1
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Aviner R, Lee TT, Masto VB, Li KH, Andino R, Frydman J. Polyglutamine-mediated ribotoxicity disrupts proteostasis and stress responses in Huntington's disease. Nat Cell Biol 2024; 26:892-902. [PMID: 38741019 DOI: 10.1038/s41556-024-01414-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/01/2024] [Indexed: 05/16/2024]
Abstract
Huntington's disease (HD) is a neurodegenerative disorder caused by expansion of a CAG trinucleotide repeat in the Huntingtin (HTT) gene, encoding a homopolymeric polyglutamine (polyQ) tract. Although mutant HTT (mHTT) protein is known to aggregate, the links between aggregation and neurotoxicity remain unclear. Here we show that both translation and aggregation of wild-type HTT and mHTT are regulated by a stress-responsive upstream open reading frame and that polyQ expansions cause abortive translation termination and release of truncated, aggregation-prone mHTT fragments. Notably, we find that mHTT depletes translation elongation factor eIF5A in brains of symptomatic HD mice and cultured HD cells, leading to pervasive ribosome pausing and collisions. Loss of eIF5A disrupts homeostatic controls and impairs recovery from acute stress. Importantly, drugs that inhibit translation initiation reduce premature termination and mitigate this escalating cascade of ribotoxic stress and dysfunction in HD.
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Affiliation(s)
- Ranen Aviner
- Department of Biology and Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub San Francisco, San Francisco, CA, USA
| | - Ting-Ting Lee
- Department of Biology and Department of Genetics, Stanford University, Stanford, CA, USA
| | - Vincent B Masto
- Department of Biology and Department of Genetics, Stanford University, Stanford, CA, USA
| | - Kathy H Li
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Judith Frydman
- Department of Biology and Department of Genetics, Stanford University, Stanford, CA, USA.
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2
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Flügel T, Schacherl M, Unbehaun A, Schroeer B, Dabrowski M, Bürger J, Mielke T, Sprink T, Diebolder CA, Guillén Schlippe YV, Spahn CMT. Transient disome complex formation in native polysomes during ongoing protein synthesis captured by cryo-EM. Nat Commun 2024; 15:1756. [PMID: 38409277 PMCID: PMC10897467 DOI: 10.1038/s41467-024-46092-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 02/13/2024] [Indexed: 02/28/2024] Open
Abstract
Structural studies of translating ribosomes traditionally rely on in vitro assembly and stalling of ribosomes in defined states. To comprehensively visualize bacterial translation, we reactivated ex vivo-derived E. coli polysomes in the PURE in vitro translation system and analyzed the actively elongating polysomes by cryo-EM. We find that 31% of 70S ribosomes assemble into disome complexes that represent eight distinct functional states including decoding and termination intermediates, and a pre-nucleophilic attack state. The functional diversity of disome complexes together with RNase digest experiments suggests that paused disome complexes transiently form during ongoing elongation. Structural analysis revealed five disome interfaces between leading and queueing ribosomes that undergo rearrangements as the leading ribosome traverses through the elongation cycle. Our findings reveal at the molecular level how bL9's CTD obstructs the factor binding site of queueing ribosomes to thwart harmful collisions and illustrate how translation dynamics reshape inter-ribosomal contacts.
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Affiliation(s)
- Timo Flügel
- Charité - Univesitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Magdalena Schacherl
- Charité - Univesitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Anett Unbehaun
- Charité - Univesitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Birgit Schroeer
- Charité - Univesitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Marylena Dabrowski
- Charité - Univesitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Jörg Bürger
- Charité - Univesitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
- Max Planck Institute for Molecular Genetics, Microscopy and Cryo-Electron Microscopy Service Group, Berlin, Germany
| | - Thorsten Mielke
- Max Planck Institute for Molecular Genetics, Microscopy and Cryo-Electron Microscopy Service Group, Berlin, Germany
| | - Thiemo Sprink
- Core Facility for Cryo-Electron Microscopy, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Technology Platform Cryo-EM, Berlin, Germany
| | - Christoph A Diebolder
- Core Facility for Cryo-Electron Microscopy, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Technology Platform Cryo-EM, Berlin, Germany
| | - Yollete V Guillén Schlippe
- Charité - Univesitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany.
| | - Christian M T Spahn
- Charité - Univesitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany.
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3
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Park EN, Mackens-Kiani T, Berhane R, Esser H, Erdenebat C, Burroughs AM, Berninghausen O, Aravind L, Beckmann R, Green R, Buskirk AR. B. subtilis MutS2 splits stalled ribosomes into subunits without mRNA cleavage. EMBO J 2024; 43:484-506. [PMID: 38177497 PMCID: PMC10897456 DOI: 10.1038/s44318-023-00010-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 11/16/2023] [Accepted: 11/21/2023] [Indexed: 01/06/2024] Open
Abstract
Stalled ribosomes are rescued by pathways that recycle the ribosome and target the nascent polypeptide for degradation. In E. coli, these pathways are triggered by ribosome collisions through the recruitment of SmrB, a nuclease that cleaves the mRNA. In B. subtilis, the related protein MutS2 was recently implicated in ribosome rescue. Here we show that MutS2 is recruited to collisions by its SMR and KOW domains, and we reveal the interaction of these domains with collided ribosomes by cryo-EM. Using a combination of in vivo and in vitro approaches, we show that MutS2 uses its ABC ATPase activity to split ribosomes, targeting the nascent peptide for degradation through the ribosome quality control pathway. However, unlike SmrB, which cleaves mRNA in E. coli, we see no evidence that MutS2 mediates mRNA cleavage or promotes ribosome rescue by tmRNA. These findings clarify the biochemical and cellular roles of MutS2 in ribosome rescue in B. subtilis and raise questions about how these pathways function differently in diverse bacteria.
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Affiliation(s)
- Esther N Park
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Timur Mackens-Kiani
- Gene Center and Department of Biochemistry, University of Munich, Munich, Germany
| | - Rebekah Berhane
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hanna Esser
- Gene Center and Department of Biochemistry, University of Munich, Munich, Germany
| | - Chimeg Erdenebat
- Gene Center and Department of Biochemistry, University of Munich, Munich, Germany
| | - A Maxwell Burroughs
- Computational Biology Branch, Intramural Research Program, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Otto Berninghausen
- Gene Center and Department of Biochemistry, University of Munich, Munich, Germany
| | - L Aravind
- Computational Biology Branch, Intramural Research Program, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Roland Beckmann
- Gene Center and Department of Biochemistry, University of Munich, Munich, Germany
| | - Rachel Green
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Allen R Buskirk
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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4
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Hou W, Harjono V, Harvey AT, Subramaniam AR, Zid BM. Quantification of elongation stalls and impact on gene expression in yeast. RNA (NEW YORK, N.Y.) 2023; 29:1928-1938. [PMID: 37783489 PMCID: PMC10653389 DOI: 10.1261/rna.079663.123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 09/21/2023] [Indexed: 10/04/2023]
Abstract
Ribosomal pauses are a critical part of cotranslational events including protein folding and localization. However, extended ribosome pauses can lead to ribosome collisions, resulting in the activation of ribosome rescue pathways and turnover of protein and mRNA. While this relationship has been known, there has been little exploration of how ribosomal stalls impact translation duration at a quantitative level. We have taken a method used to measure elongation time and adapted it for use in Saccharomyces cerevisiae to quantify the impact of elongation stalls. We find, in transcripts containing Arg CGA codon repeat-induced stalls, a Hel2-mediated dose-dependent decrease in protein expression and mRNA level and an elongation delay on the order of minutes. In transcripts that contain synonymous substitutions to nonoptimal Leu codons, there is a decrease in protein and mRNA levels, as well as similar elongation delay, but this occurs through a non-Hel2-mediated mechanism. Finally, we find that Dhh1 selectively increases protein expression, mRNA level, and elongation rate. This indicates that distinct poorly translated mRNAs will activate different rescue pathways despite similar elongation stall durations. Taken together, these results provide new quantitative mechanistic insight into the surveillance of translation and the roles of Hel2 and Dhh1 in mediating ribosome pausing events.
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Affiliation(s)
- Wanfu Hou
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Vince Harjono
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Alex T Harvey
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Arvind Rasi Subramaniam
- Basic Sciences Division and Computational Biology Section of the Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Brian M Zid
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
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5
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Hacker WC, Elcock AH. spotter: a single-nucleotide resolution stochastic simulation model of supercoiling-mediated transcription and translation in prokaryotes. Nucleic Acids Res 2023; 51:e92. [PMID: 37602419 PMCID: PMC10516669 DOI: 10.1093/nar/gkad682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 07/25/2023] [Accepted: 08/09/2023] [Indexed: 08/22/2023] Open
Abstract
Stochastic simulation models have played an important role in efforts to understand the mechanistic basis of prokaryotic transcription and translation. Despite the fundamental linkage of these processes in bacterial cells, however, most simulation models have been limited to representations of either transcription or translation. In addition, the available simulation models typically either attempt to recapitulate data from single-molecule experiments without considering cellular-scale high-throughput sequencing data or, conversely, seek to reproduce cellular-scale data without paying close attention to many of the mechanistic details. To address these limitations, we here present spotter (Simulation of Prokaryotic Operon Transcription & Translation Elongation Reactions), a flexible, user-friendly simulation model that offers highly-detailed combined representations of prokaryotic transcription, translation, and DNA supercoiling. In incorporating nascent transcript and ribosomal profiling sequencing data, spotter provides a critical bridge between data collected in single-molecule experiments and data collected at the cellular scale. Importantly, in addition to rapidly generating output that can be aggregated for comparison with next-generation sequencing and proteomics data, spotter produces residue-level positional information that can be used to visualize individual simulation trajectories in detail. We anticipate that spotter will be a useful tool in exploring the interplay of processes that are crucially linked in prokaryotes.
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Affiliation(s)
- William C Hacker
- Department of Biochemistry & Molecular Biology, University of Iowa, Iowa City, IA, USA
| | - Adrian H Elcock
- Department of Biochemistry & Molecular Biology, University of Iowa, Iowa City, IA, USA
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6
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Vidal CM, Ouyang C, Qi Y, Mendez-Dorantes C, Coblentz A, Alva-Ornelas JA, Stark JM, Seewaldt VL, Ann DK. Arginine regulates HSPA5/BiP translation through ribosome pausing in triple-negative breast cancer cells. Br J Cancer 2023; 129:444-454. [PMID: 37386138 PMCID: PMC10403569 DOI: 10.1038/s41416-023-02322-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 05/17/2023] [Accepted: 06/12/2023] [Indexed: 07/01/2023] Open
Abstract
BACKGROUND Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer with a high mortality rate due to a lack of therapeutic targets. Many TNBC cells are reliant on extracellular arginine for survival and express high levels of binding immunoglobin protein (BiP), a marker of metastasis and endoplasmic reticulum (ER) stress response. METHODS In this study, the effect of arginine shortage on BiP expression in the TNBC cell line MDA-MB-231 was evaluated. Two stable cell lines were generated in MDA-MB-231 cells: the first expressed wild-type BiP, and the second expressed a mutated BiP free of the two arginine pause-site codons, CCU and CGU, termed G-BiP. RESULTS The results showed that arginine shortage induced a non-canonical ER stress response by inhibiting BiP translation via ribosome pausing. Overexpression of G-BiP in MDA-MB-231 cells promoted cell resistance to arginine shortage compared to cells overexpressing wild-type BiP. Additionally, limiting arginine led to decreased levels of the spliced XBP1 in the G-BiP overexpressing cells, potentially contributing to their improved survival compared to the parental WT BiP overexpressing cells. CONCLUSION In conclusion, these findings suggest that the downregulation of BiP disrupts proteostasis during arginine shortage-induced non-canonical ER stress and plays a key role in cell growth inhibition, indicating BiP as a target of codon-specific ribosome pausing upon arginine shortage.
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Affiliation(s)
- Christina M Vidal
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
- Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Ching Ouyang
- Department of Computational and Quantitative Medicine, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Yue Qi
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Carlos Mendez-Dorantes
- Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Alaysia Coblentz
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Jackelyn A Alva-Ornelas
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Jeremy M Stark
- Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Victoria L Seewaldt
- Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - David K Ann
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA.
- Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA.
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7
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Abisado-Duque RG, Townsend KA, Mckee BM, Woods K, Koirala P, Holder AJ, Craddock VD, Cabeen M, Chandler JR. An Amino Acid Substitution in Elongation Factor EF-G1A Alters the Antibiotic Susceptibility of Pseudomonas aeruginosa LasR-Null Mutants. J Bacteriol 2023; 205:e0011423. [PMID: 37191503 PMCID: PMC10294626 DOI: 10.1128/jb.00114-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 04/22/2023] [Indexed: 05/17/2023] Open
Abstract
The opportunistic bacterium Pseudomonas aeruginosa uses the LasR-I quorum-sensing system to increase resistance to the aminoglycoside antibiotic tobramycin. Paradoxically, lasR-null mutants are commonly isolated from chronic human infections treated with tobramycin, suggesting there may be a mechanism that permits the emergence of lasR-null mutants under tobramycin selection. We hypothesized that some other genetic mutations that emerge in these isolates might modulate the effects of lasR-null mutations on antibiotic resistance. To test this hypothesis, we inactivated lasR in several highly tobramycin-resistant isolates from long-term evolution experiments. In some of these isolates, inactivating lasR further increased resistance, compared with decreasing resistance of the wild-type ancestor. These strain-dependent effects were due to a G61A nucleotide polymorphism in the fusA1 gene encoding amino acid substitution A21T in the translation elongation factor EF-G1A. The EF-G1A mutational effects required the MexXY efflux pump and the MexXY regulator ArmZ. The fusA1 mutation also modulated ΔlasR mutant resistance to two other antibiotics, ciprofloxacin and ceftazidime. Our results identify a gene mutation that can reverse the direction of the antibiotic selection of lasR mutants, a phenomenon known as sign epistasis, and provide a possible explanation for the emergence of lasR-null mutants in clinical isolates. IMPORTANCE One of the most common mutations in Pseudomonas aeruginosa clinical isolates is in the quorum sensing lasR gene. In laboratory strains, lasR disruption decreases resistance to the clinical antibiotic tobramycin. To understand how lasR mutations emerge in tobramycin-treated patients, we mutated lasR in highly tobramycin-resistant laboratory strains and determined the effects on resistance. Disrupting lasR enhanced the resistance of some strains. These strains had a single amino acid substitution in the translation factor EF-G1A. The EF-G1A mutation reversed the selective effects of tobramycin on lasR mutants. These results illustrate how adaptive mutations can lead to the emergence of new traits in a population and are relevant to understanding how genetic diversity contributes to the progression of disease during chronic infections.
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Affiliation(s)
| | - Kade A. Townsend
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Brielle M. Mckee
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Kathryn Woods
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Pratik Koirala
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Alexandra J. Holder
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Vaughn D. Craddock
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Matthew Cabeen
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
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8
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Park E, Mackens-Kiani T, Berhane R, Esser H, Erdenebat C, Burroughs AM, Berninghausen O, Aravind L, Beckmann R, Green R, Buskirk AR. B. subtilis MutS2 splits stalled ribosomes into subunits without mRNA cleavage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.05.539626. [PMID: 37205477 PMCID: PMC10187299 DOI: 10.1101/2023.05.05.539626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Stalled ribosomes are rescued by pathways that recycle the ribosome and target the nascent polypeptide for degradation. In E. coli, these pathways are triggered by ribosome collisions through recruitment of SmrB, a nuclease that cleaves the mRNA. In B. subtilis, the related protein MutS2 was recently implicated in ribosome rescue. Here we show that MutS2 is recruited to collisions by its SMR and KOW domains and reveal the interaction of these domains with collided ribosomes by cryo-EM. Using a combination of in vivo and in vitro approaches, we show that MutS2 uses its ABC ATPase activity to split ribosomes, targeting the nascent peptide for degradation by the ribosome quality control pathway. Notably, we see no evidence of mRNA cleavage by MutS2, nor does it promote ribosome rescue by tmRNA as SmrB cleavage does in E. coli. These findings clarify the biochemical and cellular roles of MutS2 in ribosome rescue in B. subtilis and raise questions about how these pathways function differently in various bacteria.
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Affiliation(s)
- Esther Park
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Timur Mackens-Kiani
- Gene Center and Department of Biochemistry, University of Munich, Munich, Germany
| | - Rebekah Berhane
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Hanna Esser
- Gene Center and Department of Biochemistry, University of Munich, Munich, Germany
| | - Chimeg Erdenebat
- Gene Center and Department of Biochemistry, University of Munich, Munich, Germany
| | - A. Maxwell Burroughs
- Computational Biology Branch, Intramural Research Program, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - Otto Berninghausen
- Gene Center and Department of Biochemistry, University of Munich, Munich, Germany
| | - L. Aravind
- Computational Biology Branch, Intramural Research Program, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - Roland Beckmann
- Gene Center and Department of Biochemistry, University of Munich, Munich, Germany
| | - Rachel Green
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Allen R. Buskirk
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States
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9
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Hacker WC, Elcock AH. spotter : A single-nucleotide resolution stochastic simulation model of supercoiling-mediated transcription and translation in prokaryotes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.21.537861. [PMID: 37131791 PMCID: PMC10153252 DOI: 10.1101/2023.04.21.537861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Stochastic simulation models have played an important role in efforts to understand the mechanistic basis of prokaryotic transcription and translation. Despite the fundamental linkage of these processes in bacterial cells, however, most simulation models have been limited to representations of either transcription or translation. In addition, the available simulation models typically either attempt to recapitulate data from single-molecule experiments without considering cellular-scale high-throughput sequencing data or, conversely, seek to reproduce cellular-scale data without paying close attention to many of the mechanistic details. To address these limitations, we here present spotter (Simulation of Prokaryotic Operon Transcription & Translation Elongation Reactions), a flexible, user-friendly simulation model that offers highly-detailed combined representations of prokaryotic transcription, translation, and DNA supercoiling. In incorporating nascent transcript and ribosomal profiling sequencing data, spotter provides a critical bridge between data collected in single-molecule experiments and data collected at the cellular scale. Importantly, in addition to rapidly generating output that can be aggregated for comparison with next-generation sequencing and proteomics data, spotter produces residue-level positional information that can be used to visualize individual simulation trajectories in detail. We anticipate that spotter will be a useful tool in exploring the interplay of processes that are crucially linked in prokaryotes.
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10
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Hou W, Harjono V, Harvey AT, Subramaniam AR, Zid BM. Quantification of elongation stalls and impact on gene expression in yeast. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.19.533377. [PMID: 36993688 PMCID: PMC10055187 DOI: 10.1101/2023.03.19.533377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Ribosomal pauses are a critical part of co-translational events including protein folding and localization. However, extended ribosome pauses can lead to ribosome collisions, resulting in the activation of ribosome rescue pathways and turnover of protein and mRNA. While this relationship has been known, the specific threshold between permissible pausing versus activation of rescue pathways has not been quantified. We have taken a method used to measure elongation time and adapted it for use in S. cerevisiae to quantify the impact of elongation stalls. We find, in transcripts containing Arg CGA codon repeat-induced stalls, a Hel2-mediated dose-dependent decrease in protein expression and mRNA level and an elongation delay on the order of minutes. In transcripts that contain synonymous substitutions to non-optimal Leu codons, there is a decrease in protein and mRNA levels, as well as similar elongation delay, but this occurs through a non-Hel2-mediated mechanism. Finally, we find that Dhh1 selectively increases protein expression, mRNA level, and elongation rate. This indicates that distinct poorly translated codons in an mRNA will activate different rescue pathways despite similar elongation stall durations. Taken together, these results provide new quantitative mechanistic insight into the surveillance of translation and the roles of Hel2 and Dhh1 in mediating ribosome pausing events.
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Affiliation(s)
- Wanfu Hou
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Vince Harjono
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Alex T Harvey
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Arvind Rasi Subramaniam
- Basic Sciences Division and Computational Biology Section of Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Brian M Zid
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
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11
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Abisado-Duquea RG, McKee BM, Townsend KA, Woods K, Koirala P, Holder AJ, Craddock VD, Cabeen MT, Chandler JR. Tobramycin adaptation alters the antibiotic susceptibility of Pseudomonas aeruginosa quorum sensing-null mutants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.13.523864. [PMID: 36711731 PMCID: PMC9882136 DOI: 10.1101/2023.01.13.523864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The opportunistic bacterium Pseudomonas aeruginosa uses the LasR-I quorum sensing system to increase resistance to the aminioglycoside antibiotic tobramycin. Paradoxically, lasR-null mutants are commonly isolated from chronic human infections treated with tobramycin, suggesting there may be a mechanism allowing the lasR-null mutants to persist under tobramycin selection. We hypothesized that the effects of inactivating lasR on tobramycin resistance might be dependent on the presence or absence of other gene mutations in that strain, a phenomenon known as epistasis. To test this hypothesis, we inactivated lasR in several highly tobramycin-resistant isolates from long-term evolution experiments. We show that the effects of ΔlasR on tobramycin resistance are strain dependent. The effects can be attributed to a point mutation in the gene encoding the translation elongation factor fusA1 (G61A nucleotide substitution), which confers a strong selective advantage to lasR-null PA14 under tobramycin selection. This fusA1 G61A mutation results in increased activity of the MexXY efflux pump and expression of the mexXY regulator ArmZ. The fusA1 mutation can also modulate ΔlasR mutant resistance to two other antibiotics, ciprofloxacin and ceftazidime. Our results demonstrate the importance of epistatic gene interactions on antibiotic susceptibility of lasR-null mutants. These results support of the idea that gene interactions might play a significant role in the evolution of quorum sensing in P. aeruginosa.
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12
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Jain A, Gupta AK. Modeling mRNA Translation With Ribosome Abortions. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:1600-1605. [PMID: 36044491 DOI: 10.1109/tcbb.2022.3203171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
We derive a deterministic mathematical model for the flow of ribosomes along a mRNA called the ribosome flow model with extended objects and abortions (RFMEOA). This model incorporates important cellular features such as every ribosome covers several codons and they may detach from various regions along the track due to more realistic biological situations including phenomena of ribosome-ribosome collisions. We prove that the ribosome density profile along the mRNA in the RFMEOA and in particular, the protein production rate converge to a unique steady-state. Simulations of the RFMEOA demonstrate a surprising result that an increase in the initiation rate may sometimes lead to a decrease in the production rate. We believe that this model could be helpful to provide insight into the effects of premature termination on the protein expression and be useful for understanding and re-engineering the translation process.
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13
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Bottorff TA, Park H, Geballe AP, Subramaniam AR. Translational buffering by ribosome stalling in upstream open reading frames. PLoS Genet 2022; 18:e1010460. [PMID: 36315596 PMCID: PMC9648851 DOI: 10.1371/journal.pgen.1010460] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/10/2022] [Accepted: 10/04/2022] [Indexed: 11/05/2022] Open
Abstract
Upstream open reading frames (uORFs) are present in over half of all human mRNAs. uORFs can potently regulate the translation of downstream open reading frames through several mechanisms: siphoning away scanning ribosomes, regulating re-initiation, and allowing interactions between scanning and elongating ribosomes. However, the consequences of these different mechanisms for the regulation of protein expression remain incompletely understood. Here, we performed systematic measurements on the uORF-containing 5' UTR of the cytomegaloviral UL4 mRNA to test alternative models of uORF-mediated regulation in human cells. We find that a terminal diproline-dependent elongating ribosome stall in the UL4 uORF prevents decreases in main ORF protein expression when ribosome loading onto the mRNA is reduced. This uORF-mediated buffering is insensitive to the location of the ribosome stall along the uORF. Computational kinetic modeling based on our measurements suggests that scanning ribosomes dissociate rather than queue when they collide with stalled elongating ribosomes within the UL4 uORF. We identify several human uORFs that repress main ORF protein expression via a similar terminal diproline motif. We propose that ribosome stalls in uORFs provide a general mechanism for buffering against reductions in main ORF translation during stress and developmental transitions.
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Affiliation(s)
- Ty A. Bottorff
- Basic Sciences Division and Computational Biology Program of the Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Biological Physics, Structure and Design Graduate Program, University of Washington, Seattle, Washington, United States of America
| | - Heungwon Park
- Basic Sciences Division and Computational Biology Program of the Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Adam P. Geballe
- Human Biology and Clinical Research Divisions, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Arvind Rasi Subramaniam
- Basic Sciences Division and Computational Biology Program of the Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Biological Physics, Structure and Design Graduate Program, University of Washington, Seattle, Washington, United States of America
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14
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Ribosome collisions induce mRNA cleavage and ribosome rescue in bacteria. Nature 2022; 603:503-508. [PMID: 35264790 DOI: 10.1038/s41586-022-04416-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 01/07/2022] [Indexed: 01/17/2023]
Abstract
Ribosome rescue pathways recycle stalled ribosomes and target problematic mRNAs and aborted proteins for degradation1,2. In bacteria, it remains unclear how rescue pathways distinguish ribosomes stalled in the middle of a transcript from actively translating ribosomes3-6. Here, using a genetic screen in Escherichia coli, we discovered a new rescue factor that has endonuclease activity. SmrB cleaves mRNAs upstream of stalled ribosomes, allowing the ribosome rescue factor tmRNA (which acts on truncated mRNAs3) to rescue upstream ribosomes. SmrB is recruited to ribosomes and is activated by collisions. Cryo-electron microscopy structures of collided disomes from E. coli and Bacillus subtilis show distinct and conserved arrangements of individual ribosomes and the composite SmrB-binding site. These findings reveal the underlying mechanisms by which ribosome collisions trigger ribosome rescue in bacteria.
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15
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Jain A, Margaliot M, Gupta AK. Large-scale mRNA translation and the intricate effects of competition for the finite pool of ribosomes. J R Soc Interface 2022; 19:20220033. [PMID: 35259953 PMCID: PMC8922411 DOI: 10.1098/rsif.2022.0033] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We present a new theoretical framework for large-scale mRNA translation using a network of models called the ribosome flow model with Langmuir kinetics (RFMLK), interconnected via a pool of free ribosomes. The input to each RFMLK depends on the pool density, and it affects the initiation rate and potentially also the internal ribosome entry rates along each RFMLK. Ribosomes that detach from an RFMLK owing to termination or premature drop-off are fed back into the pool. We prove that the network always converges to a steady state, and study its sensitivity to variations in the parameters. For example, we show that if the drop-off rate at some site in some RFMLK is increased then the pool density increases and consequently the steady-state production rate in all the other RFMLKs increases. Surprisingly, we also show that modifying a parameter of a certain RFMLK can lead to arbitrary effects on the densities along the modified RFMLK, depending on the parameters in the entire network. We conclude that the competition for shared resources generates an indirect and intricate web of mutual effects between the mRNA molecules that must be accounted for in any analysis of translation.
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Affiliation(s)
- Aditi Jain
- Department of Mathematics, Indian Institute of Technology Ropar, Rupnagar, Punjab 140001, India
| | - Michael Margaliot
- School of Electrical Engineering and the Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Arvind Kumar Gupta
- Department of Mathematics, Indian Institute of Technology Ropar, Rupnagar, Punjab 140001, India
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16
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Kim KQ, Zaher HS. Canary in a coal mine: collided ribosomes as sensors of cellular conditions. Trends Biochem Sci 2022; 47:82-97. [PMID: 34607755 PMCID: PMC8688274 DOI: 10.1016/j.tibs.2021.09.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 08/30/2021] [Accepted: 09/03/2021] [Indexed: 02/06/2023]
Abstract
The recent discovery that collision of ribosomes triggers quality control and stress responses in eukaryotes has shifted the perspective of the field. Collided eukaryotic ribosomes adopt a unique structure, acting as a ubiquitin signaling platform for various response factors. While several of the signals that determine which downstream pathways are activated have been uncovered, we are only beginning to learn how the specificity for the activation of each process is achieved during collisions. This review will summarize those findings and how ribosome-associated factors act as molecular sentinels, linking aberrations in translation to the overall cellular state. Insights into how cells respond to ribosome collision events will provide greater understanding of the role of the ribosome in the maintenance of cellular homeostasis.
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Affiliation(s)
| | - Hani S. Zaher
- Correspondence to: , Department of Biology, Washington University in St. Louis, Campus Box 1137, One Brookings Drive, St. Louis, MO, USA 63130, Phone: (314) 935-7832, Fax: (314) 935-4432
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17
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Felletti M, Romilly C, Wagner EGH, Jonas K. A nascent polypeptide sequence modulates DnaA translation elongation in response to nutrient availability. eLife 2021; 10:71611. [PMID: 34524083 PMCID: PMC8443254 DOI: 10.7554/elife.71611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/15/2021] [Indexed: 01/01/2023] Open
Abstract
The ability to regulate DNA replication initiation in response to changing nutrient conditions is an important feature of most cell types. In bacteria, DNA replication is triggered by the initiator protein DnaA, which has long been suggested to respond to nutritional changes; nevertheless, the underlying mechanisms remain poorly understood. Here, we report a novel mechanism that adjusts DnaA synthesis in response to nutrient availability in Caulobacter crescentus. By performing a detailed biochemical and genetic analysis of the dnaA mRNA, we identified a sequence downstream of the dnaA start codon that inhibits DnaA translation elongation upon carbon exhaustion. Our data show that the corresponding peptide sequence, but not the mRNA secondary structure or the codon choice, is critical for this response, suggesting that specific amino acids in the growing DnaA nascent chain tune translational efficiency. Our study provides new insights into DnaA regulation and highlights the importance of translation elongation as a regulatory target. We propose that translation regulation by nascent chain sequences, like the one described, might constitute a general strategy for modulating the synthesis rate of specific proteins under changing conditions.
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Affiliation(s)
- Michele Felletti
- Science for Life Laboratory and Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Cédric Romilly
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - E Gerhart H Wagner
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Kristina Jonas
- Science for Life Laboratory and Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
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18
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Abstract
Bacterial protein synthesis rates have evolved to maintain preferred stoichiometries at striking precision, from the components of protein complexes to constituents of entire pathways. Setting relative protein production rates to be well within a factor of two requires concerted tuning of transcription, RNA turnover, and translation, allowing many potential regulatory strategies to achieve the preferred output. The last decade has seen a greatly expanded capacity for precise interrogation of each step of the central dogma genome-wide. Here, we summarize how these technologies have shaped the current understanding of diverse bacterial regulatory architectures underpinning stoichiometric protein synthesis. We focus on the emerging expanded view of bacterial operons, which encode diverse primary and secondary mRNA structures for tuning protein stoichiometry. Emphasis is placed on how quantitative tuning is achieved. We discuss the challenges and open questions in the application of quantitative, genome-wide methodologies to the problem of precise protein production. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- James C Taggart
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; ,
| | - Jean-Benoît Lalanne
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; , .,Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Current affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA;
| | - Gene-Wei Li
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; ,
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19
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Lalanne J, Parker DJ, Li G. Spurious regulatory connections dictate the expression-fitness landscape of translation factors. Mol Syst Biol 2021; 17:e10302. [PMID: 33900014 PMCID: PMC8073009 DOI: 10.15252/msb.202110302] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 12/21/2022] Open
Abstract
During steady-state cell growth, individual enzymatic fluxes can be directly inferred from growth rate by mass conservation, but the inverse problem remains unsolved. Perturbing the flux and expression of a single enzyme could have pleiotropic effects that may or may not dominate the impact on cell fitness. Here, we quantitatively dissect the molecular and global responses to varied expression of translation termination factors (peptide release factors, RFs) in the bacterium Bacillus subtilis. While endogenous RF expression maximizes proliferation, deviations in expression lead to unexpected distal regulatory responses that dictate fitness reduction. Molecularly, RF depletion causes expression imbalance at specific operons, which activates master regulators and detrimentally overrides the transcriptome. Through these spurious connections, RF abundances are thus entrenched by focal points within the regulatory network, in one case located at a single stop codon. Such regulatory entrenchment suggests that predictive bottom-up models of expression-fitness landscapes will require near-exhaustive characterization of parts.
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Affiliation(s)
- Jean‐Benoît Lalanne
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of PhysicsMassachusetts Institute of TechnologyCambridgeMAUSA
- Present address:
Department of Genome SciencesUniversity of WashingtonSeattleWAUSA
| | - Darren J Parker
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMAUSA
- Present address:
Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | - Gene‐Wei Li
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMAUSA
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20
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Liu Y, Yang Q, Zhao F. Synonymous but Not Silent: The Codon Usage Code for Gene Expression and Protein Folding. Annu Rev Biochem 2021; 90:375-401. [PMID: 33441035 DOI: 10.1146/annurev-biochem-071320-112701] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Codon usage bias, the preference for certain synonymous codons, is found in all genomes. Although synonymous mutations were previously thought to be silent, a large body of evidence has demonstrated that codon usage can play major roles in determining gene expression levels and protein structures. Codon usage influences translation elongation speed and regulates translation efficiency and accuracy. Adaptation of codon usage to tRNA expression determines the proteome landscape. In addition, codon usage biases result in nonuniform ribosome decoding rates on mRNAs, which in turn influence the cotranslational protein folding process that is critical for protein function in diverse biological processes. Conserved genome-wide correlations have also been found between codon usage and protein structures. Furthermore, codon usage is a major determinant of mRNA levels through translation-dependent effects on mRNA decay and translation-independent effects on transcriptional and posttranscriptional processes. Here, we discuss the multifaceted roles and mechanisms of codon usage in different gene regulatory processes.
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Affiliation(s)
- Yi Liu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA;
| | - Qian Yang
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA;
| | - Fangzhou Zhao
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA;
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21
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Computational discovery and modeling of novel gene expression rules encoded in the mRNA. Biochem Soc Trans 2020; 48:1519-1528. [PMID: 32662820 DOI: 10.1042/bst20191048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 06/15/2020] [Accepted: 06/17/2020] [Indexed: 11/17/2022]
Abstract
The transcript is populated with numerous overlapping codes that regulate all steps of gene expression. Deciphering these codes is very challenging due to the large number of variables involved, the non-modular nature of the codes, biases and limitations in current experimental approaches, our limited knowledge in gene expression regulation across the tree of life, and other factors. In recent years, it has been shown that computational modeling and algorithms can significantly accelerate the discovery of novel gene expression codes. Here, we briefly summarize the latest developments and different approaches in the field.
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22
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Patraquim P, Mumtaz MAS, Pueyo JI, Aspden JL, Couso JP. Developmental regulation of canonical and small ORF translation from mRNAs. Genome Biol 2020; 21:128. [PMID: 32471506 PMCID: PMC7260771 DOI: 10.1186/s13059-020-02011-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 04/08/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Ribosomal profiling has revealed the translation of thousands of sequences outside annotated protein-coding genes, including small open reading frames of less than 100 codons, and the translational regulation of many genes. Here we present an improved version of Poly-Ribo-Seq and apply it to Drosophila melanogaster embryos to extend the catalog of in vivo translated small ORFs, and to reveal the translational regulation of both small and canonical ORFs from mRNAs across embryogenesis. RESULTS We obtain highly correlated samples across five embryonic stages, with nearly 500 million putative ribosomal footprints mapped to mRNAs, and compare them to existing Ribo-Seq and proteomic data. Our analysis reveals, for the first time in Drosophila, footprints mapping to codons in a phased pattern, the hallmark of productive translation. We propose a simple binomial probability metric to ascertain translation probability. Our results also reveal reproducible ribosomal binding apparently not resulting in productive translation. This non-productive ribosomal binding seems to be especially prevalent amongst upstream short ORFs located in the 5' mRNA leaders, and amongst canonical ORFs during the activation of the zygotic translatome at the maternal-to zygotic transition. CONCLUSIONS We suggest that this non-productive ribosomal binding might be due to cis-regulatory ribosomal binding and to defective ribosomal scanning of ORFs outside periods of productive translation. Our results are compatible with the main function of upstream short ORFs being to buffer the translation of canonical canonical ORFs; and show that, in general, small ORFs in mRNAs display markers compatible with an evolutionary transitory state towards full coding function.
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Affiliation(s)
- Pedro Patraquim
- Centro Andaluz de Biologia del Desarrollo, CSIC-UPO, Seville, Spain
| | | | | | - Julie Louise Aspden
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Juan-Pablo Couso
- Centro Andaluz de Biologia del Desarrollo, CSIC-UPO, Seville, Spain. .,Previous address: Brighton and Sussex Medical School, Brighton, East Sussex, UK.
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23
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Scott S, Szavits-Nossan J. Power series method for solving TASEP-based models of mRNA translation. Phys Biol 2019; 17:015004. [PMID: 31726446 DOI: 10.1088/1478-3975/ab57a0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We develop a method for solving mathematical models of messenger RNA (mRNA) translation based on the totally asymmetric simple exclusion process (TASEP). Our main goal is to demonstrate that the method is versatile and applicable to realistic models of translation. To this end we consider the TASEP with codon-dependent elongation rates, premature termination due to ribosome drop-off and translation reinitiation due to circularisation of the mRNA. We apply the method to the model organism Saccharomyces cerevisiae under physiological conditions and find an excellent agreement with the results of stochastic simulations. Our findings suggest that the common view on translation as being rate-limited by initiation is oversimplistic. Instead we find theoretical evidence for ribosome interference and also theoretical support for the ramp hypothesis which argues that codons at the beginning of genes have slower elongation rates in order to reduce ribosome density and jamming.
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Affiliation(s)
- S Scott
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
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24
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Jack BR, Wilke CO. Pinetree: a step-wise gene expression simulator with codon-specific translation rates. Bioinformatics 2019; 35:4176-4178. [PMID: 30923831 DOI: 10.1093/bioinformatics/btz203] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 12/31/2018] [Accepted: 03/27/2019] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Stochastic gene expression simulations often assume steady-state transcript levels, or they model transcription in more detail than translation. Moreover, they lack accessible programing interfaces, which limit their utility. RESULTS We present Pinetree, a step-wise gene expression simulator with codon-specific translation rates. Pinetree models both transcription and translation in a stochastic framework with individual polymerase and ribosome-level detail. Written in C++ with a Python front-end, any user familiar with Python can specify a genome and simulate gene expression. Pinetree was designed to be efficient and scale to simulate large plasmids or viral genomes. AVAILABILITY AND IMPLEMENTATION Pinetree is available on GitHub (https://github.com/benjaminjack/pinetree) and the Python Package Index (https://pypi.org/project/pinetree/).
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Affiliation(s)
- Benjamin R Jack
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Claus O Wilke
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
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25
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Park H, Subramaniam AR. Inverted translational control of eukaryotic gene expression by ribosome collisions. PLoS Biol 2019; 17:e3000396. [PMID: 31532761 PMCID: PMC6750593 DOI: 10.1371/journal.pbio.3000396] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 08/05/2019] [Indexed: 11/19/2022] Open
Abstract
The canonical model of eukaryotic translation posits that efficient translation initiation increases protein expression and mRNA stability. Contrary to this model, we find that increasing initiation rate can decrease both protein expression and stability of certain mRNAs in the budding yeast Saccharomyces cerevisiae. These mRNAs encode a stretch of polybasic residues that cause ribosome stalling. Our computational modeling predicts that the observed decrease in gene expression at high initiation rates occurs when ribosome collisions at stalls stimulate abortive termination of the leading ribosome or cause endonucleolytic mRNA cleavage. Consistent with this prediction, the collision-associated quality-control factors Asc1 and Hel2 (orthologs of human RACK1 and ZNF598, respectively) decrease gene expression from stall-containing mRNAs only at high initiation rates. Remarkably, hundreds of S. cerevisiae mRNAs that contain ribosome stall sequences also exhibit lower translation efficiency. We propose that inefficient translation initiation allows these stall-containing endogenous mRNAs to escape collision-stimulated reduction in gene expression. Higher rates of translation counterintuitively lead to lower protein levels from eukaryotic mRNAs that encode ribosome stalls; modelling suggests that this occurs when ribosome collisions at stalls trigger abortive termination of the leading ribosome or cause endonucleolytic mRNA cleavage.
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Affiliation(s)
- Heungwon Park
- Basic Sciences Division and Computational Biology Section of Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Arvind R. Subramaniam
- Basic Sciences Division and Computational Biology Section of Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail:
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26
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D'Orazio KN, Wu CCC, Sinha N, Loll-Krippleber R, Brown GW, Green R. The endonuclease Cue2 cleaves mRNAs at stalled ribosomes during No Go Decay. eLife 2019; 8:e49117. [PMID: 31219035 PMCID: PMC6598757 DOI: 10.7554/elife.49117] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 06/19/2019] [Indexed: 01/04/2023] Open
Abstract
Translation of problematic sequences in mRNAs leads to ribosome collisions that trigger a series of quality control events including ribosome rescue, degradation of the stalled nascent polypeptide, and targeting of the mRNA for decay (No Go Decay or NGD). Using a reverse genetic screen in yeast, we identify Cue2 as the conserved endonuclease that is recruited to stalled ribosomes to promote NGD. Ribosome profiling and biochemistry provide strong evidence that Cue2 cleaves mRNA within the A site of the colliding ribosome. We demonstrate that NGD primarily proceeds via Xrn1-mediated exonucleolytic decay and Cue2-mediated endonucleolytic decay normally constitutes a secondary decay pathway. Finally, we show that the Cue2-dependent pathway becomes a major contributor to NGD in cells depleted of factors required for the resolution of stalled ribosome complexes. Together these results provide insights into how multiple decay processes converge to process problematic mRNAs in eukaryotic cells..
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Affiliation(s)
- Karole N D'Orazio
- Department of Molecular Biology and GeneticsHoward Hughes Medical Institute, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Colin Chih-Chien Wu
- Department of Molecular Biology and GeneticsHoward Hughes Medical Institute, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Niladri Sinha
- Department of Molecular Biology and GeneticsHoward Hughes Medical Institute, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Raphael Loll-Krippleber
- Donnelly Centre for Cellular and Biomolecular Research, Department of BiochemistryUniversity of TorontoTorontoCanada
| | - Grant W Brown
- Donnelly Centre for Cellular and Biomolecular Research, Department of BiochemistryUniversity of TorontoTorontoCanada
| | - Rachel Green
- Department of Molecular Biology and GeneticsHoward Hughes Medical Institute, Johns Hopkins University School of MedicineBaltimoreUnited States
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27
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Ingolia NT, Hussmann JA, Weissman JS. Ribosome Profiling: Global Views of Translation. Cold Spring Harb Perspect Biol 2019; 11:cshperspect.a032698. [PMID: 30037969 DOI: 10.1101/cshperspect.a032698] [Citation(s) in RCA: 157] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The translation of messenger RNA (mRNA) into protein and the folding of the resulting protein into an active form are prerequisites for virtually every cellular process and represent the single largest investment of energy by cells. Ribosome profiling-based approaches have revolutionized our ability to monitor every step of protein synthesis in vivo, allowing one to measure the rate of protein synthesis across the proteome, annotate the protein coding capacity of genomes, monitor localized protein synthesis, and explore cotranslational folding and targeting. The rich and quantitative nature of ribosome profiling data provides an unprecedented opportunity to explore and model complex cellular processes. New analytical techniques and improved experimental protocols will provide a deeper understanding of the factors controlling translation speed and its impact on protein function and cell physiology as well as the role of ribosomal RNA and mRNA modifications in regulating translation.
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Affiliation(s)
- Nicholas T Ingolia
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720
| | - Jeffrey A Hussmann
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158.,Howard Hughes Medical Institute, San Francisco, California 94158
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158.,Howard Hughes Medical Institute, San Francisco, California 94158
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Kim S, Jacobs-Wagner C. Effects of mRNA Degradation and Site-Specific Transcriptional Pausing on Protein Expression Noise. Biophys J 2019; 114:1718-1729. [PMID: 29642040 DOI: 10.1016/j.bpj.2018.02.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 01/30/2018] [Accepted: 02/07/2018] [Indexed: 12/20/2022] Open
Abstract
Genetically identical cells exhibit diverse phenotypes even when experiencing the same environment. This phenomenon in part originates from cell-to-cell variability (noise) in protein expression. Although various kinetic schemes of stochastic transcription initiation are known to affect gene expression noise, how posttranscription initiation events contribute to noise at the protein level remains incompletely understood. To address this question, we developed a stochastic simulation-based model of bacterial gene expression that integrates well-known dependencies between transcription initiation, transcription elongation dynamics, mRNA degradation, and translation. We identified realistic conditions under which mRNA lifetime and transcriptional pauses modulate the protein expression noise initially introduced by the promoter architecture. For instance, we found that the short lifetime of bacterial mRNAs facilitates the production of protein bursts. Conversely, RNA polymerase (RNAP) pausing at specific sites during transcription elongation can attenuate protein bursts by fluidizing the RNAP traffic to the point of erasing the effect of a bursty promoter. Pause-prone sites, if located close to the promoter, can also affect noise indirectly by reducing both transcription and translation initiation due to RNAP and ribosome congestion. Our findings highlight how the interplay between transcription initiation, transcription elongation, translation, and mRNA degradation shapes the distribution in protein numbers. They also have implications for our understanding of gene evolution and suggest combinatorial strategies for modulating phenotypic variability by genetic engineering.
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Affiliation(s)
- Sangjin Kim
- Microbial Sciences Institute, West Haven, Connecticut; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut; Howard Hughes Medical Institute, New Haven, Connecticut
| | - Christine Jacobs-Wagner
- Microbial Sciences Institute, West Haven, Connecticut; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut; Howard Hughes Medical Institute, New Haven, Connecticut; Department of Microbial Pathogenesis, Yale School of Medicine, Yale University, New Haven, Connecticut.
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Darnell AM, Subramaniam AR, O'Shea EK. Translational Control through Differential Ribosome Pausing during Amino Acid Limitation in Mammalian Cells. Mol Cell 2019; 71:229-243.e11. [PMID: 30029003 DOI: 10.1016/j.molcel.2018.06.041] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 05/07/2018] [Accepted: 06/26/2018] [Indexed: 12/22/2022]
Abstract
Limitation for amino acids is thought to regulate translation in mammalian cells primarily by signaling through the kinases mTORC1 and GCN2. We find that a selective loss of arginine tRNA charging during limitation for arginine regulates translation through ribosome pausing at two of six arginine codons. Surprisingly, limitation for leucine, an essential and abundant amino acid in protein, results in little or no ribosome pausing. Chemical and genetic perturbation of mTORC1 and GCN2 signaling revealed that their robust response to leucine limitation prevents ribosome pausing, while an insufficient response to arginine limitation leads to loss of tRNA charging and ribosome pausing. Ribosome pausing decreases protein production and triggers premature ribosome termination without reducing mRNA levels. Together, our results suggest that amino acids that are not optimally sensed by the mTORC1 and GCN2 pathways still regulate translation through an evolutionarily conserved mechanism based on codon-specific ribosome pausing.
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Affiliation(s)
- Alicia M Darnell
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Arvind R Subramaniam
- Basic Sciences Division and Computational Biology Program of Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
| | - Erin K O'Shea
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA; Department of Chemistry and Chemical Biology and Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.
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30
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Juszkiewicz S, Chandrasekaran V, Lin Z, Kraatz S, Ramakrishnan V, Hegde RS. ZNF598 Is a Quality Control Sensor of Collided Ribosomes. Mol Cell 2018; 72:469-481.e7. [PMID: 30293783 PMCID: PMC6224477 DOI: 10.1016/j.molcel.2018.08.037] [Citation(s) in RCA: 234] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 08/07/2018] [Accepted: 08/22/2018] [Indexed: 01/30/2023]
Abstract
Aberrantly slow translation elicits quality control pathways initiated by the ubiquitin ligase ZNF598. How ZNF598 discriminates physiologic from pathologic translation complexes and ubiquitinates stalled ribosomes selectively is unclear. Here, we find that the minimal unit engaged by ZNF598 is the collided di-ribosome, a molecular species that arises when a trailing ribosome encounters a slower leading ribosome. The collided di-ribosome structure reveals an extensive 40S-40S interface in which the ubiquitination targets of ZNF598 reside. The paucity of 60S interactions allows for different ribosome rotation states, explaining why ZNF598 recognition is indifferent to how the leading ribosome has stalled. The use of ribosome collisions as a proxy for stalling allows the degree of tolerable slowdown to be tuned by the initiation rate on that mRNA; hence, the threshold for triggering quality control is substrate specific. These findings illustrate how higher-order ribosome architecture can be exploited by cellular factors to monitor translation status. ZNF598 is a direct sensor of ribosome collisions incurred by many unrelated causes The minimal target recognized and ubiquitinated by ZNF598 is a collided di-ribosome Collided di-ribosome structure shows that ZNF598 ubiquitin sites are near the interface Collisions are required to terminally arrest translation in ZNF598-dependent manner
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Affiliation(s)
| | | | - Zhewang Lin
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | - V Ramakrishnan
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
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31
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Liu B, Chen C. Translation Elongation Factor 4 (LepA) Contributes to Tetracycline Susceptibility by Stalling Elongating Ribosomes. Antimicrob Agents Chemother 2018; 62:e02356-17. [PMID: 29784847 PMCID: PMC6105825 DOI: 10.1128/aac.02356-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 05/13/2018] [Indexed: 12/05/2022] Open
Abstract
Even though elongation factor 4 (EF4) is the third most conserved protein in bacteria, its physiological functions remain largely unknown and its proposed molecular mechanisms are conflicting among previous studies. In the present study, we show that the growth of an Escherichia coli strain is more susceptible to tetracycline than its EF4 knockout strain. Consistent with previous studies, our results suggested that EF4 affects ribosome biogenesis when tetracycline is present. Through ribosome profiling analysis, we discovered that EF4 causes 1-nucleotide shifting of ribosomal footprints on mRNA when cells have been exposed to tetracycline. In addition, when tetracycline is present, EF4 inhibits the elongation of protein synthesis, which leads to the accumulation of ribosomes in the early segment of mRNA. Altogether, when cells are exposed to tetracycline, EF4 alters both ribosome biogenesis and the elongation phase of protein synthesis.
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Affiliation(s)
- Bin Liu
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China
| | - Chunlai Chen
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China
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32
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Van Damme P. Limitless translation limits translation. Nature 2018; 553:289-290. [PMID: 29345666 DOI: 10.1038/d41586-017-08785-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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33
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Kapur M, Ackerman SL. mRNA Translation Gone Awry: Translation Fidelity and Neurological Disease. Trends Genet 2018; 34:218-231. [PMID: 29352613 DOI: 10.1016/j.tig.2017.12.007] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 12/04/2017] [Accepted: 12/11/2017] [Indexed: 10/18/2022]
Abstract
Errors during mRNA translation can lead to a reduction in the levels of functional proteins and an increase in deleterious molecules. Advances in next-generation sequencing have led to the discovery of rare genetic disorders, many caused by mutations in genes encoding the mRNA translation machinery, as well as to a better understanding of translational dynamics through ribosome profiling. We discuss here multiple neurological disorders that are linked to errors in tRNA aminoacylation and ribosome decoding. We draw on studies from genetic models, including yeast and mice, to enhance our understanding of the translational defects observed in these diseases. Finally, we emphasize the importance of tRNA, their associated enzymes, and the inextricable link between accuracy and efficiency in the maintenance of translational fidelity.
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Affiliation(s)
- Mridu Kapur
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Section of Neurobiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Susan L Ackerman
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Section of Neurobiology, University of California, San Diego, La Jolla, CA 92093, USA.
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