51
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Thépaut M, Campos-Silva R, Renard E, Barloy-Hubler F, Ennifar E, Boujard D, Gillet R. Safe and easy in vitro evaluation of tmRNA-SmpB-mediated trans-translation from ESKAPE pathogenic bacteria. RNA (NEW YORK, N.Y.) 2021; 27:1390-1399. [PMID: 34353925 PMCID: PMC8522692 DOI: 10.1261/rna.078773.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
In bacteria, trans-translation is the major quality control system for rescuing stalled ribosomes. It is mediated by tmRNA, a hybrid RNA with properties of both a tRNA and a mRNA, and the small protein SmpB. Because trans-translation is absent in eukaryotes but necessary for bacterial fitness or survival, it is a promising target for the development of novel antibiotics. To facilitate screening of chemical libraries, various reliable in vitro and in vivo systems have been created for assessing trans-translational activity. However, the aim of the current work was to permit the safe and easy in vitro evaluation of trans-translation from pathogenic bacteria, which are obviously the ones we should be targeting. Based on green fluorescent protein (GFP) reassembly during active trans-translation, we have created a cell-free assay adapted to the rapid evaluation of trans-translation in ESKAPE bacteria, with 24 different possible combinations. It can be used for easy high-throughput screening of chemical compounds as well as for exploring the mechanism of trans-translation in these pathogens.
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Affiliation(s)
- Marion Thépaut
- Université Rennes, CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR 6290, 35043 Rennes, France
- SATT Ouest-Valorisation, 35750 Rennes, France
| | - Rodrigo Campos-Silva
- Université Rennes, CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR 6290, 35043 Rennes, France
- Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre 90610-000, Brazil
| | - Eva Renard
- Architecture et Réactivité de l'ARN-CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 67084 Strasbourg, France
| | - Frédérique Barloy-Hubler
- Université Rennes, CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR 6290, 35043 Rennes, France
| | - Eric Ennifar
- Architecture et Réactivité de l'ARN-CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 67084 Strasbourg, France
| | - Daniel Boujard
- Université Rennes, CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR 6290, 35043 Rennes, France
| | - Reynald Gillet
- Université Rennes, CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR 6290, 35043 Rennes, France
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52
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Park J, Park J, Lee J, Lim C. The trinity of ribosome-associated quality control and stress signaling for proteostasis and neuronal physiology. BMB Rep 2021. [PMID: 34488933 PMCID: PMC8505234 DOI: 10.5483/bmbrep.2021.54.9.097] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Translating ribosomes accompany co-translational regulation of nascent polypeptide chains, including subcellular targeting, protein folding, and covalent modifications. Ribosome-associated quality control (RQC) is a co-translational surveillance mechanism triggered by ribosomal collisions, an indication of atypical translation. The ribosome-associated E3 ligase ZNF598 ubiquitinates small subunit proteins at the stalled ribosomes. A series of RQC factors are then recruited to dissociate and triage aberrant translation intermediates. Regulatory ribosomal stalling may occur on endogenous transcripts for quality gene expression, whereas ribosomal collisions are more globally induced by ribotoxic stressors such as translation inhibitors, ribotoxins, and UV radiation. The latter are sensed by ribosome-associated kinases GCN2 and ZAKα, activating integrated stress response (ISR) and ribotoxic stress response (RSR), respectively. Hierarchical crosstalks among RQC, ISR, and RSR pathways are readily detectable since the collided ribosome is their common substrate for activation. Given the strong implications of RQC factors in neuronal physiology and neurological disorders, the interplay between RQC and ribosome-associated stress signaling may sustain proteostasis, adaptively determine cell fate, and contribute to neural pathogenesis. The elucidation of underlying molecular principles in relevant human diseases should thus provide unexplored therapeutic opportunities.
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Affiliation(s)
- Jumin Park
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
| | - Jongmin Park
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
| | - Jongbin Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
| | - Chunghun Lim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
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53
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Abstract
Translation of the genetic information into proteins, performed by the ribosome, is a key cellular process in all organisms. Translation usually proceeds smoothly, but, unfortunately, undesirable events can lead to stalling of translating ribosomes. To rescue these faulty arrested ribosomes, bacterial cells possess three well-characterized quality control systems, tmRNA, ArfA, and ArfB. Recently, an additional ribosome rescue mechanism has been discovered in Bacillus subtilis. In contrast to the "canonical" systems targeting the 70S bacterial ribosome, this latter mechanism operates by first splitting the ribosome into the small (30S) and large (50S) subunits to then clearing the resultant jammed large subunit from the incomplete nascent polypeptide. Here, I will discuss the recent microbiological, biochemical, and structural data regarding functioning of this novel rescue system.
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Affiliation(s)
- Maxim S Svetlov
- Center for Biomolecular Sciences, Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA.
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54
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Harwood CR, Kikuchi Y. The ins and outs of Bacillus proteases: activities, functions and commercial significance. FEMS Microbiol Rev 2021; 46:6354784. [PMID: 34410368 PMCID: PMC8767453 DOI: 10.1093/femsre/fuab046] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/17/2021] [Indexed: 12/23/2022] Open
Abstract
Because the majority of bacterial species divide by binary fission, and do not have distinguishable somatic and germline cells, they could be considered to be immortal. However, bacteria ‘age’ due to damage to vital cell components such as DNA and proteins. DNA damage can often be repaired using efficient DNA repair mechanisms. However, many proteins have a functional ‘shelf life’; some are short lived, while others are relatively stable. Specific degradation processes are built into the life span of proteins whose activities are required to fulfil a specific function during a prescribed period of time (e.g. cell cycle, differentiation process, stress response). In addition, proteins that are irreparably damaged or that have come to the end of their functional life span need to be removed by quality control proteases. Other proteases are involved in performing a variety of specific functions that can be broadly divided into three categories: processing, regulation and feeding. This review presents a systematic account of the proteases of Bacillus subtilis and their activities. It reviews the proteases found in, or associated with, the cytoplasm, the cell membrane, the cell wall and the external milieu. Where known, the impacts of the deletion of particular proteases are discussed, particularly in relation to industrial applications.
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Affiliation(s)
- Colin R Harwood
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University NE2 4AX, Newcastle upon Tyne, UK
| | - Yoshimi Kikuchi
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., Kawasaki 210-8681, JAPAN
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55
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Takada H, Crowe-McAuliffe C, Polte C, Sidorova ZY, Murina V, Atkinson GC, Konevega AL, Ignatova Z, Wilson DN, Hauryliuk V. RqcH and RqcP catalyze processive poly-alanine synthesis in a reconstituted ribosome-associated quality control system. Nucleic Acids Res 2021; 49:8355-8369. [PMID: 34255840 PMCID: PMC8373112 DOI: 10.1093/nar/gkab589] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/21/2021] [Accepted: 06/24/2021] [Indexed: 01/13/2023] Open
Abstract
In the cell, stalled ribosomes are rescued through ribosome-associated protein quality-control (RQC) pathways. After splitting of the stalled ribosome, a C-terminal polyalanine 'tail' is added to the unfinished polypeptide attached to the tRNA on the 50S ribosomal subunit. In Bacillus subtilis, polyalanine tailing is catalyzed by the NEMF family protein RqcH, in cooperation with RqcP. However, the mechanistic details of this process remain unclear. Here we demonstrate that RqcH is responsible for tRNAAla selection during RQC elongation, whereas RqcP lacks any tRNA specificity. The ribosomal protein uL11 is crucial for RqcH, but not RqcP, recruitment to the 50S subunit, and B. subtilis lacking uL11 are RQC-deficient. Through mutational mapping, we identify critical residues within RqcH and RqcP that are important for interaction with the P-site tRNA and/or the 50S subunit. Additionally, we have reconstituted polyalanine-tailing in vitro and can demonstrate that RqcH and RqcP are necessary and sufficient for processivity in a minimal system. Moreover, the in vitro reconstituted system recapitulates our in vivo findings by reproducing the importance of conserved residues of RqcH and RqcP for functionality. Collectively, our findings provide mechanistic insight into the role of RqcH and RqcP in the bacterial RQC pathway.
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Affiliation(s)
- Hiraku Takada
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo, Motoyama, Kita-ku, Kyoto 603-8555, Japan.,Department of Molecular Biology, Umeå University, 90187 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90187 Umeå, Sweden
| | - Caillan Crowe-McAuliffe
- Institute for Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany
| | - Christine Polte
- Institute for Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany
| | - Zhanna Yu Sidorova
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre "Kurchatov Institute", 188300 Gatchina, Russia.,Russian Research Institute of Hematology and Transfusiology of FMBA, 191024 Saint Petersburg, Russia
| | - Victoriia Murina
- Department of Molecular Biology, Umeå University, 90187 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90187 Umeå, Sweden
| | - Gemma C Atkinson
- National Research Centre "Kurchatov Institute", 123182 Moscow, Russia
| | - Andrey L Konevega
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre "Kurchatov Institute", 188300 Gatchina, Russia.,Peter the Great St. Petersburg Polytechnic University, 195251 Saint Petersburg, Russia.,National Research Centre "Kurchatov Institute", 123182 Moscow, Russia
| | - Zoya Ignatova
- Institute for Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany
| | - Vasili Hauryliuk
- Department of Molecular Biology, Umeå University, 90187 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90187 Umeå, Sweden.,Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden.,University of Tartu, Institute of Technology, 50411 Tartu, Estonia
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56
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Howard CJ, Frost A. Ribosome-associated quality control and CAT tailing. Crit Rev Biochem Mol Biol 2021; 56:603-620. [PMID: 34233554 DOI: 10.1080/10409238.2021.1938507] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Translation is the set of mechanisms by which ribosomes decode genetic messages as they synthesize polypeptides of a defined amino acid sequence. While the ribosome has been honed by evolution for high-fidelity translation, errors are inevitable. Aberrant mRNAs, mRNA structure, defective ribosomes, interactions between nascent proteins and the ribosomal exit tunnel, and insufficient cellular resources, including low tRNA levels, can lead to functionally irreversible stalls. Life thus depends on quality control mechanisms that detect, disassemble and recycle stalled translation intermediates. Ribosome-associated Quality Control (RQC) recognizes aberrant ribosome states and targets their potentially toxic polypeptides for degradation. Here we review recent advances in our understanding of RQC in bacteria, fungi, and metazoans. We focus in particular on an unusual modification made to the nascent chain known as a "CAT tail", or Carboxy-terminal Alanine and Threonine tail, and the mechanisms by which ancient RQC proteins catalyze CAT-tail synthesis.
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Affiliation(s)
- Conor J Howard
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Adam Frost
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
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57
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Izert MA, Klimecka MM, Górna MW. Applications of Bacterial Degrons and Degraders - Toward Targeted Protein Degradation in Bacteria. Front Mol Biosci 2021; 8:669762. [PMID: 34026843 PMCID: PMC8138137 DOI: 10.3389/fmolb.2021.669762] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/15/2021] [Indexed: 12/28/2022] Open
Abstract
A repertoire of proteolysis-targeting signals known as degrons is a necessary component of protein homeostasis in every living cell. In bacteria, degrons can be used in place of chemical genetics approaches to interrogate and control protein function. Here, we provide a comprehensive review of synthetic applications of degrons in targeted proteolysis in bacteria. We describe recent advances ranging from large screens employing tunable degradation systems and orthogonal degrons, to sophisticated tools and sensors for imaging. Based on the success of proteolysis-targeting chimeras as an emerging paradigm in cancer drug discovery, we discuss perspectives on using bacterial degraders for studying protein function and as novel antimicrobials.
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Affiliation(s)
| | | | - Maria Wiktoria Górna
- Structural Biology Group, Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland
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58
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Yip MCJ, Shao S. Detecting and Rescuing Stalled Ribosomes. Trends Biochem Sci 2021; 46:731-743. [PMID: 33966939 DOI: 10.1016/j.tibs.2021.03.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/18/2021] [Accepted: 03/30/2021] [Indexed: 11/24/2022]
Abstract
Ribosomes that stall inappropriately during protein synthesis harbor proteotoxic components linked to cellular stress and neurodegenerative diseases. Molecular mechanisms that rescue stalled ribosomes must selectively detect rare aberrant translational complexes and process the heterogeneous components. Ribosome-associated quality control pathways eliminate problematic messenger RNAs and nascent proteins on stalled translational complexes. In addition, recent studies have uncovered general principles of stall recognition upstream of quality control pathways and fail-safe mechanisms that ensure nascent proteome integrity. Here, we discuss developments in our mechanistic understanding of the detection and rescue of stalled ribosomal complexes in eukaryotes.
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Affiliation(s)
- Matthew C J Yip
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Sichen Shao
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
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59
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Thrun A, Garzia A, Kigoshi-Tansho Y, Patil PR, Umbaugh CS, Dallinger T, Liu J, Kreger S, Patrizi A, Cox GA, Tuschl T, Joazeiro CAP. Convergence of mammalian RQC and C-end rule proteolytic pathways via alanine tailing. Mol Cell 2021; 81:2112-2122.e7. [PMID: 33909987 DOI: 10.1016/j.molcel.2021.03.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 01/28/2021] [Accepted: 03/02/2021] [Indexed: 12/22/2022]
Abstract
Incompletely synthesized nascent chains obstructing large ribosomal subunits are targeted for degradation by ribosome-associated quality control (RQC). In bacterial RQC, RqcH marks the nascent chains with C-terminal alanine (Ala) tails that are directly recognized by proteasome-like proteases, whereas in eukaryotes, RqcH orthologs (Rqc2/NEMF [nuclear export mediator factor]) assist the Ltn1/Listerin E3 ligase in nascent chain ubiquitylation. Here, we study RQC-mediated proteolytic targeting of ribosome stalling products in mammalian cells. We show that mammalian NEMF has an additional, Listerin-independent proteolytic role, which, as in bacteria, is mediated by tRNA-Ala binding and Ala tailing. However, in mammalian cells Ala tails signal proteolysis indirectly, through a pathway that recognizes C-terminal degrons; we identify the CRL2KLHDC10 E3 ligase complex and the novel C-end rule E3, Pirh2/Rchy1, as bona fide RQC pathway components that directly bind to Ala-tailed ribosome stalling products and target them for degradation. As Listerin mutation causes neurodegeneration in mice, functionally redundant E3s may likewise be implicated in molecular mechanisms of neurodegeneration.
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Affiliation(s)
- Anna Thrun
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Aitor Garzia
- Laboratory of RNA Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Yu Kigoshi-Tansho
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Pratik R Patil
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Charles S Umbaugh
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Teresa Dallinger
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Jia Liu
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Sylvia Kreger
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Annarita Patrizi
- Schaller Research Group Leader at the German Cancer Research Center, DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | | | - Thomas Tuschl
- Laboratory of RNA Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Claudio A P Joazeiro
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany; Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA.
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60
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Zarechenskaia AS, Sergiev PV, Osterman IA. Quality Control Mechanisms in Bacterial Translation. Acta Naturae 2021; 13:32-44. [PMID: 34377554 PMCID: PMC8327144 DOI: 10.32607/actanaturae.11401] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 05/15/2021] [Indexed: 12/24/2022] Open
Abstract
Ribosome stalling during translation significantly reduces cell viability, because cells have to spend resources on the synthesis of new ribosomes. Therefore, all bacteria have developed various mechanisms of ribosome rescue. Usually, the release of ribosomes is preceded by hydrolysis of the tRNA-peptide bond, but, in some cases, the ribosome can continue translation thanks to the activity of certain factors. This review describes the mechanisms of ribosome rescue thanks to trans-translation and the activity of the ArfA, ArfB, BrfA, ArfT, HflX, and RqcP/H factors, as well as continuation of translation via the action of EF-P, EF-4, and EttA. Despite the ability of some systems to duplicate each other, most of them have their unique functional role, related to the quality control of bacterial translation in certain abnormalities caused by mutations, stress cultivation conditions, or antibiotics.
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Affiliation(s)
- A. S. Zarechenskaia
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Moscow, 119992 Russia
| | - P. V. Sergiev
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, 143028 Russia
- Lomonosov Moscow State University, Institute of functional genomics, Moscow, 119992 Russia
- Lomonosov Moscow State University, Department of Chemistry, Moscow, 119992 Russia
| | - I. A. Osterman
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, 143028 Russia
- Lomonosov Moscow State University, Department of Chemistry, Moscow, 119992 Russia
- Sirius University of Science and Technology, Genetics and Life Sciences Research Center, Sochi, 354340 Russia
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61
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Müller C, Crowe-McAuliffe C, Wilson DN. Ribosome Rescue Pathways in Bacteria. Front Microbiol 2021; 12:652980. [PMID: 33815344 PMCID: PMC8012679 DOI: 10.3389/fmicb.2021.652980] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 02/23/2021] [Indexed: 12/18/2022] Open
Abstract
Ribosomes that become stalled on truncated or damaged mRNAs during protein synthesis must be rescued for the cell to survive. Bacteria have evolved a diverse array of rescue pathways to remove the stalled ribosomes from the aberrant mRNA and return them to the free pool of actively translating ribosomes. In addition, some of these pathways target the damaged mRNA and the incomplete nascent polypeptide chain for degradation. This review highlights the recent developments in our mechanistic understanding of bacterial ribosomal rescue systems, including drop-off, trans-translation mediated by transfer-messenger RNA and small protein B, ribosome rescue by the alternative rescue factors ArfA and ArfB, as well as Bacillus ribosome rescue factor A, an additional rescue system found in some Gram-positive bacteria, such as Bacillus subtilis. Finally, we discuss the recent findings of ribosome-associated quality control in particular bacterial lineages mediated by RqcH and RqcP. The importance of rescue pathways for bacterial survival suggests they may represent novel targets for the development of new antimicrobial agents against multi-drug resistant pathogenic bacteria.
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Affiliation(s)
| | | | - Daniel N. Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
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62
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Abstract
C-terminal tailing is an ancient and conserved form of peptide synthesis that protects cells from incomplete and potentially toxic translation products. Filbeck et al. (2020) and Crowe-McAuliffe et al. (2020) use structural, genetic, and biochemical approaches to elucidate the mechanisms driving C-terminal tailing.
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Affiliation(s)
- Onn Brandman
- Department of Biochemistry, Stanford University, Palo Alto, CA 94305, USA.
| | - Adam Frost
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
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63
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Samatova E, Daberger J, Liutkute M, Rodnina MV. Translational Control by Ribosome Pausing in Bacteria: How a Non-uniform Pace of Translation Affects Protein Production and Folding. Front Microbiol 2021; 11:619430. [PMID: 33505387 PMCID: PMC7829197 DOI: 10.3389/fmicb.2020.619430] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/11/2020] [Indexed: 11/23/2022] Open
Abstract
Protein homeostasis of bacterial cells is maintained by coordinated processes of protein production, folding, and degradation. Translational efficiency of a given mRNA depends on how often the ribosomes initiate synthesis of a new polypeptide and how quickly they read the coding sequence to produce a full-length protein. The pace of ribosomes along the mRNA is not uniform: periods of rapid synthesis are separated by pauses. Here, we summarize recent evidence on how ribosome pausing affects translational efficiency and protein folding. We discuss the factors that slow down translation elongation and affect the quality of the newly synthesized protein. Ribosome pausing emerges as important factor contributing to the regulatory programs that ensure the quality of the proteome and integrate the cellular and environmental cues into regulatory circuits of the cell.
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Affiliation(s)
- Ekaterina Samatova
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Jan Daberger
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Marija Liutkute
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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64
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Seychell BC, Beck T. Molecular basis for protein-protein interactions. Beilstein J Org Chem 2021; 17:1-10. [PMID: 33488826 PMCID: PMC7801801 DOI: 10.3762/bjoc.17.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 12/07/2020] [Indexed: 01/11/2023] Open
Abstract
This minireview provides an overview on the current knowledge of protein-protein interactions, common characterisation methods to characterise them, and their role in protein complex formation with some examples. A deep understanding of protein-protein interactions and their molecular interactions is important for a number of applications, including drug design. Protein-protein interactions and their discovery are thus an interesting avenue for understanding how protein complexes, which make up the majority of proteins, work.
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Affiliation(s)
- Brandon Charles Seychell
- Universität Hamburg, Department of Chemistry, Institute of Physical Chemistry, Grindelallee 117, 20146 Hamburg, Germany
| | - Tobias Beck
- Universität Hamburg, Department of Chemistry, Institute of Physical Chemistry, Grindelallee 117, 20146 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Hamburg, Germany
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65
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Udagawa T, Seki M, Okuyama T, Adachi S, Natsume T, Noguchi T, Matsuzawa A, Inada T. Failure to Degrade CAT-Tailed Proteins Disrupts Neuronal Morphogenesis and Cell Survival. Cell Rep 2021; 34:108599. [PMID: 33406423 DOI: 10.1016/j.celrep.2020.108599] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 07/24/2020] [Accepted: 12/14/2020] [Indexed: 12/25/2022] Open
Abstract
Ribosome-associated quality control (RQC) relieves stalled ribosomes and eliminates potentially toxic nascent polypeptide chains (NCs) that can cause neurodegeneration. During RQC, RQC2 modifies NCs with a C-terminal alanine and threonine (CAT) tail. CAT tailing promotes ubiquitination of NCs for proteasomal degradation, while RQC failure in budding yeast disrupts proteostasis via CAT-tailed NC aggregation. However, the CAT tail and its cytotoxicity in mammals have remained largely uncharacterized. We demonstrate that NEMF, a mammalian RQC2 homolog, modifies translation products of nonstop mRNAs, major erroneous mRNAs in mammals, with a C-terminal tail mainly composed of alanine with several other amino acids. Overproduction of nonstop mRNAs induces NC aggregation and caspase-3-dependent apoptosis and impairs neuronal morphogenesis, which are ameliorated by NEMF depletion. Moreover, we found that homopolymeric alanine tailing at least partially accounts for CAT-tail cytotoxicity. These findings explain the cytotoxicity of CAT-tailed NCs and demonstrate physiological significance of RQC on proper neuronal morphogenesis and cell survival.
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Affiliation(s)
- Tsuyoshi Udagawa
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan.
| | - Moeka Seki
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Taku Okuyama
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Shungo Adachi
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan
| | - Tohru Natsume
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan
| | - Takuya Noguchi
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Atsushi Matsuzawa
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Toshifumi Inada
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan.
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66
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Crowe-McAuliffe C, Takada H, Murina V, Polte C, Kasvandik S, Tenson T, Ignatova Z, Atkinson GC, Wilson DN, Hauryliuk V. Structural Basis for Bacterial Ribosome-Associated Quality Control by RqcH and RqcP. Mol Cell 2020; 81:115-126.e7. [PMID: 33259810 DOI: 10.1016/j.molcel.2020.11.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/07/2020] [Accepted: 10/29/2020] [Indexed: 12/25/2022]
Abstract
In all branches of life, stalled translation intermediates are recognized and processed by ribosome-associated quality control (RQC) pathways. RQC begins with the splitting of stalled ribosomes, leaving an unfinished polypeptide still attached to the large subunit. Ancient and conserved NEMF family RQC proteins target these incomplete proteins for degradation by the addition of C-terminal "tails." How such tailing can occur without the regular suite of translational components is, however, unclear. Using single-particle cryo-electron microscopy (EM) of native complexes, we show that C-terminal tailing in Bacillus subtilis is mediated by NEMF protein RqcH in concert with RqcP, an Hsp15 family protein. Our structures reveal how these factors mediate tRNA movement across the ribosomal 50S subunit to synthesize polypeptides in the absence of mRNA or the small subunit.
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Affiliation(s)
- Caillan Crowe-McAuliffe
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Pl. 6, 20146 Hamburg, Germany
| | - Hiraku Takada
- Department of Molecular Biology, Umeå University, 90187 Umeå, Sweden; Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90187 Umeå, Sweden
| | - Victoriia Murina
- Department of Molecular Biology, Umeå University, 90187 Umeå, Sweden; Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90187 Umeå, Sweden
| | - Christine Polte
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Pl. 6, 20146 Hamburg, Germany
| | - Sergo Kasvandik
- University of Tartu, Institute of Technology, 50411 Tartu, Estonia
| | - Tanel Tenson
- University of Tartu, Institute of Technology, 50411 Tartu, Estonia
| | - Zoya Ignatova
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Pl. 6, 20146 Hamburg, Germany
| | - Gemma C Atkinson
- Department of Molecular Biology, Umeå University, 90187 Umeå, Sweden
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Pl. 6, 20146 Hamburg, Germany.
| | - Vasili Hauryliuk
- Department of Molecular Biology, Umeå University, 90187 Umeå, Sweden; Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90187 Umeå, Sweden; University of Tartu, Institute of Technology, 50411 Tartu, Estonia.
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67
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Filbeck S, Cerullo F, Paternoga H, Tsaprailis G, Joazeiro CAP, Pfeffer S. Mimicry of Canonical Translation Elongation Underlies Alanine Tail Synthesis in RQC. Mol Cell 2020; 81:104-114.e6. [PMID: 33259811 DOI: 10.1016/j.molcel.2020.11.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/06/2020] [Accepted: 10/29/2020] [Indexed: 12/21/2022]
Abstract
Aborted translation produces large ribosomal subunits obstructed with tRNA-linked nascent chains, which are substrates of ribosome-associated quality control (RQC). Bacterial RqcH, a widely conserved RQC factor, senses the obstruction and recruits tRNAAla(UGC) to modify nascent-chain C termini with a polyalanine degron. However, how RqcH and its eukaryotic homologs (Rqc2 and NEMF), despite their relatively simple architecture, synthesize such C-terminal tails in the absence of a small ribosomal subunit and mRNA has remained unknown. Here, we present cryoelectron microscopy (cryo-EM) structures of Bacillus subtilis RQC complexes representing different Ala tail synthesis steps. The structures explain how tRNAAla is selected via anticodon reading during recruitment to the A-site and uncover striking hinge-like movements in RqcH leading tRNAAla into a hybrid A/P-state associated with peptidyl-transfer. Finally, we provide structural, biochemical, and molecular genetic evidence identifying the Hsp15 homolog (encoded by rqcP) as a novel RQC component that completes the cycle by stabilizing the P-site tRNA conformation. Ala tailing thus follows mechanistic principles surprisingly similar to canonical translation elongation.
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Affiliation(s)
- Sebastian Filbeck
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Federico Cerullo
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Helge Paternoga
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | | | - Claudio A P Joazeiro
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany; Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA.
| | - Stefan Pfeffer
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.
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68
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Phillips BP, Miller EA. Ribosome-associated quality control of membrane proteins at the endoplasmic reticulum. J Cell Sci 2020; 133:133/22/jcs251983. [PMID: 33247003 PMCID: PMC7116877 DOI: 10.1242/jcs.251983] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Protein synthesis is an energetically costly, complex and risky process. Aberrant protein biogenesis can result in cellular toxicity and disease, with membrane-embedded proteins being particularly challenging for the cell. In order to protect the cell from consequences of defects in membrane proteins, quality control systems act to maintain protein homeostasis. The majority of these pathways act post-translationally; however, recent evidence reveals that membrane proteins are also subject to co-translational quality control during their synthesis in the endoplasmic reticulum (ER). This newly identified quality control pathway employs components of the cytosolic ribosome-associated quality control (RQC) machinery but differs from canonical RQC in that it responds to biogenesis state of the substrate rather than mRNA aberrations. This ER-associated RQC (ER-RQC) is sensitive to membrane protein misfolding and malfunctions in the ER insertion machinery. In this Review, we discuss the advantages of co-translational quality control of membrane proteins, as well as potential mechanisms of substrate recognition and degradation. Finally, we discuss some outstanding questions concerning future studies of ER-RQC of membrane proteins.
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Affiliation(s)
- Ben P Phillips
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
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69
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Fei X, Bell TA, Barkow SR, Baker TA, Sauer RT. Structural basis of ClpXP recognition and unfolding of ssrA-tagged substrates. eLife 2020; 9:61496. [PMID: 33089779 PMCID: PMC7652416 DOI: 10.7554/elife.61496] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/21/2020] [Indexed: 01/05/2023] Open
Abstract
When ribosomes fail to complete normal translation, all cells have mechanisms to ensure degradation of the resulting partial proteins to safeguard proteome integrity. In Escherichia coli and other eubacteria, the tmRNA system rescues stalled ribosomes and adds an ssrA tag or degron to the C-terminus of the incomplete protein, which directs degradation by the AAA+ ClpXP protease. Here, we present cryo-EM structures of ClpXP bound to the ssrA degron. C-terminal residues of the ssrA degron initially bind in the top of an otherwise closed ClpX axial channel and subsequently move deeper into an open channel. For short-degron protein substrates, we show that unfolding can occur directly from the initial closed-channel complex. For longer degron substrates, our studies illuminate how ClpXP transitions from specific recognition into a nonspecific unfolding and translocation machine. Many AAA+ proteases and protein-remodeling motors are likely to employ similar multistep recognition and engagement strategies.
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Affiliation(s)
- Xue Fei
- Departments of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - Tristan A Bell
- Departments of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - Sarah R Barkow
- Chemistry, Massachusetts Institute of Technology, Cambridge, United States
| | - Tania A Baker
- Departments of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - Robert T Sauer
- Departments of Biology, Massachusetts Institute of Technology, Cambridge, United States
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70
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Hickey KL, Dickson K, Cogan JZ, Replogle JM, Schoof M, D'Orazio KN, Sinha NK, Hussmann JA, Jost M, Frost A, Green R, Weissman JS, Kostova KK. GIGYF2 and 4EHP Inhibit Translation Initiation of Defective Messenger RNAs to Assist Ribosome-Associated Quality Control. Mol Cell 2020; 79:950-962.e6. [PMID: 32726578 PMCID: PMC7891188 DOI: 10.1016/j.molcel.2020.07.007] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 07/07/2020] [Accepted: 07/07/2020] [Indexed: 12/31/2022]
Abstract
Ribosome-associated quality control (RQC) pathways protect cells from toxicity caused by incomplete protein products resulting from translation of damaged or problematic mRNAs. Extensive work in yeast has identified highly conserved mechanisms that lead to degradation of faulty mRNA and partially synthesized polypeptides. Here we used CRISPR-Cas9-based screening to search for additional RQC strategies in mammals. We found that failed translation leads to specific inhibition of translation initiation on that message. This negative feedback loop is mediated by two translation inhibitors, GIGYF2 and 4EHP. Model substrates and growth-based assays established that inhibition of additional rounds of translation acts in concert with known RQC pathways to prevent buildup of toxic proteins. Inability to block translation of faulty mRNAs and subsequent accumulation of partially synthesized polypeptides could explain the neurodevelopmental and neuropsychiatric disorders observed in mice and humans with compromised GIGYF2 function.
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Affiliation(s)
- Kelsey L Hickey
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kimberley Dickson
- Department of Biology, Lawerence University, Appleton, WI 54911, USA
| | - J Zachery Cogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Joseph M Replogle
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Michael Schoof
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Karole N D'Orazio
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Niladri K Sinha
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jeffrey A Hussmann
- Department of Cellular and Molecular Pharmacology, 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
| | - Marco Jost
- Department of Cellular and Molecular Pharmacology, 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
| | - Adam Frost
- California Institute for Quantitative Biomedical Research, 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; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Rachel Green
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA; Howard Hughes Medical Institute, Carnegie Institution for Science, Baltimore, MD 21218, USA
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, 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; Howard Hughes Medical Institute, Carnegie Institution for Science, Baltimore, MD 21218, USA.
| | - Kamena K Kostova
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA.
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71
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Martin PB, Kigoshi-Tansho Y, Sher RB, Ravenscroft G, Stauffer JE, Kumar R, Yonashiro R, Müller T, Griffith C, Allen W, Pehlivan D, Harel T, Zenker M, Howting D, Schanze D, Faqeih EA, Almontashiri NAM, Maroofian R, Houlden H, Mazaheri N, Galehdari H, Douglas G, Posey JE, Ryan M, Lupski JR, Laing NG, Joazeiro CAP, Cox GA. NEMF mutations that impair ribosome-associated quality control are associated with neuromuscular disease. Nat Commun 2020; 11:4625. [PMID: 32934225 PMCID: PMC7494853 DOI: 10.1038/s41467-020-18327-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 08/11/2020] [Indexed: 12/14/2022] Open
Abstract
A hallmark of neurodegeneration is defective protein quality control. The E3 ligase Listerin (LTN1/Ltn1) acts in a specialized protein quality control pathway—Ribosome-associated Quality Control (RQC)—by mediating proteolytic targeting of incomplete polypeptides produced by ribosome stalling, and Ltn1 mutation leads to neurodegeneration in mice. Whether neurodegeneration results from defective RQC and whether defective RQC contributes to human disease have remained unknown. Here we show that three independently-generated mouse models with mutations in a different component of the RQC complex, NEMF/Rqc2, develop progressive motor neuron degeneration. Equivalent mutations in yeast Rqc2 selectively interfere with its ability to modify aberrant translation products with C-terminal tails which assist with RQC-mediated protein degradation, suggesting a pathomechanism. Finally, we identify NEMF mutations expected to interfere with function in patients from seven families presenting juvenile neuromuscular disease. These uncover NEMF’s role in translational homeostasis in the nervous system and implicate RQC dysfunction in causing neurodegeneration. Defective protein quality control is a key feature of neurodegeneration. Here, the authors show that mutations in Nemf/NEMF, a component of the Ribosome-associated Quality Control complex, have a neurodegenerative effect in mice and may underlie neuromuscular disease in seven unrelated families.
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Affiliation(s)
- Paige B Martin
- The Jackson Laboratory, Bar Harbor, ME, USA.,The University of Maine, Graduate School of Biomedical Science and Engineering, Orono, ME, USA
| | - Yu Kigoshi-Tansho
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Roger B Sher
- Department of Neurobiology & Behavior, Stony Brook University, Stony Brook, NY, USA.,Center for Nervous System Disorders, Stony Brook University, Stony Brook, NY, USA
| | - Gianina Ravenscroft
- Harry Perkins Institute of Medical Research, Centre for Medical Research, University of Western Australia, Nedlands, WA, Australia
| | | | - Rajesh Kumar
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Ryo Yonashiro
- Department of Molecular Medicine, Scripps Research, Jupiter, FL, USA
| | - Tina Müller
- Department of Molecular Medicine, Scripps Research, Jupiter, FL, USA
| | | | - William Allen
- Mission Fullerton Genetics Center, Mission Health, Asheville, NC, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Tamar Harel
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Martin Zenker
- Institute of Human Genetics, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Denise Howting
- Harry Perkins Institute of Medical Research, Centre for Medical Research, University of Western Australia, Nedlands, WA, Australia
| | - Denny Schanze
- Institute of Human Genetics, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Eissa A Faqeih
- Department of Genetics, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Naif A M Almontashiri
- The Center for Genetics and Inherited Diseases, Taibah University, Almadinah Almunwarah, Saudi Arabia.,Faculty of Applied Medical Sciences, Taibah University, Almadinah Almunwarah, Saudi Arabia
| | - Reza Maroofian
- Neurogenetics Laboratory, UCL Queen Square Institute of Neurology, London, UK.,The National Hospital for Neurology and Neurosurgery, London, UK
| | - Henry Houlden
- Neurogenetics Laboratory, UCL Queen Square Institute of Neurology, London, UK.,The National Hospital for Neurology and Neurosurgery, London, UK
| | - Neda Mazaheri
- Department of Genetics, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Hamid Galehdari
- Department of Genetics, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | | | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Monique Ryan
- Department of Neurology, The Royal Children's Hospital, Melbourne, VIC, Australia.,Murdoch Children's Research Institute and University of Melbourne, Melbourne, VIC, Australia
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Texas Children's Hospital, Houston, TX, USA
| | - Nigel G Laing
- Harry Perkins Institute of Medical Research, Centre for Medical Research, University of Western Australia, Nedlands, WA, Australia
| | - Claudio A P Joazeiro
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany. .,Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA.
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72
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Abstract
Stalled protein synthesis produces defective nascent chains that can harm cells. In response, cells degrade these nascent chains via a process called ribosome-associated quality control (RQC). Here, we review the irregularities in the translation process that cause ribosomes to stall as well as how cells use RQC to detect stalled ribosomes, ubiquitylate their tethered nascent chains, and deliver the ubiquitylated nascent chains to the proteasome. We additionally summarize how cells respond to RQC failure.
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Affiliation(s)
- Cole S Sitron
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany;
| | - Onn Brandman
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA;
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73
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Inada T. Quality controls induced by aberrant translation. Nucleic Acids Res 2020; 48:1084-1096. [PMID: 31950154 PMCID: PMC7026593 DOI: 10.1093/nar/gkz1201] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 12/01/2019] [Accepted: 12/18/2019] [Indexed: 12/31/2022] Open
Abstract
During protein synthesis, translating ribosomes encounter many challenges imposed by various types of defective mRNAs that can lead to reduced cellular fitness and, in some cases, even threaten cell viability. Aberrant translation leads to activation of one of several quality control pathways depending on the nature of the problem. These pathways promote the degradation of the problematic mRNA as well as the incomplete translation product, the nascent polypeptide chain. Many of these quality control systems feature critical roles for specialized regulatory factors that work in concert with conventional factors. This review focuses on the mechanisms used by these quality control pathways to recognize aberrant ribosome stalling and discusses the conservation of these systems.
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Affiliation(s)
- Toshifumi Inada
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
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74
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Sitron CS, Park JH, Giafaglione JM, Brandman O. Aggregation of CAT tails blocks their degradation and causes proteotoxicity in S. cerevisiae. PLoS One 2020; 15:e0227841. [PMID: 31945107 PMCID: PMC6964901 DOI: 10.1371/journal.pone.0227841] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 12/30/2019] [Indexed: 02/07/2023] Open
Abstract
The Ribosome-associated Quality Control (RQC) pathway co-translationally marks incomplete polypeptides from stalled translation with two signals that trigger their proteasome-mediated degradation. The E3 ligase Ltn1 adds ubiquitin and Rqc2 directs the large ribosomal subunit to append carboxy-terminal alanine and threonine residues (CAT tails). When excessive amounts of incomplete polypeptides evade Ltn1, CAT-tailed proteins accumulate and can self-associate into aggregates. CAT tail aggregation has been hypothesized to either protect cells by sequestering potentially toxic incomplete polypeptides or harm cells by disrupting protein homeostasis. To distinguish between these possibilities, we modulated CAT tail aggregation in Saccharomyces cerevisiae with genetic and chemical tools to analyze CAT tails in aggregated and un-aggregated states. We found that enhancing CAT tail aggregation induces proteotoxic stress and antagonizes degradation of CAT-tailed proteins, while inhibiting aggregation reverses these effects. Our findings suggest that CAT tail aggregation harms RQC-compromised cells and that preventing aggregation can mitigate this toxicity.
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Affiliation(s)
- Cole S. Sitron
- Department of Biochemistry, Stanford University, Stanford, CA, United States of America
| | - Joseph H. Park
- Department of Biochemistry, Stanford University, Stanford, CA, United States of America
- Department of Chemical & Systems Biology, Stanford University, Stanford, CA, United States of America
| | - Jenna M. Giafaglione
- Department of Biochemistry, Stanford University, Stanford, CA, United States of America
| | - Onn Brandman
- Department of Biochemistry, Stanford University, Stanford, CA, United States of America
- * E-mail:
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75
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Ayyub SA, Gao F, Lightowlers RN, Chrzanowska-Lightowlers ZM. Rescuing stalled mammalian mitoribosomes - what can we learn from bacteria? J Cell Sci 2020; 133:133/1/jcs231811. [PMID: 31896602 DOI: 10.1242/jcs.231811] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
In the canonical process of translation, newly completed proteins escape from the ribosome following cleavage of the ester bond that anchors the polypeptide to the P-site tRNA, after which the ribosome can be recycled to initiate a new round of translation. Not all protein synthesis runs to completion as various factors can impede the progression of ribosomes. Rescuing of stalled ribosomes in mammalian mitochondria, however, does not share the same mechanisms that many bacteria use. The classic method for rescuing bacterial ribosomes is trans-translation. The key components of this system are absent from mammalian mitochondria; however, four members of a translation termination factor family are present, with some evidence of homology to members of a bacterial back-up rescue system. To date, there is no definitive demonstration of any other member of this family functioning in mitoribosome rescue. Here, we provide an overview of the processes and key players of canonical translation termination in both bacteria and mammalian mitochondria, followed by a perspective of the bacterial systems used to rescue stalled ribosomes. We highlight any similarities or differences with the mitochondrial translation release factors, and suggest potential roles for these proteins in ribosome rescue in mammalian mitochondria.
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Affiliation(s)
- Shreya Ahana Ayyub
- The Wellcome Centre for Mitochondrial Research, Newcastle University, The Medical School, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Fei Gao
- The Wellcome Centre for Mitochondrial Research, Newcastle University, The Medical School, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Robert N Lightowlers
- The Wellcome Centre for Mitochondrial Research, Newcastle University, The Medical School, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Zofia M Chrzanowska-Lightowlers
- The Wellcome Centre for Mitochondrial Research, Newcastle University, The Medical School, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
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76
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Release factor-dependent ribosome rescue by BrfA in the Gram-positive bacterium Bacillus subtilis. Nat Commun 2019; 10:5397. [PMID: 31776341 PMCID: PMC6881298 DOI: 10.1038/s41467-019-13408-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/07/2019] [Indexed: 12/14/2022] Open
Abstract
Rescue of the ribosomes from dead-end translation complexes, such as those on truncated (non-stop) mRNA, is essential for the cell. Whereas bacteria use trans-translation for ribosome rescue, some Gram-negative species possess alternative and release factor (RF)-dependent rescue factors, which enable an RF to catalyze stop-codon-independent polypeptide release. We now discover that the Gram-positive Bacillus subtilis has an evolutionarily distinct ribosome rescue factor named BrfA. Genetic analysis shows that B. subtilis requires the function of either trans-translation or BrfA for growth, even in the absence of proteotoxic stresses. Biochemical and cryo-electron microscopy (cryo-EM) characterization demonstrates that BrfA binds to non-stop stalled ribosomes, recruits homologous RF2, but not RF1, and induces its transition into an open active conformation. Although BrfA is distinct from E. coli ArfA, they use convergent strategies in terms of mode of action and expression regulation, indicating that many bacteria may have evolved as yet unidentified ribosome rescue systems. In bacteria, the conserved trans-translation system serves as the primary pathway of ribosome rescue, but many species can also use alternative rescue pathways. Here the authors report that in B. subtilis, the rescue factor BrfA binds to non-stop stalled ribosomes, recruits RF2 but not RF1, and induces transition of the ribosome into an open active conformation.
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77
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Nürenberg-Goloub E, Tampé R. Ribosome recycling in mRNA translation, quality control, and homeostasis. Biol Chem 2019; 401:47-61. [DOI: 10.1515/hsz-2019-0279] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 10/22/2019] [Indexed: 02/07/2023]
Abstract
Abstract
Protein biosynthesis is a conserved process, essential for life. Ongoing research for four decades has revealed the structural basis and mechanistic details of most protein biosynthesis steps. Numerous pathways and their regulation have recently been added to the translation system describing protein quality control and messenger ribonucleic acid (mRNA) surveillance, ribosome-associated protein folding and post-translational modification as well as human disorders associated with mRNA and ribosome homeostasis. Thus, translation constitutes a key regulatory process placing the ribosome as a central hub at the crossover of numerous cellular pathways. Here, we describe the role of ribosome recycling by ATP-binding cassette sub-family E member 1 (ABCE1) as a crucial regulatory step controlling the biogenesis of functional proteins and the degradation of aberrant nascent chains in quality control processes.
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Affiliation(s)
- Elina Nürenberg-Goloub
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt , Max-von-Laue-Str. 9 , D-60438 Frankfurt/Main , Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt , Max-von-Laue-Str. 9 , D-60438 Frankfurt/Main , Germany
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