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Bianco E, Bonassera M, Uliana F, Tilma J, Winkler M, Zencir S, Gossert A, Oborská-Oplová M, Dechant R, Hugener J, Panse VG, Pilhofer M, Albert B, Kimmig P, Peter M. Stm1 regulates Ifh1 activity revealing crosstalk between ribosome biogenesis and ribosome dormancy. Mol Cell 2025; 85:1806-1823.e17. [PMID: 40315826 DOI: 10.1016/j.molcel.2025.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 01/26/2025] [Accepted: 04/04/2025] [Indexed: 05/04/2025]
Abstract
Nutrient abundance boosts ribosome biogenesis, whereas ribosome dormancy factors limit ribosome degradation upon starvation. The equilibrium between the two pathways governs cell growth. In this study, we identified suppressor of Tom1 (Stm1) as a molecular link between ribosome protection and biogenesis in Saccharomyces cerevisiae. While Stm1 was previously described as a dormancy factor, we show that it activates Ifh1, a transcriptional activator of ribosomal protein genes. Stm1 transiently localizes to the nucleolus, where it interacts with pre-ribosomes and directly binds RNA and Ifh1 through its C-terminal intrinsically disordered region (IDR). Although the IDR is dispensable for ribosome protection, its loss compromises cell growth. The IDR is phosphorylated upon nutrient starvation, which disrupts its interaction with Ifh1. Our findings reveal a molecular pathway sensing and adjusting ribosome abundance in response to nutrient availability, reinforcing the relevance of regulated ribosome homeostasis in physiology and disease.
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Affiliation(s)
- Eliana Bianco
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8093 Zürich, Switzerland.
| | - Martina Bonassera
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8093 Zürich, Switzerland; Department of Biology, Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH), 8093 Zürich, Switzerland
| | - Federico Uliana
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8093 Zürich, Switzerland
| | - Janny Tilma
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8093 Zürich, Switzerland
| | - Martin Winkler
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8093 Zürich, Switzerland
| | - Sevil Zencir
- Department of Cell Biology Sciences III, Université de Genève, 1211 Geneva, Switzerland
| | - Alvar Gossert
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8093 Zürich, Switzerland; Biomolecular NMR Spectroscopy Platform (BNSP), Department of Biology, Eidgenössische Technische Hochschule (ETH), 8093 Zürich, Switzerland
| | | | - Reinhard Dechant
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8093 Zürich, Switzerland
| | - Jannik Hugener
- Department of Biology, Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH), 8093 Zürich, Switzerland
| | - Vikram Govind Panse
- Institute of Medical Microbiology, University of Zürich, 8006 Zürich, Switzerland; Faculty of Science, University of Zürich, Zürich, Switzerland
| | - Martin Pilhofer
- Department of Biology, Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH), 8093 Zürich, Switzerland
| | - Benjamin Albert
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Philipp Kimmig
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8093 Zürich, Switzerland
| | - Matthias Peter
- Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8093 Zürich, Switzerland.
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Ma K, Zhang P, Zhao J, Qin Y. Discovery of a novel translation-machinery-associated protein that positively correlates with cellulase production. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2025; 18:20. [PMID: 39987148 PMCID: PMC11847360 DOI: 10.1186/s13068-025-02624-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2024] [Accepted: 02/11/2025] [Indexed: 02/24/2025]
Abstract
BACKGROUND The production of cellulases by filamentous fungi is a crucial aspect of sustainable bioproduction from renewable lignocellulosic biomass. Following the transcription of cellulase genes in the nucleus, a complex pathway involving translation, folding, and secretion is required to produce extracellular cellulases. Most studies about cellulase production have focused on examining transcriptional regulatory mechanisms and enhancement of enzyme gene levels; comparatively, little is known about protein translation and secretion for cellulase production. RESULTS A translation-machinery-associated (TMA) protein PoTma15 was identified in cellulosic Penicillium oxalicum. The PoTma15 is conserved in various filamentous fungi, but not in yeast, plants, or animals. All homologous proteins of PoTma15 have previously been uncharacterized. PoTma15 was initially thought to be one of the putative interactors of transcription factor PoXlnR, as it was preyed by tandem affinity purification (TAP) coupled with the mass spectrometry (TAP-MS) technique using PoXlnR as the bait. Subsequent research revealed that PoTma15 is associated with the translation machinery. The top three proteins associated with PoTma15 are orthologs of Saccharomyces cerevisiae translation-machinery-associated protein (Tma19), translation elongation factor eIF5A, and ribosomal protein S28, respectively. PoTma15 is widely distributed in fungal hyphae and positively correlates with the production of cellulases and extracellular proteins. Deleting the Potma15 gene (Δtma15) decreased cellulase production, while overexpressing the Potma15 gene (OEtma15) increased cellulase production. However, the Δtma15 mutant was not observed to have downregulated transcript levels of major (hemi)cellulase and amylase genes, compared to the P. oxalicum wild type (WT). The production of extracellular cellulases and extracellular proteins of the Δtma15 mutant was less affected by cycloheximide, an inhibitor of eukaryotic translation elongation, compared to the WT strain and OEtma15 mutant, suggesting a stronger resistance to the translation-inhibiting effects of cycloheximide in the Δtma15 mutant. The results demonstrate that PoTma15 is a translation-machinery-associated protein that affects translation elongation and, consequently, the production of enzyme proteins. CONCLUSIONS PoTma15 is the first TMA protein characterized in cellulosic filamentous fungi and the first TMA protein used in fungi to increase cellulase production. PoTma15's role in the production of cellulases and total extracellular proteins suggests that not only can it be used to widen the cellulase production pathway, but can even be engineered as a target to improve the production of other heterologous protein or bioproducts using filamentous fungi as cell factories in the future.
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Affiliation(s)
- Kexuan Ma
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- National Glycoengineering Research Center, Shandong University, Qingdao, China
| | - Panpan Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- National Glycoengineering Research Center, Shandong University, Qingdao, China
| | - Jian Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.
| | - Yuqi Qin
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.
- National Glycoengineering Research Center, Shandong University, Qingdao, China.
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3
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Dutcher HA, Gasch AP. Investigating the role of RNA-binding protein Ssd1 in aneuploidy tolerance through network analysis. RNA (NEW YORK, N.Y.) 2024; 31:100-112. [PMID: 39471998 DOI: 10.1261/rna.080199.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Accepted: 10/15/2024] [Indexed: 11/06/2024]
Abstract
RNA-binding proteins (RBPs) play critical cellular roles by mediating various stages of RNA life cycles. Ssd1, an RBP with pleiotropic effects, has been implicated in aneuploidy tolerance in Saccharomyces cerevisiae but its mechanistic role remains unclear. Here, we used a network-based approach to inform on Ssd1's role in aneuploidy tolerance, by identifying and experimentally perturbing a network of RBPs that share mRNA targets with Ssd1. We identified RBPs whose bound mRNA targets significantly overlap with Ssd1 targets. For 14 identified RBPs, we then used a genetic approach to generate all combinations of genotypes for euploid and aneuploid yeast with an extra copy of chromosome XII, with and without SSD1 and/or the RBP of interest. Deletion of 10 RBPs either exacerbated or alleviated the sensitivity of wild-type and/or ssd1Δ cells to chromosome XII duplication, in several cases indicating genetic interactions with SSD1 in the context of aneuploidy. We integrated these findings with results from a global overexpression screen that identified genes whose duplication complements ssd1Δ aneuploid sensitivity. The resulting network points to a subgroup of proteins with shared roles in translational repression and P-body formation, implicating these functions in aneuploidy tolerance. Our results reveal a role for new RBPs in aneuploidy tolerance and support a model in which Ssd1 mitigates translation-related stresses in aneuploid cells.
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Affiliation(s)
- H Auguste Dutcher
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Audrey P Gasch
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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4
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Xie Y, Shu T, Liu T, Spindler MC, Mahamid J, Hocky GM, Gresham D, Holt LJ. Polysome collapse and RNA condensation fluidize the cytoplasm. Mol Cell 2024; 84:2698-2716.e9. [PMID: 39059370 PMCID: PMC11539954 DOI: 10.1016/j.molcel.2024.06.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 03/25/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024]
Abstract
The cell interior is packed with macromolecules of mesoscale size, and this crowded milieu significantly influences cellular physiology. Cellular stress responses almost universally lead to inhibition of translation, resulting in polysome collapse and release of mRNA. The released mRNA molecules condense with RNA-binding proteins to form ribonucleoprotein (RNP) condensates known as processing bodies and stress granules. Here, we show that polysome collapse and condensation of RNA transiently fluidize the cytoplasm, and coarse-grained molecular dynamic simulations support this as a minimal mechanism for the observed biophysical changes. Increased mesoscale diffusivity correlates with the efficient formation of quality control bodies (Q-bodies), membraneless organelles that compartmentalize misfolded peptides during stress. Synthetic, light-induced RNA condensation also fluidizes the cytoplasm. Together, our study reveals a functional role for stress-induced translation inhibition and formation of RNP condensates in modulating the physical properties of the cytoplasm to enable efficient response of cells to stress conditions.
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Affiliation(s)
- Ying Xie
- Institute for Systems Genetics, New York University Langone Medical Center, New York, NY, USA; Department of Biology, New York University, New York, NY, USA
| | - Tong Shu
- Institute for Systems Genetics, New York University Langone Medical Center, New York, NY, USA
| | - Tiewei Liu
- Institute for Systems Genetics, New York University Langone Medical Center, New York, NY, USA; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Marie-Christin Spindler
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany; Cell Biology and Biophysics Unit, EMBL, Heidelberg, Germany
| | - Glen M Hocky
- Department of Chemistry and Simons Center for Computational Physical Chemistry, New York University, New York, NY, USA
| | - David Gresham
- Department of Biology, New York University, New York, NY, USA.
| | - Liam J Holt
- Institute for Systems Genetics, New York University Langone Medical Center, New York, NY, USA.
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5
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Dutcher HA, Gasch AP. Investigating the role of RNA-binding protein Ssd1 in aneuploidy tolerance through network analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.19.604323. [PMID: 39091809 PMCID: PMC11291059 DOI: 10.1101/2024.07.19.604323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
RNA-binding proteins (RBPs) play critical cellular roles by mediating various stages of RNA life cycles. Ssd1, an RBP with pleiotropic effects, has been implicated in aneuploidy tolerance in Saccharomyces cerevisiae but its mechanistic role remains unclear. Here we used a network-based approach to inform on Ssd1's role in aneuploidy tolerance, by identifying and experimentally perturbing a network of RBPs that share mRNA targets with Ssd1. We identified RBPs whose bound mRNA targets significantly overlap with Ssd1 targets. For 14 identified RBPs, we then used a genetic approach to generate all combinations of genotypes for euploid and aneuploid yeast with an extra copy of chromosome XII, with and without SSD1 and/or the RBP of interest. Deletion of 10 RBPs either exacerbated or alleviated the sensitivity of wild-type and/or ssd1 Δ cells to chromosome XII duplication, in several cases indicating genetic interactions with SSD1 in the context of aneuploidy. We integrated these findings with results from a global over-expression screen that identified genes whose duplication complements ssd1 Δ aneuploid sensitivity. The resulting network points to a sub-group of proteins with shared roles in translational repression and p-body formation, implicating these functions in aneuploidy tolerance. Our results reveal a role for new RBPs in aneuploidy tolerance and support a model in which Ssd1 mitigates translation-related stresses in aneuploid cells.
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6
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Koli S, Shetty S. Ribosomal dormancy at the nexus of ribosome homeostasis and protein synthesis. Bioessays 2024; 46:e2300247. [PMID: 38769702 DOI: 10.1002/bies.202300247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/05/2024] [Accepted: 05/02/2024] [Indexed: 05/22/2024]
Abstract
Dormancy or hibernation is a non-proliferative state of cells with low metabolic activity and gene expression. Dormant cells sequester ribosomes in a translationally inactive state, called dormant/hibernating ribosomes. These dormant ribosomes are important for the preservation of ribosomes and translation shut-off. While recent studies attempted to elucidate their modes of formation, the regulation and roles of the diverse dormant ribosomal populations are still largely understudied. The mechanistic details of the formation of dormant ribosomes in stress and especially their disassembly during recovery remain elusive. In this review, we discuss the roles of dormant ribosomes and their potential regulatory mechanisms. Furthermore, we highlight the paradigms that need to be answered in the field of ribosomal dormancy.
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Affiliation(s)
- Saloni Koli
- Advanced Centre for Treatment Research and Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, India
| | - Sunil Shetty
- Advanced Centre for Treatment Research and Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
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7
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Du M, Li X, Dong W, Zeng F. Implication of Stm1 in the protection of eIF5A, eEF2 and tRNA through dormant ribosomes. Front Mol Biosci 2024; 11:1395220. [PMID: 38698775 PMCID: PMC11063288 DOI: 10.3389/fmolb.2024.1395220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Accepted: 04/09/2024] [Indexed: 05/05/2024] Open
Abstract
Background: Dormant ribosomes are typically associated with preservation factors to protect themselves from degradation under stress conditions. Stm1/SERBP1 is one such protein that anchors the 40S and 60S subunits together. Several proteins and tRNAs bind to this complex as well, yet the molecular mechanisms remain unclear. Methods: Here, we reported the cryo-EM structures of five newly identified Stm1/SERBP1-bound ribosomes. Results: These structures highlighted that eIF5A, eEF2, and tRNA might bind to dormant ribosomes under stress to avoid their own degradation, thus facilitating protein synthesis upon the restoration of growth conditions. In addition, Ribo-seq data analysis reflected the upregulation of nutrient, metabolism, and external-stimulus-related pathways in the ∆stm1 strain, suggesting possible regulatory roles of Stm1. Discussion: The knowledge generated from the present work will facilitate in better understanding the molecular mechanism of dormant ribosomes.
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Affiliation(s)
- Mengtan Du
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, China
| | - Xin Li
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, China
| | - Wanlin Dong
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, China
| | - Fuxing Zeng
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, China
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8
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Liu B, Luo L, Shi Z, Ju H, Yu L, Li G, Cui J. Research Progress of Porcine Reproductive and Respiratory Syndrome Virus NSP2 Protein. Viruses 2023; 15:2310. [PMID: 38140551 PMCID: PMC10747760 DOI: 10.3390/v15122310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is globally prevalent and seriously harms the economic efficiency of pig farming. Because of its immunosuppression and high incidence of mutant recombination, PRRSV poses a great challenge for disease prevention and control. Nonstructural protein 2 (NSP2) is the most variable functional protein in the PRRSV genome and can generate NSP2N and NSP2TF variants due to programmed ribosomal frameshifts. These variants are broad and complex in function and play key roles in numerous aspects of viral protein maturation, viral particle assembly, regulation of immunity, autophagy, apoptosis, cell cycle and cell morphology. In this paper, we review the structural composition, programmed ribosomal frameshift and biological properties of NSP2 to facilitate basic research on PRRSV and to provide theoretical support for disease prevention and control and therapeutic drug development.
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Affiliation(s)
- Benjin Liu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150038, China; (B.L.); (L.L.); (Z.S.)
| | - Lingzhi Luo
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150038, China; (B.L.); (L.L.); (Z.S.)
| | - Ziqi Shi
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150038, China; (B.L.); (L.L.); (Z.S.)
| | - Houbin Ju
- Shanghai Animal Disease Prevention and Control Center, Shanghai 201103, China;
| | - Lingxue Yu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China;
| | - Guoxin Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China;
| | - Jin Cui
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150038, China; (B.L.); (L.L.); (Z.S.)
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9
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Bleckmann A, Spitzlberger N, Denninger P, Ehrnsberger HF, Wang L, Bruckmann A, Reich S, Holzinger P, Medenbach J, Grasser KD, Dresselhaus T. Cytosolic RGG RNA-binding proteins are temperature sensitive flowering time regulators in Arabidopsis. Biol Chem 2023; 404:1069-1084. [PMID: 37674329 DOI: 10.1515/hsz-2023-0171] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 08/03/2023] [Indexed: 09/08/2023]
Abstract
mRNA translation is tightly regulated by various classes of RNA-binding proteins (RBPs) during development and in response to changing environmental conditions. In this study, we characterize the arginine-glycine-glycine (RGG) motif containing RBP family of Arabidopsis thaliana representing homologues of the multifunctional translation regulators and ribosomal preservation factors Stm1 from yeast (ScStm1) and human SERBP1 (HsSERBP1). The Arabidopsis genome encodes three RGG proteins named AtRGGA, AtRGGB and AtRGGC. While AtRGGA is ubiquitously expressed, AtRGGB and AtRGGC are enriched in dividing cells. All AtRGGs localize almost exclusively to the cytoplasm and bind with high affinity to ssRNA, while being capable to interact with most nucleic acids, except dsRNA. A protein-interactome study shows that AtRGGs interact with ribosomal proteins and proteins involved in RNA processing and transport. In contrast to ScStm1, AtRGGs are enriched in ribosome-free fractions in polysome profiles, suggesting additional plant-specific functions. Mutant studies show that AtRGG proteins differentially regulate flowering time, with a distinct and complex temperature dependency for each AtRGG protein. In conclusion, we suggest that AtRGGs function in fine-tuning translation efficiency to control flowering time and potentially other developmental processes in response to environmental changes.
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Affiliation(s)
- Andrea Bleckmann
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Nicole Spitzlberger
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Philipp Denninger
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Hans F Ehrnsberger
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Lele Wang
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Astrid Bruckmann
- Biochemistry I, University of Regensburg, D-93053 Regensburg, Germany
| | - Stefan Reich
- Biochemistry I, University of Regensburg, D-93053 Regensburg, Germany
| | - Philipp Holzinger
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Jan Medenbach
- Biochemistry I, University of Regensburg, D-93053 Regensburg, Germany
| | - Klaus D Grasser
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Thomas Dresselhaus
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
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10
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Subbaiah S P V, Uttamrao PP, Das U, Sundaresan S, Rathinavelan T. Concentration and time-dependent amyloidogenic characteristics of intrinsically disordered N-terminal region of Saccharomyces cerevisiae Stm1. Front Microbiol 2023; 14:1206945. [PMID: 37928673 PMCID: PMC10620681 DOI: 10.3389/fmicb.2023.1206945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 10/03/2023] [Indexed: 11/07/2023] Open
Abstract
Saccharomyces cerevisiae Stm1 protein is a ribosomal association factor, which plays an important role in preserving ribosomes in a nutrition-deprived environment. It is also shown to take part in apoptosis-like cell death. Stm1 N-terminal region (Stm1_N1-113) is shown to recognize purine motif DNA triplex and G-quadruplex. Circular dichroism (CD) spectra of Stm1_N1-113 (enriched in positively-charged Lysine and Arginine; negatively-charged Aspartate; polar-uncharged Threonine, Asparagine, Proline and Serine; hydrophobic Alanine, Valine, and Glycine) collected after 0 and 24 h indicate that the protein assumes beta-sheet conformation at the higher concentrations in contrast to intrinsically disordered conformation seen for its monomeric form found in the crystal structure. Thioflavin-T kinetics experiments indicate that the lag phase is influenced by the salt concentration. Atomic force microscopy (AFM) images collected for a variety of Stm1_N1-113 concentrations (in the range of 1-400 μM) in the presence of 150 mM NaCl at 0, 24, and 48 h indicate a threshold concentration requirement to observe the time-dependent amyloid formation. This is prominent seen at the physiological salt concentration of 150 mM NaCl with the fibrillation observed for 400 μM concentration at 48 h, whereas oligomerization or proto-fibrillation is seen for the other concentrations. Such concentration-dependent fibrillation of Stm1_N1-113 explains that amyloid fibrils formed during the overexpression of Stm1_N1-113 may act as a molecular device to trigger apoptosis-like cell death.
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Affiliation(s)
- Venkata Subbaiah S P
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
| | - Patil Pranita Uttamrao
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
| | - Uttam Das
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
| | - Sruthi Sundaresan
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
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11
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Xie Y, Liu T, Gresham D, Holt LJ. mRNA condensation fluidizes the cytoplasm. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.30.542963. [PMID: 37398029 PMCID: PMC10312499 DOI: 10.1101/2023.05.30.542963] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The intracellular environment is packed with macromolecules of mesoscale size, and this crowded milieu significantly influences cell physiology. When exposed to stress, mRNAs released after translational arrest condense with RNA binding proteins, resulting in the formation of membraneless RNA protein (RNP) condensates known as processing bodies (P-bodies) and stress granules (SGs). However, the impact of the assembly of these condensates on the biophysical properties of the crowded cytoplasmic environment remains unclear. Here, we find that upon exposure to stress, polysome collapse and condensation of mRNAs increases mesoscale particle diffusivity in the cytoplasm. Increased mesoscale diffusivity is required for the efficient formation of Q-bodies, membraneless organelles that coordinate degradation of misfolded peptides that accumulate during stress. Additionally, we demonstrate that polysome collapse and stress granule formation has a similar effect in mammalian cells, fluidizing the cytoplasm at the mesoscale. We find that synthetic, light-induced RNA condensation is sufficient to fluidize the cytoplasm, demonstrating a causal effect of RNA condensation. Together, our work reveals a new functional role for stress-induced translation inhibition and formation of RNP condensates in modulating the physical properties of the cytoplasm to effectively respond to stressful conditions.
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Affiliation(s)
- Ying Xie
- Institute for Systems Genetics, New York University Langone Medical Center, New York, New York, United States
- Department of Biology, New York University, New York, New York, United States
| | - Tiewei Liu
- Institute for Systems Genetics, New York University Langone Medical Center, New York, New York, United States
| | - David Gresham
- Department of Biology, New York University, New York, New York, United States
| | - Liam J Holt
- Institute for Systems Genetics, New York University Langone Medical Center, New York, New York, United States
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12
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Shetty S, Hofstetter J, Battaglioni S, Ritz D, Hall MN. TORC1 phosphorylates and inhibits the ribosome preservation factor Stm1 to activate dormant ribosomes. EMBO J 2023; 42:e112344. [PMID: 36691768 PMCID: PMC9975950 DOI: 10.15252/embj.2022112344] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 12/23/2022] [Accepted: 12/23/2022] [Indexed: 01/25/2023] Open
Abstract
Target of rapamycin complex 1 (TORC1) promotes biogenesis and inhibits the degradation of ribosomes in response to nutrient availability. To ensure a basal supply of ribosomes, cells are known to preserve a small pool of dormant ribosomes under nutrient-limited conditions. However, the regulation of these dormant ribosomes is poorly characterized. Here, we show that upon inhibition of yeast TORC1 by rapamycin or nitrogen starvation, the ribosome preservation factor Stm1 mediates the formation of nontranslating, dormant 80S ribosomes. Furthermore, Stm1-bound 80S ribosomes are protected from proteasomal degradation. Upon nutrient replenishment, TORC1 directly phosphorylates and inhibits Stm1 to reactivate translation. Finally, we find that SERBP1, a mammalian ortholog of Stm1, is likewise required for the formation of dormant 80S ribosomes upon mTORC1 inhibition in mammalian cells. These data suggest that TORC1 regulates ribosomal dormancy in an evolutionarily conserved manner by directly targeting a ribosome preservation factor.
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Affiliation(s)
| | | | | | - Danilo Ritz
- BiozentrumUniversity of BaselBaselSwitzerland
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13
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Leesch F, Lorenzo-Orts L, Pribitzer C, Grishkovskaya I, Roehsner J, Chugunova A, Matzinger M, Roitinger E, Belačić K, Kandolf S, Lin TY, Mechtler K, Meinhart A, Haselbach D, Pauli A. A molecular network of conserved factors keeps ribosomes dormant in the egg. Nature 2023; 613:712-720. [PMID: 36653451 PMCID: PMC7614339 DOI: 10.1038/s41586-022-05623-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 12/02/2022] [Indexed: 01/20/2023]
Abstract
Ribosomes are produced in large quantities during oogenesis and are stored in the egg. However, the egg and early embryo are translationally repressed1-4. Here, using mass spectrometry and cryo-electron microscopy analyses of ribosomes isolated from zebrafish (Danio rerio) and Xenopus laevis eggs and embryos, we provide molecular evidence that ribosomes transition from a dormant state to an active state during the first hours of embryogenesis. Dormant ribosomes are associated with four conserved factors that form two modules, consisting of Habp4-eEF2 and death associated protein 1b (Dap1b) or Dap in complex with eIF5a. Both modules occupy functionally important sites and act together to stabilize ribosomes and repress translation. Dap1b (also known as Dapl1 in mammals) is a newly discovered translational inhibitor that stably inserts into the polypeptide exit tunnel. Addition of recombinant zebrafish Dap1b protein is sufficient to block translation and reconstitute the dormant egg ribosome state in a mammalian translation extract in vitro. Thus, a developmentally programmed, conserved ribosome state has a key role in ribosome storage and translational repression in the egg.
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Affiliation(s)
- Friederike Leesch
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Laura Lorenzo-Orts
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.
| | - Carina Pribitzer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Irina Grishkovskaya
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Josef Roehsner
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Anastasia Chugunova
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Manuel Matzinger
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Elisabeth Roitinger
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Katarina Belačić
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Susanne Kandolf
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Tzi-Yang Lin
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Anton Meinhart
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - David Haselbach
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.
| | - Andrea Pauli
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.
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14
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Structural remodeling of ribosome associated Hsp40-Hsp70 chaperones during co-translational folding. Nat Commun 2022; 13:3410. [PMID: 35701497 PMCID: PMC9197937 DOI: 10.1038/s41467-022-31127-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 06/02/2022] [Indexed: 11/16/2022] Open
Abstract
Ribosome associated complex (RAC), an obligate heterodimer of HSP40 and HSP70 (Zuo1 and Ssz1 in yeast), is conserved in eukaryotes and functions as co-chaperone for another HSP70 (Ssb1/2 in yeast) to facilitate co-translational folding of nascent polypeptides. Many mechanistic details, such as the coordination of one HSP40 with two HSP70s and the dynamic interplay between RAC-Ssb and growing nascent chains, remain unclear. Here, we report three sets of structures of RAC-containing ribosomal complexes isolated from Saccharomyces cerevisiae. Structural analyses indicate that RAC on the nascent-chain-free ribosome is in an autoinhibited conformation, and in the presence of a nascent chain at the peptide tunnel exit (PTE), RAC undergoes large-scale structural remodeling to make Zuo1 J-Domain more accessible to Ssb. Our data also suggest a role of Zuo1 in orienting Ssb-SBD proximal to the PTE for easy capture of the substrate. Altogether, in accordance with previous data, our work suggests a sequence of structural remodeling events for RAC-Ssb during co-translational folding, triggered by the binding and passage of growing nascent chain from one to another. Ribosome associated complex (RAC)- HSP70 (Ssb in yeast) is a eukaryotic chaperone system involved in co-translational folding. Here, authors report structures of RAC-containing ribosomal complexes, which suggest a working model for the dynamic actions of RAC-Ssb during the process.
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15
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Smith PR, Pandit SC, Loerch S, Campbell ZT. The space between notes: emerging roles for translationally silent ribosomes. Trends Biochem Sci 2022; 47:477-491. [PMID: 35246374 PMCID: PMC9106873 DOI: 10.1016/j.tibs.2022.02.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/31/2022] [Accepted: 02/04/2022] [Indexed: 01/02/2023]
Abstract
In addition to their central functions in translation, ribosomes can adopt inactive structures that are fully assembled yet devoid of mRNA. We describe how the abundance of idle eukaryotic ribosomes is influenced by a broad range of biological conditions spanning viral infection, nutrient deprivation, and developmental cues. Vacant ribosomes may provide a means to exclude ribosomes from translation while also shielding them from degradation, and the variable identity of factors that occlude ribosomes may impart distinct functionality. We propose that regulated changes in the balance of idle and active ribosomes provides a means to fine-tune translation. We provide an overview of idle ribosomes, describe what is known regarding their function, and highlight questions that may clarify their biological roles.
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Affiliation(s)
- Patrick R Smith
- The University of Texas at Dallas, Department of Biological Sciences, Richardson, TX, USA
| | - Sapna C Pandit
- University of California, Santa Cruz, Department of Chemistry and Biochemistry, Santa Cruz, CA, USA
| | - Sarah Loerch
- University of California, Santa Cruz, Department of Chemistry and Biochemistry, Santa Cruz, CA, USA
| | - Zachary T Campbell
- The University of Texas at Dallas, Department of Biological Sciences, Richardson, TX, USA; The Center for Advanced Pain Studies (CAPS), University of Texas at Dallas, Richardson, TX, USA.
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16
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Kišonaitė M, Wild K, Lapouge K, Ruppert T, Sinning I. High-resolution structures of a thermophilic eukaryotic 80S ribosome reveal atomistic details of translocation. Nat Commun 2022; 13:476. [PMID: 35079002 PMCID: PMC8789840 DOI: 10.1038/s41467-022-27967-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 01/02/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractRibosomes are complex and highly conserved ribonucleoprotein assemblies catalyzing protein biosynthesis in every organism. Here we present high-resolution cryo-EM structures of the 80S ribosome from a thermophilic fungus in two rotational states, which due to increased 80S stability provide a number of mechanistic details of eukaryotic translation. We identify a universally conserved ‘nested base-triple knot’ in the 26S rRNA at the polypeptide tunnel exit with a bulged-out nucleotide that likely serves as an adaptable element for nascent chain containment and handover. We visualize the structure and dynamics of the ribosome protective factor Stm1 upon ribosomal 40S head swiveling. We describe the structural impact of a unique and essential m1acp3 Ψ 18S rRNA hyper-modification embracing the anticodon wobble-position for eukaryotic tRNA and mRNA translocation. We complete the eEF2-GTPase switch cycle describing the GDP-bound post-hydrolysis state. Taken together, our data and their integration into the structural landscape of 80S ribosomes furthers our understanding of protein biogenesis.
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17
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Carey SB, Bolger TA. Translational control by helicases during cellular stress. Methods Enzymol 2022; 673:103-140. [DOI: 10.1016/bs.mie.2022.03.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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18
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Smith PR, Loerch S, Kunder N, Stanowick AD, Lou TF, Campbell ZT. Functionally distinct roles for eEF2K in the control of ribosome availability and p-body abundance. Nat Commun 2021; 12:6789. [PMID: 34815424 PMCID: PMC8611098 DOI: 10.1038/s41467-021-27160-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 11/07/2021] [Indexed: 11/09/2022] Open
Abstract
Processing bodies (p-bodies) are a prototypical phase-separated RNA-containing granule. Their abundance is highly dynamic and has been linked to translation. Yet, the molecular mechanisms responsible for coordinate control of the two processes are unclear. Here, we uncover key roles for eEF2 kinase (eEF2K) in the control of ribosome availability and p-body abundance. eEF2K acts on a sole known substrate, eEF2, to inhibit translation. We find that the eEF2K agonist nelfinavir abolishes p-bodies in sensory neurons and impairs translation. To probe the latter, we used cryo-electron microscopy. Nelfinavir stabilizes vacant 80S ribosomes. They contain SERBP1 in place of mRNA and eEF2 in the acceptor site. Phosphorylated eEF2 associates with inactive ribosomes that resist splitting in vitro. Collectively, the data suggest that eEF2K defines a population of inactive ribosomes resistant to recycling and protected from degradation. Thus, eEF2K activity is central to both p-body abundance and ribosome availability in sensory neurons.
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Affiliation(s)
- Patrick R. Smith
- grid.267323.10000 0001 2151 7939The University of Texas at Dallas, Department of Biological Sciences, Richardson, TX USA
| | - Sarah Loerch
- grid.443970.dJanelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA USA ,grid.205975.c0000 0001 0740 6917University of California, Santa Cruz, Department of Chemistry and Biochemistry, Santa Cruz, CA USA
| | - Nikesh Kunder
- grid.267323.10000 0001 2151 7939The University of Texas at Dallas, Department of Biological Sciences, Richardson, TX USA
| | - Alexander D. Stanowick
- grid.267323.10000 0001 2151 7939The University of Texas at Dallas, Department of Biological Sciences, Richardson, TX USA
| | - Tzu-Fang Lou
- grid.267323.10000 0001 2151 7939The University of Texas at Dallas, Department of Biological Sciences, Richardson, TX USA
| | - Zachary T. Campbell
- grid.267323.10000 0001 2151 7939The University of Texas at Dallas, Department of Biological Sciences, Richardson, TX USA ,grid.267323.10000 0001 2151 7939The Center for Advanced Pain Studies (CAPS), University of Texas at Dallas, Richardson, TX USA
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19
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Rollins MG, Shasmal M, Meade N, Astar H, Shen PS, Walsh D. Negative charge in the RACK1 loop broadens the translational capacity of the human ribosome. Cell Rep 2021; 36:109663. [PMID: 34496247 PMCID: PMC8451006 DOI: 10.1016/j.celrep.2021.109663] [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: 01/28/2021] [Revised: 03/30/2021] [Accepted: 08/13/2021] [Indexed: 12/18/2022] Open
Abstract
Although the roles of initiation factors, RNA binding proteins, and RNA elements in regulating translation are well defined, how the ribosome functionally diversifies remains poorly understood. In their human hosts, poxviruses phosphorylate serine 278 (S278) at the tip of a loop domain in the small subunit ribosomal protein RACK1, thereby mimicking negatively charged residues in the RACK1 loops of dicot plants and protists to stimulate translation of transcripts with 5′ poly(A) leaders. However, how a negatively charged RACK1 loop affects ribosome structure and its broader translational output is not known. Here, we show that although ribotoxin-induced stress signaling and stalling on poly(A) sequences are unaffected, negative charge in the RACK1 loop alters the swivel motion of the 40S head domain in a manner similar to several internal ribosome entry sites (IRESs), confers resistance to various protein synthesis inhibitors, and broadly supports noncanonical modes of translation. How ribosomes functionally diversify to selectively control translation is only beginning to be understood. Rollins et al. show that negative charge in a loop domain of the small subunit ribosomal protein RACK1 increases the swiveling motion of the 40S head and broadens the translational capacity of the human ribosome.
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Affiliation(s)
- Madeline G Rollins
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Manidip Shasmal
- Department of Biochemistry, School of Medicine, University of Utah, Salt Lake City, UT 84112, USA
| | - Nathan Meade
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Helen Astar
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Peter S Shen
- Department of Biochemistry, School of Medicine, University of Utah, Salt Lake City, UT 84112, USA.
| | - Derek Walsh
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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20
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Cao W, Zhao W, Yang B, Wang X, Shen Y, Wei T, Qin W, Li Z, Bao X. Proteomic analysis revealed the roles of YRR1 deletion in enhancing the vanillin resistance of Saccharomyces cerevisiae. Microb Cell Fact 2021; 20:142. [PMID: 34301255 PMCID: PMC8305865 DOI: 10.1186/s12934-021-01633-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 07/15/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Vanillin is one of the important phenolic inhibitors in Saccharomyces cerevisiae for bioconversion of lignocellulosic materials and has been reported to inhibit the translation process in cells. In our previous studies, it was confirmed that the deletion of the transcription factor gene YRR1 enhanced vanillin resistance by promoting some translation-related processes at the transcription level. In this work, we investigated the effects of proteomic changes upon induction of vanillin stress and deletion of YRR1 to provide unique perspectives from a transcriptome analysis for comprehending the mechanisms of YRR1 deletion in the protective response of yeast to vanillin. RESULTS In wild-type cells, vanillin reduced two dozens of ribosomal proteins contents while upregulated proteins involved in glycolysis, oxidative phosphorylation, and the pentose phosphate pathway in cells. The ratios of NADPH/NADP+ and NADH/NAD+ were increased when cells responded to vanillin stress. The differentially expressed proteins perturbed by YRR1 deletion were much more abundant than and showed no overlaps with transcriptome changes, indicating that Yrr1 affects the synthesis of certain proteins. Forty-eight of 112 upregulated proteins were involved in the stress response, translational and transcriptional regulation. YRR1 deletion increased the expression of HAA1-encoding transcriptional activator, TMA17-encoding proteasome assembly chaperone and MBF1-encoding coactivator at the protein level, as confirmed by ELISA. Cultivation data showed that the overexpression of HAA1 and TMA17 enhanced resistance to vanillin in S. cerevisiae. CONCLUSIONS Cells conserve energy by decreasing the content of ribosomal proteins, producing more energy and NAD(P)H for survival in response to vanillin stress. Yrr1 improved vanillin resistance by increasing the protein quantities of Haa1, Tma17 and Mbf1. These results showed the response of S. cerevisiae to vanillin and how YRR1 deletion increases vanillin resistance at the protein level. These findings may advance our knowledge of how YRR1 deletion protects yeast from vanillin stress and offer novel targets for genetic engineering of designing inhibitor-resistant ethanologenic yeast strains.
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Affiliation(s)
- Wenyan Cao
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Key Laboratory of Shandong Microbial Engineering, Qilu University of Technology (Shandong Academy of Sciences), 3501 Daxue Road, Jinan, 250353, China
| | - Weiquan Zhao
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Key Laboratory of Shandong Microbial Engineering, Qilu University of Technology (Shandong Academy of Sciences), 3501 Daxue Road, Jinan, 250353, China
| | - Bolun Yang
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Key Laboratory of Shandong Microbial Engineering, Qilu University of Technology (Shandong Academy of Sciences), 3501 Daxue Road, Jinan, 250353, China
| | - Xinning Wang
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Key Laboratory of Shandong Microbial Engineering, Qilu University of Technology (Shandong Academy of Sciences), 3501 Daxue Road, Jinan, 250353, China.
| | - Yu Shen
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, 266237, China
| | - Tiandi Wei
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, 266237, China
| | - Wensheng Qin
- Department of Biology, Lakehead University, 955 Oliver Rd, Thunder Bay, ON, P7B 5E1, Canada
| | - Zailu Li
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Key Laboratory of Shandong Microbial Engineering, Qilu University of Technology (Shandong Academy of Sciences), 3501 Daxue Road, Jinan, 250353, China
| | - Xiaoming Bao
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Key Laboratory of Shandong Microbial Engineering, Qilu University of Technology (Shandong Academy of Sciences), 3501 Daxue Road, Jinan, 250353, China
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21
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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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22
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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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23
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Wells JN, Buschauer R, Mackens-Kiani T, Best K, Kratzat H, Berninghausen O, Becker T, Gilbert W, Cheng J, Beckmann R. Structure and function of yeast Lso2 and human CCDC124 bound to hibernating ribosomes. PLoS Biol 2020; 18:e3000780. [PMID: 32687489 PMCID: PMC7392345 DOI: 10.1371/journal.pbio.3000780] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/30/2020] [Accepted: 07/01/2020] [Indexed: 12/20/2022] Open
Abstract
Cells adjust to nutrient deprivation by reversible translational shutdown. This is accompanied by maintaining inactive ribosomes in a hibernation state, in which they are bound by proteins with inhibitory and protective functions. In eukaryotes, such a function was attributed to suppressor of target of Myb protein 1 (Stm1; SERPINE1 mRNA-binding protein 1 [SERBP1] in mammals), and recently, late-annotated short open reading frame 2 (Lso2; coiled-coil domain containing short open reading frame 124 [CCDC124] in mammals) was found to be involved in translational recovery after starvation from stationary phase. Here, we present cryo-electron microscopy (cryo-EM) structures of translationally inactive yeast and human ribosomes. We found Lso2/CCDC124 accumulating on idle ribosomes in the nonrotated state, in contrast to Stm1/SERBP1-bound ribosomes, which display a rotated state. Lso2/CCDC124 bridges the decoding sites of the small with the GTPase activating center (GAC) of the large subunit. This position allows accommodation of the duplication of multilocus region 34 protein (Dom34)-dependent ribosome recycling system, which splits Lso2-containing, but not Stm1-containing, ribosomes. We propose a model in which Lso2 facilitates rapid translation reactivation by stabilizing the recycling-competent state of inactive ribosomes.
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Affiliation(s)
- Jennifer N. Wells
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Robert Buschauer
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Timur Mackens-Kiani
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Katharina Best
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Hanna Kratzat
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Otto Berninghausen
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Thomas Becker
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Wendy Gilbert
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Jingdong Cheng
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
| | - Roland Beckmann
- Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany
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24
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An ortholog of the Vasa intronic gene is required for small RNA-mediated translation repression in Chlamydomonas reinhardtii. Proc Natl Acad Sci U S A 2019; 117:761-770. [PMID: 31871206 PMCID: PMC6955306 DOI: 10.1073/pnas.1908356117] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Small RNAs (sRNAs) are a class of noncoding RNAs that regulate complementary mRNAs, by triggering translation repression and/or transcript decay, and influence multiple biological processes. In animals, land plants, and some protists like the alga Chlamydomonas, sRNAs can repress translation of polyribosome-associated mRNAs, without or with only minimal transcript destabilization. However, the precise silencing mechanism is poorly understood. We found that Chlamydomonas VIG1, a homolog of the Drosophila melanogaster Vasa intronic gene and a member of a widely conserved protein family in eukaryotes, is involved in this process. VIG1 appears to be an ancillary ribosomal constituent. Additionally, VIG1 copurifies with core components of sRNA effector complexes and plays a key role in the sRNA-mediated translation repression of polyribosomal transcripts. Small RNAs (sRNAs) associate with Argonaute (AGO) proteins in effector complexes, termed RNA-induced silencing complexes (RISCs), which regulate complementary transcripts by translation inhibition and/or RNA degradation. In the unicellular alga Chlamydomonas, several metazoans, and land plants, emerging evidence indicates that polyribosome-associated transcripts can be translationally repressed by RISCs without substantial messenger RNA (mRNA) destabilization. However, the mechanism of translation inhibition in a polyribosomal context is not understood. Here we show that Chlamydomonas VIG1, an ortholog of the Drosophila melanogaster Vasa intronic gene (VIG), is required for this process. VIG1 localizes predominantly in the cytosol and comigrates with monoribosomes and polyribosomes by sucrose density gradient sedimentation. A VIG1-deleted mutant shows hypersensitivity to the translation elongation inhibitor cycloheximide, suggesting that VIG1 may have a nonessential role in ribosome function/structure. Additionally, FLAG-tagged VIG1 copurifies with AGO3 and Dicer-like 3 (DCL3), consistent with it also being a component of the RISC. Indeed, VIG1 is necessary for the repression of sRNA-targeted transcripts at the translational level but is dispensable for cleavage-mediated RNA interference and for the association of the AGO3 effector with polyribosomes or target transcripts. Our results suggest that VIG1 is an ancillary ribosomal component and plays a role in sRNA-mediated translation repression of polyribosomal transcripts.
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Pilla SP, Thomas A, Bahadur RP. Dissecting macromolecular recognition sites in ribosome: implication to its self-assembly. RNA Biol 2019; 16:1300-1312. [PMID: 31179876 DOI: 10.1080/15476286.2019.1629767] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Interactions between macromolecules play a crucial role in ribosome assembly that follows a highly coordinated process involving RNA folding and binding of ribosomal proteins (r-proteins). Although extensive studies have been carried out to understand macromolecular interactions in ribosomes, most of them are confined to either large or small ribosomal-subunit of few species. A comparative analysis of macromolecular interactions across different domains is still missing. We have analyzed the structural and physicochemical properties of protein-protein (PP), protein-RNA (PR) and RNA-RNA (RR) interfaces in small and large subunits of ribosomes, as well as in between the two subunits. Additionally, we have also developed Random Forest (RF) classifier to catalog the r-proteins. We find significant differences as well as similarities in macromolecular recognition sites between ribosomal assemblies of prokaryotes and eukaryotes. PR interfaces are substantially larger and have more ionic interactions than PP and RR interfaces in both prokaryotes and eukaryotes. PP, PR and RR interfaces in eukaryotes are well packed compared to those in prokaryotes. However, the packing density between the large and the small subunit interfaces in the entire assembly is strikingly low in both prokaryotes and eukaryotes, indicating the periodic association and dissociation of the two subunits during the translation. The structural and physicochemical properties of PR interfaces are used to predict the r-proteins in the assembly pathway into early, intermediate and late binders using RF classifier with an accuracy of 80%. The results provide new insights into the classification of r-proteins in the assembly pathway.
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Affiliation(s)
- Smita P Pilla
- a Computational Structural Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur , Kharagpur , India
| | - Amal Thomas
- a Computational Structural Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur , Kharagpur , India
| | - Ranjit Prasad Bahadur
- a Computational Structural Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur , Kharagpur , India
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26
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Brodiazhenko T, Johansson MJO, Takada H, Nissan T, Hauryliuk V, Murina V. Elimination of Ribosome Inactivating Factors Improves the Efficiency of Bacillus subtilis and Saccharomyces cerevisiae Cell-Free Translation Systems. Front Microbiol 2018; 9:3041. [PMID: 30619132 PMCID: PMC6305275 DOI: 10.3389/fmicb.2018.03041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 11/26/2018] [Indexed: 12/29/2022] Open
Abstract
Cell-free translation systems based on cellular lysates optimized for in vitro protein synthesis have multiple applications both in basic and applied science, ranging from studies of translational regulation to cell-free production of proteins and ribosome-nascent chain complexes. In order to achieve both high activity and reproducibility in a translation system, it is essential that the ribosomes in the cellular lysate are enzymatically active. Here we demonstrate that genomic disruption of genes encoding ribosome inactivating factors - HPF in Bacillus subtilis and Stm1 in Saccharomyces cerevisiae - robustly improve the activities of bacterial and yeast translation systems. Importantly, the elimination of B. subtilis HPF results in a complete loss of 100S ribosomes, which otherwise interfere with disome-based approaches for preparation of stalled ribosomal complexes for cryo-electron microscopy studies.
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Affiliation(s)
- Tetiana Brodiazhenko
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
- Institute of Technology, University of Tartu, Tartu, Estonia
| | | | - Hiraku Takada
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Tracy Nissan
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Vasili Hauryliuk
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Victoriia Murina
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
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27
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Brown A, Baird MR, Yip MC, Murray J, Shao S. Structures of translationally inactive mammalian ribosomes. eLife 2018; 7:40486. [PMID: 30355441 PMCID: PMC6226290 DOI: 10.7554/elife.40486] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 10/12/2018] [Indexed: 12/23/2022] Open
Abstract
The cellular levels and activities of ribosomes directly regulate gene expression during numerous physiological processes. The mechanisms that globally repress translation are incompletely understood. Here, we use electron cryomicroscopy to analyze inactive ribosomes isolated from mammalian reticulocytes, the penultimate stage of red blood cell differentiation. We identify two types of ribosomes that are translationally repressed by protein interactions. The first comprises ribosomes sequestered with elongation factor 2 (eEF2) by SERPINE mRNA binding protein 1 (SERBP1) occupying the ribosomal mRNA entrance channel. The second type are translationally repressed by a novel ribosome-binding protein, interferon-related developmental regulator 2 (IFRD2), which spans the P and E sites and inserts a C-terminal helix into the mRNA exit channel to preclude translation. IFRD2 binds ribosomes with a tRNA occupying a noncanonical binding site, the ‘Z site’, on the ribosome. These structures provide functional insights into how ribosomal interactions may suppress translation to regulate gene expression.
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Affiliation(s)
- Alan Brown
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Matthew R Baird
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Matthew Cj Yip
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Jason Murray
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Sichen Shao
- Department of Cell Biology, Harvard Medical School, Boston, United States
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28
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Abstract
During protein synthesis, ribosomes encounter many roadblocks, the outcomes of which are largely determined by substrate availability, amino acid features and reaction kinetics. Prolonged ribosome stalling is likely to be resolved by ribosome rescue or quality control pathways, whereas shorter stalling is likely to be resolved by ongoing productive translation. How ribosome function is affected by such hindrances can therefore have a profound impact on the translational output (yield) of a particular mRNA. In this Review, we focus on these roadblocks and the resumption of normal translation elongation rather than on alternative fates wherein the stalled ribosome triggers degradation of the mRNA and the incomplete protein product. We discuss the fundamental stages of the translation process in eukaryotes, from elongation through ribosome recycling, with particular attention to recent discoveries of the complexity of the genetic code and regulatory elements that control gene expression, including ribosome stalling during elongation, the role of mRNA context in translation termination and mechanisms of ribosome rescue that resemble recycling.
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Affiliation(s)
- Anthony P Schuller
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - 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.
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29
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Muto A, Sugihara Y, Shibakawa M, Oshima K, Matsuda T, Nadano D. The mRNA-binding protein Serbp1 as an auxiliary protein associated with mammalian cytoplasmic ribosomes. Cell Biochem Funct 2018; 36:312-322. [PMID: 30039520 DOI: 10.1002/cbf.3350] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 04/23/2018] [Accepted: 06/26/2018] [Indexed: 01/27/2023]
Abstract
While transcription plays an obviously important role in gene expression, translation has recently been emerged as a key step that defines the composition and quality of the proteome in the cell of higher eukaryotes including mammals. Selective translation is supposed to be regulated by the structural heterogeneity of cytoplasmic ribosomes including differences in protein composition and chemical modifications. However, the current knowledge on the heterogeneity of mammalian ribosomes is limited. Here, we report mammalian Serbp1 as a ribosome-associated protein. The translated products of Serbp1 gene, including the longest isoform, were found to be localized in the nucleolus as well as in the cytoplasm. Subcellular fractionation indicated that most of cytoplasmic Serbp1 molecules were precipitated by ultracentrifugation. Proteomic analysis identified Serbp1 in the cytoplasmic ribosomes of the rodent testis. Polysome profiling suggested that Serbp1, as a component of the small 40S subunit, was included in translating ribosomes (polysomes). Cosedimentation of Serbp1 with the 40S subunit was observed after dissociation of the ribosomal subunits. Serbp1 was also included in the ribosomes of human cancer cells, which may lead to a mechanistic understanding of an emerging link between Serbp1 and tumour progression. SIGNIFICANCE OF THE STUDY In mammalian cells, the final protein output of their genetic program is determined not only by controlling transcription but also by regulating the posttranscriptional events. Although mRNA-binding proteins and the cytoplasmic ribosome have long been recognized as central players in the posttranscriptional regulation, their physical and functional interactions are still far from a complete understanding. Here, we describe the intracellular localization of Serbp1, an mRNA-binding protein, and the inclusion of this protein in actively translating ribosomes in normal and cancer cells. These findings shed a new light into molecular mechanisms underlying Serbp1 action in translational gene regulation and tumour progression.
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Affiliation(s)
- Akiko Muto
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Yoshihiko Sugihara
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Minami Shibakawa
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Kenzi Oshima
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Tsukasa Matsuda
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Daita Nadano
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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30
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Hayashi H, Nagai R, Abe T, Wada M, Ito K, Takeuchi-Tomita N. Tight interaction of eEF2 in the presence of Stm1 on ribosome. J Biochem 2018; 163:177-185. [PMID: 29069440 DOI: 10.1093/jb/mvx070] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 09/07/2017] [Indexed: 11/14/2022] Open
Abstract
The stress-related protein Stm1 interacts with ribosomes, and is implicated in repressing translation. Stm1 was previously studied both in vivo and in vitro by cell-free translation systems using crude yeast lysates, but its precise functional mechanism remains obscure. Using an in vitro reconstituted translation system, we now show that Stm1 severely inhibits translation through its N-terminal region, aa 1 to 107, and this inhibition is antagonized by eEF3. We found that Stm1 stabilizes eEF2 on the 80 S ribosome in the GTP-bound form, independently of eEF2's diphthamide modification, a conserved post-translational modification at the tip of domain IV. Systematic analyses of N- or C-terminal truncated mutants revealed that the core region of Stm1, aa 47 to 143, is crucial for its ribosome binding and eEF2 stabilization. Stm1 does not inhibit the 80 S-dependent GTPase activity of eEF2, at least during the first round of GTP-hydrolysis. The mechanism and the role of the stable association of eEF2 with the ribosome in the presence of Stm1 are discussed in relation to the translation repression by Stm1.
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Affiliation(s)
- Hikari Hayashi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
| | - Riku Nagai
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
| | - Taisho Abe
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
| | - Miki Wada
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
| | - Koichi Ito
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
| | - Nono Takeuchi-Tomita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
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31
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Qin P, Fan S, Deng L, Zhong G, Zhang S, Li M, Chen W, Wang G, Tu B, Wang Y, Chen X, Ma B, Li S. LML1, Encoding a Conserved Eukaryotic Release Factor 1 Protein, Regulates Cell Death and Pathogen Resistance by Forming a Conserved Complex with SPL33 in Rice. PLANT & CELL PHYSIOLOGY 2018; 59:887-902. [PMID: 29566164 DOI: 10.1093/pcp/pcy056] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 03/09/2018] [Indexed: 06/08/2023]
Abstract
Lesion mimic mutants are powerful tools for unveiling the molecular connections between cell death and pathogen resistance. Various proteins responsible for lesion mimics have been identified; however, the mechanisms underlying lesion formation and pathogen resistance are still unknown. Here, we identify a lesion mimic mutant in rice, lesion mimic leaf 1 (lml1). The lml1 mutant exhibited abnormal cell death and resistance to both bacterial blight and rice blast. LML1 is expressed in all types of leaf cells, and encodes a novel eukaryotic release factor 1 (eRF1) protein located in the endoplasmic reticulum. Protein sequences of LML1 orthologs are conserved in yeast, animals and plants. LML1 can partially rescue the growth delay phenotype of the LML1 yeast ortholog mutant, dom34. Both lml1 and mutants of AtLML1 (the LML1 Arabidopsis ortholog) exhibited a growth delay phenotype like dom34. This indicates that LML1 and its orthologs are functionally conserved. LML1 forms a functional complex with a eukaryotic elongation factor 1A (eEF1A)-like protein, SPL33/LMM5.1, whose mutant phenotype was similar to the lml1 phenotype. This complex was conserved between rice and yeast. Our work provides new insight into understanding the mechanism of cell death and pathogen resistance, and also lays a good foundation for studying the fundamental molecular function of Pelota/DOM34 and its orthologs in plants.
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Affiliation(s)
- Peng Qin
- Rice Research Institute of Sichuan Agricultural University, Chengdu Wenjiang, Sichuan 611130, China
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu Wenjiang, Sichuan 611130, China
| | - Shijun Fan
- Rice Research Institute of Sichuan Agricultural University, Chengdu Wenjiang, Sichuan 611130, China
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu Wenjiang, Sichuan 611130, China
| | - Luchang Deng
- Rice Research Institute of Sichuan Agricultural University, Chengdu Wenjiang, Sichuan 611130, China
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 610066, China
| | - Guangrong Zhong
- Hybrid Rice Research Center of Neijiang Academy of Agricultural, Neijiang, Sichuan 641000, China
| | - Siwei Zhang
- Rice Research Institute of Sichuan Agricultural University, Chengdu Wenjiang, Sichuan 611130, China
| | - Meng Li
- Rice Research Institute of Sichuan Agricultural University, Chengdu Wenjiang, Sichuan 611130, China
| | - Weilan Chen
- Rice Research Institute of Sichuan Agricultural University, Chengdu Wenjiang, Sichuan 611130, China
| | - Geling Wang
- Rice Research Institute of Sichuan Agricultural University, Chengdu Wenjiang, Sichuan 611130, China
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu Wenjiang, Sichuan 611130, China
| | - Bin Tu
- Rice Research Institute of Sichuan Agricultural University, Chengdu Wenjiang, Sichuan 611130, China
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu Wenjiang, Sichuan 611130, China
| | - Yuping Wang
- Rice Research Institute of Sichuan Agricultural University, Chengdu Wenjiang, Sichuan 611130, China
| | - Xuewei Chen
- Rice Research Institute of Sichuan Agricultural University, Chengdu Wenjiang, Sichuan 611130, China
| | - Bingtian Ma
- Rice Research Institute of Sichuan Agricultural University, Chengdu Wenjiang, Sichuan 611130, China
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu Wenjiang, Sichuan 611130, China
| | - Shigui Li
- Rice Research Institute of Sichuan Agricultural University, Chengdu Wenjiang, Sichuan 611130, China
- State Key Laboratory of Hybrid Rice, Sichuan Agricultural University, Chengdu Wenjiang, Sichuan 611130, China
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32
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Navarro-Quiles C, Mateo-Bonmatí E, Micol JL. ABCE Proteins: From Molecules to Development. FRONTIERS IN PLANT SCIENCE 2018; 9:1125. [PMID: 30127795 PMCID: PMC6088178 DOI: 10.3389/fpls.2018.01125] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 07/12/2018] [Indexed: 05/12/2023]
Abstract
Most members of the large family of ATP-Binding Cassette (ABC) proteins function as membrane transporters. However, the most evolutionarily conserved group, the ABCE protein subfamily, comprises soluble proteins that were initially denoted RNase L inhibitor (RLI) proteins. ABCE proteins are present in all eukaryotes and archaea and are encoded by a single gene in most genomes, or by two genes in a few cases. Functional analysis of ABCE genes, primarily in Saccharomyces cerevisiae, has shown that ABCE proteins have essential functions as part of the translational apparatus. In this review, we summarize the current understanding of ABCE protein function in ribosome biogenesis and recycling, with a particular focus on their known and proposed developmental roles in different species. The ABCE proteins might represent another class of factors contributing to the role of the ribosome in gene expression regulation.
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33
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Aryanpur PP, Regan CA, Collins JM, Mittelmeier TM, Renner DM, Vergara AM, Brown NP, Bolger TA. Gle1 Regulates RNA Binding of the DEAD-Box Helicase Ded1 in Its Complex Role in Translation Initiation. Mol Cell Biol 2017; 37:e00139-17. [PMID: 28784717 PMCID: PMC5640818 DOI: 10.1128/mcb.00139-17] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 05/05/2017] [Accepted: 07/21/2017] [Indexed: 02/07/2023] Open
Abstract
DEAD-box proteins (DBPs) are required in gene expression to facilitate changes to ribonucleoprotein complexes, but the cellular mechanisms and regulation of DBPs are not fully defined. Gle1 is a multifunctional regulator of DBPs with roles in mRNA export and translation. In translation, Gle1 modulates Ded1, a DBP required for initiation. However, DED1 overexpression causes defects, suggesting that Ded1 can promote or repress translation in different contexts. Here we show that GLE1 expression suppresses the repressive effects of DED1 in vivo and Gle1 counteracts Ded1 in translation assays in vitro Furthermore, both Ded1 and Gle1 affect the assembly of preinitiation complexes. Through mutation analysis and binding assays, we show that Gle1 inhibits Ded1 by reducing its affinity for RNA. Our results are consistent with a model wherein active Ded1 promotes translation but inactive or excess Ded1 leads to translation repression. Gle1 can inhibit either role of Ded1, positioning it as a gatekeeper to optimize Ded1 activity to the appropriate level for translation. This study suggests a paradigm for finely controlling the activity of DEAD-box proteins to optimize their function in RNA-based processes. It also positions the versatile regulator Gle1 as a potential node for the coordination of different steps of gene expression.
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Affiliation(s)
- Peyman P Aryanpur
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - Chelsea A Regan
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - John M Collins
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - Telsa M Mittelmeier
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - David M Renner
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - Ashley M Vergara
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - Nicolette P Brown
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - Timothy A Bolger
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
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34
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Abstract
Recent evidence indicates that codon optimality is a broad determinant of mRNA stability. A study by Radhakrishnan et al. in Cell raises the possibility that the conserved DEAD-box protein Dhh1 underlies the phenomenon.
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35
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Napthine S, Treffers EE, Bell S, Goodfellow I, Fang Y, Firth AE, Snijder EJ, Brierley I. A novel role for poly(C) binding proteins in programmed ribosomal frameshifting. Nucleic Acids Res 2016; 44:5491-503. [PMID: 27257056 PMCID: PMC4937337 DOI: 10.1093/nar/gkw480] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 05/18/2016] [Indexed: 01/16/2023] Open
Abstract
Translational control through programmed ribosomal frameshifting (PRF) is exploited widely by viruses and increasingly documented in cellular genes. Frameshifting is induced by mRNA secondary structures that compromise ribosome fidelity during decoding of a heptanucleotide 'slippery' sequence. The nsp2 PRF signal of porcine reproductive and respiratory syndrome virus is distinctive in directing both -2 and -1 PRF and in its requirement for a trans-acting protein factor, the viral replicase subunit nsp1β. Here we show that the the trans-activation of frameshifting is carried out by a protein complex composed of nsp1β and a cellular poly(C) binding protein (PCBP). From the results of in vitro translation and electrophoretic mobility shift assays, we demonstrate that a PCBP/nsp1β complex binds to a C-rich sequence downstream of the slippery sequence and here mimics the activity of a structured mRNA stimulator of PRF. This is the first description of a role for a trans-acting cellular protein in PRF. The discovery broadens the repertoire of activities associated with poly(C) binding proteins and prototypes a new class of virus-host interactions.
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Affiliation(s)
- Sawsan Napthine
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | - Emmely E Treffers
- Department of Medical Microbiology, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Susanne Bell
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | - Ian Goodfellow
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | - Ying Fang
- College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506-5705, USA
| | - Andrew E Firth
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | - Eric J Snijder
- Department of Medical Microbiology, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Ian Brierley
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
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36
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Zinoviev A, Hellen CUT, Pestova TV. Multiple mechanisms of reinitiation on bicistronic calicivirus mRNAs. Mol Cell 2016; 57:1059-1073. [PMID: 25794616 DOI: 10.1016/j.molcel.2015.01.039] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 12/31/2014] [Accepted: 01/26/2015] [Indexed: 02/05/2023]
Abstract
Reinitiation is a strategy used by viruses to express several cistrons from one mRNA. Although extremely weak after translation of long open reading frames (ORFs) on cellular mRNAs, reinitiation occurs efficiently on subgenomic bicistronic calicivirus mRNAs, enabling synthesis of minor capsid proteins. The process is governed by a short element upstream of the restart AUG, designated "termination upstream ribosomal binding site" (TURBS). It contains the conserved Motif 1 complementary to h26 of 18S rRNA, displayed in the loop of a hairpin formed by species-specific Motifs 2/2(∗). To determine the advantages conferred on reinitiation by TURBS, we reconstituted this process in vitro on two model bicistronic calicivirus mRNAs. We found that post-termination ribosomal tethering of mRNA by TURBS allows reinitiation by post-termination 80S ribosomes and diminishes dependence on eukaryotic initiation factor 3 (eIF3) of reinitiation by recycled 40S subunits, which can be mediated either by eIFs 2/1/1A or by Ligatin following ABCE1-dependent or -independent splitting of post-termination complexes.
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Affiliation(s)
- Alexandra Zinoviev
- Department of Cell Biology, SUNY Downstate Medical Center, 450 Clarkson Avenue, Brooklyn, NY 11203, USA
| | - Christopher U T Hellen
- Department of Cell Biology, SUNY Downstate Medical Center, 450 Clarkson Avenue, Brooklyn, NY 11203, USA
| | - Tatyana V Pestova
- Department of Cell Biology, SUNY Downstate Medical Center, 450 Clarkson Avenue, Brooklyn, NY 11203, USA.
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37
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Wolf AS, Grayhack EJ. Asc1, homolog of human RACK1, prevents frameshifting in yeast by ribosomes stalled at CGA codon repeats. RNA (NEW YORK, N.Y.) 2015; 21:935-45. [PMID: 25792604 PMCID: PMC4408800 DOI: 10.1261/rna.049080.114] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 01/14/2015] [Indexed: 05/09/2023]
Abstract
Quality control systems monitor and stop translation at some ribosomal stalls, but it is unknown if halting translation at such stalls actually prevents synthesis of abnormal polypeptides. In yeast, ribosome stalling occurs at Arg CGA codon repeats, with even two consecutive CGA codons able to reduce translation by up to 50%. The conserved eukaryotic Asc1 protein limits translation through internal Arg CGA codon repeats. We show that, in the absence of Asc1 protein, ribosomes continue translating at CGA codons, but undergo substantial frameshifting with dramatically higher levels of frameshifting occurring with additional repeats of CGA codons. Frameshifting depends upon the slow or inefficient decoding of these codons, since frameshifting is suppressed by increased expression of the native tRNA(Arg(ICG)) that decodes CGA codons by wobble decoding. Moreover, the extent of frameshifting is modulated by the position of the CGA codon repeat relative to the translation start site. Thus, translation fidelity depends upon Asc1-mediated quality control.
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Affiliation(s)
- Andrew S Wolf
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA
| | - Elizabeth J Grayhack
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
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38
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Fragile X mental retardation protein and the ribosome. Mol Cell 2014; 54:330-2. [PMID: 24813710 DOI: 10.1016/j.molcel.2014.04.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In this issue of Molecular Cell, Chen et al. (2014) provide evidence that FMRP represses translation by binding the ribosome, suggesting a novel form of translational control.
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Huch S, Nissan T. Interrelations between translation and general mRNA degradation in yeast. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 5:747-63. [PMID: 24944158 PMCID: PMC4285117 DOI: 10.1002/wrna.1244] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 04/28/2014] [Accepted: 05/02/2014] [Indexed: 12/31/2022]
Abstract
Messenger RNA (mRNA) degradation is an important element of gene expression that can be modulated by alterations in translation, such as reductions in initiation or elongation rates. Reducing translation initiation strongly affects mRNA degradation by driving mRNA toward the assembly of a decapping complex, leading to decapping. While mRNA stability decreases as a consequence of translational inhibition, in apparent contradiction several external stresses both inhibit translation initiation and stabilize mRNA. A key difference in these processes is that stresses induce multiple responses, one of which stabilizes mRNAs at the initial and rate-limiting step of general mRNA decay. Because this increase in mRNA stability is directly induced by stress, it is independent of the translational effects of stress, which provide the cell with an opportunity to assess its response to changing environmental conditions. After assessment, the cell can store mRNAs, reinitiate their translation or, alternatively, embark on a program of enhanced mRNA decay en masse. Finally, recent results suggest that mRNA decay is not limited to non-translating messages and can occur when ribosomes are not initiating but are still elongating on mRNA. This review will discuss the models for the mechanisms of these processes and recent developments in understanding the relationship between translation and general mRNA degradation, with a focus on yeast as a model system. How to cite this article: WIREs RNA 2014, 5:747–763. doi: 10.1002/wrna.1244
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Affiliation(s)
- Susanne Huch
- Department of Molecular Biology, Umeå University, Umeå, Sweden
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40
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Guydosh NR, Green R. Dom34 rescues ribosomes in 3' untranslated regions. Cell 2014; 156:950-62. [PMID: 24581494 DOI: 10.1016/j.cell.2014.02.006] [Citation(s) in RCA: 278] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 11/18/2013] [Accepted: 02/04/2014] [Indexed: 10/25/2022]
Abstract
Ribosomes that stall before completing peptide synthesis must be recycled and returned to the cytoplasmic pool. The protein Dom34 and cofactors Hbs1 and Rli1 can dissociate stalled ribosomes in vitro, but the identity of targets in the cell is unknown. Here, we extend ribosome profiling methodology to reveal a high-resolution molecular characterization of Dom34 function in vivo. Dom34 removes stalled ribosomes from truncated mRNAs, but, in contrast, does not generally dissociate ribosomes on coding sequences known to trigger stalling, such as polyproline. We also show that Dom34 targets arrested ribosomes near the ends of 3' UTRs. These ribosomes appear to gain access to the 3' UTR via a mechanism that does not require decoding of the mRNA. These results suggest that ribosomes frequently enter downstream noncoding regions and that Dom34 carries out the important task of rescuing them.
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Affiliation(s)
- Nicholas R Guydosh
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Rachel Green
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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41
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Abstract
The high-resolution structure of the eukaryotic ribosome from yeast, determined at 3.0-Å resolution, permitted the unambiguous determination of the protein side chains, eukaryote-specific proteins, protein insertions, and ribosomal RNA expansion segments of the 80 proteins and ∼5,500 RNA bases that constitute the 80S ribosome. A comparison between this first atomic model of the entire 80S eukaryotic ribosome and previously determined structures of bacterial ribosomes confirmed early genetic and structural data indicating that they share an evolutionarily conserved core of ribosomal RNA and proteins. It also confirmed the conserved organization of essential functional sites, such as the peptidyl transferase center and the decoding site. New structural information about eukaryote-specific elements, such as expansion segments and new ribosomal proteins, forms the structural framework for the design and analysis of experiments that will explore the eukaryotic translational apparatus and the evolutionary forces that shaped it. New nomenclature for ribosomal proteins, based on the names of protein families, has been proposed.
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Affiliation(s)
- Gulnara Yusupova
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg F-67000, France
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42
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van den Elzen AMG, Schuller A, Green R, Séraphin B. Dom34-Hbs1 mediated dissociation of inactive 80S ribosomes promotes restart of translation after stress. EMBO J 2014; 33:265-76. [PMID: 24424461 DOI: 10.1002/embj.201386123] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Following translation termination, ribosomal subunits dissociate to become available for subsequent rounds of protein synthesis. In many translation-inhibiting stress conditions, e.g. glucose starvation in yeast, free ribosomal subunits reassociate to form a large pool of non-translating 80S ribosomes stabilized by the 'clamping' Stm1 factor. The subunits of these inactive ribosomes need to be mobilized for translation restart upon stress relief. The Dom34-Hbs1 complex, together with the Rli1 NTPase (also known as ABCE1), have been shown to split ribosomes stuck on mRNAs in the context of RNA quality control mechanisms. Here, using in vitro and in vivo methods, we report a new role for the Dom34-Hbs1 complex and Rli1 in dissociating inactive ribosomes, thereby facilitating translation restart in yeast recovering from glucose starvation stress. Interestingly, we found that this new role is not restricted to stress conditions, indicating that in growing yeast there is a dynamic pool of inactive ribosomes that needs to be split by Dom34-Hbs1 and Rli1 to participate in protein synthesis. We propose that this provides a new level of translation regulation.
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Affiliation(s)
- Antonia M G van den Elzen
- Equipe Labellisée La Ligue, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) Centre National de Recherche Scientifique (CNRS) UMR 7104/Institut National de Santé et de Recherche Médicale (INSERM) U964/Université de Strasbourg, Illkirch, France
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43
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Roy B, Jacobson A. The intimate relationships of mRNA decay and translation. Trends Genet 2013; 29:691-9. [PMID: 24091060 DOI: 10.1016/j.tig.2013.09.002] [Citation(s) in RCA: 129] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 08/21/2013] [Accepted: 09/03/2013] [Indexed: 11/18/2022]
Abstract
The decay rate of an mRNA and the efficiency with which it is translated are key determinants of eukaryotic gene expression. Although it was once thought that mRNA stability and translational efficiency were directly linked, the interrelationships between the two processes are considerably more complex. The decay of individual mRNAs can be triggered or antagonized by translational impairment, and alterations in the half-life of certain mRNAs can even alter translational fidelity. In this review we consider whether mRNA translation and turnover are distinct or overlapping phases of an mRNA life cycle, and then address some of the many ways in which the two processes influence each other in eukaryotic cells.
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Affiliation(s)
- Bijoyita Roy
- Department of Microbiology and Physiological Systems, Albert Sherman Center, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
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44
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Klass DM, Scheibe M, Butter F, Hogan GJ, Mann M, Brown PO. Quantitative proteomic analysis reveals concurrent RNA-protein interactions and identifies new RNA-binding proteins in Saccharomyces cerevisiae. Genome Res 2013; 23:1028-38. [PMID: 23636942 PMCID: PMC3668357 DOI: 10.1101/gr.153031.112] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A growing body of evidence supports the existence of an extensive network of RNA-binding proteins (RBPs) whose combinatorial binding affects the post-transcriptional fate of every mRNA in the cell—yet we still do not have a complete understanding of which proteins bind to mRNA, which of these bind concurrently, and when and where in the cell they bind. We describe here a method to identify the proteins that bind to RNA concurrently with an RBP of interest, using quantitative mass spectrometry combined with RNase treatment of affinity-purified RNA–protein complexes. We applied this method to the known RBPs Pab1, Nab2, and Puf3. Our method significantly enriched for known RBPs and is a clear improvement upon previous approaches in yeast. Our data reveal that some reported protein–protein interactions may instead reflect simultaneous binding to shared RNA targets. We also discovered more than 100 candidate RBPs, and we independently confirmed that 77% (23/30) bind directly to RNA. The previously recognized functions of the confirmed novel RBPs were remarkably diverse, and we mapped the RNA-binding region of one of these proteins, the transcriptional coactivator Mbf1, to a region distinct from its DNA-binding domain. Our results also provided new insights into the roles of Nab2 and Puf3 in post-transcriptional regulation by identifying other RBPs that bind simultaneously to the same mRNAs. While existing methods can identify sets of RBPs that interact with common RNA targets, our approach can determine which of those interactions are concurrent—a crucial distinction for understanding post-transcriptional regulation.
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Affiliation(s)
- Daniel M Klass
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA
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45
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Structures of the human and Drosophila 80S ribosome. Nature 2013; 497:80-5. [DOI: 10.1038/nature12104] [Citation(s) in RCA: 410] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 03/19/2013] [Indexed: 12/19/2022]
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46
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Hooper C, Hilliker A. Packing them up and dusting them off: RNA helicases and mRNA storage. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:824-34. [PMID: 23528738 DOI: 10.1016/j.bbagrm.2013.03.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 03/16/2013] [Accepted: 03/18/2013] [Indexed: 12/31/2022]
Abstract
Cytoplasmic mRNA can be translated, translationally repressed, localized or degraded. Regulation of translation is an important step in control of gene expression and the cell can change whether and to what extent an mRNA is translated. If an mRNA is not translating, it will associate with translation repression factors; the mRNA can be stored in these non-translating states. The movement of mRNA into storage and back to translation is dictated by the recognition of the mRNA by trans factors. So, remodeling the factors that bind mRNA is critical for changing the fate of mRNA. RNA helicases, which have the ability to remodel RNA or RNA-protein complexes, are excellent candidates for facilitating such rearrangements. This review will focus on the RNA helicases implicated in translation repression and/or mRNA storage and how their study has illuminated mechanisms of mRNA regulation. This article is part of a Special Issue entitled: The Biology of RNA helicases - Modulation for life.
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Affiliation(s)
- Christopher Hooper
- Department of Neonatology, Vanderbilt Children's Hospital, Nashville, TN, USA
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47
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Eukaryotic mRNA decay: methodologies, pathways, and links to other stages of gene expression. J Mol Biol 2013; 425:3750-75. [PMID: 23467123 DOI: 10.1016/j.jmb.2013.02.029] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 02/24/2013] [Accepted: 02/26/2013] [Indexed: 01/15/2023]
Abstract
mRNA concentration depends on the balance between transcription and degradation rates. On both sides of the equilibrium, synthesis and degradation show, however, interesting differences that have conditioned the evolution of gene regulatory mechanisms. Here, we discuss recent genome-wide methods for determining mRNA half-lives in eukaryotes. We also review pre- and posttranscriptional regulons that coordinate the fate of functionally related mRNAs by using protein- or RNA-based trans factors. Some of these factors can regulate both transcription and decay rates, thereby maintaining proper mRNA homeostasis during eukaryotic cell life.
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48
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Grousl T, Ivanov P, Malcova I, Pompach P, Frydlova I, Slaba R, Senohrabkova L, Novakova L, Hasek J. Heat shock-induced accumulation of translation elongation and termination factors precedes assembly of stress granules in S. cerevisiae. PLoS One 2013; 8:e57083. [PMID: 23451152 PMCID: PMC3581570 DOI: 10.1371/journal.pone.0057083] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 01/17/2013] [Indexed: 12/26/2022] Open
Abstract
In response to severe environmental stresses eukaryotic cells shut down translation and accumulate components of the translational machinery in stress granules (SGs). Since they contain mainly mRNA, translation initiation factors and 40S ribosomal subunits, they have been referred to as dominant accumulations of stalled translation preinitiation complexes. Here we present evidence that the robust heat shock-induced SGs of S. cerevisiae also contain translation elongation factors eEF3 (Yef3p) and eEF1Bγ2 (Tef4p) as well as translation termination factors eRF1 (Sup45p) and eRF3 (Sup35p). Despite the presence of the yeast prion protein Sup35 in heat shock-induced SGs, we found out that its prion-like domain is not involved in the SGs assembly. Factors eEF3, eEF1Bγ2 and eRF1 were accumulated and co-localized with Dcp2 foci even upon a milder heat shock at 42°C independently of P-bodies scaffolding proteins. We also show that eEF3 accumulations at 42°C determine sites of the genuine SGs assembly at 46°C. We suggest that identification of translation elongation and termination factors in SGs might help to understand the mechanism of the eIF2α factor phosphorylation-independent repression of translation and SGs assembly.
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Affiliation(s)
- Tomas Grousl
- Institute of Microbiology of AS CR, v.v.i., Prague, Czech Republic
| | - Pavel Ivanov
- Institute of Microbiology of AS CR, v.v.i., Prague, Czech Republic
| | - Ivana Malcova
- Institute of Microbiology of AS CR, v.v.i., Prague, Czech Republic
| | - Petr Pompach
- Institute of Microbiology of AS CR, v.v.i., Prague, Czech Republic
| | - Ivana Frydlova
- Institute of Microbiology of AS CR, v.v.i., Prague, Czech Republic
| | - Renata Slaba
- Institute of Microbiology of AS CR, v.v.i., Prague, Czech Republic
| | | | - Lenka Novakova
- Institute of Microbiology of AS CR, v.v.i., Prague, Czech Republic
| | - Jiri Hasek
- Institute of Microbiology of AS CR, v.v.i., Prague, Czech Republic
- * E-mail:
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49
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Decker CJ, Parker R. P-bodies and stress granules: possible roles in the control of translation and mRNA degradation. Cold Spring Harb Perspect Biol 2012; 4:a012286. [PMID: 22763747 DOI: 10.1101/cshperspect.a012286] [Citation(s) in RCA: 566] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The control of translation and mRNA degradation is important in the regulation of eukaryotic gene expression. In general, translation and steps in the major pathway of mRNA decay are in competition with each other. mRNAs that are not engaged in translation can aggregate into cytoplasmic mRNP granules referred to as processing bodies (P-bodies) and stress granules, which are related to mRNP particles that control translation in early development and neurons. Analyses of P-bodies and stress granules suggest a dynamic process, referred to as the mRNA Cycle, wherein mRNPs can move between polysomes, P-bodies and stress granules although the functional roles of mRNP assembly into higher order structures remain poorly understood. In this article, we review what is known about the coupling of translation and mRNA degradation, the properties of P-bodies and stress granules, and how assembly of mRNPs into larger structures might influence cellular function.
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Affiliation(s)
- Carolyn J Decker
- Department of Molecular and Cellular Biology and Howard Hughes Medical Institute, University of Arizona, Tucson, Arizona 85721-0206, USA
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50
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Kong J, Lasko P. Translational control in cellular and developmental processes. Nat Rev Genet 2012; 13:383-94. [PMID: 22568971 DOI: 10.1038/nrg3184] [Citation(s) in RCA: 135] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Growing evidence indicates that translational control of specific mRNAs contributes importantly to genetic regulation across the breadth of cellular and developmental processes. Synthesis of protein from a specific mRNA can be controlled by RNA-binding proteins at the level of translational initiation and elongation, and translational control is also sometimes coupled to mRNA localization mechanisms. Recent discoveries from invertebrate and vertebrate systems have uncovered novel modes of translational regulation, have provided new insights into how specific regulators target the general translational machinery and have identified several new links between translational control and human disease.
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Affiliation(s)
- Jian Kong
- Department of Biology, McGill University, 3649 Promenade Sir William Osler, Montreal, Quebec H3G 0T5, Canada
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