.,Amgen Discovery Research, Thousand Oaks, CA, USA
| | - Kurt M Reichermeier
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.,Genentech, South San Francisco, CA, USA
| | - A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Robert S Oania
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA.,Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Justin M Reitsma
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
| | - Raymond J Deshaies
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA. .,Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA. .,Amgen Discovery Research, Thousand Oaks, CA, USA.
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119
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Ibrahim F, Maragkakis M, Alexiou P, Mourelatos Z. Ribothrypsis, a novel process of canonical mRNA decay, mediates ribosome-phased mRNA endonucleolysis. Nat Struct Mol Biol 2018; 25:302-310. [PMID: 29507394 PMCID: PMC5889319 DOI: 10.1038/s41594-018-0042-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 01/30/2018] [Indexed: 01/06/2023]
Abstract
mRNAs transmit the genetic information that dictates protein production and are a nexus for numerous pathways that regulate gene expression. The prevailing view of canonical mRNA decay is that it is mediated by deadenylation and decapping followed by exonucleolysis from the 3' and 5' ends. By developing Akron-seq, a novel approach that captures the native 3' and 5' ends of capped and polyadenylated RNAs, respectively, we show that canonical human mRNAs are subject to repeated cotranslational and ribosome-phased endonucleolytic cuts at the exit site of the mRNA ribosome channel, in a process that we term ribothrypsis. We uncovered RNA G quadruplexes among likely ribothrypsis triggers and show that ribothrypsis is a conserved process. Strikingly, we found that mRNA fragments are abundant in living cells and thus have important implications for the interpretation of experiments, such as RNA-seq, that rely on the assumption that mRNAs exist largely as full-length molecules in vivo.
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Affiliation(s)
- Fadia Ibrahim
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Medicine Translational Neuroscience Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Manolis Maragkakis
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Medicine Translational Neuroscience Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Panagiotis Alexiou
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Medicine Translational Neuroscience Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Zissimos Mourelatos
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Penn Medicine Translational Neuroscience Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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120
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Zuzow N, Ghosh A, Leonard M, Liao J, Yang B, Bennett EJ. Mapping the mammalian ribosome quality control complex interactome using proximity labeling approaches. Mol Biol Cell 2018. [PMID: 29540532 PMCID: PMC5935074 DOI: 10.1091/mbc.e17-12-0714] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Previous genetic and biochemical studies from Saccharomyces cerevisiae have identified a critical ribosome-associated quality control complex (RQC) that facilitates resolution of stalled ribosomal complexes. While components of the mammalian RQC have been examined in vitro, a systematic characterization of RQC protein interactions in mammalian cells has yet to be described. Here we utilize both proximity-labeling proteomic approaches, BioID and APEX, and traditional affinity-based strategies to both identify interacting proteins of mammalian RQC members and putative substrates for the RQC resident E3 ligase, Ltn1. Surprisingly, validation studies revealed that a subset of substrates are ubiquitylated by Ltn1 in a regulatory manner that does not result in subsequent substrate degradation. We demonstrate that Ltn1 catalyzes the regulatory ubiquitylation of ribosomal protein S6 kinase 1 and 2 (RPS6KA1, RPS6KA3). Further, loss of Ltn1 function results in hyperactivation of RSK1/2 signaling without impacting RSK1/2 protein turnover. These results suggest that Ltn1-mediated RSK1/2 ubiquitylation is inhibitory and establishes a new role for Ltn1 in regulating mitogen-activated kinase signaling via regulatory RSK1/2 ubiquitylation. Taken together, our results suggest that mammalian RQC interactions are difficult to observe and may be more transient than the homologous complex in S. cerevisiae and that Ltn1 has RQC-independent functions.
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Affiliation(s)
- Nathan Zuzow
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Arit Ghosh
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Marilyn Leonard
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Jeffrey Liao
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Bing Yang
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Eric J Bennett
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
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121
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Nillegoda NB, Wentink AS, Bukau B. Protein Disaggregation in Multicellular Organisms. Trends Biochem Sci 2018; 43:285-300. [PMID: 29501325 DOI: 10.1016/j.tibs.2018.02.003] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 01/29/2018] [Accepted: 02/01/2018] [Indexed: 12/13/2022]
Abstract
Protein aggregates are formed in cells with profoundly perturbed proteostasis, where the generation of misfolded proteins exceeds the cellular refolding and degradative capacity. They are a hallmark of protein conformational disorders and aged and/or environmentally stressed cells. Protein aggregation is a reversible process in vivo, which counteracts proteotoxicities derived from aggregate persistence, but the chaperone machineries involved in protein disaggregation in Metazoa were uncovered only recently. Here we highlight recent advances in the mechanistic understanding of the major protein disaggregation machinery mediated by the Hsp70 chaperone system and discuss emerging alternative disaggregation activities in multicellular organisms.
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Affiliation(s)
- Nadinath B Nillegoda
- Center for Molecular Biology of Heidelberg University (ZMBH), Im Neuenheimer Feld 282, 69120 Heidelberg, Germany; German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany.
| | - Anne S Wentink
- Center for Molecular Biology of Heidelberg University (ZMBH), Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Bernd Bukau
- Center for Molecular Biology of Heidelberg University (ZMBH), Im Neuenheimer Feld 282, 69120 Heidelberg, Germany; German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany.
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122
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Limoncelli KA, Merrikh CN, Moore MJ. ASC1 and RPS3: new actors in 18S nonfunctional rRNA decay. RNA (NEW YORK, N.Y.) 2017; 23:1946-1960. [PMID: 28956756 PMCID: PMC5689013 DOI: 10.1261/rna.061671.117] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 09/23/2017] [Indexed: 06/07/2023]
Abstract
In budding yeast, inactivating mutations within the 40S ribosomal subunit decoding center lead to 18S rRNA clearance by a quality control mechanism known as nonfunctional 18S rRNA decay (18S NRD). We previously showed that 18S NRD is functionally related to No-Go mRNA Decay (NGD), a pathway for clearing translation complexes stalled on aberrant mRNAs. Whereas the NGD factors Dom34p and Hbs1p contribute to 18S NRD, their genetic deletion (either singly or in combination) only partially stabilizes mutant 18S rRNA. Here we identify Asc1p (aka RACK1) and Rps3p, both stable 40S subunit components, as additional 18S NRD factors. Complete stabilization of mutant 18S rRNA in dom34Δ;asc1Δ and hbs1Δ;asc1Δ strains indicates the existence of two genetically separable 18S NRD pathways. A small region of the Rps3p C-terminal tail known to be subject to post-translational modification is also crucial for 18S NRD. We combine these findings with the effects of mutations in the 5' → 3' and 3' → 5' decay machinery to propose a model wherein multiple targeting and decay pathways kinetically contribute to 18S NRD.
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Affiliation(s)
- Kelly A Limoncelli
- Department of Biochemistry and Molecular Pharmacology, RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Christopher N Merrikh
- Department of Biochemistry and Molecular Pharmacology, RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Melissa J Moore
- Department of Biochemistry and Molecular Pharmacology, RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
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123
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VCP/p97-Mediated Unfolding as a Principle in Protein Homeostasis and Signaling. Mol Cell 2017; 69:182-194. [PMID: 29153394 DOI: 10.1016/j.molcel.2017.10.028] [Citation(s) in RCA: 262] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 10/06/2017] [Accepted: 10/20/2017] [Indexed: 01/14/2023]
Abstract
The AAA+-type ATPase p97 governs an ever-expanding number of cellular processes reaching from degradation of damaged proteins and organelles to key signaling events and chromatin regulation with thousands of client proteins. With its relevance for cellular homeostasis and genome stability, it is linked to muscular and neuronal degeneration and, conversely, constitutes an attractive anti-cancer drug target. Its molecular function is ATP-driven protein unfolding, which is directed by ubiquitin and assisted by a host of cofactor proteins. This activity underlies p97's diverse ability to pull proteins out of membranes, unfold proteins for proteasomal degradation, or segregate proteins from partners for downstream activity. Recent advances in structural analysis and biochemical reconstitution have underscored this notion, resolved detailed molecular motions within the p97 hexamer, and suggested substrate threading through the central channel of the p97 hexamer as the driving mechanism. We will discuss the mechanisms and open questions in the context of the diverse cellular activities.
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124
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Preribosomes escaping from the nucleus are caught during translation by cytoplasmic quality control. Nat Struct Mol Biol 2017; 24:1107-1115. [PMID: 29083413 DOI: 10.1038/nsmb.3495] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 10/04/2017] [Indexed: 12/28/2022]
Abstract
Assembly of fully functional ribosomes is a prerequisite for failsafe translation. This explains why maturing preribosomal subunits have to pass through an array of quality-control checkpoints, including nuclear export, to ensure that only properly assembled ribosomes engage in translation. Despite these safeguards, we found that nuclear pre-60S particles unable to remove a transient structure composed of ITS2 pre-rRNA and associated assembly factors, termed the 'foot', escape to the cytoplasm, where they can join with mature 40S subunits to catalyze protein synthesis. However, cells harboring these abnormal ribosomes show translation defects indicated by the formation of 80S ribosomes poised with pre-60S subunits carrying tRNAs in trapped hybrid states. To overcome this translational stress, the cytoplasmic surveillance machineries RQC and Ski-exosome target these malfunctioning ribosomes. Thus, pre-60S subunits that escape nuclear quality control can enter translation, but are caught by cytoplasmic surveillance mechanisms.
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125
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Izawa T, Park SH, Zhao L, Hartl FU, Neupert W. Cytosolic Protein Vms1 Links Ribosome Quality Control to Mitochondrial and Cellular Homeostasis. Cell 2017; 171:890-903.e18. [PMID: 29107329 DOI: 10.1016/j.cell.2017.10.002] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 07/15/2017] [Accepted: 09/27/2017] [Indexed: 01/09/2023]
Abstract
Eukaryotic cells have evolved extensive protein quality-control mechanisms to remove faulty translation products. Here, we show that yeast cells continually produce faulty mitochondrial polypeptides that stall on the ribosome during translation but are imported into the mitochondria. The cytosolic protein Vms1, together with the E3 ligase Ltn1, protects against the mitochondrial toxicity of these proteins and maintains cell viability under respiratory conditions. In the absence of these factors, stalled polypeptides aggregate after import and sequester critical mitochondrial chaperone and translation machinery. Aggregation depends on C-terminal alanyl/threonyl sequences (CAT-tails) that are attached to stalled polypeptides on 60S ribosomes by Rqc2. Vms1 binds to 60S ribosomes at the mitochondrial surface and antagonizes Rqc2, thereby facilitating import, impeding aggregation, and directing aberrant polypeptides to intra-mitochondrial quality control. Vms1 is a key component of a rescue pathway for ribosome-stalled mitochondrial polypeptides that are inaccessible to ubiquitylation due to coupling of translation and translocation.
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Affiliation(s)
- Toshiaki Izawa
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany; Division of Cell Biology, Biomedical Center, Faculty of Medicine, University of Munich, Großhaderner Strasse 9, 82152 Martinsried, Germany
| | - Sae-Hun Park
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Liang Zhao
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
| | - Walter Neupert
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany; Division of Cell Biology, Biomedical Center, Faculty of Medicine, University of Munich, Großhaderner Strasse 9, 82152 Martinsried, Germany.
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126
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Simms CL, Yan LL, Zaher HS. Ribosome Collision Is Critical for Quality Control during No-Go Decay. Mol Cell 2017; 68:361-373.e5. [PMID: 28943311 DOI: 10.1016/j.molcel.2017.08.019] [Citation(s) in RCA: 186] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 05/08/2017] [Accepted: 08/21/2017] [Indexed: 10/18/2022]
Abstract
No-go decay (NGD) is a eukaryotic quality control mechanism that evolved to cope with translational arrests. The process is characterized by an endonucleolytic cleavage near the stall sequence, but the mechanistic details are unclear. Our analysis of cleavage sites indicates that cleavage requires multiple ribosomes on the mRNA. We also show that reporters harboring stall sequences near the initiation codon, which cannot accommodate multiple ribosomes, are not subject to NGD. Consistent with our model, we uncover an inverse correlation between ribosome density per mRNA and cleavage efficiency. Furthermore, promoting global ribosome collision in vivo resulted in ubiquitination of ribosomal proteins, suggesting that collision is sensed by the cell to initiate downstream quality control processes. Collectively, our data suggest that NGD and subsequent quality control are triggered by ribosome collision. This model provides insight into the regulation of quality control processes and the manner by which they reduce off-target effects.
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Affiliation(s)
- Carrie L Simms
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Liewei L Yan
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Hani S Zaher
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA.
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127
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Zheng J, Yang J, Choe YJ, Hao X, Cao X, Zhao Q, Zhang Y, Franssens V, Hartl FU, Nyström T, Winderickx J, Liu B. Role of the ribosomal quality control machinery in nucleocytoplasmic translocation of polyQ-expanded huntingtin exon-1. Biochem Biophys Res Commun 2017; 493:708-717. [PMID: 28864412 DOI: 10.1016/j.bbrc.2017.08.126] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Accepted: 08/28/2017] [Indexed: 10/19/2022]
Abstract
The subcellular localization of polyQ-expanded huntingtin exon1 (Httex1) modulates polyQ toxicity in models of Huntington's disease. Using genome-wide screens in a yeast model system, we report that the ribosome quality control (RQC) machinery, recently implicated in neurodegeneration, is a key determinant for the nucleocytoplasmic distribution of Httex1-103Q. Deletion of the RQC genes, LTN1 or RQC1, caused the accumulation of Httex1-103Q in the nucleus through a process that required the CAT-tail tagging activity of Rqc2 and transport via the nuclear pore complex. We provide evidence that nuclear accumulation of Httex1-103Q enhances its cytotoxicity, suggesting that the RQC machinery plays an important role in protecting cells against the adverse effects of polyQ expansion proteins.
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Affiliation(s)
- Ju Zheng
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-413 90, Göteborg, Sweden; Department of Biology, Functional Biology, KU Leuven, 3001, Heverlee, Belgium
| | - Junsheng Yang
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-413 90, Göteborg, Sweden
| | - Young-Jun Choe
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, 82152, Germany
| | - Xinxin Hao
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-413 90, Göteborg, Sweden
| | - Xiuling Cao
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-413 90, Göteborg, Sweden
| | - Qian Zhao
- School of Life Sciences, Shandong University of Technology, 266 New Village West Road, Zhangdian District, Zibo, Shandong, China
| | - Yuejie Zhang
- School of Life Sciences, Shandong University of Technology, 266 New Village West Road, Zhangdian District, Zibo, Shandong, China
| | - Vanessa Franssens
- Department of Biology, Functional Biology, KU Leuven, 3001, Heverlee, Belgium
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, 82152, Germany
| | - Thomas Nyström
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-413 90, Göteborg, Sweden
| | - Joris Winderickx
- Department of Biology, Functional Biology, KU Leuven, 3001, Heverlee, Belgium
| | - Beidong Liu
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-413 90, Göteborg, Sweden.
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128
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Ubiquitination of stalled ribosome triggers ribosome-associated quality control. Nat Commun 2017; 8:159. [PMID: 28757607 PMCID: PMC5534433 DOI: 10.1038/s41467-017-00188-1] [Citation(s) in RCA: 205] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 06/08/2017] [Indexed: 11/08/2022] Open
Abstract
Translation arrest by polybasic sequences induces ribosome stalling, and the arrest product is degraded by the ribosome-mediated quality control (RQC) system. Here we report that ubiquitination of the 40S ribosomal protein uS10 by the E3 ubiquitin ligase Hel2 (or RQT1) is required for RQC. We identify a RQC-trigger (RQT) subcomplex composed of the RNA helicase-family protein Slh1/Rqt2, the ubiquitin-binding protein Cue3/Rqt3, and yKR023W/Rqt4 that is required for RQC. The defects in RQC of the RQT mutants correlate with sensitivity to anisomycin, which stalls ribosome at the rotated form. Cryo-electron microscopy analysis reveals that Hel2-bound ribosome are dominantly the rotated form with hybrid tRNAs. Ribosome profiling reveals that ribosomes stalled at the rotated state with specific pairs of codons at P-A sites serve as RQC substrates. Rqt1 specifically ubiquitinates these arrested ribosomes to target them to the RQT complex, allowing subsequent RQC reactions including dissociation of the stalled ribosome into subunits.Several protein quality control mechanisms are in place to trigger the rapid degradation of aberrant polypeptides and mRNAs. Here the authors describe a mechanism of ribosome-mediated quality control that involves the ubiquitination of ribosomal proteins by the E3 ubiquitin ligase Hel2/RQT1.
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129
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Kostova KK, Hickey KL, Osuna BA, Hussmann JA, Frost A, Weinberg DE, Weissman JS. CAT-tailing as a fail-safe mechanism for efficient degradation of stalled nascent polypeptides. Science 2017; 357:414-417. [PMID: 28751611 PMCID: PMC5673106 DOI: 10.1126/science.aam7787] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 05/04/2017] [Accepted: 06/28/2017] [Indexed: 12/27/2022]
Abstract
Ribosome stalling leads to recruitment of the ribosome quality control complex (RQC), which targets the partially synthesized polypeptide for proteasomal degradation through the action of the ubiquitin ligase Ltn1p. A second core RQC component, Rqc2p, modifies the nascent polypeptide by adding a carboxyl-terminal alanine and threonine (CAT) tail through a noncanonical elongation reaction. Here we examined the role of CAT-tailing in nascent-chain degradation in budding yeast. We found that Ltn1p efficiently accessed only nascent-chain lysines immediately proximal to the ribosome exit tunnel. For substrates without Ltn1p-accessible lysines, CAT-tailing enabled degradation by exposing lysines sequestered in the ribosome exit tunnel. Thus, CAT-tails do not serve as a degron, but rather provide a fail-safe mechanism that expands the range of RQC-degradable substrates.
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Affiliation(s)
- Kamena K Kostova
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kelsey L Hickey
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Beatriz A Osuna
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jeffrey A Hussmann
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Adam Frost
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - David E Weinberg
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA
- Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
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130
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Osuna BA, Howard CJ, KC S, Frost A, Weinberg DE. In vitro analysis of RQC activities provides insights into the mechanism and function of CAT tailing. eLife 2017; 6:e27949. [PMID: 28718767 PMCID: PMC5562442 DOI: 10.7554/elife.27949] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 07/11/2017] [Indexed: 12/25/2022] Open
Abstract
Ribosomes can stall during translation due to defects in the mRNA template or translation machinery, leading to the production of incomplete proteins. The Ribosome-associated Quality control Complex (RQC) engages stalled ribosomes and targets nascent polypeptides for proteasomal degradation. However, how each RQC component contributes to this process remains unclear. Here we demonstrate that key RQC activities-Ltn1p-dependent ubiquitination and Rqc2p-mediated Carboxy-terminal Alanine and Threonine (CAT) tail elongation-can be recapitulated in vitro with a yeast cell-free system. Using this approach, we determined that CAT tailing is mechanistically distinct from canonical translation, that Ltn1p-mediated ubiquitination depends on the poorly characterized RQC component Rqc1p, and that the process of CAT tailing enables robust ubiquitination of the nascent polypeptide. These findings establish a novel system to study the RQC and provide a framework for understanding how RQC factors coordinate their activities to facilitate clearance of incompletely synthesized proteins.
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Affiliation(s)
- Beatriz A Osuna
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Conor J Howard
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
- California Institute for Quantitative Biomedical Research, San Francisco, United States
- Chan Zuckerberg Biohub, San Francisco, United States
| | - Subheksha KC
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - Adam Frost
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
- California Institute for Quantitative Biomedical Research, San Francisco, United States
- Chan Zuckerberg Biohub, San Francisco, United States
- Department of Biochemistry, University of Utah, Salt Lake City, United States
| | - David E Weinberg
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
- Sandler Faculty Fellows Program, University of California, San Francisco, San Francisco, United States
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131
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Joazeiro CAP. Ribosomal Stalling During Translation: Providing Substrates for Ribosome-Associated Protein Quality Control. Annu Rev Cell Dev Biol 2017; 33:343-368. [PMID: 28715909 DOI: 10.1146/annurev-cellbio-111315-125249] [Citation(s) in RCA: 136] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cells of all organisms survey problems during translation elongation, which may happen as a consequence of mRNA aberrations, inefficient decoding, or other sources. In eukaryotes, ribosome-associated quality control (RQC) senses elongation-stalled ribosomes and promotes dissociation of ribosomal subunits. This so-called ribosomal rescue releases the mRNA for degradation and allows 40S subunits to be recycled for new rounds of translation. However, the nascent polypeptide chains remain linked to tRNA and associated with the rescued 60S subunits. As a final critical step in this pathway, the Ltn1/Listerin E3 ligase subunit of the RQC complex (RQCc) ubiquitylates the nascent chain, which promotes clearance of the 60S subunit while simultaneously marking the nascent chain for elimination. Here we review the ribosomal stalling and rescue steps upstream of the RQCc, where one witnesses intersection with cellular machineries implicated in translation elongation, translation termination, ribosomal subunit recycling, and mRNA quality control. We emphasize both recent progress and future directions in this area, as well as examples linking ribosomal rescue with the production of Ltn1-RQCc substrates.
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Affiliation(s)
- Claudio A P Joazeiro
- ZMBH, University of Heidelberg, 69120 Heidelberg, Germany; .,The Scripps Research Institute, La Jolla, California 92037
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132
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Schmidt C, Kowalinski E, Shanmuganathan V, Defenouillère Q, Braunger K, Heuer A, Pech M, Namane A, Berninghausen O, Fromont-Racine M, Jacquier A, Conti E, Becker T, Beckmann R. The cryo-EM structure of a ribosome-Ski2-Ski3-Ski8 helicase complex. Science 2017; 354:1431-1433. [PMID: 27980209 DOI: 10.1126/science.aaf7520] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 09/26/2016] [Accepted: 11/21/2016] [Indexed: 01/06/2023]
Abstract
Ski2-Ski3-Ski8 (Ski) is a helicase complex functioning with the RNA-degrading exosome to mediate the 3'-5' messenger RNA (mRNA) decay in turnover and quality-control pathways. We report that the Ski complex directly associates with 80S ribosomes presenting a short mRNA 3' overhang. We determined the structure of an endogenous ribosome-Ski complex using cryo-electron microscopy (EM) with a local resolution of the Ski complex ranging from 4 angstroms (Å) in the core to about 10 Å for intrinsically flexible regions. Ribosome binding displaces the autoinhibitory domain of the Ski2 helicase, positioning it in an open conformation near the ribosomal mRNA entry tunnel. We observe that the mRNA 3' overhang is threaded directly from the small ribosomal subunit to the helicase channel of Ski2, primed for ongoing exosome-mediated 3'-5' degradation.
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Affiliation(s)
- Christian Schmidt
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, Feodor-Lynen-Strasse 25, University of Munich, 81377 Munich, Germany
| | - Eva Kowalinski
- Max Planck Institute of Biochemistry, Department of Structural Cell Biology, Am Klopferspitz 18, 82152 Martinsried, Munich, Germany
| | - Vivekanandan Shanmuganathan
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, Feodor-Lynen-Strasse 25, University of Munich, 81377 Munich, Germany
| | - Quentin Defenouillère
- Institut Pasteur, Génétique des Interactions Macromoléculaires, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 3525, Rue du Docteur Roux 25-28, 75724 Paris, France.,Sorbonne Universités, UPMC Paris 6, Complexité du Vivant, 75252 Paris Cedex 05, France
| | - Katharina Braunger
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, Feodor-Lynen-Strasse 25, University of Munich, 81377 Munich, Germany
| | - André Heuer
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, Feodor-Lynen-Strasse 25, University of Munich, 81377 Munich, Germany
| | - Markus Pech
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, Feodor-Lynen-Strasse 25, University of Munich, 81377 Munich, Germany
| | - Abdelkader Namane
- Institut Pasteur, Génétique des Interactions Macromoléculaires, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 3525, Rue du Docteur Roux 25-28, 75724 Paris, France
| | - Otto Berninghausen
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, Feodor-Lynen-Strasse 25, University of Munich, 81377 Munich, Germany
| | - Micheline Fromont-Racine
- Institut Pasteur, Génétique des Interactions Macromoléculaires, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 3525, Rue du Docteur Roux 25-28, 75724 Paris, France
| | - Alain Jacquier
- Institut Pasteur, Génétique des Interactions Macromoléculaires, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 3525, Rue du Docteur Roux 25-28, 75724 Paris, France
| | - Elena Conti
- Max Planck Institute of Biochemistry, Department of Structural Cell Biology, Am Klopferspitz 18, 82152 Martinsried, Munich, Germany.
| | - Thomas Becker
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, Feodor-Lynen-Strasse 25, University of Munich, 81377 Munich, Germany.
| | - Roland Beckmann
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, Feodor-Lynen-Strasse 25, University of Munich, 81377 Munich, Germany.
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133
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Ye Y, Tang WK, Zhang T, Xia D. A Mighty "Protein Extractor" of the Cell: Structure and Function of the p97/CDC48 ATPase. Front Mol Biosci 2017; 4:39. [PMID: 28660197 PMCID: PMC5468458 DOI: 10.3389/fmolb.2017.00039] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 05/22/2017] [Indexed: 12/13/2022] Open
Abstract
p97/VCP (known as Cdc48 in S. cerevisiae or TER94 in Drosophila) is one of the most abundant cytosolic ATPases. It is highly conserved from archaebacteria to eukaryotes. In conjunction with a large number of cofactors and adaptors, it couples ATP hydrolysis to segregation of polypeptides from immobile cellular structures such as protein assemblies, membranes, ribosome, and chromatin. This often results in proteasomal degradation of extracted polypeptides. Given the diversity of p97 substrates, this "segregase" activity has profound influence on cellular physiology ranging from protein homeostasis to DNA lesion sensing, and mutations in p97 have been linked to several human diseases. Here we summarize our current understanding of the structure and function of this important cellular machinery and discuss the relevant clinical implications.
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Affiliation(s)
- Yihong Ye
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesda, MD, United States
| | - Wai Kwan Tang
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of HealthBethesda, MD, United States
| | - Ting Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesda, MD, United States
| | - Di Xia
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of HealthBethesda, MD, United States
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134
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Defenouillère Q, Fromont-Racine M. The ribosome-bound quality control complex: from aberrant peptide clearance to proteostasis maintenance. Curr Genet 2017; 63:997-1005. [PMID: 28528489 DOI: 10.1007/s00294-017-0708-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 05/16/2017] [Accepted: 05/17/2017] [Indexed: 01/01/2023]
Abstract
Proteostasis in eukaryotes is maintained by compartment-specific quality control pathways, which enable the refolding or the degradation of defective polypeptides to prevent the toxicity that may arise from their aggregation. Among these processes, translational protein quality control is performed by the Ribosome-bound Quality Control complex (RQC), which recognizes nascent peptides translated from aberrant mRNAs, polyubiquitylates these aberrant peptides, extracts them from the stalled 60S subunit and finally escorts them to the proteasome for degradation. In this review, we focus on the mechanism of action of the RQC complex from stalled 60S binding to aberrant peptide delivery to the proteasome and describe the cellular consequences of a deficiency in the RQC pathway, such as aberrant protein aggregation. In addition, this review covers the recent discoveries concerning the role of cytosolic chaperones, as well as Tom1, to prevent the accumulation of aberrant protein aggregates in case of a deficiency in the RQC pathway.
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Affiliation(s)
- Quentin Defenouillère
- Institut Pasteur, Génétique des Interactions Macromoléculaires, Centre National de la Recherche Scientifique, UMR 3525, 75724, Paris Cedex 15, France. .,Membrane Trafficking, Ubiquitin and Signaling, Institut Jacques Monod, UMR7592 CNRS/Université Paris-Diderot, 15 Rue Hélène Brion, Bât. Buffon, 75205, Paris Cedex 13, France.
| | - Micheline Fromont-Racine
- Institut Pasteur, Génétique des Interactions Macromoléculaires, Centre National de la Recherche Scientifique, UMR 3525, 75724, Paris Cedex 15, France
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135
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Ubiquitin- and ATP-dependent unfoldase activity of P97/VCP•NPLOC4•UFD1L is enhanced by a mutation that causes multisystem proteinopathy. Proc Natl Acad Sci U S A 2017; 114:E4380-E4388. [PMID: 28512218 DOI: 10.1073/pnas.1706205114] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
p97 is a "segregase" that plays a key role in numerous ubiquitin (Ub)-dependent pathways such as ER-associated degradation. It has been hypothesized that p97 extracts proteins from membranes or macromolecular complexes to enable their proteasomal degradation; however, the complex nature of p97 substrates has made it difficult to directly observe the fundamental basis for this activity. To address this issue, we developed a soluble p97 substrate-Ub-GFP modified with K48-linked ubiquitin chains-for in vitro p97 activity assays. We demonstrate that WT p97 can unfold proteins and that this activity is dependent on the p97 adaptor NPLOC4-UFD1L, ATP hydrolysis, and substrate ubiquitination, with branched chains providing maximal stimulation. Furthermore, we show that a p97 mutant that causes inclusion body myopathy, Paget's disease of bone, and frontotemporal dementia in humans unfolds substrate faster, suggesting that excess activity may underlie pathogenesis. This work overcomes a significant barrier in the study of p97 and will allow the future dissection of p97 mechanism at a level of detail previously unattainable.
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136
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Sitron CS, Park JH, Brandman O. Asc1, Hel2, and Slh1 couple translation arrest to nascent chain degradation. RNA (NEW YORK, N.Y.) 2017; 23:798-810. [PMID: 28223409 PMCID: PMC5393187 DOI: 10.1261/rna.060897.117] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 02/17/2017] [Indexed: 05/17/2023]
Abstract
Premature arrest of protein synthesis within the open reading frame elicits a protective response that degrades the incomplete nascent chain. In this response, arrested 80S ribosomes are split into their large and small subunits, allowing assembly of the ribosome quality control complex (RQC), which targets nascent chains for degradation. How the cell recognizes arrested nascent chains among the vast pool of actively translating polypeptides is poorly understood. We systematically examined translation arrest and modification of nascent chains in Saccharomyces cerevisiae to characterize the steps that couple arrest to RQC targeting. We focused our analysis on two poorly understood 80S ribosome-binding proteins previously implicated in the response to failed translation, Asc1 and Hel2, as well as a new component of the pathway, Slh1, that we identified here. We found that premature arrest at ribosome stalling sequences still occurred robustly in the absence of Asc1, Hel2, and Slh1. However, these three factors were required for the RQC to modify the nascent chain. We propose that Asc1, Hel2, and Slh1 target arresting ribosomes and that this targeting event is a precondition for the RQC to engage the incomplete nascent chain and facilitate its degradation.
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Affiliation(s)
- Cole S Sitron
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA
| | - Joseph H Park
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA
| | - Onn Brandman
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA
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137
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Alberti S, Mateju D, Mediani L, Carra S. Granulostasis: Protein Quality Control of RNP Granules. Front Mol Neurosci 2017; 10:84. [PMID: 28396624 PMCID: PMC5367262 DOI: 10.3389/fnmol.2017.00084] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 03/10/2017] [Indexed: 12/14/2022] Open
Abstract
Ribonucleoprotein (RNP) granules transport, store, or degrade messenger RNAs, thereby indirectly regulating protein synthesis. Normally, RNP granules are highly dynamic compartments. However, because of aging or severe environmental stress, RNP granules, in particular stress granules (SGs), convert into solid, aggregate-like inclusions. There is increasing evidence that such RNA-protein inclusions are associated with several age-related neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS), fronto-temporal dementia (FTD) and Alzheimer's disease (AD). Thus, understanding what triggers the conversion of RNP granules into aggregates and identifying the cellular players that control RNP granules will be critical to develop treatments for these diseases. In this review article, we discuss recent insight into RNP and SG formation. More specifically, we examine the evidence for liquid-liquid phase separation (LLPS) as an organizing principle of RNP granules and the role of aggregation-prone RNA-binding proteins (RBPs) in this process. We further discuss recent findings that liquid-like SGs can sequester misfolded proteins, which promote an aberrant conversion of liquid SGs into solid aggregates. Importantly, very recent studies show that a specific protein quality control (PQC) process prevents the accumulation of misfolding-prone proteins in SGs and, by doing so, maintains the dynamic state of SGs. This quality control process has been referred to as granulostasis and it relies on the specific action of the HSPB8-BAG3-HSP70 complex. Additional players such as p97/valosin containing protein (VCP) and other molecular chaperones (e.g., HSPB1) participate, directly or indirectly, in granulostasis, and ensure the timely elimination of defective ribosomal products and other misfolded proteins from SGs. Finally, we discuss recent findings that, in the stress recovery phase, SGs are preferentially disassembled with the assistance of chaperones, and we discuss evidence for a back-up system that targets aberrant SGs to the aggresome for autophagy-mediated clearance. Altogether the findings discussed here provide evidence for an intricate network of interactions between RNP granules and various components of the PQC machinery. Molecular chaperones in particular are emerging as key players that control the composition and dynamics of RNP granules, which may be important to protect against age-related diseases.
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Affiliation(s)
- Simon Alberti
- Alberti Lab, Max Planck Institute of Molecular Cell Biology and Genetics Dresden, Germany
| | - Daniel Mateju
- Alberti Lab, Max Planck Institute of Molecular Cell Biology and Genetics Dresden, Germany
| | - Laura Mediani
- Department of Biomedical, Metabolic and Neural Sciences, Center for Neuroscience and Nanotechnology, University of Modena and Reggio Emilia Modena, Italy
| | - Serena Carra
- Department of Biomedical, Metabolic and Neural Sciences, Center for Neuroscience and Nanotechnology, University of Modena and Reggio Emilia Modena, Italy
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138
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Defenouillère Q, Namane A, Mouaikel J, Jacquier A, Fromont-Racine M. The ribosome-bound quality control complex remains associated to aberrant peptides during their proteasomal targeting and interacts with Tom1 to limit protein aggregation. Mol Biol Cell 2017; 28:1165-1176. [PMID: 28298488 PMCID: PMC5415013 DOI: 10.1091/mbc.e16-10-0746] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 03/03/2017] [Accepted: 03/03/2017] [Indexed: 11/16/2022] Open
Abstract
The RQC complex involved in protein quality control mechanisms also exists as a ribosome-unbound complex during the escort of aberrant peptides to the proteasome. The E3 ubiquitin ligase Tom1 is a newly identified partner of this light version of the RQC complex and is required for aggregate prevention. Protein quality control mechanisms eliminate defective polypeptides to ensure proteostasis and to avoid the toxicity of protein aggregates. In eukaryotes, the ribosome-bound quality control (RQC) complex detects aberrant nascent peptides that remain stalled in 60S ribosomal particles due to a dysfunction in translation termination. The RQC complex polyubiquitylates aberrant polypeptides and recruits a Cdc48 hexamer to extract them from 60S particles in order to escort them to the proteasome for degradation. Whereas the steps from stalled 60S recognition to aberrant peptide polyubiquitylation by the RQC complex have been described, the mechanism leading to proteasomal degradation of these defective translation products remains unknown. We show here that the RQC complex also exists as a ribosome-unbound complex during the escort of aberrant peptides to the proteasome. In addition, we identify a new partner of this light version of the RQC complex, the E3 ubiquitin ligase Tom1. Tom1 interacts with aberrant nascent peptides and is essential to limit their accumulation and aggregation in the absence of Rqc1; however, its E3 ubiquitin ligase activity is not required. Taken together, these results reveal new roles for Tom1 in protein quality control, aggregate prevention, and, therefore, proteostasis maintenance.
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Affiliation(s)
- Quentin Defenouillère
- Institut Pasteur, Génétique des Interactions Macromoléculaires, Centre National de la Recherche Scientifique, UMR 3525, F-75724 Paris Cedex 15, France.,Sorbonne Universités, UPMC Paris 6, Complexité Du Vivant, 75252 Paris Cedex 05, France
| | - Abdelkader Namane
- Institut Pasteur, Génétique des Interactions Macromoléculaires, Centre National de la Recherche Scientifique, UMR 3525, F-75724 Paris Cedex 15, France
| | - John Mouaikel
- Institut Pasteur, Génétique des Interactions Macromoléculaires, Centre National de la Recherche Scientifique, UMR 3525, F-75724 Paris Cedex 15, France
| | - Alain Jacquier
- Institut Pasteur, Génétique des Interactions Macromoléculaires, Centre National de la Recherche Scientifique, UMR 3525, F-75724 Paris Cedex 15, France
| | - Micheline Fromont-Racine
- Institut Pasteur, Génétique des Interactions Macromoléculaires, Centre National de la Recherche Scientifique, UMR 3525, F-75724 Paris Cedex 15, France
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139
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Juszkiewicz S, Hegde RS. Initiation of Quality Control during Poly(A) Translation Requires Site-Specific Ribosome Ubiquitination. Mol Cell 2017; 65:743-750.e4. [PMID: 28065601 PMCID: PMC5316413 DOI: 10.1016/j.molcel.2016.11.039] [Citation(s) in RCA: 212] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 11/16/2016] [Accepted: 11/28/2016] [Indexed: 11/19/2022]
Abstract
Diverse cellular stressors have been observed to trigger site-specific ubiquitination on several ribosomal proteins. However, the ubiquitin ligases, biochemical consequences, and physiologic pathways linked to these modifications are not known. Here, we show in mammalian cells that the ubiquitin ligase ZNF598 is required for ribosomes to terminally stall during translation of poly(A) sequences. ZNF598-mediated stalling initiated the ribosome-associated quality control (RQC) pathway for degradation of nascent truncated proteins. Biochemical ubiquitination reactions identified two sites of mono-ubiquitination on the 40S protein eS10 as the primary ribosomal target of ZNF598. Cells lacking ZNF598 activity or containing ubiquitination-resistant eS10 ribosomes failed to stall efficiently on poly(A) sequences. In the absence of stalling, read-through of poly(A) produces a poly-lysine tag, which might alter the localization and solubility of the associated protein. Thus, ribosome ubiquitination can modulate translation elongation and impacts co-translational quality control to minimize production of aberrant proteins. Poly(A), not poly-basic tracts, are the main trigger of ribosome stalling in mammals The ubiquitin ligase ZNF598 is required to stall ribosomes during poly(A) translation ZNF598 primarily mono-ubiquitinates two lysines on the 40S ribosomal protein eS10 ZNF598 deletion or mutation of its eS10 target permits increased poly(A) translation
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140
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Inada T. The Ribosome as a Platform for mRNA and Nascent Polypeptide Quality Control. Trends Biochem Sci 2017; 42:5-15. [DOI: 10.1016/j.tibs.2016.09.005] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 09/05/2016] [Accepted: 09/13/2016] [Indexed: 11/28/2022]
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141
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Dempsey PW. CTCs and ctDNA: Two Tales of a Complex Biology. LIQUID BIOPSIES IN SOLID TUMORS 2017. [DOI: 10.1007/978-3-319-50956-3_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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142
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Belyy A, Raoux-Barbot D, Saveanu C, Namane A, Ogryzko V, Worpenberg L, David V, Henriot V, Fellous S, Merrifield C, Assayag E, Ladant D, Renault L, Mechold U. Actin activates Pseudomonas aeruginosa ExoY nucleotidyl cyclase toxin and ExoY-like effector domains from MARTX toxins. Nat Commun 2016; 7:13582. [PMID: 27917880 PMCID: PMC5150216 DOI: 10.1038/ncomms13582] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 10/13/2016] [Indexed: 12/15/2022] Open
Abstract
The nucleotidyl cyclase toxin ExoY is one of the virulence factors injected by the Pseudomonas aeruginosa type III secretion system into host cells. Inside cells, it is activated by an unknown eukaryotic cofactor to synthesize various cyclic nucleotide monophosphates. ExoY-like adenylate cyclases are also found in Multifunctional-Autoprocessing Repeats-in-ToXin (MARTX) toxins produced by various Gram-negative pathogens. Here we demonstrate that filamentous actin (F-actin) is the hitherto unknown cofactor of ExoY. Association with F-actin stimulates ExoY activity more than 10,000 fold in vitro and results in stabilization of actin filaments. ExoY is recruited to actin filaments in transfected cells and alters F-actin turnover. Actin also activates an ExoY-like adenylate cyclase MARTX effector domain from Vibrio nigripulchritudo. Finally, using a yeast genetic screen, we identify actin mutants that no longer activate ExoY. Our results thus reveal a new sub-group within the class II adenylyl cyclase family, namely actin-activated nucleotidyl cyclase (AA-NC) toxins.
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Affiliation(s)
- Alexander Belyy
- Institut Pasteur, CNRS UMR3528, Unité de Biochimie des Interactions Macromoléculaires, Département de Biologie Structurale et Chimie, 25-28 rue du Docteur Roux, 75724 Paris cedex 15, France
- Department of Bacterial Infections, Gamaleya Research Center, Moscow 123098, Russia
| | - Dorothée Raoux-Barbot
- Institut Pasteur, CNRS UMR3528, Unité de Biochimie des Interactions Macromoléculaires, Département de Biologie Structurale et Chimie, 25-28 rue du Docteur Roux, 75724 Paris cedex 15, France
| | - Cosmin Saveanu
- Institut Pasteur, CNRS UMR3525, Génétique des Interactions Macromoléculaires, Département de Génomes et Génétique, 25-28 rue du Docteur Roux, 75724 Paris cedex 15, France
| | - Abdelkader Namane
- Institut Pasteur, CNRS UMR3525, Génétique des Interactions Macromoléculaires, Département de Génomes et Génétique, 25-28 rue du Docteur Roux, 75724 Paris cedex 15, France
| | - Vasily Ogryzko
- Institut Gustave Roussy, CNRS UMR 8126, Unité de Signaling, Nuclei and Innovations in Oncology, 94805 Villejuif, France
| | - Lina Worpenberg
- Institut Pasteur, CNRS UMR3528, Unité de Biochimie des Interactions Macromoléculaires, Département de Biologie Structurale et Chimie, 25-28 rue du Docteur Roux, 75724 Paris cedex 15, France
| | - Violaine David
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Veronique Henriot
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Souad Fellous
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Christien Merrifield
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Elodie Assayag
- Institut Pasteur, CNRS UMR3528, Unité de Biochimie des Interactions Macromoléculaires, Département de Biologie Structurale et Chimie, 25-28 rue du Docteur Roux, 75724 Paris cedex 15, France
| | - Daniel Ladant
- Institut Pasteur, CNRS UMR3528, Unité de Biochimie des Interactions Macromoléculaires, Département de Biologie Structurale et Chimie, 25-28 rue du Docteur Roux, 75724 Paris cedex 15, France
| | - Louis Renault
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Undine Mechold
- Institut Pasteur, CNRS UMR3528, Unité de Biochimie des Interactions Macromoléculaires, Département de Biologie Structurale et Chimie, 25-28 rue du Docteur Roux, 75724 Paris cedex 15, France
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143
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Harper JW, Bennett EJ. Proteome complexity and the forces that drive proteome imbalance. Nature 2016; 537:328-38. [PMID: 27629639 DOI: 10.1038/nature19947] [Citation(s) in RCA: 163] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 07/29/2016] [Indexed: 12/28/2022]
Abstract
The cellular proteome is a complex microcosm of structural and regulatory networks that requires continuous surveillance and modification to meet the dynamic needs of the cell. It is therefore crucial that the protein flux of the cell remains in balance to ensure proper cell function. Genetic alterations that range from chromosome imbalance to oncogene activation can affect the speed, fidelity and capacity of protein biogenesis and degradation systems, which often results in proteome imbalance. An improved understanding of the causes and consequences of proteome imbalance is helping to reveal how these systems can be targeted to treat diseases such as cancer.
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Affiliation(s)
- J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Eric J Bennett
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093, USA
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144
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Ikeuchi K, Yazaki E, Kudo K, Inada T. Conserved functions of human Pelota in mRNA quality control of nonstop mRNA. FEBS Lett 2016; 590:3254-63. [DOI: 10.1002/1873-3468.12366] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 08/12/2016] [Accepted: 08/15/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Ken Ikeuchi
- Graduate School of Pharmaceutical Science; Tohoku University; Aoba-ku Sendai Japan
| | - Erina Yazaki
- Graduate School of Pharmaceutical Science; Tohoku University; Aoba-ku Sendai Japan
| | - Kazuhei Kudo
- Graduate School of Pharmaceutical Science; Tohoku University; Aoba-ku Sendai Japan
| | - Toshifumi Inada
- Graduate School of Pharmaceutical Science; Tohoku University; Aoba-ku Sendai Japan
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145
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Sung MK, Porras-Yakushi TR, Reitsma JM, Huber FM, Sweredoski MJ, Hoelz A, Hess S, Deshaies RJ. A conserved quality-control pathway that mediates degradation of unassembled ribosomal proteins. eLife 2016; 5. [PMID: 27552055 PMCID: PMC5026473 DOI: 10.7554/elife.19105] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Accepted: 08/19/2016] [Indexed: 12/17/2022] Open
Abstract
Overproduced yeast ribosomal protein (RP) Rpl26 fails to assemble into ribosomes and is degraded in the nucleus/nucleolus by a ubiquitin-proteasome system quality control pathway comprising the E2 enzymes Ubc4/Ubc5 and the ubiquitin ligase Tom1. tom1 cells show reduced ubiquitination of multiple RPs, exceptional accumulation of detergent-insoluble proteins including multiple RPs, and hypersensitivity to imbalances in production of RPs and rRNA, indicative of a profound perturbation to proteostasis. Tom1 directly ubiquitinates unassembled RPs primarily via residues that are concealed in mature ribosomes. Together, these data point to an important role for Tom1 in normal physiology and prompt us to refer to this pathway as ERISQ, for excess ribosomal protein quality control. A similar pathway, mediated by the Tom1 homolog Huwe1, restricts accumulation of overexpressed hRpl26 in human cells. We propose that ERISQ is a key element of the quality control machinery that sustains protein homeostasis and cellular fitness in eukaryotes.
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Affiliation(s)
- Min-Kyung Sung
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Tanya R Porras-Yakushi
- Proteome Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institue, California Institute of Technology, Pasadena, United States
| | - Justin M Reitsma
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Ferdinand M Huber
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, United States
| | - Michael J Sweredoski
- Proteome Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institue, California Institute of Technology, Pasadena, United States
| | - André Hoelz
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, United States
| | - Sonja Hess
- Proteome Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institue, California Institute of Technology, Pasadena, United States
| | - Raymond J Deshaies
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States.,Howard Hughes Medical Institute, California Institute of Technology, Pasadena, United States
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146
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Vekaria PH, Home T, Weir S, Schoenen FJ, Rao R. Targeting p97 to Disrupt Protein Homeostasis in Cancer. Front Oncol 2016; 6:181. [PMID: 27536557 PMCID: PMC4971439 DOI: 10.3389/fonc.2016.00181] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 07/22/2016] [Indexed: 12/11/2022] Open
Abstract
Cancer cells are addicted to numerous non-oncogenic traits that enable them to thrive. Proteotoxic stress is one such non-oncogenic trait that is experienced by all tumor cells owing to increased genomic abnormalities and the resulting synthesis and accumulation of non-stoichiometric amounts of cellular proteins. This imbalance in the amounts of proteins ultimately culminates in proteotoxic stress. p97, or valosin-containing protein (VCP), is an ATPase whose function is essential to restore protein homeostasis in the cells. Working in concert with the ubiquitin proteasome system, p97 promotes the retrotranslocation from cellular organelles and/or degradation of misfolded proteins. Consequently, p97 inhibition has emerged as a novel therapeutic target in cancer cells, especially those that have a highly secretory phenotype. This review summarizes our current understanding of the function of p97 in maintaining protein homeostasis and its inhibition with small molecule inhibitors as an emerging strategy to target cancer cells.
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Affiliation(s)
| | - Trisha Home
- Division of Hematologic Malignancies and Cellular Therapeutics, Kansas University Medical Center , Kansas City, KS , USA
| | - Scott Weir
- The University of Kansas Cancer Center, University of Kansas , Kansas City, KS , USA
| | - Frank J Schoenen
- Specialized Chemistry Center, University of Kansas , Lawrence, KS , USA
| | - Rekha Rao
- Division of Hematologic Malignancies and Cellular Therapeutics, Kansas University Medical Center , Kansas City, KS , USA
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147
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Doamekpor SK, Lee JW, Hepowit NL, Wu C, Charenton C, Leonard M, Bengtson MH, Rajashankar KR, Sachs MS, Lima CD, Joazeiro CAP. Structure and function of the yeast listerin (Ltn1) conserved N-terminal domain in binding to stalled 60S ribosomal subunits. Proc Natl Acad Sci U S A 2016; 113:E4151-60. [PMID: 27385828 PMCID: PMC4961192 DOI: 10.1073/pnas.1605951113] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The Ltn1 E3 ligase (listerin in mammals) has emerged as a paradigm for understanding ribosome-associated ubiquitylation. Ltn1 binds to 60S ribosomal subunits to ubiquitylate nascent polypeptides that become stalled during synthesis; among Ltn1's substrates are aberrant products of mRNA lacking stop codons [nonstop translation products (NSPs)]. Here, we report the reconstitution of NSP ubiquitylation in Neurospora crassa cell extracts. Upon translation in vitro, ribosome-stalled NSPs were ubiquitylated in an Ltn1-dependent manner, while still ribosome-associated. Furthermore, we provide biochemical evidence that the conserved N-terminal domain (NTD) plays a significant role in the binding of Ltn1 to 60S ribosomal subunits and that NTD mutations causing defective 60S binding also lead to defective NSP ubiquitylation, without affecting Ltn1's intrinsic E3 ligase activity. Finally, we report the crystal structure of the Ltn1 NTD at 2.4-Å resolution. The structure, combined with additional mutational studies, provides insight to NTD's role in binding stalled 60S subunits. Our findings show that Neurospora extracts can be used as a tool to dissect mechanisms underlying ribosome-associated protein quality control and are consistent with a model in which Ltn1 uses 60S subunits as adapters, at least in part via its NTD, to target stalled NSPs for ubiquitylation.
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Affiliation(s)
- Selom K Doamekpor
- Structural Biology Program, Sloan-Kettering Institute, New York, NY 10065
| | - Joong-Won Lee
- Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Nathaniel L Hepowit
- Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Cheng Wu
- Department of Biology, Texas A&M University, College Station, TX 77843-3258
| | - Clement Charenton
- Structural Biology Program, Sloan-Kettering Institute, New York, NY 10065
| | - Marilyn Leonard
- Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Mario H Bengtson
- Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Kanagalaghatta R Rajashankar
- Northeastern Collaborative Access Team, Advanced Photon Source, Argonne, IL 60439; Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
| | - Matthew S Sachs
- Department of Biology, Texas A&M University, College Station, TX 77843-3258;
| | - Christopher D Lima
- Structural Biology Program, Sloan-Kettering Institute, New York, NY 10065; Howard Hughes Medical Institute, Sloan-Kettering Institute, New York, NY 10065;
| | - Claudio A P Joazeiro
- Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037; Zentrum für Molekulare Biologie der Universität Heidelberg, Heidelberg D-69120, Germany; Deutsches Krebsforschungszentrum-Zentrum für Molekulare Biologie der Universität Heidelberg Alliance (ZMBH-DKFZ), Heidelberg D-69120, Germany
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148
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Xue L, Blythe EE, Freiberger EC, Mamrosh JL, Hebert AS, Reitsma JM, Hess S, Coon JJ, Deshaies RJ. Valosin-containing protein (VCP)-Adaptor Interactions are Exceptionally Dynamic and Subject to Differential Modulation by a VCP Inhibitor. Mol Cell Proteomics 2016; 15:2970-86. [PMID: 27406709 DOI: 10.1074/mcp.m116.061036] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Indexed: 11/06/2022] Open
Abstract
Protein quality control (PQC) plays an important role in stemming neurodegenerative diseases and is essential for the growth of some cancers. Valosin-containing protein (VCP)/p97 plays a pivotal role in multiple PQC pathways by interacting with numerous adaptors that link VCP to specific PQC pathways and substrates and influence the post-translational modification state of substrates. However, our poor understanding of the specificity and architecture of the adaptors, and the dynamic properties of their interactions with VCP hinders our understanding of fundamental features of PQC and how modulation of VCP activity can best be exploited therapeutically. In this study we use multiple mass spectrometry-based proteomic approaches combined with biophysical studies to characterize the interaction of adaptors with VCP. Our results reveal that most VCP-adaptor interactions are characterized by rapid dynamics that in some cases are modulated by the VCP inhibitor NMS873. These findings have significant implications for both the regulation of VCP function and the impact of VCP inhibition on different VCP-adaptor complexes.
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Affiliation(s)
- Liang Xue
- From the ‡Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, California 91125
| | - Emily E Blythe
- From the ‡Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, California 91125
| | - Elyse C Freiberger
- §Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Jennifer L Mamrosh
- From the ‡Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, California 91125
| | | | - Justin M Reitsma
- From the ‡Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, California 91125
| | - Sonja Hess
- **Proteome Exploration Laboratory (PEL), Beckman Institute, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
| | - Joshua J Coon
- §Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706; ¶Genome Center of Wisconsin, 425 Henry Mall, Madison, Wisconsin 53706; ‖Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Raymond J Deshaies
- From the ‡Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, California 91125; ‡‡Howard Hughes Medical Institute, Pasadena, California 91125
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149
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Sung MK, Reitsma JM, Sweredoski MJ, Hess S, Deshaies RJ. Ribosomal proteins produced in excess are degraded by the ubiquitin-proteasome system. Mol Biol Cell 2016; 27:2642-52. [PMID: 27385339 PMCID: PMC5007085 DOI: 10.1091/mbc.e16-05-0290] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 06/30/2016] [Indexed: 01/08/2023] Open
Abstract
Overexpression of ribosomal proteins in yeast is prevented by ubiquitination of unassembled ribosomal proteins in the nucleus and/or nucleolus followed by proteasome-dependent degradation. Brief inhibition of proteasome causes strong accumulation of multiple ribosomal proteins in an insoluble fraction, suggesting that this is a general phenomenon. Ribosome assembly is an essential process that consumes prodigious quantities of cellular resources. Ribosomal proteins cannot be overproduced in Saccharomyces cerevisiae because the excess proteins are rapidly degraded. However, the responsible quality control (QC) mechanisms remain poorly characterized. Here we demonstrate that overexpression of multiple proteins of the small and large yeast ribosomal subunits is suppressed. Rpl26 overexpressed from a plasmid can be detected in the nucleolus and nucleoplasm, but it largely fails to assemble into ribosomes and is rapidly degraded. However, if the endogenous RPL26 loci are deleted, plasmid-encoded Rpl26 assembles into ribosomes and localizes to the cytosol. Chemical and genetic perturbation studies indicate that overexpressed ribosomal proteins are degraded by the ubiquitin–proteasome system and not by autophagy. Inhibition of the proteasome led to accumulation of multiple endogenous ribosomal proteins in insoluble aggregates, consistent with the operation of this QC mechanism in the absence of ribosomal protein overexpression. Our studies reveal that ribosomal proteins that fail to assemble into ribosomes are rapidly distinguished from their assembled counterparts and ubiquitinated and degraded within the nuclear compartment.
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Affiliation(s)
- Min-Kyung Sung
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Justin M Reitsma
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Michael J Sweredoski
- Proteome Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institute, California Institute of Technology, Pasadena, CA 91125
| | - Sonja Hess
- Proteome Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institute, California Institute of Technology, Pasadena, CA 91125
| | - Raymond J Deshaies
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125 Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125
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150
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Shcherbik N, Chernova TA, Chernoff YO, Pestov DG. Distinct types of translation termination generate substrates for ribosome-associated quality control. Nucleic Acids Res 2016; 44:6840-52. [PMID: 27325745 PMCID: PMC5001609 DOI: 10.1093/nar/gkw566] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Accepted: 06/13/2016] [Indexed: 11/24/2022] Open
Abstract
Cotranslational degradation of polypeptide nascent chains plays a critical role in quality control of protein synthesis and the rescue of stalled ribosomes. In eukaryotes, ribosome stalling triggers release of 60S subunits with attached nascent polypeptides, which undergo ubiquitination by the E3 ligase Ltn1 and proteasomal degradation facilitated by the ATPase Cdc48. However, the identity of factors acting upstream in this process is less clear. Here, we examined how the canonical release factors Sup45–Sup35 (eRF1–eRF3) and their paralogs Dom34-Hbs1 affect the total population of ubiquitinated nascent chains associated with yeast ribosomes. We found that the availability of the functional release factor complex Sup45–Sup35 strongly influences the amount of ubiquitinated polypeptides associated with 60S ribosomal subunits, while Dom34-Hbs1 generate 60S-associated peptidyl-tRNAs that constitute a relatively minor fraction of Ltn1 substrates. These results uncover two separate pathways that target nascent polypeptides for Ltn1-Cdc48-mediated degradation and suggest that in addition to canonical termination on stop codons, eukaryotic release factors contribute to cotranslational protein quality control.
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Affiliation(s)
- Natalia Shcherbik
- Department of Cell Biology, Rowan University, School of Osteopathic Medicine, Stratford, NJ 08084, USA
| | - Tatiana A Chernova
- Department of Biochemistry, Emory University, School of Medicine, Atlanta, GA 30322, USA
| | - Yury O Chernoff
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30322, USA Laboratory of Amyloid Biology & Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Dimitri G Pestov
- Department of Cell Biology, Rowan University, School of Osteopathic Medicine, Stratford, NJ 08084, USA
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