1
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Joiret M, Kerff F, Rapino F, Close P, Geris L. Reversing the relative time courses of the peptide bond reaction with oligopeptides of different lengths and charged amino acid distributions in the ribosome exit tunnel. Comput Struct Biotechnol J 2024; 23:2453-2464. [PMID: 38882677 PMCID: PMC11179572 DOI: 10.1016/j.csbj.2024.05.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/10/2024] [Accepted: 05/27/2024] [Indexed: 06/18/2024] Open
Abstract
The kinetics of the protein elongation cycle by the ribosome depends on intertwined factors. One of these factors is the electrostatic interaction of the nascent protein with the ribosome exit tunnel. In this computational biology theoretical study, we focus on the rate of the peptide bond formation and its dependence on the ribosome exit tunnel electrostatic potential profile. We quantitatively predict how oligopeptides of variable lengths can affect the peptide bond formation rate. We applied the Michaelis-Menten model as previously extended to incorporate the mechano-biochemical effects of forces on the rate of reaction at the catalytic site of the ribosome. For a given pair of carboxy-terminal amino acid substrate at the P- and an aminoacyl-tRNA at the A-sites, the relative time courses of the peptide bond formation reaction can be reversed depending on the oligopeptide sequence embedded in the tunnel and their variable lengths from the P-site. The reversal is predicted to occur from a shift in positions of charged amino acids upstream in the oligopeptidyl-tRNA at the P-site. The position shift must be adjusted by clever design of the oligopeptide probes using the electrostatic potential profile along the exit tunnel axial path. These predicted quantitative results bring strong evidence of the importance and relative contribution of the electrostatic interaction of the ribosome exit tunnel with the nascent peptide chain during elongation.
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Affiliation(s)
- Marc Joiret
- Biomechanics Research Unit, GIGA In Silico Medicine, Liège University, CHU-B34(+5) 1 Avenue de l'Hôpital, 4000 Liège, Belgium
| | - Frederic Kerff
- UR InBios Centre d'Ingénierie des Protéines, Liège University, Bât B6a, Allèe du 6 Août, 19, B-4000 Liège, Belgium
| | - Francesca Rapino
- Cancer Signaling, GIGA Stem Cells, Liège University, CHU-B34(+2) 1 Avenue de l'Hôpital, B-4000 Liège, Belgium
| | - Pierre Close
- Cancer Signaling, GIGA Stem Cells, Liège University, CHU-B34(+2) 1 Avenue de l'Hôpital, B-4000 Liège, Belgium
| | - Liesbet Geris
- Biomechanics Research Unit, GIGA In Silico Medicine, Liège University, CHU-B34(+5) 1 Avenue de l'Hôpital, 4000 Liège, Belgium
- Skeletal Biology & Engineering Research Center, KU Leuven, ON I Herestraat 49 - Box 813, 3000 Leuven, Belgium
- Biomechanics Section, KU Leuven, Celestijnenlaan 300C - Box 2419, B-3001 Heverlee, Belgium
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2
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Chadani Y, Yamanouchi S, Uemura E, Yamasaki K, Niwa T, Ikeda T, Kurihara M, Iwasaki W, Taguchi H. The ABCF proteins in Escherichia coli individually cope with 'hard-to-translate' nascent peptide sequences. Nucleic Acids Res 2024; 52:5825-5840. [PMID: 38661232 PMCID: PMC11162784 DOI: 10.1093/nar/gkae309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 03/18/2024] [Accepted: 04/10/2024] [Indexed: 04/26/2024] Open
Abstract
Organisms possess a wide variety of proteins with diverse amino acid sequences, and their synthesis relies on the ribosome. Empirical observations have led to the misconception that ribosomes are robust protein factories, but in reality, they have several weaknesses. For instance, ribosomes stall during the translation of the proline-rich sequences, but the elongation factor EF-P assists in synthesizing proteins containing the poly-proline sequences. Thus, living organisms have evolved to expand the translation capability of ribosomes through the acquisition of translation elongation factors. In this study, we have revealed that Escherichia coli ATP-Binding Cassette family-F (ABCF) proteins, YheS, YbiT, EttA and Uup, individually cope with various problematic nascent peptide sequences within the exit tunnel. The correspondence between noncanonical translations and ABCFs was YheS for the translational arrest by nascent SecM, YbiT for poly-basic sequence-dependent stalling and poly-acidic sequence-dependent intrinsic ribosome destabilization (IRD), EttA for IRD at the early stage of elongation, and Uup for poly-proline-dependent stalling. Our results suggest that ATP hydrolysis-coupled structural rearrangement and the interdomain linker sequence are pivotal for handling 'hard-to-translate' nascent peptides. Our study highlights a new aspect of ABCF proteins to reduce the potential risks that are encoded within the nascent peptide sequences.
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Affiliation(s)
- Yuhei Chadani
- Faculty of Environmental, Life, Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
| | - Shun Yamanouchi
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Eri Uemura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Kohei Yamasaki
- Faculty of Science, Okayama University, Okayama 700-8530, Japan
| | - Tatsuya Niwa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Toma Ikeda
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Miku Kurihara
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Wataru Iwasaki
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba 277-0882, Japan
| | - Hideki Taguchi
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8503, Japan
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3
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Chen KY, Park H, Subramaniam AR. Massively parallel identification of sequence motifs triggering ribosome-associated mRNA quality control. Nucleic Acids Res 2024:gkae285. [PMID: 38647082 DOI: 10.1093/nar/gkae285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 02/28/2024] [Accepted: 04/04/2024] [Indexed: 04/25/2024] Open
Abstract
Decay of mRNAs can be triggered by ribosome slowdown at stretches of rare codons or positively charged amino acids. However, the full diversity of sequences that trigger co-translational mRNA decay is poorly understood. To comprehensively identify sequence motifs that trigger mRNA decay, we use a massively parallel reporter assay to measure the effect of all possible combinations of codon pairs on mRNA levels in S. cerevisiae. In addition to known mRNA-destabilizing sequences, we identify several dipeptide repeats whose translation reduces mRNA levels. These include combinations of positively charged and bulky residues, as well as proline-glycine and proline-aspartate dipeptide repeats. Genetic deletion of the ribosome collision sensor Hel2 rescues the mRNA effects of these motifs, suggesting that they trigger ribosome slowdown and activate the ribosome-associated quality control (RQC) pathway. Deep mutational scanning of an mRNA-destabilizing dipeptide repeat reveals a complex interplay between the charge, bulkiness, and location of amino acid residues in conferring mRNA instability. Finally, we show that the mRNA effects of codon pairs are predictive of the effects of endogenous sequences. Our work highlights the complexity of sequence motifs driving co-translational mRNA decay in eukaryotes, and presents a high throughput approach to dissect their requirements at the codon level.
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Affiliation(s)
- Katharine Y Chen
- Basic Sciences Division and Computational Biology Section of the Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Heungwon Park
- Basic Sciences Division and Computational Biology Section of the Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Arvind Rasi Subramaniam
- Basic Sciences Division and Computational Biology Section of the Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
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4
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Shao B, Yan J, Zhang J, Liu L, Chen Y, Buskirk AR. Riboformer: a deep learning framework for predicting context-dependent translation dynamics. Nat Commun 2024; 15:2011. [PMID: 38443396 PMCID: PMC10915169 DOI: 10.1038/s41467-024-46241-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 02/18/2024] [Indexed: 03/07/2024] Open
Abstract
Translation elongation is essential for maintaining cellular proteostasis, and alterations in the translational landscape are associated with a range of diseases. Ribosome profiling allows detailed measurements of translation at the genome scale. However, it remains unclear how to disentangle biological variations from technical artifacts in these data and identify sequence determinants of translation dysregulation. Here we present Riboformer, a deep learning-based framework for modeling context-dependent changes in translation dynamics. Riboformer leverages the transformer architecture to accurately predict ribosome densities at codon resolution. When trained on an unbiased dataset, Riboformer corrects experimental artifacts in previously unseen datasets, which reveals subtle differences in synonymous codon translation and uncovers a bottleneck in translation elongation. Further, we show that Riboformer can be combined with in silico mutagenesis to identify sequence motifs that contribute to ribosome stalling across various biological contexts, including aging and viral infection. Our tool offers a context-aware and interpretable approach for standardizing ribosome profiling datasets and elucidating the regulatory basis of translation kinetics.
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Affiliation(s)
- Bin Shao
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Jiawei Yan
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Jing Zhang
- Biological Design Center, Boston University, Boston, MA, USA
| | - Lili Liu
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Ye Chen
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Allen R Buskirk
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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5
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Masse M, Hutchinson RB, Morgan CE, Allaman HJ, Guan H, Yu EW, Cavagnero S. Mapping Protein-Protein Interactions at Birth: Single-Particle Cryo-EM Analysis of a Ribosome-Nascent Globin Complex. ACS CENTRAL SCIENCE 2024; 10:385-401. [PMID: 38435509 PMCID: PMC10906257 DOI: 10.1021/acscentsci.3c00777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 12/29/2023] [Accepted: 01/03/2024] [Indexed: 03/05/2024]
Abstract
Interactions between ribosome-bound nascent chains (RNCs) and ribosomal components are critical to elucidate the mechanism of cotranslational protein folding. Nascent protein-ribosome contacts within the ribosomal exit tunnel were previously assessed mostly in the presence of C-terminal stalling sequences, yet little is known about contacts taking place in the absence of these strongly interacting motifs. Further, there is nearly no information about ribosomal proteins (r-proteins) interacting with nascent chains within the outer surface of the ribosome. Here, we combine chemical cross-linking, single-particle cryo-EM, and fluorescence anisotropy decays to determine the structural features of ribosome-bound apomyoglobin (apoMb). Within the ribosomal exit tunnel core, interactions are similar to those identified in previous reports. However, once the RNC enters the tunnel vestibule, it becomes more dynamic and interacts with ribosomal RNA (rRNA) and the L23 r-protein. Remarkably, on the outer surface of the ribosome, RNCs interact mainly with a highly conserved nonpolar patch of the L23 r-protein. RNCs also comprise a compact and dynamic N-terminal region lacking contact with the ribosome. In all, apoMb traverses the ribosome and interacts with it via its C-terminal region, while N-terminal residues sample conformational space and form a compact subdomain before the entire nascent protein sequence departs from the ribosome.
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Affiliation(s)
- Meranda
M. Masse
- Department
of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Rachel B. Hutchinson
- Department
of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Christopher E. Morgan
- Department
of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Heather J. Allaman
- Department
of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Hongqing Guan
- Department
of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Edward W. Yu
- Department
of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Silvia Cavagnero
- Department
of Chemistry, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
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6
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Samatova E, Komar AA, Rodnina MV. How the ribosome shapes cotranslational protein folding. Curr Opin Struct Biol 2024; 84:102740. [PMID: 38071940 DOI: 10.1016/j.sbi.2023.102740] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/15/2023] [Accepted: 11/16/2023] [Indexed: 02/09/2024]
Abstract
During protein synthesis, the growing nascent peptide chain moves inside the polypeptide exit tunnel of the ribosome from the peptidyl transferase center towards the exit port where it emerges into the cytoplasm. The ribosome defines the unique energy landscape of the pioneering round of protein folding. The spatial confinement and the interactions of the nascent peptide with the tunnel walls facilitate formation of secondary structures, such as α-helices. The vectorial nature of protein folding inside the tunnel favors local intra- and inter-molecular interactions, thereby inducing cotranslational folding intermediates that do not form upon protein refolding in solution. Tertiary structures start to fold in the lower part of the tunnel, where interactions with the ribosome destabilize native protein folds. The present review summarizes the recent progress in understanding the driving forces of nascent protein folding inside the tunnel and at the surface of the ribosome.
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Affiliation(s)
- Ekaterina Samatova
- Department of Physical Biochemistry, Max Planck Institute for Multidisciplinary Sciences, Goettingen 37077, Germany
| | - Anton A Komar
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological and Environmental Sciences, Cleveland State University, 2121 Euclid Avenue, Cleveland, OH 44115, USA; Department of Biochemistry and Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Multidisciplinary Sciences, Goettingen 37077, Germany.
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7
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Dos Santos OAL, Carneiro RL, Requião RD, Ribeiro-Alves M, Domitrovic T, Palhano FL. Transcriptional profile of ribosome-associated quality control components and their associated phenotypes in mammalian cells. Sci Rep 2024; 14:1439. [PMID: 38228636 PMCID: PMC10792078 DOI: 10.1038/s41598-023-50811-z] [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: 08/30/2023] [Accepted: 12/26/2023] [Indexed: 01/18/2024] Open
Abstract
During protein synthesis, organisms detect translation defects that induce ribosome stalling and result in protein aggregation. The Ribosome-associated Quality Control (RQC) complex, comprising TCF25, LTN1, and NEMF, is responsible for identifying incomplete protein products from unproductive translation events, targeting them for degradation. Although RQC disruption causes adverse effects on vertebrate neurons, data regarding mRNA/protein expression and regulation across tissues are lacking. Employing high-throughput methods, we analyzed public datasets to explore RQC gene expression and phenotypes. Our findings revealed widespread expression of RQC components in human tissues; however, silencing of RQC yielded only mild negative effects on cell growth. Notably, TCF25 exhibited elevated mRNA levels that were not reflected in the protein content. We experimentally demonstrated that this disparity arose from post-translational protein degradation by the proteasome. Additionally, we observed that cellular aging marginally influenced RQC expression, leading to reduced mRNA levels in specific tissues. Our results suggest the necessity of RQC expression in all mammalian tissues. Nevertheless, when RQC falters, alternative mechanisms seem to compensate, ensuring cell survival under nonstress conditions.
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Affiliation(s)
- Otávio Augusto Leitão Dos Santos
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Rodolfo L Carneiro
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Rodrigo D Requião
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Marcelo Ribeiro-Alves
- Fundação Oswaldo Cruz, Instituto Nacional de Infectologia Evandro Chagas, Rio de Janeiro, 21040-900, Brazil
| | - Tatiana Domitrovic
- Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Fernando L Palhano
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil.
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8
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Komar AA, Samatova E, Rodnina MV. Translation Rates and Protein Folding. J Mol Biol 2023:168384. [PMID: 38065274 DOI: 10.1016/j.jmb.2023.168384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/01/2023] [Accepted: 12/02/2023] [Indexed: 12/19/2023]
Abstract
The mRNA coding sequence defines not only the amino acid sequence of the protein, but also the speed at which the ribosomes move along the mRNA while making the protein. The non-uniform local kinetics - denoted as translational rhythm - is similar among mRNAs coding for related protein folds. Deviations from this conserved rhythm can result in protein misfolding. In this review we summarize the experimental evidence demonstrating how local translation rates affect cotranslational protein folding, with the focus on the synonymous codons and patches of charged residues in the nascent peptide as best-studied examples. Alterations in nascent protein conformations due to disturbed translational rhythm can persist off the ribosome, as demonstrated by the effects of synonymous codon variants of several disease-related proteins. Charged amino acid patches in nascent chains also modulate translation and cotranslational protein folding, and can abrogate translation when placed at the N-terminus of the nascent peptide. During cotranslational folding, incomplete nascent chains navigate through a unique conformational landscape in which earlier intermediate states become inaccessible as the nascent peptide grows. Precisely tuned local translation rates, as well as interactions with the ribosome, guide the folding pathway towards the native structure, whereas deviations from the natural translation rhythm may favor pathways leading to trapped misfolded states. Deciphering the 'folding code' of the mRNA will contribute to understanding the diseases caused by protein misfolding and to rational protein design.
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Affiliation(s)
- Anton A Komar
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological and Environmental Sciences, Cleveland State University, 2121 Euclid Avenue, Cleveland, OH 44115, USA; Department of Biochemistry and Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.
| | - Ekaterina Samatova
- Max Planck Department of Physical Biochemistry, Max Planck Institute for Multidisciplinary Sciences, 37077 Goettingen, Germany
| | - Marina V Rodnina
- Max Planck Department of Physical Biochemistry, Max Planck Institute for Multidisciplinary Sciences, 37077 Goettingen, Germany.
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9
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Li X, Mariappan M. Nascent Chain Ubiquitination is Uncoupled from Degradation to Enable Protein Maturation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.09.561585. [PMID: 37873109 PMCID: PMC10592752 DOI: 10.1101/2023.10.09.561585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
A significant proportion of nascent proteins undergo polyubiquitination on ribosomes in mammalian cells, yet the fate of these proteins remains elusive. The ribosome-associated quality control (RQC) is a mechanism that mediates the ubiquitination of nascent chains on stalled ribosomes. Here, we find that nascent proteins ubiquitinated on stalled ribosomes by the RQC E3 ligase LTN1 are insufficient for proteasomal degradation. Our biochemical reconstitution studies reveal that ubiquitinated nascent chains are promptly deubiquitinated in the cytosol upon release from stalled ribosomes, as they are no longer associated with LTN1 E3 ligase for continuous ubiquitination to compete with cytosolic deubiquitinases. These deubiquitinated nascent chains can mature into stable proteins. However, if they misfold and expose a degradation signal, the cytosolic quality control recognizes them for re-ubiquitination and subsequent proteasomal degradation. Thus, our findings suggest that cycles of ubiquitination and deubiquitination spare foldable nascent proteins while ensuring the degradation of terminally misfolded proteins.
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Affiliation(s)
- Xia Li
- Department of Cell Biology, Nanobiology Institute, Yale School of Medicine, Yale University West Campus, West Haven, CT 06516, USA
| | - Malaiyalam Mariappan
- Department of Cell Biology, Nanobiology Institute, Yale School of Medicine, Yale University West Campus, West Haven, CT 06516, USA
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10
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Sogawa A, Komori R, Yanagitani K, Ohfurudono M, Tsuru A, Kadoi K, Kimata Y, Yoshida H, Kohno K. Signal sequence-triage is activated by translocon obstruction sensed by an ER stress sensor IRE1α. Cell Struct Funct 2023; 48:211-221. [PMID: 37766570 DOI: 10.1247/csf.23072] [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] [Indexed: 09/29/2023] Open
Abstract
Secretory pathway proteins are cotranslationally translocated into the endoplasmic reticulum (ER) of metazoan cells through the protein channel, translocon. Given that there are far fewer translocons than ribosomes in a cell, it is essential that secretory protein-translating ribosomes only occupy translocons transiently. Therefore, if translocons are obstructed by ribosomes stalled or slowed in translational elongation, it possibly results in deleterious consequences to cellular function. Hence, we investigated how translocon clogging by stalled ribosomes affects mammalian cells. First, we constructed ER-destined translational arrest proteins (ER-TAP) as an artificial protein that clogged the translocon in the ER membrane. Here, we show that the translocon clogging by ER-TAP expression activates triage of signal sequences (SS) in which secretory pathway proteins harboring highly efficient SS are preferentially translocated into the ER lumen. Interestingly, the translocon obstructed status specifically activates inositol requiring enzyme 1α (IRE1α) but not protein kinase R-like ER kinase (PERK). Given that the IRE1α-XBP1 pathway mainly induces the translocon components, our discovery implies that lowered availability of translocon activates IRE1α, which induces translocon itself. This results in rebalance between protein influx into the ER and the cellular translocation capacity.Key words: endoplasmic reticulum, translocation capacity, translocon clogging, IRE1, signal sequence.
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Affiliation(s)
- Ashuei Sogawa
- Laboratory of Molecular and Cell Genetics, Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST)
- Osaka International Cancer Institute (OICI)
| | - Ryota Komori
- Institute for Research Initiatives, Nara Institute of Science and Technology (NAIST)
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST)
- Department of Biochemistry and Molecular Biology, Graduate School of Science, University of Hyogo
| | - Kota Yanagitani
- Institute for Research Initiatives, Nara Institute of Science and Technology (NAIST)
- Ubiquitin Biology Laboratory, Graduate School of Frontier Biosciences, Osaka University
| | - Miku Ohfurudono
- Laboratory of Molecular and Cell Genetics, Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST)
- Institute for Research Initiatives, Nara Institute of Science and Technology (NAIST)
| | - Akio Tsuru
- Laboratory of Molecular and Cell Genetics, Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST)
- Institute for Research Initiatives, Nara Institute of Science and Technology (NAIST)
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST)
| | - Koji Kadoi
- Laboratory of Molecular and Cell Genetics, Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST)
| | - Yukio Kimata
- Laboratory of Molecular and Cell Genetics, Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST)
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST)
| | - Hiderou Yoshida
- Department of Biochemistry and Molecular Biology, Graduate School of Science, University of Hyogo
| | - Kenji Kohno
- Laboratory of Molecular and Cell Genetics, Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST)
- Institute for Research Initiatives, Nara Institute of Science and Technology (NAIST)
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST)
- Department of Biochemistry and Molecular Biology, Graduate School of Science, University of Hyogo
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11
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Bian B, Kumagai T, Saito Y. VeloPro: A pipeline integrating Ribo-seq and AlphaFold deciphers association patterns between translation velocity and protein structure features. IMETA 2023; 2:e148. [PMID: 38868219 PMCID: PMC10989810 DOI: 10.1002/imt2.148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 10/22/2023] [Indexed: 06/14/2024]
Abstract
VeloPro integrates Ribo-seq data and AlphaFold2-predicted 3D protein structure information for characterization of the association patterns between translation velocity and many protein structure features in prokaryotic and eukaryotic organisms across different taxonomical clades such as bacteria, fungi, protozoa, nematode, plants, insect, and mammals. We illustrated that association patterns between translation velocity and protein structure features differ across organisms, partially reflecting their taxonomical relationship.
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Affiliation(s)
- Bian Bian
- Department of Computational Biology and Medical SciencesGraduate School of Frontier Sciences, The University of TokyoKashiwaJapan
- Artificial Intelligence Research CenterNational Institute of Advanced Industrial Science and Technology (AIST)Koto‐kuJapan
| | | | - Yutaka Saito
- Department of Computational Biology and Medical SciencesGraduate School of Frontier Sciences, The University of TokyoKashiwaJapan
- Artificial Intelligence Research CenterNational Institute of Advanced Industrial Science and Technology (AIST)Koto‐kuJapan
- AIST‐Waseda University Computational Bio Big‐Data Open Innovation Laboratory (CBBD‐OIL)Shinjuku‐kuJapan
- Department of Data Science, School of Frontier EngineeringKitasato UniversitySagamiharaJapan
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12
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Alagar Boopathy LR, Beadle E, Garcia-Bueno Rico A, Vera M. Proteostasis regulation through ribosome quality control and no-go-decay. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1809. [PMID: 37488089 DOI: 10.1002/wrna.1809] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 06/14/2023] [Accepted: 06/30/2023] [Indexed: 07/26/2023]
Abstract
Cell functionality relies on the existing pool of proteins and their folding into functional conformations. This is achieved through the regulation of protein synthesis, which requires error-free mRNAs and ribosomes. Ribosomes are quality control hubs for mRNAs and proteins. Problems during translation elongation slow down the decoding rate, leading to ribosome halting and the eventual collision with the next ribosome. Collided ribosomes form a specific disome structure recognized and solved by ribosome quality control (RQC) mechanisms. RQC pathways orchestrate the degradation of the problematic mRNA by no-go decay and the truncated nascent peptide, the repression of translation initiation, and the recycling of the stalled ribosomes. All these events maintain protein homeostasis and return valuable ribosomes to translation. As such, cell homeostasis and function are maintained at the mRNA level by preventing the production of aberrant or unnecessary proteins. It is becoming evident that the crosstalk between RQC and the protein homeostasis network is vital for cell function, as the absence of RQC components leads to the activation of stress response and neurodegenerative diseases. Here, we review the molecular events of RQC discovered through well-designed stalling reporters. Given the impact of RQC in proteostasis, we discuss the relevance of identifying endogenous mRNA regulated by RQC and their preservation in stress conditions. This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms Translation > Regulation.
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Affiliation(s)
| | - Emma Beadle
- Department of Biochemistry, McGill University, Montreal, Canada
| | | | - Maria Vera
- Department of Biochemistry, McGill University, Montreal, Canada
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13
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Chen KY, Park H, Subramaniam AR. Massively parallel identification of sequence motifs triggering ribosome-associated mRNA quality control. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.27.559793. [PMID: 37808677 PMCID: PMC10557687 DOI: 10.1101/2023.09.27.559793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Decay of mRNAs can be triggered by ribosome slowdown at stretches of rare codons or positively charged amino acids. However, the full diversity of sequences that trigger co-translational mRNA decay is poorly understood. To comprehensively identify sequence motifs that trigger mRNA decay, we use a massively parallel reporter assay to measure the effect of all possible combinations of codon pairs on mRNA levels in S. cerevisiae. In addition to known mRNA-destabilizing sequences, we identify several dipeptide repeats whose translation reduces mRNA levels. These include combinations of positively charged and bulky residues, as well as proline-glycine and proline-aspartate dipeptide repeats. Genetic deletion of the ribosome collision sensor Hel2 rescues the mRNA effects of these motifs, suggesting that they trigger ribosome slowdown and activate the ribosome-associated quality control (RQC) pathway. Deep mutational scanning of an mRNA-destabilizing dipeptide repeat reveals a complex interplay between the charge, bulkiness, and location of amino acid residues in conferring mRNA instability. Finally, we show that the mRNA effects of codon pairs are predictive of the effects of endogenous sequences. Our work highlights the complexity of sequence motifs driving co-translational mRNA decay in eukaryotes, and presents a high throughput approach to dissect their requirements at the codon level.
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Affiliation(s)
- Katharine Y. Chen
- Basic Sciences Division and Computational Biology Section of the Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Heungwon Park
- Basic Sciences Division and Computational Biology Section of the Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Arvind Rasi Subramaniam
- Basic Sciences Division and Computational Biology Section of the Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
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14
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Höpfler M, Hegde RS. Control of mRNA fate by its encoded nascent polypeptide. Mol Cell 2023; 83:2840-2855. [PMID: 37595554 PMCID: PMC10501990 DOI: 10.1016/j.molcel.2023.07.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/03/2023] [Accepted: 07/11/2023] [Indexed: 08/20/2023]
Abstract
Cells tightly regulate mRNA processing, localization, and stability to ensure accurate gene expression in diverse cellular states and conditions. Most of these regulatory steps have traditionally been thought to occur before translation by the action of RNA-binding proteins. Several recent discoveries highlight multiple co-translational mechanisms that modulate mRNA translation, localization, processing, and stability. These mechanisms operate by recognition of the nascent protein, which is necessarily coupled to its encoding mRNA during translation. Hence, the distinctive sequence or structure of a particular nascent chain can recruit recognition factors with privileged access to the corresponding mRNA in an otherwise crowded cellular environment. Here, we draw on both well-established and recent examples to provide a conceptual framework for how cells exploit nascent protein recognition to direct mRNA fate. These mechanisms allow cells to dynamically and specifically regulate their transcriptomes in response to changes in cellular states to maintain protein homeostasis.
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15
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Shao B, Yan J, Zhang J, Buskirk AR. Riboformer: A Deep Learning Framework for Predicting Context-Dependent Translation Dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.24.538053. [PMID: 37163112 PMCID: PMC10168224 DOI: 10.1101/2023.04.24.538053] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Translation elongation is essential for maintaining cellular proteostasis, and alterations in the translational landscape are associated with a range of diseases. Ribosome profiling allows detailed measurement of translation at genome scale. However, it remains unclear how to disentangle biological variations from technical artifacts and identify sequence determinant of translation dysregulation. Here we present Riboformer, a deep learning-based framework for modeling context-dependent changes in translation dynamics. Riboformer leverages the transformer architecture to accurately predict ribosome densities at codon resolution. It corrects experimental artifacts in previously unseen datasets, reveals subtle differences in synonymous codon translation and uncovers a bottleneck in protein synthesis. Further, we show that Riboformer can be combined with in silico mutagenesis analysis to identify sequence motifs that contribute to ribosome stalling across various biological contexts, including aging and viral infection. Our tool offers a context-aware and interpretable approach for standardizing ribosome profiling datasets and elucidating the regulatory basis of translation kinetics.
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Affiliation(s)
- Bin Shao
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
- Present address: Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jiawei Yan
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Jing Zhang
- Biological Design Center, Boston University, Boston, MA, USA
| | - Allen R. Buskirk
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, USA
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16
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Baquero F, Martínez JL, Sánchez A, Fernández-de-Bobadilla MD, San-Millán A, Rodríguez-Beltrán J. Bacterial Subcellular Architecture, Structural Epistasis, and Antibiotic Resistance. BIOLOGY 2023; 12:biology12050640. [PMID: 37237454 DOI: 10.3390/biology12050640] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/08/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023]
Abstract
Epistasis refers to the way in which genetic interactions between some genetic loci affect phenotypes and fitness. In this study, we propose the concept of "structural epistasis" to emphasize the role of the variable physical interactions between molecules located in particular spaces inside the bacterial cell in the emergence of novel phenotypes. The architecture of the bacterial cell (typically Gram-negative), which consists of concentrical layers of membranes, particles, and molecules with differing configurations and densities (from the outer membrane to the nucleoid) determines and is in turn determined by the cell shape and size, depending on the growth phases, exposure to toxic conditions, stress responses, and the bacterial environment. Antibiotics change the bacterial cell's internal molecular topology, producing unexpected interactions among molecules. In contrast, changes in shape and size may alter antibiotic action. The mechanisms of antibiotic resistance (and their vectors, as mobile genetic elements) also influence molecular connectivity in the bacterial cell and can produce unexpected phenotypes, influencing the action of other antimicrobial agents.
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Affiliation(s)
- Fernando Baquero
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), 28034 Madrid, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), 28034 Madrid, Spain
| | | | - Alvaro Sánchez
- Centro Nacional de Biotecnología, CSIC, 28049 Madrid, Spain
| | - Miguel D Fernández-de-Bobadilla
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), 28034 Madrid, Spain
- CIBER en Enfermedades Infecciosas (CIBERINFECT), 28034 Madrid, Spain
| | - Alvaro San-Millán
- Centro Nacional de Biotecnología, CSIC, 28049 Madrid, Spain
- CIBER en Enfermedades Infecciosas (CIBERINFECT), 28034 Madrid, Spain
| | - Jerónimo Rodríguez-Beltrán
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), 28034 Madrid, Spain
- CIBER en Enfermedades Infecciosas (CIBERINFECT), 28034 Madrid, Spain
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17
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Fages-Lartaud M, Mueller Y, Elie F, Courtade G, Hohmann-Marriott MF. Standard Intein Gene Expression Ramps (SIGER) for Protein-Independent Expression Control. ACS Synth Biol 2023; 12:1058-1071. [PMID: 36920366 PMCID: PMC10127266 DOI: 10.1021/acssynbio.2c00530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Coordination of multigene expression is one of the key challenges of metabolic engineering for the development of cell factories. Constraints on translation initiation and early ribosome kinetics of mRNA are imposed by features of the 5'UTR in combination with the start of the gene, referred to as the "gene ramp", such as rare codons and mRNA secondary structures. These features strongly influence the translation yield and protein quality by regulating the ribosome distribution on mRNA strands. The utilization of genetic expression sequences, such as promoters and 5'UTRs in combination with different target genes, leads to a wide variety of gene ramp compositions with irregular translation rates, leading to unpredictable levels of protein yield and quality. Here, we present the Standard Intein Gene Expression Ramp (SIGER) system for controlling protein expression. The SIGER system makes use of inteins to decouple the translation initiation features from the gene of a target protein. We generated sequence-specific gene expression sequences for two inteins (DnaB and DnaX) that display defined levels of protein expression. Additionally, we used inteins that possess the ability to release the C-terminal fusion protein in vivo to avoid the impairment of protein functionality by the fused intein. Overall, our results show that SIGER systems are unique tools to mitigate the undesirable effects of gene ramp variation and to control the relative ratios of enzymes involved in molecular pathways. As a proof of concept of the potential of the system, we also used a SIGER system to express two difficult-to-produce proteins, GumM and CBM73.
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Affiliation(s)
- Maxime Fages-Lartaud
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim N-7491, Norway
| | - Yasmin Mueller
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim N-7491, Norway
| | - Florence Elie
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim N-7491, Norway
| | - Gaston Courtade
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim N-7491, Norway
| | - Martin Frank Hohmann-Marriott
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim N-7491, Norway.,United Scientists CORE (Limited), Dunedin 9016, Aotearoa, New Zealand
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18
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Lee J, Moon B, Lee DW, Hwang I. Translation rate underpins specific targeting of N-terminal transmembrane proteins to mitochondria. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023. [PMID: 36897023 DOI: 10.1111/jipb.13475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
Protein biogenesis is a complex process, and complexity is greatly increased in eukaryotic cells through specific targeting of proteins to different organelles. To direct targeting, organellar proteins carry an organelle-specific targeting signal for recognition by organelle-specific import machinery. However, the situation is confusing for transmembrane domain (TMD)-containing signal-anchored (SA) proteins of various organelles because TMDs function as an endoplasmic reticulum (ER) targeting signal. Although ER targeting of SA proteins is well understood, how they are targeted to mitochondria and chloroplasts remains elusive. Here, we investigated how the targeting specificity of SA proteins is determined for specific targeting to mitochondria and chloroplasts. Mitochondrial targeting requires multiple motifs around and within TMDs: a basic residue and an arginine-rich region flanking the N- and C-termini of TMDs, respectively, and an aromatic residue in the C-terminal side of the TMD that specify mitochondrial targeting in an additive manner. These motifs play a role in slowing down the elongation speed during translation, thereby ensuring mitochondrial targeting in a co-translational manner. By contrast, the absence of any of these motifs individually or together causes at varying degrees chloroplast targeting that occurs in a post-translational manner.
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Affiliation(s)
- Junho Lee
- Department of Life Science, Pohang University of Science and Technology, Pohang, 790-784, South Korea
| | - Byeongho Moon
- Department of Life Science, Pohang University of Science and Technology, Pohang, 790-784, South Korea
| | - Dong Wook Lee
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, 61186, South Korea
- Department Bioenergy Science and Technology, Chonnam National University, Gwangju, 61186, South Korea
| | - Inhwan Hwang
- Department of Life Science, Pohang University of Science and Technology, Pohang, 790-784, South Korea
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19
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Metabolic Sensing of Extracytoplasmic Copper Availability via Translational Control by a Nascent Exported Protein. mBio 2023; 14:e0304022. [PMID: 36598193 PMCID: PMC9973294 DOI: 10.1128/mbio.03040-22] [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] [Indexed: 01/05/2023] Open
Abstract
Metabolic sensing is a crucial prerequisite for cells to adjust their physiology to rapidly changing environments. In bacteria, the response to intra- and extracellular ligands is primarily controlled by transcriptional regulators, which activate or repress gene expression to ensure metabolic acclimation. Translational control, such as ribosomal stalling, can also contribute to cellular acclimation and has been shown to mediate responses to changing intracellular molecules. In the current study, we demonstrate that the cotranslational export of the Rhodobacter capsulatus protein CutF regulates the translation of the downstream cutO-encoded multicopper oxidase CutO in response to extracellular copper (Cu). Our data show that CutF, acting as a Cu sensor, is cotranslationally exported by the signal recognition particle pathway. The binding of Cu to the periplasmically exposed Cu-binding motif of CutF delays its cotranslational export via its C-terminal ribosome stalling-like motif. This allows for the unfolding of an mRNA stem-loop sequence that shields the ribosome-binding site of cutO, which favors its subsequent translation. Bioinformatic analyses reveal that CutF-like proteins are widely distributed in bacteria and are often located upstream of genes involved in transition metal homeostasis. Our overall findings illustrate a highly conserved control mechanism using the cotranslational export of a protein acting as a sensor to integrate the changing availability of extracellular nutrients into metabolic acclimation. IMPORTANCE Metabolite sensing is a fundamental biological process, and the perception of dynamic changes in the extracellular environment is of paramount importance for the survival of organisms. Bacteria usually adjust their metabolisms to changing environments via transcriptional regulation. Here, using Rhodobacter capsulatus, we describe an alternative translational mechanism that controls the bacterial response to the presence of copper, a toxic micronutrient. This mechanism involves a cotranslationally secreted protein that, in the presence of copper, undergoes a process resembling ribosomal stalling. This allows for the unfolding of a downstream mRNA stem-loop and enables the translation of the adjacent Cu-detoxifying multicopper oxidase. Bioinformatic analyses reveal that such proteins are widespread, suggesting that metabolic sensing using ribosome-arrested nascent secreted proteins acting as sensors may be a common strategy for the integration of environmental signals into metabolic adaptations.
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20
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Bigman LS, Levy Y. Conformational Analysis of Charged Homo-Polypeptides. Biomolecules 2023; 13:biom13020363. [PMID: 36830732 PMCID: PMC9953673 DOI: 10.3390/biom13020363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 02/17/2023] Open
Abstract
Many proteins have intrinsically disordered regions (IDRs), which are often characterized by a high fraction of charged residues with polyampholytic (i.e., mixed charge) or polyelectrolytic (i.e., uniform charge) characteristics. Polyelectrolytic IDRs include consecutive positively charged Lys or Arg residues (K/R repeats) or consecutive negatively charged Asp or Glu residues (D/E repeats). In previous research, D/E repeats were found to be about five times longer than K/R repeats and to be much more common in eukaryotes. Within these repeats, a preference is often observed for E over D and for K over R. To understand the greater prevalence of D/E over K/R repeats and the higher abundance of E and K, we simulated the conformational ensemble of charged homo-polypeptides (polyK, polyR, polyD, and polyE) using molecular dynamics simulations. The conformational preferences and dynamics of these polyelectrolytic polypeptides change with changes in salt concentration. In particular, polyD and polyE are more sensitive to salt than polyK and polyR, as polyD and polyE tend to adsorb more divalent cations, which leads to their having more compact conformations. We conclude with a discussion of biophysical explanations for the relative abundance of charged amino acids and particularly for the greater abundance of D/E repeats over K/R repeats.
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21
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A dynamical stochastic model of yeast translation across the cell cycle. Heliyon 2023; 9:e13101. [PMID: 36793957 PMCID: PMC9922973 DOI: 10.1016/j.heliyon.2023.e13101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 01/04/2023] [Accepted: 01/16/2023] [Indexed: 01/27/2023] Open
Abstract
Translation is a central step in gene expression, however its quantitative and time-resolved regulation is poorly understood. We developed a discrete, stochastic model for protein translation in S. cerevisiae in a whole-transcriptome, single-cell context. A "base case" scenario representing an average cell highlights translation initiation rates as the main co-translational regulatory parameters. Codon usage bias emerges as a secondary regulatory mechanism through ribosome stalling. Demand for anticodons with low abundancy is shown to cause above-average ribosome dwelling times. Codon usage bias correlates strongly both with protein synthesis rates and elongation rates. Applying the model to a time-resolved transcriptome estimated by combining data from FISH and RNA-Seq experiments, it could be shown that increased total transcript abundance during the cell cycle decreases translation efficiency at single transcript level. Translation efficiency grouped by gene function shows highest values for ribosomal and glycolytic genes. Ribosomal proteins peak in S phase while glycolytic proteins rank highest in later cell cycle phases.
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22
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Monem PC, Vidyasagar N, Piatt AL, Sehgal E, Arribere JA. Ubiquitination of stalled ribosomes enables mRNA decay via HBS-1 and NONU-1 in vivo. PLoS Genet 2023; 19:e1010577. [PMID: 36626369 PMCID: PMC9870110 DOI: 10.1371/journal.pgen.1010577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/23/2023] [Accepted: 12/18/2022] [Indexed: 01/11/2023] Open
Abstract
As ribosomes translate the genetic code, they can encounter a variety of obstacles that hinder their progress. If ribosomes stall for prolonged times, cells suffer due to the loss of translating ribosomes and the accumulation of aberrant protein products. Thus to protect cells, stalled ribosomes experience a series of reactions to relieve the stall and degrade the offending mRNA, a process known as No-Go mRNA Decay (NGD). While much of the machinery for NGD is known, the precise ordering of events and factors along this pathway has not been tested. Here, we deploy C. elegans to unravel the coordinated events comprising NGD. Utilizing a novel reporter and forward and reverse genetics, we identify the machinery required for NGD. Our subsequent molecular analyses define a functional requirement for ubiquitination on at least two ribosomal proteins (eS10 and uS10), and we show that ribosomes lacking ubiquitination sites on eS10 and uS10 fail to perform NGD in vivo. We show that the nuclease NONU-1 acts after the ubiquitin ligase ZNF-598, and discover a novel requirement for the ribosome rescue factors HBS-1/PELO-1 in mRNA decay via NONU-1. Taken together, our work demonstrates mechanisms by which ribosomes signal to effectors of mRNA repression, and we delineate links between repressive factors working toward a well-defined NGD pathway.
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Affiliation(s)
- Parissa C. Monem
- Department of Molecular, Cell, and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California, United States of America
| | - Nitin Vidyasagar
- Department of Molecular, Cell, and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California, United States of America
| | - Audrey L. Piatt
- Department of Molecular, Cell, and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California, United States of America
| | - Enisha Sehgal
- Department of Molecular, Cell, and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California, United States of America
| | - Joshua A. Arribere
- Department of Molecular, Cell, and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California, United States of America
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23
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McGrath H, Černeková M, Kolář MH. Binding of the peptide deformylase on the ribosome surface modulates the exit tunnel interior. Biophys J 2022; 121:4443-4451. [PMID: 36335428 PMCID: PMC9748369 DOI: 10.1016/j.bpj.2022.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/26/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
Proteosynthesis on ribosomes is regulated at many levels. Conformational changes of the ribosome, possibly induced by external factors, may transfer over large distances and contribute to the regulation. The molecular principles of this long-distance allostery within the ribosome remain poorly understood. Here, we use structural analysis and atomistic molecular dynamics simulations to investigate peptide deformylase (PDF), an enzyme that binds to the ribosome surface near the ribosomal protein uL22 during translation and chemically modifies the emerging nascent peptide. Our simulations of the entire ribosome-PDF complex reveal that the PDF undergoes a swaying motion on the ribosome surface at the submicrosecond timescale. We show that the PDF affects the conformational dynamics of parts of the ribosome over distances of more than 5 nm. Using a supervised-learning algorithm, we demonstrate that the exit tunnel is influenced by the presence or absence of PDF. Our findings suggest a possible effect of the PDF on the nascent peptide translocation through the ribosome exit tunnel.
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Affiliation(s)
- Hugo McGrath
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Czech Republic
| | - Michaela Černeková
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Czech Republic
| | - Michal H Kolář
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Czech Republic.
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24
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Kriachkov V, Ormsby AR, Kusnadi EP, McWilliam HE, Mintern JD, Amarasinghe SL, Ritchie ME, Furic L, Hatters DM. Arginine-rich C9ORF72 ALS proteins stall ribosomes in a manner distinct from a canonical ribosome-associated quality control substrate. J Biol Chem 2022; 299:102774. [PMID: 36481270 PMCID: PMC9830226 DOI: 10.1016/j.jbc.2022.102774] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 11/23/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
Hexanucleotide expansion mutations in C9ORF72 are a frequent cause of amyotrophic lateral sclerosis. We previously reported that long arginine-rich dipeptide repeats (DPRs), mimicking abnormal proteins expressed from the hexanucleotide expansion, caused translation stalling when expressed in cell culture models. Whether this stalling provides a mechanism of pathogenicity remains to be determined. Here, we explored the molecular features of DPR-induced stalling and examined whether known mechanisms such as ribosome quality control (RQC) regulate translation elongation on sequences that encode arginine-rich DPRs. We demonstrate that arginine-rich DPRs lead to stalling in a length-dependent manner, with lengths longer than 40 repeats invoking severe translation arrest. Mutational screening of 40×Gly-Xxx DPRs shows that stalling is most pronounced when Xxx is a charged amino acid (Arg, Lys, Glu, or Asp). Through a genome-wide knockout screen, we find that genes regulating stalling on polyadenosine mRNA coding for poly-Lys, a canonical RQC substrate, act differently in the case of arginine-rich DPRs. Indeed, these findings point to a limited scope for natural regulatory responses to resolve the arginine-rich DPR stalls, even though the stalls may be sensed, as evidenced by an upregulation of RQC gene expression. These findings therefore implicate arginine-rich DPR-mediated stalled ribosomes as a source of stress and toxicity and may be a crucial component in pathomechanisms.
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Affiliation(s)
- Viacheslav Kriachkov
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Angelique R. Ormsby
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Eric P. Kusnadi
- Translational Prostate Cancer Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Hamish E.G. McWilliam
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia,Department of Microbiology and Immunology, Peter Doherty Institute of Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Justine D. Mintern
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | | | - Matthew E. Ritchie
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Luc Furic
- Translational Prostate Cancer Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia,Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute Cancer Program, Monash University, Clayton, Victoria, Australia
| | - Danny M. Hatters
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia,For correspondence: Danny M. Hatters
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25
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Ito Y, Chadani Y, Niwa T, Yamakawa A, Machida K, Imataka H, Taguchi H. Nascent peptide-induced translation discontinuation in eukaryotes impacts biased amino acid usage in proteomes. Nat Commun 2022; 13:7451. [PMID: 36460666 PMCID: PMC9718836 DOI: 10.1038/s41467-022-35156-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 11/18/2022] [Indexed: 12/04/2022] Open
Abstract
Robust translation elongation of any given amino acid sequence is required to shape proteomes. Nevertheless, nascent peptides occasionally destabilize ribosomes, since consecutive negatively charged residues in bacterial nascent chains can stochastically induce discontinuation of translation, in a phenomenon termed intrinsic ribosome destabilization (IRD). Here, using budding yeast and a human factor-based reconstituted translation system, we show that IRD also occurs in eukaryotic translation. Nascent chains enriched in aspartic acid (D) or glutamic acid (E) in their N-terminal regions alter canonical ribosome dynamics, stochastically aborting translation. Although eukaryotic ribosomes are more robust to ensure uninterrupted translation, we find many endogenous D/E-rich peptidyl-tRNAs in the N-terminal regions in cells lacking a peptidyl-tRNA hydrolase, indicating that the translation of the N-terminal D/E-rich sequences poses an inherent risk of failure. Indeed, a bioinformatics analysis reveals that the N-terminal regions of ORFs lack D/E enrichment, implying that the translation defect partly restricts the overall amino acid usage in proteomes.
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Affiliation(s)
- Yosuke Ito
- grid.32197.3e0000 0001 2179 2105School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8503 Japan
| | - Yuhei Chadani
- grid.32197.3e0000 0001 2179 2105Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503 Japan
| | - Tatsuya Niwa
- grid.32197.3e0000 0001 2179 2105School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8503 Japan ,grid.32197.3e0000 0001 2179 2105Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503 Japan
| | - Ayako Yamakawa
- grid.32197.3e0000 0001 2179 2105School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8503 Japan
| | - Kodai Machida
- grid.266453.00000 0001 0724 9317Graduate School of Engineering, University of Hyogo, Himeji, Hyogo 671-2280 Japan
| | - Hiroaki Imataka
- grid.266453.00000 0001 0724 9317Graduate School of Engineering, University of Hyogo, Himeji, Hyogo 671-2280 Japan
| | - Hideki Taguchi
- grid.32197.3e0000 0001 2179 2105School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8503 Japan ,grid.32197.3e0000 0001 2179 2105Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503 Japan
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26
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A male germ-cell-specific ribosome controls male fertility. Nature 2022; 612:725-731. [PMID: 36517592 DOI: 10.1038/s41586-022-05508-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 11/01/2022] [Indexed: 12/23/2022]
Abstract
Ribosomes are highly sophisticated translation machines that have been demonstrated to be heterogeneous in the regulation of protein synthesis1,2. Male germ cell development involves complex translational regulation during sperm formation3. However, it remains unclear whether translation during sperm formation is performed by a specific ribosome. Here we report a ribosome with a specialized nascent polypeptide exit tunnel, RibosomeST, that is assembled with the male germ-cell-specific protein RPL39L, the paralogue of core ribosome (RibosomeCore) protein RPL39. Deletion of RibosomeST in mice causes defective sperm formation, resulting in substantially reduced fertility. Our comparison of single-particle cryo-electron microscopy structures of ribosomes from mouse kidneys and testes indicates that RibosomeST features a ribosomal polypeptide exit tunnel of distinct size and charge states compared with RibosomeCore. RibosomeST predominantly cotranslationally regulates the folding of a subset of male germ-cell-specific proteins that are essential for the formation of sperm. Moreover, we found that specialized functions of RibosomeST were not replaceable by RibosomeCore. Taken together, identification of this sperm-specific ribosome should greatly expand our understanding of ribosome function and tissue-specific regulation of protein expression pattern in mammals.
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27
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Burke PC, Park H, Subramaniam AR. A nascent peptide code for translational control of mRNA stability in human cells. Nat Commun 2022; 13:6829. [PMID: 36369503 PMCID: PMC9652226 DOI: 10.1038/s41467-022-34664-0] [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: 12/01/2021] [Accepted: 11/02/2022] [Indexed: 11/13/2022] Open
Abstract
Stability of eukaryotic mRNAs is associated with their codon, amino acid, and GC content. Yet, coding sequence motifs that predictably alter mRNA stability in human cells remain poorly defined. Here, we develop a massively parallel assay to measure mRNA effects of thousands of synthetic and endogenous coding sequence motifs in human cells. We identify several families of simple dipeptide repeats whose translation triggers mRNA destabilization. Rather than individual amino acids, specific combinations of bulky and positively charged amino acids are critical for the destabilizing effects of dipeptide repeats. Remarkably, dipeptide sequences that form extended β strands in silico and in vitro slowdown ribosomes and reduce mRNA levels in vivo. The resulting nascent peptide code underlies the mRNA effects of hundreds of endogenous peptide sequences in the human proteome. Our work suggests an intrinsic role for the ribosome as a selectivity filter against the synthesis of bulky and aggregation-prone peptides.
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Affiliation(s)
- Phillip C. Burke
- grid.270240.30000 0001 2180 1622Basic Sciences Division and Computational Biology Section of the Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109 USA ,grid.34477.330000000122986657Department of Microbiology, University of Washington, Seattle, WA 98195 USA
| | - Heungwon Park
- grid.270240.30000 0001 2180 1622Basic Sciences Division and Computational Biology Section of the Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109 USA
| | - Arvind Rasi Subramaniam
- grid.270240.30000 0001 2180 1622Basic Sciences Division and Computational Biology Section of the Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109 USA ,grid.34477.330000000122986657Department of Microbiology, University of Washington, Seattle, WA 98195 USA
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28
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Fages‐Lartaud M, Hundvin K, Hohmann‐Marriott MF. Mechanisms governing codon usage bias and the implications for protein expression in the chloroplast of Chlamydomonas reinhardtii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:919-945. [PMID: 36071273 PMCID: PMC9828097 DOI: 10.1111/tpj.15970] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 08/29/2022] [Accepted: 09/01/2022] [Indexed: 05/30/2023]
Abstract
Chloroplasts possess a considerably reduced genome that is decoded via an almost minimal set of tRNAs. These features make an excellent platform for gaining insights into fundamental mechanisms that govern protein expression. Here, we present a comprehensive and revised perspective of the mechanisms that drive codon selection in the chloroplast of Chlamydomonas reinhardtii and the functional consequences for protein expression. In order to extract this information, we applied several codon usage descriptors to genes with different expression levels. We show that highly expressed genes strongly favor translationally optimal codons, while genes with lower functional importance are rather affected by directional mutational bias. We demonstrate that codon optimality can be deduced from codon-anticodon pairing affinity and, for a small number of amino acids (leucine, arginine, serine, and isoleucine), tRNA concentrations. Finally, we review, analyze, and expand on the impact of codon usage on protein yield, secondary structures of mRNA, translation initiation and termination, and amino acid composition of proteins, as well as cotranslational protein folding. The comprehensive analysis of codon choice provides crucial insights into heterologous gene expression in the chloroplast of C. reinhardtii, which may also be applicable to other chloroplast-containing organisms and bacteria.
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Affiliation(s)
- Maxime Fages‐Lartaud
- Department of BiotechnologyNorwegian University of Science and TechnologyTrondheimN‐7491Norway
| | - Kristoffer Hundvin
- Department of BiotechnologyNorwegian University of Science and TechnologyTrondheimN‐7491Norway
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29
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Hassell D, Denney A, Singer E, Benson A, Roth A, Ceglowski J, Steingesser M, McMurray M. Chaperone Requirements for De Novo Folding of Saccharomyces cerevisiae Septins. Mol Biol Cell 2022; 33:ar111. [PMID: 35947497 DOI: 10.1091/mbc.e22-07-0262] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Polymers of septin protein complexes play cytoskeletal roles in eukaryotic cells. The specific subunit composition within complexes controls functions and higher-order structural properties. All septins have globular GTPase domains. The other eukaryotic cytoskeletal NTPases strictly require assistance from molecular chaperones of the cytosol, particularly the cage-like chaperonins, to fold into oligomerization-competent conformations. We previously identified cytosolic chaperones that bind septins and influence the oligomerization ability of septins carrying mutations linked to human disease, but it was unknown to what extent wild-type septins require chaperone assistance for their native folding. Here we use a combination of in vivo and in vitro approaches to demonstrate chaperone requirements for de novo folding and complex assembly by budding yeast septins. Individually purified septins adopted non-native conformations and formed non-native homodimers. In chaperonin- or Hsp70-deficient cells, septins folded slower and were unable to assemble post-translationally into native complexes. One septin, Cdc12, was so dependent on co-translational chaperonin assistance that translation failed without it. Our findings point to distinct translation elongation rates for different septins as a possible mechanism to direct a stepwise, co-translational assembly pathway in which general cytosolic chaperones act as key intermediaries.
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Affiliation(s)
- Daniel Hassell
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Ashley Denney
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Emily Singer
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Aleyna Benson
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Andrew Roth
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Julia Ceglowski
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Marc Steingesser
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
| | - Michael McMurray
- University of Colorado Anschutz Medical Campus, Aurora, CO 80045
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30
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Wright SE, Rodriguez CM, Monroe J, Xing J, Krans A, Flores BN, Barsur V, Ivanova MI, Koutmou KS, Barmada SJ, Todd PK. CGG repeats trigger translational frameshifts that generate aggregation-prone chimeric proteins. Nucleic Acids Res 2022; 50:8674-8689. [PMID: 35904811 PMCID: PMC9410890 DOI: 10.1093/nar/gkac626] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 07/13/2022] [Indexed: 11/25/2022] Open
Abstract
CGG repeat expansions in the FMR1 5’UTR cause the neurodegenerative disease Fragile X-associated tremor/ataxia syndrome (FXTAS). These repeats form stable RNA secondary structures that support aberrant translation in the absence of an AUG start codon (RAN translation), producing aggregate-prone peptides that accumulate within intranuclear neuronal inclusions and contribute to neurotoxicity. Here, we show that the most abundant RAN translation product, FMRpolyG, is markedly less toxic when generated from a construct with a non-repetitive alternating codon sequence in place of the CGG repeat. While exploring the mechanism of this differential toxicity, we observed a +1 translational frameshift within the CGG repeat from the arginine to glycine reading frame. Frameshifts occurred within the first few translated repeats and were triggered predominantly by RNA sequence and structural features. Short chimeric R/G peptides form aggregates distinct from those formed by either pure arginine or glycine, and these chimeras induce toxicity in cultured rodent neurons. Together, this work suggests that CGG repeats support translational frameshifting and that chimeric RAN translated peptides may contribute to CGG repeat-associated toxicity in FXTAS and related disorders.
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Affiliation(s)
- Shannon E Wright
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA.,Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Caitlin M Rodriguez
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA.,Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA 84305, USA
| | - Jeremy Monroe
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jiazheng Xing
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Amy Krans
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA.,VA Ann Arbor Healthcare System, Ann Arbor, MI 48105, USA
| | - Brittany N Flores
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA.,Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Venkatesha Barsur
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Magdalena I Ivanova
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA.,Biophysics Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kristin S Koutmou
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sami J Barmada
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter K Todd
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA.,VA Ann Arbor Healthcare System, Ann Arbor, MI 48105, USA
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31
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mRNA and tRNA modification states influence ribosome speed and frame maintenance during poly(lysine) peptide synthesis. J Biol Chem 2022; 298:102039. [PMID: 35595100 PMCID: PMC9207662 DOI: 10.1016/j.jbc.2022.102039] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 12/16/2022] Open
Abstract
Ribosome speed is dictated by multiple factors including substrate availability, cellular conditions, and product (peptide) formation. Translation slows during the synthesis of cationic peptide sequences, potentially influencing the expression of thousands of proteins. Available evidence suggests that ionic interactions between positively charged nascent peptides and the negatively charged ribosome exit tunnel impede translation. However, this hypothesis was difficult to test directly because of inability to decouple the contributions of amino acid charge from mRNA sequence and tRNA identity/abundance in cells. Furthermore, it is unclear if other components of the translation system central to ribosome function (e.g., RNA modification) influence the speed and accuracy of positively charged peptide synthesis. In this study, we used a fully reconstituted Escherichia coli translation system to evaluate the effects of peptide charge, mRNA sequence, and RNA modification status on the translation of lysine-rich peptides. Comparison of translation reactions on poly(lysine)-encoding mRNAs conducted with either Lys-tRNALys or Val-tRNALys reveals that that amino acid charge, while important, only partially accounts for slowed translation on these transcripts. We further find that in addition to peptide charge, mRNA sequence and both tRNA and mRNA modification status influence the rates of amino acid addition and the ribosome’s ability to maintain frame (instead of entering the −2, −1, and +1 frames) during poly(lysine) peptide synthesis. Our observations lead us to expand the model for explaining how the ribosome slows during poly(lysine) peptide synthesis and suggest that posttranscriptional RNA modifications can provide cells a mechanism to precisely control ribosome movements along an mRNA.
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32
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Eisen TJ, Li JJ, Bartel DP. The interplay between translational efficiency, poly(A) tails, microRNAs, and neuronal activation. RNA (NEW YORK, N.Y.) 2022; 28:808-831. [PMID: 35273099 PMCID: PMC9074895 DOI: 10.1261/rna.079046.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
Neurons provide a rich setting for studying post-transcriptional control. Here, we investigate the landscape of translational control in neurons and search for mRNA features that explain differences in translational efficiency (TE), considering the interplay between TE, mRNA poly(A)-tail lengths, microRNAs, and neuronal activation. In neurons and brain tissues, TE correlates with tail length, and a few dozen mRNAs appear to undergo cytoplasmic polyadenylation upon light or chemical stimulation. However, the correlation between TE and tail length is modest, explaining <5% of TE variance, and even this modest relationship diminishes when accounting for other mRNA features. Thus, tail length appears to affect TE only minimally. Accordingly, miRNAs, which accelerate deadenylation of their mRNA targets, primarily influence target mRNA levels, with no detectable effect on either steady-state tail lengths or TE. Larger correlates with TE include codon composition and predicted mRNA folding energy. When combined in a model, the identified correlates explain 38%-45% of TE variance. These results provide a framework for considering the relative impact of factors that contribute to translational control in neurons. They indicate that when examined in bulk, translational control in neurons largely resembles that of other types of post-embryonic cells. Thus, detection of more specialized control might require analyses that can distinguish translation occurring in neuronal processes from that occurring in cell bodies.
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Affiliation(s)
- Timothy J Eisen
- Howard Hughes Medical Institute, Cambridge, Massachusetts 02142, USA
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
| | - Jingyi Jessica Li
- Department of Statistics, Department of Biostatistics, Department of Computational Medicine, and Department of Human Genetics, University of California, Los Angeles, California 90095, USA
| | - David P Bartel
- Howard Hughes Medical Institute, Cambridge, Massachusetts 02142, USA
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
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33
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Bigman LS, Iwahara J, Levy Y. Negatively Charged Disordered Regions are Prevalent and Functionally Important Across Proteomes. J Mol Biol 2022; 434:167660. [PMID: 35659505 DOI: 10.1016/j.jmb.2022.167660] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/20/2022] [Accepted: 05/24/2022] [Indexed: 01/12/2023]
Abstract
Intrinsically disordered regions (IDRs) of proteins are often characterized by a high fraction of charged residues, but differ in their overall net charge and in the organization of the charged residues. The function-encoding information stored via IDR charge composition and organization remains elusive. Here, we aim to decipher the sequence-function relationship in IDRs by presenting a comprehensive bioinformatic analysis of the charge properties of IDRs in the human, mouse, and yeast proteomes. About 50% of the proteins comprise at least a single IDR, which is either positively or negatively charged. Highly negatively charged IDRs are longer and possess greater net charge per residue compared with highly positively charged IDRs. A striking difference between positively and negatively charged IDRs is the characteristics of the repeated units, specifically, of consecutive Lys or Arg residues (K/R repeats) and Asp or Glu (D/E repeats) residues. D/E repeats are found to be about five times longer than K/R repeats, with the longest found containing 49 residues. Long stretches of consecutive D and E are found to be more prevalent in nucleic acid-related proteins. They are less common in prokaryotes, and in eukaryotes their abundance increases with genome size. The functional role of D/E repeats and the profound differences between them and K/R repeats are discussed.
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Affiliation(s)
- Lavi S Bigman
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel. https://twitter.com/LaviBigman
| | - Junji Iwahara
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, United States
| | - Yaakov Levy
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel.
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34
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Filbeck S, Cerullo F, Pfeffer S, Joazeiro CAP. Ribosome-associated quality-control mechanisms from bacteria to humans. Mol Cell 2022; 82:1451-1466. [PMID: 35452614 PMCID: PMC9034055 DOI: 10.1016/j.molcel.2022.03.038] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/23/2022] [Accepted: 03/28/2022] [Indexed: 11/16/2022]
Abstract
Ribosome-associated quality-control (RQC) surveys incomplete nascent polypeptides produced by interrupted translation. Central players in RQC are the human ribosome- and tRNA-binding protein, NEMF, and its orthologs, yeast Rqc2 and bacterial RqcH, which sense large ribosomal subunits obstructed with nascent chains and then promote nascent-chain proteolysis. In canonical eukaryotic RQC, NEMF stabilizes the LTN1/Listerin E3 ligase binding to obstructed ribosomal subunits for nascent-chain ubiquitylation. Furthermore, NEMF orthologs across evolution modify nascent chains by mediating C-terminal, untemplated polypeptide elongation. In eukaryotes, this process exposes ribosome-buried nascent-chain lysines, the ubiquitin acceptor sites, to LTN1. Remarkably, in both bacteria and eukaryotes, C-terminal tails also have an extra-ribosomal function as degrons. Here, we discuss recent findings on RQC mechanisms and briefly review how ribosomal stalling is sensed upstream of RQC, including via ribosome collisions, from an evolutionary perspective. Because RQC defects impair cellular fitness and cause neurodegeneration, this knowledge provides a framework for pathway-related biology and disease studies.
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Affiliation(s)
- Sebastian Filbeck
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Federico Cerullo
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Stefan Pfeffer
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany.
| | - Claudio A P Joazeiro
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany; Department of Molecular Medicine, Scripps Florida, Jupiter, FL 33458, USA.
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35
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Fujita T, Yokoyama T, Shirouzu M, Taguchi H, Ito T, Iwasaki S. The landscape of translational stall sites in bacteria revealed by monosome and disome profiling. RNA (NEW YORK, N.Y.) 2022; 28:290-302. [PMID: 34906996 PMCID: PMC8848927 DOI: 10.1261/rna.078188.120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 11/24/2021] [Indexed: 05/29/2023]
Abstract
Ribosome pauses are associated with various cotranslational events and determine the fate of mRNAs and proteins. Thus, the identification of precise pause sites across the transcriptome is desirable; however, the landscape of ribosome pauses in bacteria remains ambiguous. Here, we harness monosome and disome (or collided ribosome) profiling strategies to survey ribosome pause sites in Escherichia coli Compared to eukaryotes, ribosome collisions in bacteria showed remarkable differences: a low frequency of disomes at stop codons, collisions occurring immediately after 70S assembly on start codons, and shorter queues of ribosomes trailing upstream. The pause sites corresponded with the biochemical validation by integrated nascent chain profiling (iNP) to detect polypeptidyl-tRNA, an elongation intermediate. Moreover, the subset of those sites showed puromycin resistance, presenting slow peptidyl transfer. Among the identified sites, the ribosome pause at Asn586 of ycbZ was validated by biochemical reporter assay, tRNA sequencing (tRNA-seq), and cryo-electron microscopy (cryo-EM) experiments. Our results provide a useful resource for ribosome stalling sites in bacteria.
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Affiliation(s)
- Tomoya Fujita
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198 Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8503, Japan
| | - Takeshi Yokoyama
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama 230-0045, Japan
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8577, Japan
| | - Mikako Shirouzu
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Hideki Taguchi
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8503, Japan
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Midori-ku, Yokohama 226-8503, Japan
| | - Takuhiro Ito
- Laboratory for Translation Structural Biology, RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198 Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan
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36
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Yang CI, Kim J, Shan SO. Ribosome-nascent chain interaction regulates N-terminal protein modification. J Mol Biol 2022; 434:167535. [PMID: 35278477 PMCID: PMC9126151 DOI: 10.1016/j.jmb.2022.167535] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 03/01/2022] [Accepted: 03/04/2022] [Indexed: 01/02/2023]
Abstract
Numerous proteins initiate their folding, localization, and modifications early during translation, and emerging data show that the ribosome actively participates in diverse protein biogenesis pathways. Here we show that the ribosome imposes an additional layer of substrate selection during N-terminal methionine excision (NME), an essential protein modification in bacteria. Biochemical analyses show that cotranslational NME is exquisitely sensitive to a hydrophobic signal sequence or transmembrane domain near the N terminus of the nascent polypeptide. The ability of the nascent chain to access the active site of NME enzymes dictates NME efficiency, which is inhibited by confinement of the nascent chain on the ribosome surface and exacerbated by signal recognition particle. In vivo measurements corroborate the inhibition of NME by an N-terminal hydrophobic sequence, suggesting the retention of formylmethionine on a substantial fraction of the secretory and membrane proteome. Our work demonstrates how molecular features of a protein regulate its cotranslational modification and highlights the active participation of the ribosome in protein biogenesis pathways via interactions of the ribosome surface with the nascent protein.
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37
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Mishima Y, Han P, Ishibashi K, Kimura S, Iwasaki S. Ribosome slowdown triggers codon-mediated mRNA decay independently of ribosome quality control. EMBO J 2022; 41:e109256. [PMID: 35040509 PMCID: PMC8886528 DOI: 10.15252/embj.2021109256] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 12/06/2021] [Accepted: 12/09/2021] [Indexed: 12/11/2022] Open
Abstract
The control of mRNA stability plays a central role in regulating gene expression patterns. Recent studies have revealed that codon composition in the open reading frame determines mRNA stability in multiple organisms. Based on genome-wide correlation approaches, this previously unrecognized role for the genetic code is attributable to the kinetics of the codon-decoding process by the ribosome. However, complementary experimental analyses are required to clarify the codon effects on mRNA stability and the related cotranslational mRNA decay pathways, for example, those triggered by aberrant ribosome stalling. In the current study, we performed a set of reporter-based analyses to define codon-mediated mRNA decay and ribosome stall-dependent mRNA decay in zebrafish embryos. Our analysis showed that the effect of codons on mRNA stability stems from the decoding process, independent of the ribosome quality control factor Znf598 and stalling-dependent mRNA decay. We propose that codon-mediated mRNA decay is rather triggered by transiently slowed ribosomes engaging in a productive translation cycle in zebrafish embryos.
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Affiliation(s)
- Yuichiro Mishima
- Department of Frontier Life SciencesFaculty of Life SciencesKyoto Sangyo UniversityKyotoJapan,RNA Systems Biochemistry LaboratoryRIKEN Cluster for Pioneering ResearchSaitamaJapan
| | - Peixun Han
- RNA Systems Biochemistry LaboratoryRIKEN Cluster for Pioneering ResearchSaitamaJapan,Department of Computational Biology and Medical SciencesGraduate School of Frontier SciencesThe University of TokyoChibaJapan
| | - Kota Ishibashi
- Department of Frontier Life SciencesFaculty of Life SciencesKyoto Sangyo UniversityKyotoJapan
| | - Seisuke Kimura
- Department of Industrial Life SciencesFaculty of Life SciencesKyoto Sangyo UniversityKyotoJapan,Center for Plant SciencesKyoto Sangyo UniversityKyotoJapan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry LaboratoryRIKEN Cluster for Pioneering ResearchSaitamaJapan,Department of Computational Biology and Medical SciencesGraduate School of Frontier SciencesThe University of TokyoChibaJapan
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38
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Kolář MH, Nagy G, Kunkel J, Vaiana SM, Bock LV, Grubmüller H. Folding of VemP into translation-arresting secondary structure is driven by the ribosome exit tunnel. Nucleic Acids Res 2022; 50:2258-2269. [PMID: 35150281 PMCID: PMC8887479 DOI: 10.1093/nar/gkac038] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 11/30/2021] [Accepted: 01/25/2022] [Indexed: 01/09/2023] Open
Abstract
The ribosome is a fundamental biomolecular complex that synthesizes proteins in cells. Nascent proteins emerge from the ribosome through a tunnel, where they may interact with the tunnel walls or small molecules such as antibiotics. These interactions can cause translational arrest with notable physiological consequences. Here, we studied the arrest caused by the regulatory peptide VemP, which is known to form α-helices inside the ribosome tunnel near the peptidyl transferase center under specific conditions. We used all-atom molecular dynamics simulations of the entire ribosome and circular dichroism spectroscopy to study the driving forces of helix formation and how VemP causes the translational arrest. To that aim, we compared VemP dynamics in the ribosome tunnel with its dynamics in solution. We show that the VemP peptide has a low helical propensity in water and that the propensity is higher in mixtures of water and trifluorethanol. We propose that helix formation within the ribosome is driven by the interactions of VemP with the tunnel and that a part of VemP acts as an anchor. This anchor might slow down VemP progression through the tunnel enabling α-helix formation, which causes the elongation arrest.
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Affiliation(s)
- Michal H Kolář
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 370 77 Göttingen, Germany.,Department of Physical Chemistry, University of Chemistry and Technology in Prague, Technická 5, 166 28 Prague, Czech Republic
| | - Gabor Nagy
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 370 77 Göttingen, Germany
| | - John Kunkel
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Sara M Vaiana
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Lars V Bock
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 370 77 Göttingen, Germany
| | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 370 77 Göttingen, Germany
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Joiret M, Kerff F, Rapino F, Close P, Geris L. Ribosome exit tunnel electrostatics. Phys Rev E 2022; 105:014409. [PMID: 35193250 DOI: 10.1103/physreve.105.014409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
The impact of ribosome exit tunnel electrostatics on the protein elongation rate or on forces acting upon the nascent polypeptide chain are currently not fully elucidated. In the past, researchers have measured the electrostatic potential inside the ribosome polypeptide exit tunnel at a limited number of spatial points, at least in rabbit reticulocytes. Here we present a basic electrostatic model of the exit tunnel of the ribosome, providing a quantitative physical description of the tunnel interaction with the nascent proteins at all centro-axial points inside the tunnel. We show that a strong electrostatic screening is due to water molecules (not mobile ions) attracted to the ribosomal nucleic acid phosphate moieties buried in the immediate vicinity of the tunnel wall. We also show how the tunnel wall components and local ribosomal protein protrusions impact on the electrostatic potential profile and impede charged amino acid residues from progressing through the tunnel, affecting the elongation rate in a range of -40% to +85% when compared to the average elongation rate. The time spent by the ribosome to decode the genetic encrypted message is constrained accordingly. We quantitatively derive, at single-residue resolution, the axial forces acting on the nascent peptide from its particular sequence embedded in the tunnel. The model sheds light on how the experimental data point measurements of the potential are linked to the local structural chemistry of the inner wall, shape, and size of the tunnel. The model consistently connects experimental observations coming from different fields in molecular biology, x-ray crystallography, physical chemistry, biomechanics, and synthetic and multiomics biology. Our model should be a valuable tool to gain insight into protein synthesis dynamics, translational control, and the role of the ribosome's mechanochemistry in the cotranslational protein folding.
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Affiliation(s)
- Marc Joiret
- Biomechanics Research Unit, GIGA In Silico Medicine, Liège University, CHU-B34(+5) 1 Avenue de l'Hôpital, 4000 Liège, Belgium
| | - Frederic Kerff
- UR InBios, Centre d'Ingénierie des Protéines, Bât B6a, Allée du 6 Août, 19, B-4000 Liège, Belgium
| | - Francesca Rapino
- Cancer Signaling, GIGA Stem Cells, CHU-B34(+2) 1 Avenue de l'Hôpital, B-4000 Liège, Belgium
| | - Pierre Close
- Cancer Signaling, GIGA Stem Cells, CHU-B34(+2) 1 Avenue de l'Hôpital, B-4000 Liège, Belgium
| | - Liesbet Geris
- Biomechanics Research Unit, GIGA In Silico Medicine, Liège University, CHU-B34(+5) 1 Avenue de l'Hôpital, 4000 Liège, Belgium
- Skeletal Biology & Engineering Research Center, KU Leuven, ON I Herestraat 49 - box 813, 3000 Leuven, Belgium
- Biomechanics Section, KU Leuven, Celestijnenlaan 300C box 2419, B-3001 Heverlee, Belgium
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40
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Kim KQ, Zaher HS. Canary in a coal mine: collided ribosomes as sensors of cellular conditions. Trends Biochem Sci 2022; 47:82-97. [PMID: 34607755 PMCID: PMC8688274 DOI: 10.1016/j.tibs.2021.09.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 08/30/2021] [Accepted: 09/03/2021] [Indexed: 02/06/2023]
Abstract
The recent discovery that collision of ribosomes triggers quality control and stress responses in eukaryotes has shifted the perspective of the field. Collided eukaryotic ribosomes adopt a unique structure, acting as a ubiquitin signaling platform for various response factors. While several of the signals that determine which downstream pathways are activated have been uncovered, we are only beginning to learn how the specificity for the activation of each process is achieved during collisions. This review will summarize those findings and how ribosome-associated factors act as molecular sentinels, linking aberrations in translation to the overall cellular state. Insights into how cells respond to ribosome collision events will provide greater understanding of the role of the ribosome in the maintenance of cellular homeostasis.
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Affiliation(s)
| | - Hani S. Zaher
- Correspondence to: , Department of Biology, Washington University in St. Louis, Campus Box 1137, One Brookings Drive, St. Louis, MO, USA 63130, Phone: (314) 935-7832, Fax: (314) 935-4432
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41
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Tirincsi A, Sicking M, Hadzibeganovic D, Haßdenteufel S, Lang S. The Molecular Biodiversity of Protein Targeting and Protein Transport Related to the Endoplasmic Reticulum. Int J Mol Sci 2021; 23:143. [PMID: 35008565 PMCID: PMC8745461 DOI: 10.3390/ijms23010143] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 12/15/2022] Open
Abstract
Looking at the variety of the thousands of different polypeptides that have been focused on in the research on the endoplasmic reticulum from the last five decades taught us one humble lesson: no one size fits all. Cells use an impressive array of components to enable the safe transport of protein cargo from the cytosolic ribosomes to the endoplasmic reticulum. Safety during the transit is warranted by the interplay of cytosolic chaperones, membrane receptors, and protein translocases that together form functional networks and serve as protein targeting and translocation routes. While two targeting routes to the endoplasmic reticulum, SRP (signal recognition particle) and GET (guided entry of tail-anchored proteins), prefer targeting determinants at the N- and C-terminus of the cargo polypeptide, respectively, the recently discovered SND (SRP-independent) route seems to preferentially cater for cargos with non-generic targeting signals that are less hydrophobic or more distant from the termini. With an emphasis on targeting routes and protein translocases, we will discuss those functional networks that drive efficient protein topogenesis and shed light on their redundant and dynamic nature in health and disease.
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Affiliation(s)
- Andrea Tirincsi
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
| | - Mark Sicking
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
| | - Drazena Hadzibeganovic
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
| | - Sarah Haßdenteufel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sven Lang
- Department of Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany; (A.T.); (M.S.); (D.H.)
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Tirumalai MR, Anane-Bediakoh D, Rajesh S, Fox GE. Net Charges of the Ribosomal Proteins of the S10 and spc Clusters of Halophiles Are Inversely Related to the Degree of Halotolerance. Microbiol Spectr 2021; 9:e0178221. [PMID: 34908470 PMCID: PMC8672879 DOI: 10.1128/spectrum.01782-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 11/24/2021] [Indexed: 11/20/2022] Open
Abstract
Net positive charge(s) on ribosomal proteins (r-proteins) have been reported to influence the assembly and folding of ribosomes. A high percentage of r-proteins from extremely halophilic archaea are known to be acidic or even negatively charged. Those proteins that remain positively charged are typically far less positively charged. Here, the analysis is extended to non-archaeal halophilic bacteria, eukaryotes, and halotolerant archaea. The net charges (pH 7.4) of the r-proteins that comprise the S10-spc operon/cluster from individual microbial and eukaryotic genomes were estimated and intercompared. It was observed that, as a general rule, the net charges of individual proteins remained mostly basic as the salt tolerance of the bacterial strains increased from 5 to 15%. The most striking exceptions were the extremely halophilic bacterial strains, Salinibacter ruber SD01, Acetohalobium arabaticum DSM 5501 and Selenihalanaerobacter shriftii ATCC BAA-73, which are reported to require a minimum of 18% to 21% salt for their growth. All three strains have higher numbers of acidic S10-spc cluster r-proteins than what is seen in the moderate halophiles or the halotolerant strains. Of the individual proteins, only uL2 never became acidic. uS14 and uL16 also seldom became acidic. The net negative charges on several of the S10-spc cluster r-proteins are a feature generally shared by all extremely halophilic archaea and bacteria. The S10-spc cluster r-proteins of halophilic fungi and algae (eukaryotes) were exceptions: these were positively charged despite the halophilicity of the organisms. IMPORTANCE The net charges (at pH 7.4) of the ribosomal proteins (r-proteins) that comprise the S10-spc cluster show an inverse relationship with the halophilicity/halotolerance levels in both bacteria and archaea. In non-halophilic bacteria, the S10-spc cluster r-proteins are generally basic (positively charged), while the rest of the proteomes in these strains are generally acidic. On the other hand, the whole proteomes of the extremely halophilic strains are overall negatively charged, including the S10-spc cluster r-proteins. Given that the distribution of charged residues in the ribosome exit tunnel influences cotranslational folding, the contrasting charges observed in the S10-spc cluster r-proteins have potential implications for the rate of passage of these proteins through the ribosomal exit tunnel. Furthermore, the universal protein uL2, which lies in the oldest part of the ribosome, is always positively charged irrespective of the strain/organism it belongs to. This has implications for its role in the prebiotic context.
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Affiliation(s)
- Madhan R. Tirumalai
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| | | | - Sidharth Rajesh
- Clements High School (Class of 2023), Fort Bend Independent School District, Sugar Land, Texas, USA
| | - George E. Fox
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
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43
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Ubiquitin Ligase Redundancy and Nuclear-Cytoplasmic Localization in Yeast Protein Quality Control. Biomolecules 2021; 11:biom11121821. [PMID: 34944465 PMCID: PMC8698790 DOI: 10.3390/biom11121821] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 12/12/2022] Open
Abstract
The diverse functions of proteins depend on their proper three-dimensional folding and assembly. Misfolded cellular proteins can potentially harm cells by forming aggregates in their resident compartments that can interfere with vital cellular processes or sequester important factors. Protein quality control (PQC) pathways are responsible for the repair or destruction of these abnormal proteins. Most commonly, the ubiquitin-proteasome system (UPS) is employed to recognize and degrade those proteins that cannot be refolded by molecular chaperones. Misfolded substrates are ubiquitylated by a subset of ubiquitin ligases (also called E3s) that operate in different cellular compartments. Recent research in Saccharomyces cerevisiae has shown that the most prominent ligases mediating cytoplasmic and nuclear PQC have overlapping yet distinct substrate specificities. Many substrates have been characterized that can be targeted by more than one ubiquitin ligase depending on their localization, and cytoplasmic PQC substrates can be directed to the nucleus for ubiquitylation and degradation. Here, we review some of the major yeast PQC ubiquitin ligases operating in the nucleus and cytoplasm, as well as current evidence indicating how these ligases can often function redundantly toward substrates in these compartments.
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44
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Perach M, Zafrir Z, Tuller T, Lewinson O. Identification of conserved slow codons that are important for protein expression and function. RNA Biol 2021; 18:2296-2307. [PMID: 33691590 PMCID: PMC8632084 DOI: 10.1080/15476286.2021.1901185] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 02/28/2021] [Accepted: 03/06/2021] [Indexed: 10/21/2022] Open
Abstract
ABSTRASTDue to the redundancy of the genetic code most amino acids are encoded by several 'synonymous' codons. These codons are used unevenly, and each organism demonstrates its own unique codon usage bias, where the 'preferred' codons are associated with tRNAs that are found in high concentrations. Therefore, for decades, the prevailing view had been that preferred and non-preferred codons are linked to high or slow translation rates, respectively.However, this simplified view is contrasted by the frequent failures of codon-optimization efforts and by evidence of non-preferred (i.e. 'slow') codons having specific roles important for efficient production of functional proteins. One such specific role of slower codons is the regulation of co-translational protein folding, a complex biophysical process that is very challenging to model or to measure.Here, we combined a genome-wide approach with experiments to investigate the role of slow codons in protein production and co-translational folding. We analysed homologous gene groups from divergent bacteria and identified positions of inter-species conservation of bias towards slow codons. We then generated mutants where the conserved slow codons are substituted with 'fast' ones, and experimentally studied the effects of these codon substitutions. Using cellular and biochemical approaches we find that at certain locations, slow-to-fast codon substitutions reduce protein expression, increase protein aggregation, and impair protein function.This report provides an approach for identifying functionally relevant regions with slower codons and demonstrates that such codons are important for protein expression and function.
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Affiliation(s)
- Michal Perach
- Department of Molecular Microbiology, the Bruce and Ruth Rappaport Faculty of Medicine, The Technion-Israel Institute of Technology, Haifa, Israel
| | - Zohar Zafrir
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Oded Lewinson
- Department of Molecular Microbiology, the Bruce and Ruth Rappaport Faculty of Medicine, The Technion-Israel Institute of Technology, Haifa, Israel
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45
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Park J, Lee J, Kim JH, Lee J, Park H, Lim C. ZNF598 co-translationally titrates poly(GR) protein implicated in the pathogenesis of C9ORF72-associated ALS/FTD. Nucleic Acids Res 2021; 49:11294-11311. [PMID: 34551427 PMCID: PMC8565315 DOI: 10.1093/nar/gkab834] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 09/09/2021] [Indexed: 11/13/2022] Open
Abstract
C9ORF72-derived dipeptide repeat proteins have emerged as the pathogenic cause of neurodegeneration in amyotrophic lateral sclerosis and frontotemporal dementia (C9-ALS/FTD). However, the mechanisms underlying their expression are not fully understood. Here, we demonstrate that ZNF598, the rate-limiting factor for ribosome-associated quality control (RQC), co-translationally titrates the expression of C9ORF72-derived poly(GR) protein. A Drosophila genetic screen identified key RQC factors as potent modifiers of poly(GR)-induced neurodegeneration. ZNF598 overexpression in human neuroblastoma cells inhibited the nuclear accumulation of poly(GR) protein and decreased its cytotoxicity, whereas ZNF598 deletion had opposing effects. Poly(GR)-encoding sequences in the reporter RNAs caused translational stalling and generated ribosome-associated translation products, sharing molecular signatures with canonical RQC substrates. Furthermore, ZNF598 and listerin 1, the RQC E3 ubiquitin-protein ligase, promoted poly(GR) degradation via the ubiquitin-proteasome pathway. An ALS-relevant ZNF598R69C mutant displayed loss-of-function effects on poly(GR) expression, as well as on general RQC. Moreover, RQC function was impaired in C9-ALS patient-derived neurons, whereas lentiviral overexpression of ZNF598 lowered their poly(GR) expression and suppressed proapoptotic caspase-3 activation. Taken together, we propose that an adaptive nature of the RQC-relevant ZNF598 activity allows the co-translational surveillance to cope with the atypical expression of pathogenic poly(GR) protein, thereby acquiring a neuroprotective function in C9-ALS/FTD.
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Affiliation(s)
- Jumin Park
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Jongbo Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Ji-Hyung Kim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Jongbin Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Heeju Park
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Chunghun Lim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
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46
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Plessa E, Chu LP, Chan SHS, Thomas OL, Cassaignau AME, Waudby CA, Christodoulou J, Cabrita LD. Nascent chains can form co-translational folding intermediates that promote post-translational folding outcomes in a disease-causing protein. Nat Commun 2021; 12:6447. [PMID: 34750347 PMCID: PMC8576036 DOI: 10.1038/s41467-021-26531-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 10/01/2021] [Indexed: 01/16/2023] Open
Abstract
During biosynthesis, proteins can begin folding co-translationally to acquire their biologically-active structures. Folding, however, is an imperfect process and in many cases misfolding results in disease. Less is understood of how misfolding begins during biosynthesis. The human protein, alpha-1-antitrypsin (AAT) folds under kinetic control via a folding intermediate; its pathological variants readily form self-associated polymers at the site of synthesis, leading to alpha-1-antitrypsin deficiency. We observe that AAT nascent polypeptides stall during their biosynthesis, resulting in full-length nascent chains that remain bound to ribosome, forming a persistent ribosome-nascent chain complex (RNC) prior to release. We analyse the structure of these RNCs, which reveals compacted, partially-folded co-translational folding intermediates possessing molten-globule characteristics. We find that the highly-polymerogenic mutant, Z AAT, forms a distinct co-translational folding intermediate relative to wild-type. Its very modest structural differences suggests that the ribosome uniquely tempers the impact of deleterious mutations during nascent chain emergence. Following nascent chain release however, these co-translational folding intermediates guide post-translational folding outcomes thus suggesting that Z's misfolding is initiated from co-translational structure. Our findings demonstrate that co-translational folding intermediates drive how some proteins fold under kinetic control, and may thus also serve as tractable therapeutic targets for human disease.
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Affiliation(s)
- Elena Plessa
- Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Lien P Chu
- Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Sammy H S Chan
- Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Oliver L Thomas
- Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Anaïs M E Cassaignau
- Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Christopher A Waudby
- Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - John Christodoulou
- Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK. .,School of Crystallography, Birkbeck College, University of London, Malet Street, London, WC1E 7HX, UK.
| | - Lisa D Cabrita
- Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK.
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47
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Leininger SE, Rodriguez J, Vu QV, Jiang Y, Li MS, Deutsch C, O'Brien EP. Ribosome Elongation Kinetics of Consecutively Charged Residues Are Coupled to Electrostatic Force. Biochemistry 2021; 60:3223-3235. [PMID: 34652913 DOI: 10.1021/acs.biochem.1c00507] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The speed of protein synthesis can dramatically change when consecutively charged residues are incorporated into an elongating nascent protein by the ribosome. The molecular origins of this class of allosteric coupling remain unknown. We demonstrate, using multiscale simulations, that positively charged residues generate large forces that move the P-site amino acid away from the A-site amino acid. Negatively charged residues generate forces of similar magnitude but move the A- and P-sites closer together. These conformational changes, respectively, increase and decrease the transition state barrier height to peptide bond formation, explaining how charged residues mechanochemically alter translation speed. This mechanochemical mechanism is consistent with in vivo ribosome profiling data exhibiting proportionality between translation speed and the number of charged residues, experimental data characterizing nascent chain conformations, and a previously published cryo-EM structure of a ribosome-nascent chain complex containing consecutive lysines. These results expand the role of mechanochemistry in translation and provide a framework for interpreting experimental results on translation speed.
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Affiliation(s)
- Sarah E Leininger
- Department of Chemistry, Penn State University, University Park, Pennsylvania 16802, United States
| | - Judith Rodriguez
- Bioinformatics and Genomics Graduate Program, Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania 16802, United States
| | - Quyen V Vu
- Institute of Physics, Polish Academy of Sciences, Warsaw 02-668, Poland
| | - Yang Jiang
- Department of Chemistry, Penn State University, University Park, Pennsylvania 16802, United States
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Warsaw 02-668, Poland.,Institute for Computational Sciences and Technology, Ho Chi Minh City 700000, Vietnam
| | - Carol Deutsch
- Department of Physiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Edward P O'Brien
- Department of Chemistry, Penn State University, University Park, Pennsylvania 16802, United States.,Bioinformatics and Genomics Graduate Program, Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania 16802, United States.,Institute for Computational and Data Sciences, Penn State University, University Park, Pennsylvania 16802, United States
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48
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Bui PT, Hoang TX. Hydrophobic and electrostatic interactions modulate protein escape at the ribosomal exit tunnel. Biophys J 2021; 120:4798-4808. [PMID: 34555360 DOI: 10.1016/j.bpj.2021.09.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 08/04/2021] [Accepted: 09/15/2021] [Indexed: 11/17/2022] Open
Abstract
After translation, nascent proteins must escape the ribosomal exit tunnel to attain complete folding to their native states. This escape process also frees up the ribosome tunnel for a new translation job. In this study, we investigate the impacts of energetic interactions between the ribosomal exit tunnel and nascent proteins on the protein escape process by molecular dynamics simulations using partially coarse-grained models that incorporate hydrophobic and electrostatic interactions of the ribosome tunnel of Haloarcula marismortui with nascent proteins. We find that, in general, attractive interactions slow down the protein escape process, whereas repulsive interactions speed it up. For the small globular proteins considered, the median escape time correlates with both the number of hydrophobic residues, Nh, and the net charge, Q, of a nascent protein. A correlation coefficient exceeding 0.96 is found for the relation between the median escape time and a combined quantity of Nh + 5.9Q, suggesting that it is ∼6 times more efficient to modulate the escape time by changing the total charge than the number of hydrophobic residues. The estimated median escape times are found in the submillisecond-to-millisecond range, indicating that the escape does not delay the ribosome recycling. For various types of the tunnel model, with and without hydrophobic and electrostatic interactions, the escape time distribution always follows a simple diffusion model that describes the escape process as a downhill drift of a Brownian particle, suggesting that nascent proteins escape along barrier-less pathways at the ribosome tunnel.
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Affiliation(s)
- Phuong Thuy Bui
- Institute of Theoretical and Applied Research, Duy Tan University, Hanoi, Vietnam; Faculty of Pharmacy, Duy Tan University, Da Nang, Vietnam
| | - Trinh Xuan Hoang
- Institute of Physics, Vietnam Academy of Science and Technology, Ba Dinh, Hanoi, Vietnam; Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Cau Giay, Hanoi, Vietnam.
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49
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Morris C, Cluet D, Ricci EP. Ribosome dynamics and mRNA turnover, a complex relationship under constant cellular scrutiny. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 12:e1658. [PMID: 33949788 PMCID: PMC8519046 DOI: 10.1002/wrna.1658] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/26/2021] [Accepted: 03/26/2021] [Indexed: 12/01/2022]
Abstract
Eukaryotic gene expression is closely regulated by translation and turnover of mRNAs. Recent advances highlight the importance of translation in the control of mRNA degradation, both for aberrant and apparently normal mRNAs. During translation, the information contained in mRNAs is decoded by ribosomes, one codon at a time, and tRNAs, by specifically recognizing codons, translate the nucleotide code into amino acids. Such a decoding step does not process regularly, with various obstacles that can hinder ribosome progression, then leading to ribosome stalling or collisions. The progression of ribosomes is constantly monitored by the cell which has evolved several translation-dependent mRNA surveillance pathways, including nonsense-mediated decay (NMD), no-go decay (NGD), and non-stop decay (NSD), to degrade certain problematic mRNAs and the incomplete protein products. Recent progress in sequencing and ribosome profiling has made it possible to discover new mechanisms controlling ribosome dynamics, with numerous crosstalks between translation and mRNA decay. We discuss here various translation features critical for mRNA decay, with particular focus on current insights from the complexity of the genetic code and also the emerging role for the ribosome as a regulatory hub orchestrating mRNA decay, quality control, and stress signaling. Even if the interplay between mRNA translation and degradation is no longer to be demonstrated, a better understanding of their precise coordination is worthy of further investigation. This article is categorized under: RNA Turnover and Surveillance > Regulation of RNA Stability Translation > Translation Regulation RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
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Affiliation(s)
- Christelle Morris
- Laboratory of Biology and Modeling of the CellUniversité de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, Inserm U1293LyonFrance
| | - David Cluet
- Laboratory of Biology and Modeling of the CellUniversité de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, Inserm U1293LyonFrance
| | - Emiliano P. Ricci
- Laboratory of Biology and Modeling of the CellUniversité de Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, Inserm U1293LyonFrance
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Jakutis G, Stainier DYR. Genotype-Phenotype Relationships in the Context of Transcriptional Adaptation and Genetic Robustness. Annu Rev Genet 2021; 55:71-91. [PMID: 34314597 DOI: 10.1146/annurev-genet-071719-020342] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genetic manipulations with a robust and predictable outcome are critical to investigate gene function, as well as for therapeutic genome engineering. For many years, knockdown approaches and reagents including RNA interference and antisense oligonucleotides dominated functional studies; however, with the advent of precise genome editing technologies, CRISPR-based knockout systems have become the state-of-the-art tools for such studies. These technologies have helped decipher the role of thousands of genes in development and disease. Their use has also revealed how limited our understanding of genotype-phenotype relationships is. The recent discovery that certain mutations can trigger the transcriptional modulation of other genes, a phenomenon called transcriptional adaptation, has provided an additional explanation for the contradicting phenotypes observed in knockdown versus knockout models and increased awareness about the use of each of these approaches. In this review, we first cover the strengths and limitations of different gene perturbation strategies. Then we highlight the diverse ways in which the genotype-phenotype relationship can be discordant between these different strategies. Finally, we review the genetic robustness mechanisms that can lead to such discrepancies, paying special attention to the recently discovered phenomenon of transcriptional adaptation. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Gabrielius Jakutis
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany;
| | - Didier Y R Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany; .,German Centre for Cardiovascular Research (DZHK), Partner site Rhine-Main, 60590 Frankfurt am Main, Germany.,Excellence Cluster Cardio-Pulmonary Institute (CPI), 35392 Giessen, Germany
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