101
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Hill CH, Cook GM, Napthine S, Kibe A, Brown K, Caliskan N, Firth AE, Graham SC, Brierley I. Investigating molecular mechanisms of 2A-stimulated ribosomal pausing and frameshifting in Theilovirus. Nucleic Acids Res 2021; 49:11938-11958. [PMID: 34751406 PMCID: PMC8599813 DOI: 10.1093/nar/gkab969] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 10/01/2021] [Accepted: 10/06/2021] [Indexed: 12/02/2022] Open
Abstract
The 2A protein of Theiler's murine encephalomyelitis virus (TMEV) acts as a switch to stimulate programmed -1 ribosomal frameshifting (PRF) during infection. Here, we present the X-ray crystal structure of TMEV 2A and define how it recognises the stimulatory RNA element. We demonstrate a critical role for bases upstream of the originally predicted stem-loop, providing evidence for a pseudoknot-like conformation and suggesting that the recognition of this pseudoknot by beta-shell proteins is a conserved feature in cardioviruses. Through examination of PRF in TMEV-infected cells by ribosome profiling, we identify a series of ribosomal pauses around the site of PRF induced by the 2A-pseudoknot complex. Careful normalisation of ribosomal profiling data with a 2A knockout virus facilitated the identification, through disome analysis, of ribosome stacking at the TMEV frameshifting signal. These experiments provide unparalleled detail of the molecular mechanisms underpinning Theilovirus protein-stimulated frameshifting.
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Affiliation(s)
- Chris H Hill
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Georgia M Cook
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Sawsan Napthine
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Anuja Kibe
- Helmholtz Institute for RNA-based Infection Research (HIRI), Josef-Schneider-Straße 2/D15, 97080 Würzburg, Germany
| | - Katherine Brown
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Neva Caliskan
- Helmholtz Institute for RNA-based Infection Research (HIRI), Josef-Schneider-Straße 2/D15, 97080 Würzburg, Germany
- Medical Faculty, Julius-Maximilians University Würzburg, 97074 Würzburg, Germany
| | - Andrew E Firth
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Stephen C Graham
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Ian Brierley
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
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102
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Fusco CM, Desch K, Dörrbaum AR, Wang M, Staab A, Chan ICW, Vail E, Villeri V, Langer JD, Schuman EM. Neuronal ribosomes exhibit dynamic and context-dependent exchange of ribosomal proteins. Nat Commun 2021; 12:6127. [PMID: 34675203 PMCID: PMC8531293 DOI: 10.1038/s41467-021-26365-x] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 09/29/2021] [Indexed: 12/11/2022] Open
Abstract
Owing to their morphological complexity and dense network connections, neurons modify their proteomes locally, using mRNAs and ribosomes present in the neuropil (tissue enriched for dendrites and axons). Although ribosome biogenesis largely takes place in the nucleus and perinuclear region, neuronal ribosomal protein (RP) mRNAs have been frequently detected remotely, in dendrites and axons. Here, using imaging and ribosome profiling, we directly detected the RP mRNAs and their translation in the neuropil. Combining brief metabolic labeling with mass spectrometry, we found that a group of RPs rapidly associated with translating ribosomes in the cytoplasm and that this incorporation was independent of canonical ribosome biogenesis. Moreover, the incorporation probability of some RPs was regulated by location (neurites vs. cell bodies) and changes in the cellular environment (following oxidative stress). Our results suggest new mechanisms for the local activation, repair and/or specialization of the translational machinery within neuronal processes, potentially allowing neuronal synapses a rapid means to regulate local protein synthesis.
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Affiliation(s)
- Claudia M. Fusco
- grid.419505.c0000 0004 0491 3878Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Kristina Desch
- grid.419505.c0000 0004 0491 3878Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Aline R. Dörrbaum
- grid.419505.c0000 0004 0491 3878Max Planck Institute for Brain Research, Frankfurt, Germany ,Present Address: MOS, Center for Mass Spectrometry and Optical Spectroscopy, Mannheim, Germany
| | - Mantian Wang
- grid.419505.c0000 0004 0491 3878Max Planck Institute for Brain Research, Frankfurt, Germany ,grid.508836.0Present Address: Institute of Molecular and Clinical Ophthalmology, Basel, Switzerland
| | - Anja Staab
- grid.419505.c0000 0004 0491 3878Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Ivy C. W. Chan
- grid.419505.c0000 0004 0491 3878Max Planck Institute for Brain Research, Frankfurt, Germany ,grid.424247.30000 0004 0438 0426Present Address: German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Eleanor Vail
- grid.419505.c0000 0004 0491 3878Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Veronica Villeri
- grid.419505.c0000 0004 0491 3878Max Planck Institute for Brain Research, Frankfurt, Germany ,grid.412041.20000 0001 2106 639XPresent Address: Department of Neuroscience, University of Bordeaux, Bordeaux, France
| | - Julian D. Langer
- grid.419505.c0000 0004 0491 3878Max Planck Institute for Brain Research, Frankfurt, Germany ,grid.419494.50000 0001 1018 9466Max Planck Institute for Biophysics, Frankfurt, Germany
| | - Erin M. Schuman
- grid.419505.c0000 0004 0491 3878Max Planck Institute for Brain Research, Frankfurt, Germany
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103
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Andreev DE, Smirnova VV, Shatsky IN. Modifications of Ribosome Profiling that Provide New Data on the Translation Regulation. BIOCHEMISTRY (MOSCOW) 2021; 86:1095-1106. [PMID: 34565313 DOI: 10.1134/s0006297921090054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Ribosome profiling (riboseq) has opened the possibilities for the genome-wide studies of translation in all living organisms. This method is based on deep sequencing of mRNA fragments protected by the ribosomes from hydrolysis by ribonucleases, the so-called ribosomal footprints (RFPs). Ribosomal profiling together with RNA sequencing allows not only to identify with a reasonable accuracy translated reading frames in the transcriptome, but also to track changes in gene expression in response to various stimuli. Notably, ribosomal profiling in its classical version has certain limitations. The size of the selected mRNA fragments is 25-35 nts, while RFPs of other sizes are usually omitted from analysis. Also, ribosomal profiling "averages" the data from all ribosomes and does not allow to study specific ribosomal complexes associated with particular translation factors. However, recently developed modifications of ribosomal profiling provide answers to a number of questions. Thus, it has become possible to analyze not only elongating, but also scanning and reinitiating ribosomes, to study events associated with the collision of ribosomes during mRNA translation, to discover new ways of cotranslational assembly of multisubunit protein complexes during translation, and to selectively isolate ribosomal complexes associated with certain protein factors. New data obtained using these modified approaches provide a better understanding of the mechanisms of translation regulation and the functional roles of translational apparatus components.
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Affiliation(s)
- Dmitry E Andreev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russia
| | - Viktoriya V Smirnova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Ivan N Shatsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia.
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104
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Mendonsa S, von Kuegelgen N, Bujanic L, Chekulaeva M. Charcot-Marie-Tooth mutation in glycyl-tRNA synthetase stalls ribosomes in a pre-accommodation state and activates integrated stress response. Nucleic Acids Res 2021; 49:10007-10017. [PMID: 34403468 PMCID: PMC8464049 DOI: 10.1093/nar/gkab730] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 08/12/2021] [Indexed: 11/14/2022] Open
Abstract
Toxic gain-of-function mutations in aminoacyl-tRNA synthetases cause a degeneration of peripheral motor and sensory axons, known as Charcot-Marie-Tooth (CMT) disease. While these mutations do not disrupt overall aminoacylation activity, they interfere with translation via an unknown mechanism. Here, we dissect the mechanism of function of CMT mutant glycyl-tRNA synthetase (CMT-GARS), using high-resolution ribosome profiling and reporter assays. We find that CMT-GARS mutants deplete the pool of glycyl-tRNAGly available for translation and inhibit the first stage of elongation, the accommodation of glycyl-tRNA into the ribosomal A-site, which causes ribosomes to pause at glycine codons. Moreover, ribosome pausing activates a secondary repression mechanism at the level of translation initiation, by inducing the phosphorylation of the alpha subunit of eIF2 and the integrated stress response. Thus, CMT-GARS mutant triggers translational repression via two interconnected mechanisms, affecting both elongation and initiation of translation.
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Affiliation(s)
- Samantha Mendonsa
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Free University, Berlin, Germany
| | - Nicolai von Kuegelgen
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Free University, Berlin, Germany
| | - Lucija Bujanic
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Marina Chekulaeva
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
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105
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Lyu X, Yang Q, Zhao F, Liu Y. Codon usage and protein length-dependent feedback from translation elongation regulates translation initiation and elongation speed. Nucleic Acids Res 2021; 49:9404-9423. [PMID: 34417614 PMCID: PMC8450115 DOI: 10.1093/nar/gkab729] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/26/2021] [Accepted: 08/17/2021] [Indexed: 12/26/2022] Open
Abstract
Essential cellular functions require efficient production of many large proteins but synthesis of large proteins encounters many obstacles in cells. Translational control is mostly known to be regulated at the initiation step. Whether translation elongation process can feedback to regulate initiation efficiency is unclear. Codon usage bias, a universal feature of all genomes, plays an important role in determining gene expression levels. Here, we discovered that there is a conserved but codon usage-dependent genome-wide negative correlation between protein abundance and CDS length. The codon usage effects on protein expression and ribosome flux on mRNAs are influenced by CDS length; optimal codon usage preferentially promotes production of large proteins. Translation of mRNAs with long CDS and non-optimal codon usage preferentially induces phosphorylation of initiation factor eIF2α, which inhibits translation initiation efficiency. Deletion of the eIF2α kinase CPC-3 (GCN2 homolog) in Neurospora preferentially up-regulates large proteins encoded by non-optimal codons. Surprisingly, CPC-3 also inhibits translation elongation rate in a codon usage and CDS length-dependent manner, resulting in slow elongation rates for long CDS mRNAs. Together, these results revealed a codon usage and CDS length-dependent feedback mechanism from translation elongation to regulate both translation initiation and elongation kinetics.
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Affiliation(s)
- Xueliang Lyu
- Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA.,State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Qian Yang
- Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Fangzhou Zhao
- Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Yi Liu
- Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
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106
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Koga Y, Hoang EM, Park Y, Keszei AFA, Murray J, Shao S, Liau BB. Discovery of C13-Aminobenzoyl Cycloheximide Derivatives that Potently Inhibit Translation Elongation. J Am Chem Soc 2021; 143:13473-13477. [PMID: 34403584 DOI: 10.1021/jacs.1c05146] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Employed for over half a century to study protein synthesis, cycloheximide (CHX, 1) is a small molecule natural product that reversibly inhibits translation elongation. More recently, CHX has been applied to ribosome profiling, a method for mapping ribosome positions on mRNA genome-wide. Despite CHX's extensive use, CHX treatment often results in incomplete translation inhibition due to its rapid reversibility, prompting the need for improved reagents. Here, we report the concise synthesis of C13-amide-functionalized CHX derivatives with increased potencies toward protein synthesis inhibition. Cryogenic electron microscopy (cryo-EM) revealed that C13-aminobenzoyl CHX (8) occupies the same site as CHX, competing with the 3' end of E-site tRNA. We demonstrate that 8 is superior to CHX for ribosome profiling experiments, enabling more effective capture of ribosome conformations through sustained stabilization of polysomes. Our studies identify powerful chemical reagents to study protein synthesis and reveal the molecular basis of their enhanced potency.
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Affiliation(s)
- Yumi Koga
- Department of Chemistry and Chemical Biology, Cambridge, Massachusetts 02138, United States
| | - Eileen M Hoang
- Department of Chemistry and Chemical Biology, Cambridge, Massachusetts 02138, United States
| | - Yongho Park
- Department of Chemistry and Chemical Biology, Cambridge, Massachusetts 02138, United States
| | - Alexander F A Keszei
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Jason Murray
- Department of Pathology, The Johns Hopkins Hospital, Baltimore, Maryland 21287, United States
| | - Sichen Shao
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Brian B Liau
- Department of Chemistry and Chemical Biology, Cambridge, Massachusetts 02138, United States
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107
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Humans and other commonly used model organisms are resistant to cycloheximide-mediated biases in ribosome profiling experiments. Nat Commun 2021; 12:5094. [PMID: 34429433 PMCID: PMC8384890 DOI: 10.1038/s41467-021-25411-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 08/10/2021] [Indexed: 12/26/2022] Open
Abstract
Ribosome profiling measures genome-wide translation dynamics at sub-codon resolution. Cycloheximide (CHX), a widely used translation inhibitor to arrest ribosomes in these experiments, has been shown to induce biases in yeast, questioning its use. However, whether such biases are present in datasets of other organisms including humans is unknown. Here we compare different CHX-treatment conditions in human cells and yeast in parallel experiments using an optimized protocol. We find that human ribosomes are not susceptible to conformational restrictions by CHX, nor does it distort gene-level measurements of ribosome occupancy, measured decoding speed or the translational ramp. Furthermore, CHX-induced codon-specific biases on ribosome occupancy are not detectable in human cells or other model organisms. This shows that reported biases of CHX are species-specific and that CHX does not affect the outcome of ribosome profiling experiments in most settings. Our findings provide a solid framework to conduct and analyze ribosome profiling experiments. Ribosome profiling has become the gold standard to analyze mRNA translation dynamics, and the translation inhibitor cycloheximide (CHX) is often used in its application. Here the authors systematically demonstrate that CHX does not bias the outcome of ribosome profiling experiments in most organisms.
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108
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Kim Y, Eggers C, Shvetsova E, Kleemann L, Sin O, Leidel SA. Analysis of codon-specific translation by ribosome profiling. Methods Enzymol 2021; 658:191-223. [PMID: 34517947 DOI: 10.1016/bs.mie.2021.06.025] [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] [Indexed: 01/04/2023]
Abstract
Chemical modifications of RNA molecules can affect translation in multiple ways. Therefore, it is critical to understand how their absence changes cellular translation dynamics and in particular codon-specific translation. In this chapter, we discuss the application of ribosome profiling to analyze changes in codon-specific translation and differential translation in Saccharomyces cerevisiae and human cells.
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Affiliation(s)
- Yeji Kim
- University of Bern, Department of Chemistry, Biochemistry and Pharmaceutical Sciences, Bern, Switzerland
| | - Cristian Eggers
- University of Bern, Department of Chemistry, Biochemistry and Pharmaceutical Sciences, Bern, Switzerland
| | - Ekaterina Shvetsova
- University of Bern, Department of Chemistry, Biochemistry and Pharmaceutical Sciences, Bern, Switzerland
| | - Leon Kleemann
- University of Bern, Department of Chemistry, Biochemistry and Pharmaceutical Sciences, Bern, Switzerland
| | - Olga Sin
- University of Bern, Department of Chemistry, Biochemistry and Pharmaceutical Sciences, Bern, Switzerland
| | - Sebastian A Leidel
- University of Bern, Department of Chemistry, Biochemistry and Pharmaceutical Sciences, Bern, Switzerland.
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109
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Lawson MR, Lessen LN, Wang J, Prabhakar A, Corsepius NC, Green R, Puglisi JD. Mechanisms that ensure speed and fidelity in eukaryotic translation termination. Science 2021; 373:876-882. [PMID: 34413231 PMCID: PMC9017434 DOI: 10.1126/science.abi7801] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 07/07/2021] [Indexed: 11/02/2022]
Abstract
Translation termination, which liberates a nascent polypeptide from the ribosome specifically at stop codons, must occur accurately and rapidly. We established single-molecule fluorescence assays to track the dynamics of ribosomes and two requisite release factors (eRF1 and eRF3) throughout termination using an in vitro-reconstituted yeast translation system. We found that the two eukaryotic release factors bound together to recognize stop codons rapidly and elicit termination through a tightly regulated, multistep process that resembles transfer RNA selection during translation elongation. Because the release factors are conserved from yeast to humans, the molecular events that underlie yeast translation termination are likely broadly fundamental to eukaryotic protein synthesis.
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Affiliation(s)
- Michael R Lawson
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Laura N Lessen
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Program in Molecular Biophysics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jinfan Wang
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Arjun Prabhakar
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Nicholas C Corsepius
- Program in Molecular Biophysics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Rachel Green
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- 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
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
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110
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Ichihara K, Matsumoto A, Nishida H, Kito Y, Shimizu H, Shichino Y, Iwasaki S, Imami K, Ishihama Y, Nakayama KI. Combinatorial analysis of translation dynamics reveals eIF2 dependence of translation initiation at near-cognate codons. Nucleic Acids Res 2021; 49:7298-7317. [PMID: 34226921 PMCID: PMC8287933 DOI: 10.1093/nar/gkab549] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/08/2021] [Accepted: 06/11/2021] [Indexed: 02/05/2023] Open
Abstract
Although ribosome-profiling and translation initiation sequencing (TI-seq) analyses have identified many noncanonical initiation codons, the precise detection of translation initiation sites (TISs) remains a challenge, mainly because of experimental artifacts of such analyses. Here, we describe a new method, TISCA (TIS detection by translation Complex Analysis), for the accurate identification of TISs. TISCA proved to be more reliable for TIS detection compared with existing tools, and it identified a substantial number of near-cognate codons in Kozak-like sequence contexts. Analysis of proteomics data revealed the presence of methionine at the NH2-terminus of most proteins derived from near-cognate initiation codons. Although eukaryotic initiation factor 2 (eIF2), eIF2A and eIF2D have previously been shown to contribute to translation initiation at near-cognate codons, we found that most noncanonical initiation events are most probably dependent on eIF2, consistent with the initial amino acid being methionine. Comprehensive identification of TISs by TISCA should facilitate characterization of the mechanism of noncanonical initiation.
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Affiliation(s)
- Kazuya Ichihara
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Akinobu Matsumoto
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Hiroshi Nishida
- Department of Molecular and Cellular Bioanalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yuki Kito
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Hideyuki Shimizu
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Yuichi Shichino
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan.,AMED-CREST, Japan Agency for Medical Research and Development, Wako, Saitama 351-0198, Japan
| | - Koshi Imami
- Department of Molecular and Cellular Bioanalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yasushi Ishihama
- Department of Molecular and Cellular Bioanalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Keiichi I Nakayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
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111
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Nuebel E, Morgan JT, Fogarty S, Winter JM, Lettlova S, Berg JA, Chen YC, Kidwell CU, Maschek JA, Clowers KJ, Argyriou C, Chen L, Wittig I, Cox JE, Roh-Johnson M, Braverman N, Bonkowsky J, Gygi SP, Rutter J. The biochemical basis of mitochondrial dysfunction in Zellweger Spectrum Disorder. EMBO Rep 2021; 22:e51991. [PMID: 34351705 DOI: 10.15252/embr.202051991] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 06/21/2021] [Accepted: 07/12/2021] [Indexed: 01/09/2023] Open
Abstract
Peroxisomal biogenesis disorders (PBDs) are genetic disorders of peroxisome biogenesis and metabolism that are characterized by profound developmental and neurological phenotypes. The most severe class of PBDs-Zellweger spectrum disorder (ZSD)-is caused by mutations in peroxin genes that result in both non-functional peroxisomes and mitochondrial dysfunction. It is unclear, however, how defective peroxisomes contribute to mitochondrial impairment. In order to understand the molecular basis of this inter-organellar relationship, we investigated the fate of peroxisomal mRNAs and proteins in ZSD model systems. We found that peroxins were still expressed and a subset of them accumulated on the mitochondrial membrane, which resulted in gross mitochondrial abnormalities and impaired mitochondrial metabolic function. We showed that overexpression of ATAD1, a mitochondrial quality control factor, was sufficient to rescue several aspects of mitochondrial function in human ZSD fibroblasts. Together, these data suggest that aberrant peroxisomal protein localization is necessary and sufficient for the devastating mitochondrial morphological and metabolic phenotypes in ZSDs.
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Affiliation(s)
- Esther Nuebel
- Howard Hughes Medical Institute, Salt Lake City, UT, USA.,Department of Biochemistry, University of Utah, Salt Lake City, UT, USA.,Department of Biomedical Sciences, Noorda College of Osteopathic Medicine, Provo, USA
| | - Jeffrey T Morgan
- Howard Hughes Medical Institute, Salt Lake City, UT, USA.,Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Sarah Fogarty
- Howard Hughes Medical Institute, Salt Lake City, UT, USA.,Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Jacob M Winter
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Sandra Lettlova
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Jordan A Berg
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Yu-Chan Chen
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Chelsea U Kidwell
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - J Alan Maschek
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA.,Diabetes & Metabolism Research Center, University of Utah, Salt Lake City, UT, USA.,Metabolomics, Proteomics and Mass Spectrometry Core Research Facilities, University of Utah, Salt Lake City, UT, USA
| | - Katie J Clowers
- Department of Cell Biology, Harvard University School of Medicine, Boston, MA, USA
| | | | - Lingxiao Chen
- Department of Pathology, McGill University, Montreal, ON, Canada
| | - Ilka Wittig
- Functional Proteomics, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
| | - James E Cox
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA.,Diabetes & Metabolism Research Center, University of Utah, Salt Lake City, UT, USA.,Metabolomics, Proteomics and Mass Spectrometry Core Research Facilities, University of Utah, Salt Lake City, UT, USA
| | - Minna Roh-Johnson
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Nancy Braverman
- Department of Human Genetics, McGill University, Montreal, ON, Canada.,Department of Pediatrics, Research Institute of the McGill University Health Centre, Montreal, ON, Canada
| | - Joshua Bonkowsky
- Primary Children's Hospital, University of Utah, Salt Lake City, UT, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard University School of Medicine, Boston, MA, USA
| | - Jared Rutter
- Howard Hughes Medical Institute, Salt Lake City, UT, USA.,Department of Biochemistry, University of Utah, Salt Lake City, UT, USA.,Diabetes & Metabolism Research Center, University of Utah, Salt Lake City, UT, USA
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112
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Dmitriev SE, Vladimirov DO, Lashkevich KA. A Quick Guide to Small-Molecule Inhibitors of Eukaryotic Protein Synthesis. BIOCHEMISTRY (MOSCOW) 2021; 85:1389-1421. [PMID: 33280581 PMCID: PMC7689648 DOI: 10.1134/s0006297920110097] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Eukaryotic ribosome and cap-dependent translation are attractive targets in the antitumor, antiviral, anti-inflammatory, and antiparasitic therapies. Currently, a broad array of small-molecule drugs is known that specifically inhibit protein synthesis in eukaryotic cells. Many of them are well-studied ribosome-targeting antibiotics that block translocation, the peptidyl transferase center or the polypeptide exit tunnel, modulate the binding of translation machinery components to the ribosome, and induce miscoding, premature termination or stop codon readthrough. Such inhibitors are widely used as anticancer, anthelmintic and antifungal agents in medicine, as well as fungicides in agriculture. Chemicals that affect the accuracy of stop codon recognition are promising drugs for the nonsense suppression therapy of hereditary diseases and restoration of tumor suppressor function in cancer cells. Other compounds inhibit aminoacyl-tRNA synthetases, translation factors, and components of translation-associated signaling pathways, including mTOR kinase. Some of them have antidepressant, immunosuppressive and geroprotective properties. Translation inhibitors are also used in research for gene expression analysis by ribosome profiling, as well as in cell culture techniques. In this article, we review well-studied and less known inhibitors of eukaryotic protein synthesis (with the exception of mitochondrial and plastid translation) classified by their targets and briefly describe the action mechanisms of these compounds. We also present a continuously updated database (http://eupsic.belozersky.msu.ru/) that currently contains information on 370 inhibitors of eukaryotic protein synthesis.
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Affiliation(s)
- S E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia. .,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia.,Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - D O Vladimirov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - K A Lashkevich
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
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113
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Han P, Shichino Y, Schneider-Poetsch T, Mito M, Hashimoto S, Udagawa T, Kohno K, Yoshida M, Mishima Y, Inada T, Iwasaki S. Genome-wide Survey of Ribosome Collision. Cell Rep 2021; 31:107610. [PMID: 32375038 DOI: 10.1016/j.celrep.2020.107610] [Citation(s) in RCA: 114] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 03/18/2020] [Accepted: 04/13/2020] [Indexed: 12/31/2022] Open
Abstract
Ribosome movement is not always smooth and is rather often impeded. For ribosome pauses, fundamental issues remain to be addressed, including where ribosomes pause on mRNAs, what kind of RNA/amino acid sequence causes this pause, and the physiological significance of this attenuation of protein synthesis. Here, we survey the positions of ribosome collisions caused by ribosome pauses in humans and zebrafish using modified ribosome profiling. Collided ribosomes, i.e., disomes, emerge at various sites: Pro-Pro/Gly/Asp motifs; Arg-X-Lys motifs; stop codons; and 3' untranslated regions. The electrostatic interaction between the charged nascent chain and the ribosome exit tunnel determines the eIF5A-mediated disome rescue at the Pro-Pro sites. In particular, XBP1u, a precursor of endoplasmic reticulum (ER)-stress-responsive transcription factor, shows striking queues of collided ribosomes and thus acts as a degradation substrate by ribosome-associated quality control. Our results provide insight into the causes and consequences of ribosome pause by dissecting collided ribosomes.
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Affiliation(s)
- Peixun Han
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan; RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Yuichi Shichino
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Tilman Schneider-Poetsch
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Mari Mito
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
| | - Satoshi Hashimoto
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Tsuyoshi Udagawa
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Kenji Kohno
- Institute for Research Initiatives, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Minoru Yoshida
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan; Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yuichiro Mishima
- Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
| | - Toshifumi Inada
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Shintaro Iwasaki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan; RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan.
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114
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Young DJ, Meydan S, Guydosh NR. 40S ribosome profiling reveals distinct roles for Tma20/Tma22 (MCT-1/DENR) and Tma64 (eIF2D) in 40S subunit recycling. Nat Commun 2021; 12:2976. [PMID: 34016977 PMCID: PMC8137927 DOI: 10.1038/s41467-021-23223-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 04/14/2021] [Indexed: 12/21/2022] Open
Abstract
The recycling of ribosomes at stop codons for use in further rounds of translation is critical for efficient protein synthesis. Removal of the 60S subunit is catalyzed by the ATPase Rli1 (ABCE1) while removal of the 40S is thought to require Tma64 (eIF2D), Tma20 (MCT-1), and Tma22 (DENR). However, it remains unclear how these Tma proteins cause 40S removal and control reinitiation of downstream translation. Here we used a 40S ribosome footprinting strategy to directly observe intermediate steps of ribosome recycling in cells. Deletion of the genes encoding these Tma proteins resulted in broad accumulation of unrecycled 40S subunits at stop codons, directly establishing their role in 40S recycling. Furthermore, the Tma20/Tma22 heterodimer was responsible for a majority of 40S recycling events while Tma64 played a minor role. Introduction of an autism-associated mutation into TMA22 resulted in a loss of 40S recycling activity, linking ribosome recycling and neurological disease.
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Affiliation(s)
- David J Young
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sezen Meydan
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
- Postdoctoral Research Associate Training Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Nicholas R Guydosh
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
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115
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RiboDoc: A Docker-based package for ribosome profiling analysis. Comput Struct Biotechnol J 2021; 19:2851-2860. [PMID: 34093996 PMCID: PMC8141510 DOI: 10.1016/j.csbj.2021.05.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 05/03/2021] [Accepted: 05/05/2021] [Indexed: 11/29/2022] Open
Abstract
Ribosome profiling (RiboSeq) has emerged as a powerful technique for studying the genome-wide regulation of translation in various cells. Several steps in the biological protocol have been improved, but the bioinformatics part of RiboSeq suffers from a lack of standardization, preventing the straightforward and complete reproduction of published results. Too many published studies provide insufficient detail about the bioinformatics pipeline used. The broad range of questions that can be asked with RiboSeq makes it difficult to use a single bioinformatics tool. Indeed, many scripts have been published for addressing diverse questions. Here (https://github.com/equipeGST/RiboDoc), we propose a unique tool (for use with multiple operating systems, OS) to standardize the general steps that must be performed systematically in RiboSeq analysis, together with the statistical analysis and quality control of the sample. The data generated can then be exploited with more specific tools. We hope that this tool will help to standardize bioinformatics analyses pipelines in the field of translation.
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116
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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: 63] [Impact Index Per Article: 15.8] [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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117
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Arella D, Dilucca M, Giansanti A. Codon usage bias and environmental adaptation in microbial organisms. Mol Genet Genomics 2021; 296:751-762. [PMID: 33818631 PMCID: PMC8144148 DOI: 10.1007/s00438-021-01771-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 02/22/2021] [Indexed: 01/01/2023]
Abstract
In each genome, synonymous codons are used with different frequencies; this general phenomenon is known as codon usage bias. It has been previously recognised that codon usage bias could affect the cellular fitness and might be associated with the ecology of microbial organisms. In this exploratory study, we investigated the relationship between codon usage bias, lifestyles (thermophiles vs. mesophiles; pathogenic vs. non-pathogenic; halophilic vs. non-halophilic; aerobic vs. anaerobic and facultative) and habitats (aquatic, terrestrial, host-associated, specialised, multiple) of 615 microbial organisms (544 bacteria and 71 archaea). Principal component analysis revealed that species with given phenotypic traits and living in similar environmental conditions have similar codon preferences, as represented by the relative synonymous codon usage (RSCU) index, and similar spectra of tRNA availability, as gauged by the tRNA gene copy number (tGCN). Moreover, by measuring the average tRNA adaptation index (tAI) for each genome, an index that can be associated with translational efficiency, we observed that organisms able to live in multiple habitats, including facultative organisms, mesophiles and pathogenic bacteria, are characterised by a reduced translational efficiency, consistently with their need to adapt to different environments. Our results show that synonymous codon choices might be under strong translational selection, which modulates the choice of the codons to differently match tRNA availability, depending on the organism's lifestyle needs. To our knowledge, this is the first large-scale study that examines the role of codon bias and translational efficiency in the adaptation of microbial organisms to the environment in which they live.
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Affiliation(s)
- Davide Arella
- Department of Physics, Sapienza University of Rome, 00185, Rome, Italy.
| | - Maddalena Dilucca
- Department of Physics, Sapienza University of Rome, 001885, Rome, Italy
| | - Andrea Giansanti
- Department of Physics, Sapienza University of Rome, 00185, Rome, Italy
- INFN, Roma1 Unit, 00185, Rome, Italy
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118
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Mangkalaphiban K, He F, Ganesan R, Wu C, Baker R, Jacobson A. Transcriptome-wide investigation of stop codon readthrough in Saccharomyces cerevisiae. PLoS Genet 2021; 17:e1009538. [PMID: 33878104 PMCID: PMC8087045 DOI: 10.1371/journal.pgen.1009538] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 04/30/2021] [Accepted: 04/06/2021] [Indexed: 11/18/2022] Open
Abstract
Translation of mRNA into a polypeptide is terminated when the release factor eRF1 recognizes a UAA, UAG, or UGA stop codon in the ribosomal A site and stimulates nascent peptide release. However, stop codon readthrough can occur when a near-cognate tRNA outcompetes eRF1 in decoding the stop codon, resulting in the continuation of the elongation phase of protein synthesis. At the end of a conventional mRNA coding region, readthrough allows translation into the mRNA 3'-UTR. Previous studies with reporter systems have shown that the efficiency of termination or readthrough is modulated by cis-acting elements other than stop codon identity, including two nucleotides 5' of the stop codon, six nucleotides 3' of the stop codon in the ribosomal mRNA channel, and stem-loop structures in the mRNA 3'-UTR. It is unknown whether these elements are important at a genome-wide level and whether other mRNA features proximal to the stop codon significantly affect termination and readthrough efficiencies in vivo. Accordingly, we carried out ribosome profiling analyses of yeast cells expressing wild-type or temperature-sensitive eRF1 and developed bioinformatics strategies to calculate readthrough efficiency, and to identify mRNA and peptide features which influence that efficiency. We found that the stop codon (nt +1 to +3), the nucleotide after it (nt +4), the codon in the P site (nt -3 to -1), and 3'-UTR length are the most influential features in the control of readthrough efficiency, while nts +5 to +9 had milder effects. Additionally, we found low readthrough genes to have shorter 3'-UTRs compared to high readthrough genes in cells with thermally inactivated eRF1, while this trend was reversed in wild-type cells. Together, our results demonstrated the general roles of known regulatory elements in genome-wide regulation and identified several new mRNA or peptide features affecting the efficiency of translation termination and readthrough.
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Affiliation(s)
- Kotchaphorn Mangkalaphiban
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Feng He
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Robin Ganesan
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Chan Wu
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Richard Baker
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Allan Jacobson
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- * E-mail:
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119
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Moon SL, Morisaki T, Stasevich TJ, Parker R. Coupling of translation quality control and mRNA targeting to stress granules. J Cell Biol 2021; 219:151851. [PMID: 32520986 PMCID: PMC7401812 DOI: 10.1083/jcb.202004120] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 02/07/2023] Open
Abstract
Stress granules are dynamic assemblies of proteins and nontranslating RNAs that form when translation is inhibited in response to diverse stresses. Defects in ubiquitin–proteasome system factors including valosin-containing protein (VCP) and the proteasome impact the kinetics of stress granule induction and dissolution as well as being implicated in neuropathogenesis. However, the impacts of dysregulated proteostasis on mRNA regulation and stress granules are not well understood. Using single mRNA imaging, we discovered ribosomes stall on some mRNAs during arsenite stress, and the release of transcripts from stalled ribosomes for their partitioning into stress granules requires the activities of VCP, components of the ribosome-associated quality control (RQC) complex, and the proteasome. This is an unexpected contribution of the RQC system in releasing mRNAs from translation under stress, thus identifying a new type of stress-activated RQC (saRQC) distinct from canonical RQC pathways in mRNA substrates, cellular context, and mRNA fate.
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Affiliation(s)
- Stephanie L Moon
- Department of Human Genetics, University of Michigan, Ann Arbor, MI.,Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI
| | - Tatsuya Morisaki
- Department of Biochemistry, Colorado State University, Fort Collins, CO
| | - Timothy J Stasevich
- Department of Biochemistry, Colorado State University, Fort Collins, CO.,World Research Hub Initiative, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Roy Parker
- Department of Biochemistry, University of Colorado, Boulder, CO.,Howard Hughes Medical Institute, Chevy Chase, MD
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120
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Ranjan N, Pochopien AA, Chih-Chien Wu C, Beckert B, Blanchet S, Green R, V Rodnina M, Wilson DN. Yeast translation elongation factor eEF3 promotes late stages of tRNA translocation. EMBO J 2021; 40:e106449. [PMID: 33555093 PMCID: PMC7957392 DOI: 10.15252/embj.2020106449] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 12/10/2020] [Accepted: 12/21/2020] [Indexed: 11/21/2022] Open
Abstract
In addition to the conserved translation elongation factors eEF1A and eEF2, fungi require a third essential elongation factor, eEF3. While eEF3 has been implicated in tRNA binding and release at the ribosomal A and E sites, its exact mechanism of action is unclear. Here, we show that eEF3 acts at the mRNA–tRNA translocation step by promoting the dissociation of the tRNA from the E site, but independent of aminoacyl‐tRNA recruitment to the A site. Depletion of eEF3 in vivo leads to a general slowdown in translation elongation due to accumulation of ribosomes with an occupied A site. Cryo‐EM analysis of native eEF3‐ribosome complexes shows that eEF3 facilitates late steps of translocation by favoring non‐rotated ribosomal states, as well as by opening the L1 stalk to release the E‐site tRNA. Additionally, our analysis provides structural insights into novel translation elongation states, enabling presentation of a revised yeast translation elongation cycle.
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Affiliation(s)
- Namit Ranjan
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Agnieszka A Pochopien
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, Munich, Germany.,Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Colin Chih-Chien Wu
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Bertrand Beckert
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Sandra Blanchet
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, 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
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Daniel N Wilson
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, Munich, Germany.,Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
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121
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Thompson JD, Ripp R, Mayer C, Poch O, Michel CJ. Potential role of the X circular code in the regulation of gene expression. Biosystems 2021; 203:104368. [PMID: 33567309 DOI: 10.1016/j.biosystems.2021.104368] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 02/06/2023]
Abstract
The X circular code is a set of 20 trinucleotides (codons) that has been identified in the protein-coding genes of most organisms (bacteria, archaea, eukaryotes, plasmids, viruses). It has been shown previously that the X circular code has the important mathematical property of being an error-correcting code. Thus, motifs of the X circular code, i.e. a series of codons belonging to X and called X motifs, allow identification and maintenance of the reading frame in genes. X motifs are significantly enriched in protein-coding genes, but have also been identified in many transfer RNA (tRNA) genes and in important functional regions of the ribosomal RNA (rRNA), notably in the peptidyl transferase center and the decoding center. Here, we investigate the potential role of X motifs as functional elements of protein-coding genes. First, we identify the codons of the X circular code which are frequent or rare in each domain of life (archaea, bacteria, eukaryota) and show that, for the amino acids with the highest codon bias, the preferred codon is often an X codon. We also observe a correlation between the 20 X codons and the optimal codons/dicodons that have been shown to influence translation efficiency. Then, we examined recently published experimental results concerning gene expression levels in diverse organisms. The approach used is the analysis of X motifs according to their density ds(X), i.e. the number of X motifs per kilobase in a gene sequence s. Surprisingly, this simple parameter identifies several unexpected relations between the X circular code and gene expression. For example, the X motifs are significantly enriched in the minimal gene set belonging to the three domains of life, and in codon-optimized genes. Furthermore, the density of X motifs generally correlates with experimental measures of translation efficiency and mRNA stability. Taken together, these results lead us to propose that the X motifs may represent a genetic signal contributing to the maintenance of the correct reading frame and the optimization and regulation of gene expression.
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Affiliation(s)
- Julie D Thompson
- Department of Computer Science, ICube, CNRS, University of Strasbourg, Strasbourg, France.
| | - Raymond Ripp
- Department of Computer Science, ICube, CNRS, University of Strasbourg, Strasbourg, France.
| | - Claudine Mayer
- Department of Computer Science, ICube, CNRS, University of Strasbourg, Strasbourg, France; Unité de Microbiologie Structurale, Institut Pasteur, CNRS, 75724, Paris Cedex 15, France; Université Paris Diderot, Sorbonne Paris Cité, 75724, Paris Cedex 15, France.
| | - Olivier Poch
- Department of Computer Science, ICube, CNRS, University of Strasbourg, Strasbourg, France.
| | - Christian J Michel
- Department of Computer Science, ICube, CNRS, University of Strasbourg, Strasbourg, France.
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122
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do Couto Bordignon P, Pechmann S. Inferring translational heterogeneity from Saccharomyces cerevisiae ribosome profiling. FEBS J 2021; 288:4541-4559. [PMID: 33539640 DOI: 10.1111/febs.15748] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 01/27/2021] [Accepted: 02/02/2021] [Indexed: 11/30/2022]
Abstract
Translation of mRNAs into proteins by the ribosome is the most important step of protein biosynthesis. Accordingly, translation is tightly controlled and heavily regulated to maintain cellular homeostasis. Ribosome profiling (Ribo-seq) has revolutionized the study of translation by revealing many of its underlying mechanisms. However, equally many aspects of translation remain mysterious, in part also due to persisting challenges in the interpretation of data obtained from Ribo-seq experiments. Here, we show that some of the variability observed in Ribo-seq data has biological origins and reflects programmed heterogeneity of translation. Through a comparative analysis of Ribo-seq data from Saccharomyces cerevisiae, we systematically identify short 3-codon sequences that are differentially translated (DT) across mRNAs, that is, identical sequences that are translated sometimes fast and sometimes slowly beyond what can be attributed to variability between experiments. Remarkably, the thus identified DT sequences link to mechanisms known to regulate translation elongation and are enriched in genes important for protein and organelle biosynthesis. Our results thus highlight examples of translational heterogeneity that are encoded in the genomic sequences and tuned to optimizing cellular homeostasis. More generally, our work highlights the power of Ribo-seq to understand the complexities of translation regulation.
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123
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Huh D, Passarelli MC, Gao J, Dusmatova SN, Goin C, Fish L, Pinzaru AM, Molina H, Ren Z, McMillan EA, Asgharian H, Goodarzi H, Tavazoie SF. A stress-induced tyrosine-tRNA depletion response mediates codon-based translational repression and growth suppression. EMBO J 2021; 40:e106696. [PMID: 33346941 PMCID: PMC7809793 DOI: 10.15252/embj.2020106696] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 12/16/2022] Open
Abstract
Eukaryotic transfer RNAs can become selectively fragmented upon various stresses, generating tRNA-derived small RNA fragments. Such fragmentation has been reported to impact a small fraction of the tRNA pool and thus presumed to not directly impact translation. We report that oxidative stress can rapidly generate tyrosine-tRNAGUA fragments in human cells-causing significant depletion of the precursor tRNA. Tyrosine-tRNAGUA depletion impaired translation of growth and metabolic genes enriched in cognate tyrosine codons. Depletion of tyrosine tRNAGUA or its translationally regulated targets USP3 and SCD repressed proliferation-revealing a dedicated tRNA-regulated growth-suppressive pathway for oxidative stress response. Tyrosine fragments are generated in a DIS3L2 exoribonuclease-dependent manner and inhibit hnRNPA1-mediated transcript destabilization. Moreover, tyrosine fragmentation is conserved in C. elegans. Thus, tRNA fragmentation can coordinately generate trans-acting small RNAs and functionally deplete a tRNA. Our findings reveal the existence of an underlying adaptive codon-based regulatory response inherent to the genetic code.
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Affiliation(s)
- Doowon Huh
- Laboratory of Systems Cancer BiologyThe Rockefeller UniversityNew YorkNYUSA
| | - Maria C Passarelli
- Laboratory of Systems Cancer BiologyThe Rockefeller UniversityNew YorkNYUSA
| | - Jenny Gao
- Laboratory of Systems Cancer BiologyThe Rockefeller UniversityNew YorkNYUSA
| | | | - Clara Goin
- Laboratory of Systems Cancer BiologyThe Rockefeller UniversityNew YorkNYUSA
| | - Lisa Fish
- Department of Biochemistry & BiophysicsUniversity of California, San FranciscoSan FranciscoCAUSA
| | | | - Henrik Molina
- Proteome Resource CenterThe Rockefeller UniversityNew YorkNYUSA
| | - Zhiji Ren
- Laboratory of Systems Cancer BiologyThe Rockefeller UniversityNew YorkNYUSA
| | | | - Hosseinali Asgharian
- Department of Biochemistry & BiophysicsUniversity of California, San FranciscoSan FranciscoCAUSA
| | - Hani Goodarzi
- Department of Biochemistry & BiophysicsUniversity of California, San FranciscoSan FranciscoCAUSA
| | - Sohail F Tavazoie
- Laboratory of Systems Cancer BiologyThe Rockefeller UniversityNew YorkNYUSA
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124
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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: 104] [Impact Index Per Article: 26.0] [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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125
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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: 40] [Impact Index Per Article: 10.0] [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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126
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Zhang S, Chen Y, Wang Y, Zhang P, Chen G, Zhou Y. Insights Into Translatomics in the Nervous System. Front Genet 2021; 11:599548. [PMID: 33408739 PMCID: PMC7779767 DOI: 10.3389/fgene.2020.599548] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 11/30/2020] [Indexed: 12/11/2022] Open
Abstract
Most neurological disorders are caused by abnormal gene translation. Generally, dysregulation of elements involved in the translational process disrupts homeostasis in neurons and neuroglia. Better understanding of how the gene translation process occurs requires detailed analysis of transcriptomic and proteomic profile data. However, a lack of strictly direct correlations between mRNA and protein levels limits translational investigation by combining transcriptomic and proteomic profiling. The much better correlation between proteins and translated mRNAs than total mRNAs in abundance and insufficiently sensitive proteomics approach promote the requirement of advances in translatomics technology. Translatomics which capture and sequence the mRNAs associated with ribosomes has been effective in identifying translational changes by genetics or projections, ribosome stalling, local translation, and transcript isoforms in the nervous system. Here, we place emphasis on the main three translatomics methods currently used to profile mRNAs attached to ribosome-nascent chain complex (RNC-mRNA). Their prominent applications in neurological diseases including glioma, neuropathic pain, depression, fragile X syndrome (FXS), neurodegenerative disorders are outlined. The content reviewed here expands our understanding on the contributions of aberrant translation to neurological disease development.
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Affiliation(s)
- Shuxia Zhang
- Department of Anesthesiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yeru Chen
- Department of Anesthesiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yongjie Wang
- Key Laboratory of Elemene Anti-Cancer Medicine of Zhejiang Province and Holistic Integrative Pharmacy Institutes, Hangzhou Normal University, Hangzhou, China.,Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province, Holistic Integrative Pharmacy Institutes, Hangzhou Normal University, Hangzhou, China
| | - Piao Zhang
- Department of Anesthesiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Gang Chen
- Department of Anesthesiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Youfa Zhou
- Department of Anesthesiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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127
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Zhao T, Chen YM, Li Y, Wang J, Chen S, Gao N, Qian W. Disome-seq reveals widespread ribosome collisions that promote cotranslational protein folding. Genome Biol 2021; 22:16. [PMID: 33402206 PMCID: PMC7784341 DOI: 10.1186/s13059-020-02256-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 12/20/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The folding of proteins is challenging in the highly crowded and sticky environment of a cell. Regulation of translation elongation may play a crucial role in ensuring the correct folding of proteins. Much of our knowledge regarding translation elongation comes from the sequencing of mRNA fragments protected by single ribosomes by ribo-seq. However, larger protected mRNA fragments have been observed, suggesting the existence of an alternative and previously hidden layer of regulation. RESULTS In this study, we performed disome-seq to sequence mRNA fragments protected by two stacked ribosomes, a product of translational pauses during which the 5'-elongating ribosome collides with the 3'-paused one. We detected widespread ribosome collisions that are related to slow ribosome release when stop codons are at the A-site, slow peptide bond formation from proline, glycine, asparagine, and cysteine when they are at the P-site, and slow leaving of polylysine from the exit tunnel of ribosomes. The structure of disomes obtained by cryo-electron microscopy suggests a different conformation from the substrate of the ribosome-associated protein quality control pathway. Collisions occurred more frequently in the gap regions between α-helices, where a translational pause can prevent the folding interference from the downstream peptides. Paused or collided ribosomes are associated with specific chaperones, which can aid in the cotranslational folding of the nascent peptides. CONCLUSIONS Therefore, cells use regulated ribosome collisions to ensure protein homeostasis.
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Affiliation(s)
- Taolan Zhao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China. .,Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Yan-Ming Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.,Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu Li
- Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, School of Life Science, Tsinghua University, Beijing, 100084, China.,State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Jia Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.,Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Siyu Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.,Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ning Gao
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, 100871, China.
| | - Wenfeng Qian
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China. .,Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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128
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Wang YJ, Gilbert WV. Quantitative Comparisons of Translation Activity by Ribosome Profiling with Internal Standards. Methods Mol Biol 2021; 2252:127-149. [PMID: 33765273 DOI: 10.1007/978-1-0716-1150-0_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Ribosome profiling is a genome-wide approach to map the positions of ribosomes on messenger RNAs. The abundance of ribosome-protected fragments can be used within condition to compare relative translation activities between different transcripts and between distinct conditions for the same transcript. A unified and routine method is currently lacking, however, to normalize between conditions for differences in global translation levels. Here we describe experimental and computational methods to use an orthogonal species spike-in, or internal standard, to enable absolute comparisons of translation activity between conditions. This simple modification of standard ribosome profiling provides a robust approach for accurately interpreting the effects of diverse genetic, chemical, and environmental perturbations of translation.
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Affiliation(s)
- Yinuo J Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Arrakis Therapeutics, Waltham, MA, USA
| | - Wendy V Gilbert
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
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129
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Barros GC, Requião RD, Carneiro RL, Masuda CA, Moreira MH, Rossetto S, Domitrovic T, Palhano FL. Rqc1 and other yeast proteins containing highly positively charged sequences are not targets of the RQC complex. J Biol Chem 2021; 296:100586. [PMID: 33774050 PMCID: PMC8102910 DOI: 10.1016/j.jbc.2021.100586] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 03/12/2021] [Accepted: 03/23/2021] [Indexed: 02/06/2023] Open
Abstract
Previous work has suggested that highly positively charged protein segments coded by rare codons or poly (A) stretches induce ribosome stalling and translational arrest through electrostatic interactions with the negatively charged ribosome exit tunnel, leading to inefficient elongation. This arrest leads to the activation of the Ribosome Quality Control (RQC) pathway and results in low expression of these reporter proteins. However, the only endogenous yeast proteins known to activate the RQC are Rqc1, a protein essential for RQC function, and Sdd1, a protein with unknown function, both of which contain polybasic sequences. To explore the generality of this phenomenon, we investigated whether the RQC complex controls the expression of other proteins with polybasic sequences. We showed by ribosome profiling data analysis and western blot that proteins containing polybasic sequences similar to, or even more positively charged than those of Rqc1 and Sdd1, were not targeted by the RQC complex. We also observed that the previously reported Ltn1-dependent regulation of Rqc1 is posttranslational, independent of the RQC activity. Taken together, our results suggest that RQC should not be regarded as a general regulatory pathway for the expression of highly positively charged proteins in yeast.
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Affiliation(s)
- Géssica C Barros
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Rodrigo D Requião
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Rodolfo L Carneiro
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Claudio A Masuda
- Programa de Biologia Molecular e Biotecnologia, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Mariana H Moreira
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Silvana Rossetto
- Departamento de Ciência da Computação, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Tatiana Domitrovic
- Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
| | - Fernando L Palhano
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
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130
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Abstract
Translation is a central biological process in living cells. Ribosome profiling approach enables assessing translation on a global, cell-wide level. Extracting versatile information from the ribosome profiling data usually requires specialized expertise for handling the sequencing data that is not available to the broad community of experimentalists. Here, we provide an easy-to-use and modifiable workflow that uses a small set of commands and enables full data analysis in a standardized way, including precise positioning of the ribosome-protected fragments, for determining codon-specific translation features. The workflow is complemented with simple step-by-step explanations and is accessible to scientists with no computational background.
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Affiliation(s)
| | - Zoya Ignatova
- Institute for Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, Hamburg, Germany.
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131
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Expression of transgenes enriched in rare codons is enhanced by the MAPK pathway. Sci Rep 2020; 10:22166. [PMID: 33335127 PMCID: PMC7746698 DOI: 10.1038/s41598-020-78453-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 11/23/2020] [Indexed: 11/10/2022] Open
Abstract
The ability to translate three nucleotide sequences, or codons, into amino acids to form proteins is conserved across all organisms. All but two amino acids have multiple codons, and the frequency that such synonymous codons occur in genomes ranges from rare to common. Transcripts enriched in rare codons are typically associated with poor translation, but in certain settings can be robustly expressed, suggestive of codon-dependent regulation. Given this, we screened a gain-of-function library for human genes that increase the expression of a GFPrare reporter encoded by rare codons. This screen identified multiple components of the mitogen activated protein kinase (MAPK) pathway enhancing GFPrare expression. This effect was reversed with inhibitors of this pathway and confirmed to be both codon-dependent and occur with ectopic transcripts naturally coded with rare codons. Finally, this effect was associated, at least in part, with enhanced translation. We thus identify a potential regulatory module that takes advantage of the redundancy in the genetic code to modulate protein expression.
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132
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Yan LL, Zaher HS. Ribosome quality control antagonizes the activation of the integrated stress response on colliding ribosomes. Mol Cell 2020; 81:614-628.e4. [PMID: 33338396 DOI: 10.1016/j.molcel.2020.11.033] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 11/17/2020] [Accepted: 11/17/2020] [Indexed: 12/28/2022]
Abstract
Stalling during translation triggers ribosome quality control (RQC) to maintain proteostasis. Recently, stalling has also been linked to the activation of integrated stress response (ISR) by Gcn2. How the two processes are coordinated is unclear. Here, we show that activation of RQC by Hel2 suppresses that of Gcn2. We further show that Hel2 and Gcn2 are activated by a similar set of agents that cause ribosome stalling, with maximal activation of Hel2 observed at a lower frequency of stalling. Interestingly, inactivation of one pathway was found to result in the overactivation of the other, suggesting that both are activated by the same signal of ribosome collisions. Notably, the processes do not appear to be in direct competition with each other; ISR prefers a vacant A site, whereas RQC displays no preference. Collectively, our findings provide important details about how multiple pathways that recognize stalled ribosomes coordinate to mount the appropriate response.
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Affiliation(s)
- Liewei L Yan
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Hani S Zaher
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA.
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133
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Li K, Hope CM, Wang XA, Wang JP. RiboDiPA: a novel tool for differential pattern analysis in Ribo-seq data. Nucleic Acids Res 2020; 48:12016-12029. [PMID: 33211868 PMCID: PMC7708064 DOI: 10.1093/nar/gkaa1049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 10/14/2020] [Accepted: 10/20/2020] [Indexed: 12/18/2022] Open
Abstract
Ribosome profiling, also known as Ribo-seq, has become a popular approach to investigate regulatory mechanisms of translation in a wide variety of biological contexts. Ribo-seq not only provides a measurement of translation efficiency based on the relative abundance of ribosomes bound to transcripts, but also has the capacity to reveal dynamic and local regulation at different stages of translation based on positional information of footprints across individual transcripts. While many computational tools exist for the analysis of Ribo-seq data, no method is currently available for rigorous testing of the pattern differences in ribosome footprints. In this work, we develop a novel approach together with an R package, RiboDiPA, for Differential Pattern Analysis of Ribo-seq data. RiboDiPA allows for quick identification of genes with statistically significant differences in ribosome occupancy patterns for model organisms ranging from yeast to mammals. We show that differential pattern analysis reveals information that is distinct and complimentary to existing methods that focus on translational efficiency analysis. Using both simulated Ribo-seq footprint data and three benchmark data sets, we illustrate that RiboDiPA can uncover meaningful pattern differences across multiple biological conditions on a global scale, and pinpoint characteristic ribosome occupancy patterns at single codon resolution.
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Affiliation(s)
- Keren Li
- Department of Statistics, Northwestern University, 633 Clark Street, Evanston, IL 60208, USA.,NSF-Simons Center for Quantitative Biology, Northwestern University, 633 Clark Street, Evanston, IL 60208, USA
| | - C Matthew Hope
- NSF-Simons Center for Quantitative Biology, Northwestern University, 633 Clark Street, Evanston, IL 60208, USA.,Department of Molecular Biosciences, Northwestern University, 633 Clark Street, Evanston, IL 60208, USA
| | - Xiaozhong A Wang
- NSF-Simons Center for Quantitative Biology, Northwestern University, 633 Clark Street, Evanston, IL 60208, USA.,Department of Molecular Biosciences, Northwestern University, 633 Clark Street, Evanston, IL 60208, USA
| | - Ji-Ping Wang
- Department of Statistics, Northwestern University, 633 Clark Street, Evanston, IL 60208, USA.,NSF-Simons Center for Quantitative Biology, Northwestern University, 633 Clark Street, Evanston, IL 60208, USA
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134
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García-Martínez J, Pérez-Martínez ME, Pérez-Ortín JE, Alepuz P. Recruitment of Xrn1 to stress-induced genes allows efficient transcription by controlling RNA polymerase II backtracking. RNA Biol 2020; 18:1458-1474. [PMID: 33258404 DOI: 10.1080/15476286.2020.1857521] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
A new paradigm has emerged proposing that the crosstalk between nuclear transcription and cytoplasmic mRNA stability keeps robust mRNA levels in cells under steady-state conditions. A key piece in this crosstalk is the highly conserved 5'-3' RNA exonuclease Xrn1, which degrades most cytoplasmic mRNAs but also associates with nuclear chromatin to activate transcription by not well-understood mechanisms. Here, we investigated the role of Xrn1 in the transcriptional response of Saccharomyces cerevisiae cells to osmotic stress. We show that a lack of Xrn1 results in much lower transcriptional induction of the upregulated genes but in similar high levels of their transcripts because of parallel mRNA stabilization. Unexpectedly, lower transcription in xrn1 occurs with a higher accumulation of RNA polymerase II (RNAPII) at stress-inducible genes, suggesting that this polymerase remains inactive backtracked. Xrn1 seems to be directly implicated in the formation of a competent elongation complex because Xrn1 is recruited to the osmotic stress-upregulated genes in parallel with the RNAPII complex, and both are dependent on the mitogen-activated protein kinase Hog1. Our findings extend the role of Xrn1 in preventing the accumulation of inactive RNAPII at highly induced genes to other situations of rapid and strong transcriptional upregulation.
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Affiliation(s)
- José García-Martínez
- ERI Biotecmed, Facultad De Ciencias Biológicas, Universitat De València, Burjassot, Spain.,Departamento De Genética, Facultad De Ciencias Biológicas, Universitat De València, Burjassot, Spain
| | - María E Pérez-Martínez
- ERI Biotecmed, Facultad De Ciencias Biológicas, Universitat De València, Burjassot, Spain.,Departamento De Bioquímica Y Biología Molecular, Facultad De Ciencias Biológicas, Universitat De València, Burjassot, Spain
| | - José E Pérez-Ortín
- ERI Biotecmed, Facultad De Ciencias Biológicas, Universitat De València, Burjassot, Spain.,Departamento De Bioquímica Y Biología Molecular, Facultad De Ciencias Biológicas, Universitat De València, Burjassot, Spain
| | - Paula Alepuz
- ERI Biotecmed, Facultad De Ciencias Biológicas, Universitat De València, Burjassot, Spain.,Departamento De Bioquímica Y Biología Molecular, Facultad De Ciencias Biológicas, Universitat De València, Burjassot, Spain
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135
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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: 24] [Impact Index Per Article: 4.8] [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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136
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Ahmed N, Friedrich UA, Sormanni P, Ciryam P, Altman NS, Bukau B, Kramer G, O'Brien EP. Pairs of amino acids at the P- and A-sites of the ribosome predictably and causally modulate translation-elongation rates. J Mol Biol 2020; 432:166696. [PMID: 33152326 DOI: 10.1016/j.jmb.2020.10.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 08/30/2020] [Accepted: 10/19/2020] [Indexed: 12/31/2022]
Abstract
Variation in translation-elongation kinetics along a transcript's coding sequence plays an important role in the maintenance of cellular protein homeostasis by regulating co-translational protein folding, localization, and maturation. Translation-elongation speed is influenced by molecular factors within mRNA and protein sequences. For example, the presence of proline in the ribosome's P- or A-site slows down translation, but the effect of other pairs of amino acids, in the context of all 400 possible pairs, has not been characterized. Here, we study Saccharomyces cerevisiae using a combination of bioinformatics, mutational experiments, and evolutionary analyses, and show that many different pairs of amino acids and their associated tRNA molecules predictably and causally encode translation rate information when these pairs are present in the A- and P-sites of the ribosome independent of other factors known to influence translation speed including mRNA structure, wobble base pairing, tripeptide motifs, positively charged upstream nascent chain residues, and cognate tRNA concentration. The fast-translating pairs of amino acids that we identify are enriched four-fold relative to the slow-translating pairs across Saccharomyces cerevisiae's proteome, while the slow-translating pairs are enriched downstream of domain boundaries. Thus, the chemical identity of amino acid pairs contributes to variability in translation rates, elongation kinetics are causally encoded in the primary structure of proteins, and signatures of evolutionary selection indicate their potential role in co-translational processes.
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Affiliation(s)
- Nabeel Ahmed
- Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Ulrike A Friedrich
- Center for Molecular Biology of the Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany; German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Pietro Sormanni
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Prajwal Ciryam
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Naomi S Altman
- Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA; Department of Statistics, Pennsylvania State University, University Park, PA, 16802, USA
| | - Bernd Bukau
- Center for Molecular Biology of the Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany; German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Günter Kramer
- Center for Molecular Biology of the Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany; German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Edward P O'Brien
- Bioinformatics and Genomics Graduate Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA; Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA; Institute for Computational and Data Sciences, Pennsylvania State University, University Park, PA 16802, USA.
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137
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Zinshteyn B, Wangen JR, Hua B, Green R. Nuclease-mediated depletion biases in ribosome footprint profiling libraries. RNA (NEW YORK, N.Y.) 2020; 26:1481-1488. [PMID: 32503920 PMCID: PMC7491325 DOI: 10.1261/rna.075523.120] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/01/2020] [Indexed: 05/14/2023]
Abstract
Ribosome footprint profiling is a high-throughput sequencing-based technique that provides detailed and global views of translation in living cells. An essential part of this technology is removal of unwanted, normally very abundant, ribosomal RNA sequences that dominate libraries and increase sequencing costs. The most effective commercial solution (Ribo-Zero) has been discontinued as a standalone product and a number of new, experimentally distinct commercial applications have emerged on the market. Here we evaluated several commercially available alternatives designed for RNA-seq of human samples and find them generally unsuitable for ribosome footprint profiling. We instead recommend the use of custom-designed biotinylated oligos, which were widely used in early ribosome profiling studies. Importantly, we warn that depletion solutions based on targeted nuclease cleavage significantly perturb the high-resolution information that can be derived from the data, and thus do not recommend their use for any applications that require precise determination of the ends of RNA fragments.
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Affiliation(s)
- Boris Zinshteyn
- Howard Hughes Medical Institute (HHMI)
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Jamie R Wangen
- Howard Hughes Medical Institute (HHMI)
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Boyang Hua
- Howard Hughes Medical Institute (HHMI)
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Rachel Green
- Howard Hughes Medical Institute (HHMI)
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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138
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Lauria F, Bernabò P, Tebaldi T, Groen EJN, Perenthaler E, Maniscalco F, Rossi A, Donzel D, Clamer M, Marchioretto M, Omersa N, Orri J, Dalla Serra M, Anderluh G, Quattrone A, Inga A, Gillingwater TH, Viero G. SMN-primed ribosomes modulate the translation of transcripts related to spinal muscular atrophy. Nat Cell Biol 2020; 22:1239-1251. [PMID: 32958857 PMCID: PMC7610479 DOI: 10.1038/s41556-020-00577-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 08/13/2020] [Indexed: 12/20/2022]
Abstract
The contribution of ribosome heterogeneity and ribosome-associated proteins to the molecular control of proteomes in health and disease remains unclear. Here, we demonstrate that survival motor neuron (SMN) protein-the loss of which causes the neuromuscular disease spinal muscular atrophy (SMA)-binds to ribosomes and that this interaction is tissue-dependent. SMN-primed ribosomes are preferentially positioned within the first five codons of a set of mRNAs that are enriched for translational enhancer sequences in the 5' untranslated region (UTR) and rare codons at the beginning of their coding sequence. These SMN-specific mRNAs are associated with neurogenesis, lipid metabolism, ubiquitination, chromatin regulation and translation. Loss of SMN induces ribosome depletion, especially at the beginning of the coding sequence of SMN-specific mRNAs, leading to impairment of proteins that are involved in motor neuron function and stability, including acetylcholinesterase. Thus, SMN plays a crucial role in the regulation of ribosome fluxes along mRNAs encoding proteins that are relevant to SMA pathogenesis.
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Affiliation(s)
- Fabio Lauria
- Institute of Biophysics, CNR Unit at Trento, Trento, Italy
| | - Paola Bernabò
- Institute of Biophysics, CNR Unit at Trento, Trento, Italy
| | - Toma Tebaldi
- Department CIBIO, University of Trento, Trento, Italy
- Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Ewout Joan Nicolaas Groen
- Edinburgh Medical School, Biomedical Sciences & Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh, UK
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, Utrecht, the Netherlands
| | - Elena Perenthaler
- Institute of Biophysics, CNR Unit at Trento, Trento, Italy
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Federica Maniscalco
- Institute of Biophysics, CNR Unit at Trento, Trento, Italy
- Department CIBIO, University of Trento, Trento, Italy
| | | | - Deborah Donzel
- Institute of Biophysics, CNR Unit at Trento, Trento, Italy
| | | | | | - Neža Omersa
- National Institute of Chemistry, Ljubljana, Slovenia
| | - Julia Orri
- Institute of Biophysics, CNR Unit at Trento, Trento, Italy
- La Fundació Jesuïtes Educació, Barcelona, Spain
| | | | | | | | - Alberto Inga
- Department CIBIO, University of Trento, Trento, Italy
| | - Thomas Henry Gillingwater
- Edinburgh Medical School, Biomedical Sciences & Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh, UK
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139
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Wu LY, Lv YQ, Ye Y, Liang YR, Ye JH. Transcriptomic and Translatomic Analyses Reveal Insights into the Developmental Regulation of Secondary Metabolism in the Young Shoots of Tea Plants ( Camellia sinensis L.). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:10750-10762. [PMID: 32818378 DOI: 10.1021/acs.jafc.0c03341] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Accumulation of secondary metabolites in the young shoots of tea plants is developmentally modulated, especially flavonoids. Here, we investigate the developmental regulation mechanism of secondary metabolism in the developing leaves of tea plants using an integrated multiomic approach. For the pair of Leaf2/Bud, the correlation coefficient of the fold change of mRNA and RPFs abundances involved in flavonoid biosynthesis was 0.9359, being higher than that of RPFs and protein (R2 = 0.6941). These correlations were higher than the corresponding correlation coefficients for secondary metabolisms and genome-wide scale. Metabolomic analysis demonstrates that the developmental modulations of the structural genes for flavonoid biosynthesis-related pathways align with the concentration changes of catechin and flavonol glycoside groups. Relatively high translational efficiency (TE > 2) was observed in the four flavonoid structural genes (chalcone isomerase, dihydroflavonol 4-reductase, anthocyanidin synthase, and flavonol synthase). In addition, we originally provided the information on identified small open reading frames (small ORFs) and main ORFs in tea leaves and elaborated that the presence of upstream ORFs may have a repressive effect on the translation of downstream ORFs. Our data suggest that transcriptional regulation coordinates with translational regulation and may contribute to the elevation of translational efficiencies for the structural genes involved in the flavonoid biosynthesis pathways during tea leaf development.
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Affiliation(s)
- Liang-Yu Wu
- College of Horticulture, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, Fuzhou, China
| | - Yi-Qing Lv
- Tea Research Institute, Zhejiang University, Hangzhou 310013, China
| | - Ying Ye
- Tea Research Institute, Zhejiang University, Hangzhou 310013, China
| | - Yue-Rong Liang
- Tea Research Institute, Zhejiang University, Hangzhou 310013, China
| | - Jian-Hui Ye
- Tea Research Institute, Zhejiang University, Hangzhou 310013, China
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140
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Jalihal AP, Pitchiaya S, Xiao L, Bawa P, Jiang X, Bedi K, Parolia A, Cieslik M, Ljungman M, Chinnaiyan AM, Walter NG. Multivalent Proteins Rapidly and Reversibly Phase-Separate upon Osmotic Cell Volume Change. Mol Cell 2020; 79:978-990.e5. [PMID: 32857953 PMCID: PMC7502480 DOI: 10.1016/j.molcel.2020.08.004] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 06/11/2020] [Accepted: 08/05/2020] [Indexed: 12/12/2022]
Abstract
Processing bodies (PBs) and stress granules (SGs) are prominent examples of subcellular, membraneless compartments that are observed under physiological and stress conditions, respectively. We observe that the trimeric PB protein DCP1A rapidly (within ∼10 s) phase-separates in mammalian cells during hyperosmotic stress and dissolves upon isosmotic rescue (over ∼100 s) with minimal effect on cell viability even after multiple cycles of osmotic perturbation. Strikingly, this rapid intracellular hyperosmotic phase separation (HOPS) correlates with the degree of cell volume compression, distinct from SG assembly, and is exhibited broadly by homo-multimeric (valency ≥ 2) proteins across several cell types. Notably, HOPS sequesters pre-mRNA cleavage factor components from actively transcribing genomic loci, providing a mechanism for hyperosmolarity-induced global impairment of transcription termination. Our data suggest that the multimeric proteome rapidly responds to changes in hydration and molecular crowding, revealing an unexpected mode of globally programmed phase separation and sequestration.
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Affiliation(s)
- Ameya P Jalihal
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA; Cell and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sethuramasundaram Pitchiaya
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109-1055, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Lanbo Xiao
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109-1055, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Pushpinder Bawa
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109-1055, USA
| | - Xia Jiang
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109-1055, USA
| | - Karan Bedi
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Abhijit Parolia
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109-1055, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marcin Cieslik
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109-1055, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mats Ljungman
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA; Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109-1055, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109, USA; Department of Urology, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA.
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141
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Borchardt EK, Martinez NM, Gilbert WV. Regulation and Function of RNA Pseudouridylation in Human Cells. Annu Rev Genet 2020; 54:309-336. [PMID: 32870730 DOI: 10.1146/annurev-genet-112618-043830] [Citation(s) in RCA: 136] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Recent advances in pseudouridine detection reveal a complex pseudouridine landscape that includes messenger RNA and diverse classes of noncoding RNA in human cells. The known molecular functions of pseudouridine, which include stabilizing RNA conformations and destabilizing interactions with varied RNA-binding proteins, suggest that RNA pseudouridylation could have widespread effects on RNA metabolism and gene expression. Here, we emphasize how much remains to be learned about the RNA targets of human pseudouridine synthases, their basis for recognizing distinct RNA sequences, and the mechanisms responsible for regulated RNA pseudouridylation. We also examine the roles of noncoding RNA pseudouridylation in splicing and translation and point out the potential effects of mRNA pseudouridylation on protein production, including in the context of therapeutic mRNAs.
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Affiliation(s)
- Erin K Borchardt
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, Yale University, New Haven, Connecticut 06520, USA; , ,
| | - Nicole M Martinez
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, Yale University, New Haven, Connecticut 06520, USA; , ,
| | - Wendy V Gilbert
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, Yale University, New Haven, Connecticut 06520, USA; , ,
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142
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Structural impact of K63 ubiquitin on yeast translocating ribosomes under oxidative stress. Proc Natl Acad Sci U S A 2020; 117:22157-22166. [PMID: 32855298 DOI: 10.1073/pnas.2005301117] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Subpopulations of ribosomes are responsible for fine tuning the control of protein synthesis in dynamic environments. K63 ubiquitination of ribosomes has emerged as a new posttranslational modification that regulates protein synthesis during cellular response to oxidative stress. K63 ubiquitin, a type of ubiquitin chain that functions independently of the proteasome, modifies several sites at the surface of the ribosome, however, we lack a molecular understanding on how this modification affects ribosome structure and function. Using cryoelectron microscopy (cryo-EM), we resolved the first three-dimensional (3D) structures of K63 ubiquitinated ribosomes from oxidatively stressed yeast cells at 3.5-3.2 Å resolution. We found that K63 ubiquitinated ribosomes are also present in a polysome arrangement, similar to that observed in yeast polysomes, which we determined using cryoelectron tomography (cryo-ET). We further showed that K63 ubiquitinated ribosomes are captured uniquely at the rotated pretranslocation stage of translation elongation. In contrast, cryo-EM structures of ribosomes from mutant cells lacking K63 ubiquitin resolved at 4.4-2.7 Å showed 80S ribosomes represented in multiple states of translation, suggesting that K63 ubiquitin regulates protein synthesis at a selective stage of elongation. Among the observed structural changes, ubiquitin mediates the destabilization of proteins in the 60S P-stalk and in the 40S beak, two binding regions of the eukaryotic elongation factor eEF2. These changes would impact eEF2 function, thus, inhibiting translocation. Our findings help uncover the molecular effects of K63 ubiquitination on ribosomes, providing a model of translation control during oxidative stress, which supports elongation halt at pretranslocation.
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143
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Young DJ, Guydosh NR. Hcr1/eIF3j Is a 60S Ribosomal Subunit Recycling Accessory Factor In Vivo. Cell Rep 2020; 28:39-50.e4. [PMID: 31269449 DOI: 10.1016/j.celrep.2019.05.111] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 04/26/2019] [Accepted: 05/30/2019] [Indexed: 02/07/2023] Open
Abstract
Hcr1/eIF3j is a sub-stoichiometric subunit of eukaryotic initiation factor 3 (eIF3) that can dissociate the post-termination 40S ribosomal subunit from mRNA in vitro. We examine this ribosome recycling role in vivo by ribosome profiling and reporter assays and find that loss of Hcr1 leads to reinitiation of translation in 3' UTRs, consistent with a defect in recycling. However, the defect appears to be in the recycling of the 60S subunit, rather than the 40S subunit, because reinitiation does not require an AUG codon and is suppressed by overexpression of the 60S dissociation factor Rli1/ABCE1. Consistent with a 60S recycling role, overexpression of Hcr1 cannot compensate for loss of 40S recycling factors Tma64/eIF2D and Tma20/MCT-1. Intriguingly, loss of Hcr1 triggers greater expression of RLI1 via an apparent feedback loop. These findings suggest Hcr1/eIF3j is recruited to ribosomes at stop codons and may coordinate the transition to a new round of translation.
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Affiliation(s)
- David J Young
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA
| | - Nicholas R Guydosh
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA.
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144
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Wagner S, Herrmannová A, Hronová V, Gunišová S, Sen ND, Hannan RD, Hinnebusch AG, Shirokikh NE, Preiss T, Valášek LS. Selective Translation Complex Profiling Reveals Staged Initiation and Co-translational Assembly of Initiation Factor Complexes. Mol Cell 2020; 79:546-560.e7. [PMID: 32589964 PMCID: PMC7447980 DOI: 10.1016/j.molcel.2020.06.004] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 04/10/2020] [Accepted: 05/18/2020] [Indexed: 11/25/2022]
Abstract
Translational control targeting the initiation phase is central to the regulation of gene expression. Understanding all of its aspects requires substantial technological advancements. Here we modified yeast translation complex profile sequencing (TCP-seq), related to ribosome profiling, and adapted it for mammalian cells. Human TCP-seq, capable of capturing footprints of 40S subunits (40Ss) in addition to 80S ribosomes (80Ss), revealed that mammalian and yeast 40Ss distribute similarly across 5'TRs, indicating considerable evolutionary conservation. We further developed yeast and human selective TCP-seq (Sel-TCP-seq), enabling selection of 40Ss and 80Ss associated with immuno-targeted factors. Sel-TCP-seq demonstrated that eIF2 and eIF3 travel along 5' UTRs with scanning 40Ss to successively dissociate upon AUG recognition; notably, a proportion of eIF3 lingers on during the initial elongation cycles. Highlighting Sel-TCP-seq versatility, we also identified four initiating 48S conformational intermediates, provided novel insights into ATF4 and GCN4 mRNA translational control, and demonstrated co-translational assembly of initiation factor complexes.
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Affiliation(s)
- Susan Wagner
- EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia; Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, Czech Republic.
| | - Anna Herrmannová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, Czech Republic
| | - Vladislava Hronová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, Czech Republic
| | - Stanislava Gunišová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, Czech Republic
| | - Neelam D Sen
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ross D Hannan
- Australian Cancer Research Foundation Department of Cancer Biology and Therapeutics, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia
| | - Alan G Hinnebusch
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nikolay E Shirokikh
- EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia
| | - Thomas Preiss
- EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia; Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia.
| | - Leoš Shivaya Valášek
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, Czech Republic.
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145
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Karousis ED, Gurzeler LA, Annibaldis G, Dreos R, Mühlemann O. Human NMD ensues independently of stable ribosome stalling. Nat Commun 2020; 11:4134. [PMID: 32807779 PMCID: PMC7431590 DOI: 10.1038/s41467-020-17974-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 07/20/2020] [Indexed: 12/18/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a translation-dependent RNA degradation pathway that is important for the elimination of faulty, and the regulation of normal, mRNAs. The molecular details of the early steps in NMD are not fully understood but previous work suggests that NMD activation occurs as a consequence of ribosome stalling at the termination codon (TC). To test this hypothesis, we established an in vitro translation-coupled toeprinting assay based on lysates from human cells that allows monitoring of ribosome occupancy at the TC of reporter mRNAs. In contrast to the prevailing NMD model, our in vitro system reveals similar ribosomal occupancy at the stop codons of NMD-sensitive and NMD-insensitive reporter mRNAs. Moreover, ribosome profiling reveals a similar density of ribosomes at the TC of endogenous NMD-sensitive and NMD-insensitive mRNAs in vivo. Together, these data show that NMD activation is not accompanied by stable stalling of ribosomes at TCs. Nonsense-mediated mRNA decay (NMD) was thought to ensue when ribosomes fail to terminate translation properly. However, the authors observe similar ribosome occupancy at stop codons of NMD sensitive and insensitive mRNAs, showing that human NMD is not activated by stable ribosome stalling as previously suggested.
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Affiliation(s)
- Evangelos D Karousis
- Department of Chemistry and Biochemistry, University of Bern, CH-3012, Bern, Switzerland
| | - Lukas-Adrian Gurzeler
- Department of Chemistry and Biochemistry, University of Bern, CH-3012, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, CH-3012, Bern, Switzerland
| | - Giuditta Annibaldis
- Department of Chemistry and Biochemistry, University of Bern, CH-3012, Bern, Switzerland
| | - René Dreos
- Center for Integrative Genomics, Université de Lausanne, CH-1015, Lausanne, Switzerland
| | - Oliver Mühlemann
- Department of Chemistry and Biochemistry, University of Bern, CH-3012, Bern, Switzerland.
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146
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Bohlen J, Fenzl K, Kramer G, Bukau B, Teleman AA. Selective 40S Footprinting Reveals Cap-Tethered Ribosome Scanning in Human Cells. Mol Cell 2020; 79:561-574.e5. [DOI: 10.1016/j.molcel.2020.06.005] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 04/10/2020] [Accepted: 05/18/2020] [Indexed: 11/27/2022]
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147
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Parker DJ, Lalanne JB, Kimura S, Johnson GE, Waldor MK, Li GW. Growth-Optimized Aminoacyl-tRNA Synthetase Levels Prevent Maximal tRNA Charging. Cell Syst 2020; 11:121-130.e6. [PMID: 32726597 DOI: 10.1016/j.cels.2020.07.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 05/07/2020] [Accepted: 07/02/2020] [Indexed: 01/28/2023]
Abstract
Aminoacyl-tRNA synthetases (aaRSs) serve a dual role in charging tRNAs. Their enzymatic activities both provide protein synthesis flux and reduce uncharged tRNA levels. Although uncharged tRNAs can negatively impact bacterial growth, substantial concentrations of tRNAs remain deacylated even under nutrient-rich conditions. Here, we show that tRNA charging in Bacillus subtilis is not maximized due to optimization of aaRS production during rapid growth, which prioritizes demands in protein synthesis over charging levels. The presence of uncharged tRNAs is alleviated by precisely tuned translation kinetics and the stringent response, both insensitive to aaRS overproduction but sharply responsive to underproduction, allowing for just enough aaRS production atop a "fitness cliff." Notably, we find that the stringent response mitigates fitness defects at all aaRS underproduction levels even without external starvation. Thus, adherence to minimal, flux-satisfying protein production drives limited tRNA charging and provides a basis for the sensitivity and setpoints of an integrated growth-control network.
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Affiliation(s)
- Darren J Parker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jean-Benoît Lalanne
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Satoshi Kimura
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Grace E Johnson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Matthew K Waldor
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Gene-Wei Li
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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148
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Wu CCC, Peterson A, Zinshteyn B, Regot S, Green R. Ribosome Collisions Trigger General Stress Responses to Regulate Cell Fate. Cell 2020; 182:404-416.e14. [PMID: 32610081 PMCID: PMC7384957 DOI: 10.1016/j.cell.2020.06.006] [Citation(s) in RCA: 321] [Impact Index Per Article: 64.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/18/2020] [Accepted: 06/02/2020] [Indexed: 01/01/2023]
Abstract
Problems arising during translation of mRNAs lead to ribosome stalling and collisions that trigger a series of quality control events. However, the global cellular response to ribosome collisions has not been explored. Here, we uncover a function for ribosome collisions in signal transduction. Using translation elongation inhibitors and general cellular stress conditions, including amino acid starvation and UV irradiation, we show that ribosome collisions activate the stress-activated protein kinase (SAPK) and GCN2-mediated stress response pathways. We show that the MAPKKK ZAK functions as the sentinel for ribosome collisions and is required for immediate early activation of both SAPK (p38/JNK) and GCN2 signaling pathways. Selective ribosome profiling and biochemistry demonstrate that although ZAK generally associates with elongating ribosomes on polysomal mRNAs, it specifically auto-phosphorylates on the minimal unit of colliding ribosomes, the disome. Together, these results provide molecular insights into how perturbation of translational homeostasis regulates cell fate.
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Affiliation(s)
- Colin Chih-Chien Wu
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Amy Peterson
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Boris Zinshteyn
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sergi Regot
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Rachel Green
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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149
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Arpat AB, Liechti A, De Matos M, Dreos R, Janich P, Gatfield D. Transcriptome-wide sites of collided ribosomes reveal principles of translational pausing. Genome Res 2020; 30:985-999. [PMID: 32703885 PMCID: PMC7397865 DOI: 10.1101/gr.257741.119] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 06/29/2020] [Indexed: 01/28/2023]
Abstract
Translation initiation is the major regulatory step defining the rate of protein production from an mRNA. Meanwhile, the impact of nonuniform ribosomal elongation rates is largely unknown. Using a modified ribosome profiling protocol based on footprints from two closely packed ribosomes (disomes), we have mapped ribosomal collisions transcriptome-wide in mouse liver. We uncover that the stacking of an elongating onto a paused ribosome occurs frequently and scales with translation rate, trapping ∼10% of translating ribosomes in the disome state. A distinct class of pause sites is indicative of deterministic pausing signals. Pause site association with specific amino acids, peptide motifs, and nascent polypeptide structure is suggestive of programmed pausing as a widespread mechanism associated with protein folding. Evolutionary conservation at disome sites indicates functional relevance of translational pausing. Collectively, our disome profiling approach allows unique insights into gene regulation occurring at the step of translation elongation.
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Affiliation(s)
- Alaaddin Bulak Arpat
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Angélica Liechti
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Mara De Matos
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - René Dreos
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Peggy Janich
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - David Gatfield
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
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Jones JD, Monroe J, Koutmou KS. A molecular-level perspective on the frequency, distribution, and consequences of messenger RNA modifications. WILEY INTERDISCIPLINARY REVIEWS. RNA 2020; 11:e1586. [PMID: 31960607 PMCID: PMC8243748 DOI: 10.1002/wrna.1586] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 12/21/2019] [Accepted: 01/04/2020] [Indexed: 01/16/2023]
Abstract
Cells use chemical modifications to alter the sterics, charge, and conformations of large biomolecules, modulating their biogenesis, function, and stability. Until recently post-transcriptional RNA modifications were thought to be largely limited to nonprotein coding RNA species. However, this dogma has rapidly transformed with the discovery of a host of modifications in protein coding messenger RNAs (mRNAs). Recent advancements in genome-wide sequencing technologies have enabled the identification of mRNA modifications as a potential new frontier in gene regulation-leading to the development of the epitranscriptome field. As a result, there has been a flurry of multiple groundbreaking discoveries, including new modifications, nucleoside modifying enzymes ("writers" and "erasers"), and RNA binding proteins that recognize chemical modifications ("readers"). These discoveries opened the door to understanding how post-transcriptional mRNA modifications can modulate the mRNA lifecycle, and established a link between the epitranscriptome and human health and disease. Despite a rapidly growing recognition of their importance, fundamental questions regarding the identity, prevalence, and functional consequences of mRNA modifications remain to be answered. Here, we highlight quantitative studies that characterize mRNA modification abundance, frequency, and interactions with cellular machinery. As the field progresses, we see a need for the further integration of quantitative and reductionist approaches to complement transcriptome wide studies in order to establish a molecular-level framework for understanding the consequences of mRNA chemical modifications on biological processes. This article is categorized under: RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry RNA Processing > RNA Editing and Modification.
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Affiliation(s)
- Joshua D. Jones
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan
| | - Jeremy Monroe
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan
| | - Kristin S. Koutmou
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan
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