51
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D'Orazio KN, Green R. Ribosome states signal RNA quality control. Mol Cell 2021; 81:1372-1383. [PMID: 33713598 PMCID: PMC8041214 DOI: 10.1016/j.molcel.2021.02.022] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/04/2021] [Accepted: 02/17/2021] [Indexed: 12/18/2022]
Abstract
Eukaryotic cells integrate multiple quality control (QC) responses during protein synthesis in the cytoplasm. These QC responses are signaled by slow or stalled elongating ribosomes. Depending on the nature of the delay, the signal may lead to translational repression, messenger RNA decay, ribosome rescue, and/or nascent protein degradation. Here, we discuss how the structure and composition of an elongating ribosome in a troubled state determine the downstream quality control pathway(s) that ensue. We highlight the intersecting pathways involved in RNA decay and the crosstalk that occurs between RNA decay and ribosome rescue.
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Affiliation(s)
- Karole N D'Orazio
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rachel Green
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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52
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Yang J, Han YH, Im J, Seo SW. Synthetic protein quality control to enhance full-length translation in bacteria. Nat Chem Biol 2021; 17:421-427. [PMID: 33542534 DOI: 10.1038/s41589-021-00736-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 01/08/2021] [Indexed: 01/30/2023]
Abstract
Coupled transcription and translation processes in bacteria cause indiscriminate translation of intact and truncated messenger RNAs, inevitably generating nonfunctional polypeptides. Here, we devised a synthetic protein quality control (ProQC) system that enables translation only when both ends of mRNAs are present and followed by circularization based on sequence-specific RNA-RNA hybridization. We demonstrate that the ProQC system dramatically improved the fraction of full-length proteins among all synthesized polypeptides by selectively translating intact mRNA and reducing abortive translation. As a result, full-length protein synthesis increased up to 2.5-fold without changing the transcription or translation efficiency. Furthermore, we applied the ProQC system for 3-hydroxypropionic acid, violacein and lycopene production by ensuring full-length expression of enzymes in biosynthetic pathways, resulting in 1.6- to 2.3-fold greater biochemical production. We believe that our ProQC system can be universally applied to improve not only the quality of recombinant protein production but also efficiencies of metabolic pathways.
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Affiliation(s)
- Jina Yang
- School of Chemical and Biological Engineering, Seoul National University, Seoul, Korea.,Institute of Chemical Processes, Seoul National University, Seoul, Korea
| | - Yong Hee Han
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, Korea
| | - Jongwon Im
- School of Chemical and Biological Engineering, Seoul National University, Seoul, Korea
| | - Sang Woo Seo
- School of Chemical and Biological Engineering, Seoul National University, Seoul, Korea. .,Institute of Chemical Processes, Seoul National University, Seoul, Korea. .,Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, Korea. .,Bio-MAX Institute, Seoul National University, Seoul, Korea. .,Institute of Engineering Research, Seoul National University, Seoul, Korea.
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53
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Influence of nascent polypeptide positive charges on translation dynamics. Biochem J 2021; 477:2921-2934. [PMID: 32797214 DOI: 10.1042/bcj20200303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 07/17/2020] [Accepted: 07/23/2020] [Indexed: 01/05/2023]
Abstract
Protein segments with a high concentration of positively charged amino acid residues are often used in reporter constructs designed to activate ribosomal mRNA/protein decay pathways, such as those involving nonstop mRNA decay (NSD), no-go mRNA decay (NGD) and the ribosome quality control (RQC) complex. It has been proposed that the electrostatic interaction of the positively charged nascent peptide with the negatively charged ribosomal exit tunnel leads to translation arrest. When stalled long enough, the translation process is terminated with the degradation of the transcript and an incomplete protein. Although early experiments made a strong argument for this mechanism, other features associated with positively charged reporters, such as codon bias and mRNA and protein structure, have emerged as potent inducers of ribosome stalling. We carefully reviewed the published data on the protein and mRNA expression of artificial constructs with diverse compositions as assessed in different organisms. We concluded that, although polybasic sequences generally lead to lower translation efficiency, it appears that an aggravating factor, such as a nonoptimal codon composition, is necessary to cause translation termination events.
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54
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Udagawa T, Seki M, Okuyama T, Adachi S, Natsume T, Noguchi T, Matsuzawa A, Inada T. Failure to Degrade CAT-Tailed Proteins Disrupts Neuronal Morphogenesis and Cell Survival. Cell Rep 2021; 34:108599. [PMID: 33406423 DOI: 10.1016/j.celrep.2020.108599] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 07/24/2020] [Accepted: 12/14/2020] [Indexed: 12/25/2022] Open
Abstract
Ribosome-associated quality control (RQC) relieves stalled ribosomes and eliminates potentially toxic nascent polypeptide chains (NCs) that can cause neurodegeneration. During RQC, RQC2 modifies NCs with a C-terminal alanine and threonine (CAT) tail. CAT tailing promotes ubiquitination of NCs for proteasomal degradation, while RQC failure in budding yeast disrupts proteostasis via CAT-tailed NC aggregation. However, the CAT tail and its cytotoxicity in mammals have remained largely uncharacterized. We demonstrate that NEMF, a mammalian RQC2 homolog, modifies translation products of nonstop mRNAs, major erroneous mRNAs in mammals, with a C-terminal tail mainly composed of alanine with several other amino acids. Overproduction of nonstop mRNAs induces NC aggregation and caspase-3-dependent apoptosis and impairs neuronal morphogenesis, which are ameliorated by NEMF depletion. Moreover, we found that homopolymeric alanine tailing at least partially accounts for CAT-tail cytotoxicity. These findings explain the cytotoxicity of CAT-tailed NCs and demonstrate physiological significance of RQC on proper neuronal morphogenesis and cell survival.
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Affiliation(s)
- Tsuyoshi Udagawa
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan.
| | - Moeka Seki
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Taku Okuyama
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Shungo Adachi
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan
| | - Tohru Natsume
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan
| | - Takuya Noguchi
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Atsushi Matsuzawa
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Toshifumi Inada
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan.
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55
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Barros GC, Requião RD, Carneiro RL, Masuda CA, Moreira MH, Rossetto S, Domitrovic T, Palhano FL. Rqc1 and other yeast proteins containing highly positively charged sequences are not targets of the RQC complex. J Biol Chem 2021; 296:100586. [PMID: 33774050 PMCID: PMC8102910 DOI: 10.1016/j.jbc.2021.100586] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 03/12/2021] [Accepted: 03/23/2021] [Indexed: 02/06/2023] Open
Abstract
Previous work has suggested that highly positively charged protein segments coded by rare codons or poly (A) stretches induce ribosome stalling and translational arrest through electrostatic interactions with the negatively charged ribosome exit tunnel, leading to inefficient elongation. This arrest leads to the activation of the Ribosome Quality Control (RQC) pathway and results in low expression of these reporter proteins. However, the only endogenous yeast proteins known to activate the RQC are Rqc1, a protein essential for RQC function, and Sdd1, a protein with unknown function, both of which contain polybasic sequences. To explore the generality of this phenomenon, we investigated whether the RQC complex controls the expression of other proteins with polybasic sequences. We showed by ribosome profiling data analysis and western blot that proteins containing polybasic sequences similar to, or even more positively charged than those of Rqc1 and Sdd1, were not targeted by the RQC complex. We also observed that the previously reported Ltn1-dependent regulation of Rqc1 is posttranslational, independent of the RQC activity. Taken together, our results suggest that RQC should not be regarded as a general regulatory pathway for the expression of highly positively charged proteins in yeast.
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Affiliation(s)
- Géssica C Barros
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Rodrigo D Requião
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Rodolfo L Carneiro
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Claudio A Masuda
- Programa de Biologia Molecular e Biotecnologia, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Mariana H Moreira
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Silvana Rossetto
- Departamento de Ciência da Computação, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Tatiana Domitrovic
- Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
| | - Fernando L Palhano
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
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56
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Roudko V, Bozkus CC, Orfanelli T, McClain CB, Carr C, O'Donnell T, Chakraborty L, Samstein R, Huang KL, Blank SV, Greenbaum B, Bhardwaj N. Shared Immunogenic Poly-Epitope Frameshift Mutations in Microsatellite Unstable Tumors. Cell 2020; 183:1634-1649.e17. [PMID: 33259803 PMCID: PMC8025604 DOI: 10.1016/j.cell.2020.11.004] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 06/22/2020] [Accepted: 11/02/2020] [Indexed: 12/20/2022]
Abstract
Microsatellite instability-high (MSI-H) tumors are characterized by high tumor mutation burden and responsiveness to checkpoint blockade. We identified tumor-specific frameshifts encoding multiple epitopes that originated from indel mutations shared among patients with MSI-H endometrial, colorectal, and stomach cancers. Epitopes derived from these shared frameshifts have high population occurrence rates, wide presence in many tumor subclones, and are predicted to bind to the most frequent MHC alleles in MSI-H patient cohorts. Neoantigens arising from these mutations are distinctly unlike self and viral antigens, signifying novel groups of potentially highly immunogenic tumor antigens. We further confirmed the immunogenicity of frameshift peptides in T cell stimulation experiments using blood mononuclear cells isolated from both healthy donors and MSI-H cancer patients. Our study uncovers the widespread occurrence and strong immunogenicity of tumor-specific antigens derived from shared frameshift mutations in MSI-H cancer and Lynch syndrome patients, suitable for the design of common "off-the-shelf" cancer vaccines.
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Affiliation(s)
- Vladimir Roudko
- Department of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, USA
| | - Cansu Cimen Bozkus
- Department of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, USA
| | - Theofano Orfanelli
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, USA; The Blavatnik Family Women's Health Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Christopher B McClain
- Department of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, USA
| | - Caitlin Carr
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, USA; The Blavatnik Family Women's Health Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Timothy O'Donnell
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, USA
| | - Lauren Chakraborty
- Department of Biological Sciences, University of Chicago, Chicago, IL, USA
| | - Robert Samstein
- Department of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, USA
| | - Kuan-Lin Huang
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, USA
| | - Stephanie V Blank
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, USA; The Blavatnik Family Women's Health Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Benjamin Greenbaum
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nina Bhardwaj
- Department of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, USA.
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57
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Desai N, Yang H, Chandrasekaran V, Kazi R, Minczuk M, Ramakrishnan V. Elongational stalling activates mitoribosome-associated quality control. Science 2020; 370:1105-1110. [PMID: 33243891 PMCID: PMC7116630 DOI: 10.1126/science.abc7782] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 09/24/2020] [Indexed: 02/02/2023]
Abstract
The human mitochondrial ribosome (mitoribosome) and associated proteins regulate the synthesis of 13 essential subunits of the oxidative phosphorylation complexes. We report the discovery of a mitoribosome-associated quality control pathway that responds to interruptions during elongation, and we present structures at 3.1- to 3.3-angstrom resolution of mitoribosomal large subunits trapped during ribosome rescue. Release factor homolog C12orf65 (mtRF-R) and RNA binding protein C6orf203 (MTRES1) eject the nascent chain and peptidyl transfer RNA (tRNA), respectively, from stalled ribosomes. Recruitment of mitoribosome biogenesis factors to these quality control intermediates suggests additional roles for these factors during mitoribosome rescue. We also report related cryo-electron microscopy structures (3.7 to 4.4 angstrom resolution) of elongating mitoribosomes bound to tRNAs, nascent polypeptides, the guanosine triphosphatase elongation factors mtEF-Tu and mtEF-G1, and the Oxa1L translocase.
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Affiliation(s)
- Nirupa Desai
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Hanting Yang
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | - Razina Kazi
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Michal Minczuk
- MRC Mitochondrial Biology Unit, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - V. Ramakrishnan
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK,Corresponding author.
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58
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Phillips BP, Miller EA. Ribosome-associated quality control of membrane proteins at the endoplasmic reticulum. J Cell Sci 2020; 133:133/22/jcs251983. [PMID: 33247003 PMCID: PMC7116877 DOI: 10.1242/jcs.251983] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Protein synthesis is an energetically costly, complex and risky process. Aberrant protein biogenesis can result in cellular toxicity and disease, with membrane-embedded proteins being particularly challenging for the cell. In order to protect the cell from consequences of defects in membrane proteins, quality control systems act to maintain protein homeostasis. The majority of these pathways act post-translationally; however, recent evidence reveals that membrane proteins are also subject to co-translational quality control during their synthesis in the endoplasmic reticulum (ER). This newly identified quality control pathway employs components of the cytosolic ribosome-associated quality control (RQC) machinery but differs from canonical RQC in that it responds to biogenesis state of the substrate rather than mRNA aberrations. This ER-associated RQC (ER-RQC) is sensitive to membrane protein misfolding and malfunctions in the ER insertion machinery. In this Review, we discuss the advantages of co-translational quality control of membrane proteins, as well as potential mechanisms of substrate recognition and degradation. Finally, we discuss some outstanding questions concerning future studies of ER-RQC of membrane proteins.
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Affiliation(s)
- Ben P Phillips
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
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59
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Hickey KL, Dickson K, Cogan JZ, Replogle JM, Schoof M, D'Orazio KN, Sinha NK, Hussmann JA, Jost M, Frost A, Green R, Weissman JS, Kostova KK. GIGYF2 and 4EHP Inhibit Translation Initiation of Defective Messenger RNAs to Assist Ribosome-Associated Quality Control. Mol Cell 2020; 79:950-962.e6. [PMID: 32726578 PMCID: PMC7891188 DOI: 10.1016/j.molcel.2020.07.007] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 07/07/2020] [Accepted: 07/07/2020] [Indexed: 12/31/2022]
Abstract
Ribosome-associated quality control (RQC) pathways protect cells from toxicity caused by incomplete protein products resulting from translation of damaged or problematic mRNAs. Extensive work in yeast has identified highly conserved mechanisms that lead to degradation of faulty mRNA and partially synthesized polypeptides. Here we used CRISPR-Cas9-based screening to search for additional RQC strategies in mammals. We found that failed translation leads to specific inhibition of translation initiation on that message. This negative feedback loop is mediated by two translation inhibitors, GIGYF2 and 4EHP. Model substrates and growth-based assays established that inhibition of additional rounds of translation acts in concert with known RQC pathways to prevent buildup of toxic proteins. Inability to block translation of faulty mRNAs and subsequent accumulation of partially synthesized polypeptides could explain the neurodevelopmental and neuropsychiatric disorders observed in mice and humans with compromised GIGYF2 function.
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Affiliation(s)
- Kelsey L Hickey
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kimberley Dickson
- Department of Biology, Lawerence University, Appleton, WI 54911, USA
| | - J Zachery Cogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Joseph M Replogle
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Michael Schoof
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Karole N D'Orazio
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Niladri K Sinha
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jeffrey A Hussmann
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Marco Jost
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Adam Frost
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Rachel Green
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA; Howard Hughes Medical Institute, Carnegie Institution for Science, Baltimore, MD 21218, USA
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, Carnegie Institution for Science, Baltimore, MD 21218, USA.
| | - Kamena K Kostova
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA.
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60
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Dhamija S, Yang CM, Seiler J, Myacheva K, Caudron-Herger M, Wieland A, Abdelkarim M, Sharma Y, Riester M, Groß M, Maurer J, Diederichs S. A pan-cancer analysis reveals nonstop extension mutations causing SMAD4 tumour suppressor degradation. Nat Cell Biol 2020; 22:999-1010. [DOI: 10.1038/s41556-020-0551-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 06/25/2020] [Indexed: 12/26/2022]
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61
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Powers KT, Szeto JYA, Schaffitzel C. New insights into no-go, non-stop and nonsense-mediated mRNA decay complexes. Curr Opin Struct Biol 2020; 65:110-118. [PMID: 32688260 DOI: 10.1016/j.sbi.2020.06.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 06/10/2020] [Accepted: 06/18/2020] [Indexed: 11/26/2022]
Abstract
Eukaryotes possess a variety of translational control mechanisms which function in the surveillance of mRNAs, discriminating between normal and aberrant translation elongation and termination, triggering mRNA decay. The three major evolutionarily conserved eukaryotic pathways are No-Go, Non-Stop and Nonsense-Mediated mRNA Decay. Recent findings suggest that stalling of the ribosome, due to mRNA secondary structure or translation into poly(A)-stretches, leads to ribosome collisions which are detected by No-Go/Non-Stop mRNA decay factors. Subsequent ribosome ubiquitination at the interface of two collided ribosomes is considered the signal for mRNA decay. Similarly, translation termination at a premature stop codon is slower than normal, leading to recruitment and activation of nonsense-mediated mRNA decay factors, including SMG1-8-9. Here, we detail new insights into the molecular mechanisms of these pathways.
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Affiliation(s)
- Kyle T Powers
- University of Bristol, School of Biochemistry, University Walk, Bristol, BS8 1TD, United Kingdom
| | - Jenn-Yeu Alvin Szeto
- University of Bristol, School of Biochemistry, University Walk, Bristol, BS8 1TD, United Kingdom
| | - Christiane Schaffitzel
- University of Bristol, School of Biochemistry, University Walk, Bristol, BS8 1TD, United Kingdom.
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62
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Kramarski L, Arbely E. Translational read-through promotes aggregation and shapes stop codon identity. Nucleic Acids Res 2020; 48:3747-3760. [PMID: 32128584 PMCID: PMC7144920 DOI: 10.1093/nar/gkaa136] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 02/07/2020] [Accepted: 02/22/2020] [Indexed: 12/14/2022] Open
Abstract
Faithful translation of genetic information depends on the ability of the translational machinery to decode stop codons as termination signals. Although termination of protein synthesis is highly efficient, errors in decoding of stop codons may lead to the synthesis of C-terminally extended proteins. It was found that in eukaryotes such elongated proteins do not accumulate in cells. However, the mechanism for sequestration of C-terminally extended proteins is still unknown. Here we show that 3′-UTR-encoded polypeptides promote aggregation of the C-terminally extended proteins, and targeting to lysosomes. We demonstrate that 3′-UTR-encoded polypeptides can promote different levels of protein aggregation, similar to random sequences. We also show that aggregation of endogenous proteins can be induced by aminoglycoside antibiotics that promote stop codon read-through, by UAG suppressor tRNA, or by knokcdown of release factor 1. Furthermore, we find correlation between the fidelity of termination signals, and the predicted propensity of downstream 3′-UTR-encoded polypeptides to form intrinsically disordered regions. Our data highlight a new quality control mechanism for elimination of C-terminally elongated proteins.
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Affiliation(s)
- Lior Kramarski
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Eyal Arbely
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel.,Department of Chemistry and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
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63
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Nagao M, Tsuchiya F, Motohashi R, Abo T. Ribosome rescue activity of an Arabidopsis thaliana ArfB homolog. Genes Genet Syst 2020; 95:119-131. [PMID: 32611934 DOI: 10.1266/ggs.20-00007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
A homolog of the bacterial ribosome rescue factor ArfB was identified in Arabidopsis thaliana. The factor, named AtArfB for Arabidopsis thaliana ArfB, showed ribosome rescue activity in both in vivo and in vitro assays based on the bacterial translation system. As has been shown for ArfB, the ribosome rescue activity of AtArfB was dependent on the GGQ motif, the crucial motif for the function of class I release factors and ArfB. The C-terminal region of AtArfB was also important for its function. The N-terminal region of AtArfB, which is absent in bacterial ArfB, functioned as a transit peptide for chloroplast targeting in tobacco cells. These results strongly suggest that AtArfB is a ribosome rescue factor that functions in chloroplasts.
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Affiliation(s)
- Michiaki Nagao
- Graduate School of Natural Science and Technology, Okayama University
| | - Fumina Tsuchiya
- Graduate School of Integrated Science and Technology, Shizuoka University
| | - Reiko Motohashi
- Graduate School of Integrated Science and Technology, Shizuoka University.,Research Institute of Green Science and Technology, Shizuoka University
| | - Tatsuhiko Abo
- Graduate School of Natural Science and Technology, Okayama University
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64
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Arribere JA, Kuroyanagi H, Hundley HA. mRNA Editing, Processing and Quality Control in Caenorhabditis elegans. Genetics 2020; 215:531-568. [PMID: 32632025 PMCID: PMC7337075 DOI: 10.1534/genetics.119.301807] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 05/03/2020] [Indexed: 02/06/2023] Open
Abstract
While DNA serves as the blueprint of life, the distinct functions of each cell are determined by the dynamic expression of genes from the static genome. The amount and specific sequences of RNAs expressed in a given cell involves a number of regulated processes including RNA synthesis (transcription), processing, splicing, modification, polyadenylation, stability, translation, and degradation. As errors during mRNA production can create gene products that are deleterious to the organism, quality control mechanisms exist to survey and remove errors in mRNA expression and processing. Here, we will provide an overview of mRNA processing and quality control mechanisms that occur in Caenorhabditis elegans, with a focus on those that occur on protein-coding genes after transcription initiation. In addition, we will describe the genetic and technical approaches that have allowed studies in C. elegans to reveal important mechanistic insight into these processes.
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Affiliation(s)
| | - Hidehito Kuroyanagi
- Laboratory of Gene Expression, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan, and
| | - Heather A Hundley
- Medical Sciences Program, Indiana University School of Medicine-Bloomington, Indiana 47405
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65
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Abstract
Stalled protein synthesis produces defective nascent chains that can harm cells. In response, cells degrade these nascent chains via a process called ribosome-associated quality control (RQC). Here, we review the irregularities in the translation process that cause ribosomes to stall as well as how cells use RQC to detect stalled ribosomes, ubiquitylate their tethered nascent chains, and deliver the ubiquitylated nascent chains to the proteasome. We additionally summarize how cells respond to RQC failure.
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Affiliation(s)
- Cole S Sitron
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany;
| | - Onn Brandman
- Department of Biochemistry, Stanford University, Stanford, California 94305, USA;
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66
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Abstract
Aminoacyl-tRNA synthetases (ARSs) are a family of essential "housekeeping" enzymes ubiquitous in the three major domains of life. ARSs uniquely connect the essential minimal units of both major oligomer classes-the 3-nucleotide codons of oligonucleotides and the amino acids of proteins. They catalyze the esterification of amino acids to the 3'-end of cognate transfer RNAs (tRNAs) bearing the correct anticodon triplet to ensure accurate transfer of information from mRNA to protein according to the genetic code. As an essential translation factor responsible for the first biochemical reaction in protein biosynthesis, ARSs control protein production by catalyzing aminoacylation, and by editing of mischarged aminoacyl-tRNAs to maintain translational fidelity. In addition to their primary enzymatic activities, many ARSs have noncanonical functions unrelated to their catalytic activity in protein synthesis. Among the ARSs with "moonlighting" activities, several, including GluProRS (or EPRS), LeuRS, LysRS, SerRS, TyrRS, and TrpRS, exhibit cell signaling-related activities that sense environmental signals, regulate gene expression, and modulate cellular functions. ARS signaling functions generally depend on catalytically-inactive, appended domains not present in ancient enzyme forms, and are activated by stimulus-dependent post-translational modification. Activation often results in cellular re-localization and gain of new interacting partners. The newly formed ARS-bearing complexes conduct a host of signal transduction functions, including immune response, mTORC1 pathway signaling, and fibrogenic and angiogenic signaling, among others. Because noncanonical functions of ARSs in signal transduction are uncoupled from canonical aminoacylation functions, function-specific inhibitors can be developed, thus providing promising opportunities and therapeutic targets for treatment of human disease.
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Affiliation(s)
- Peng Yao
- Aab Cardiovascular Research Institute, Department of Medicine and Department of Biochemistry & Biophysics, The Center for RNA Biology, The Center for Biomedical Informatics, University of Rochester School of Medicine & Dentistry, Rochester, NY, United States.
| | - Paul L Fox
- Department of Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States.
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67
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Chakrabarti M, de Lorenzo L, Abdel-Ghany SE, Reddy ASN, Hunt AG. Wide-ranging transcriptome remodelling mediated by alternative polyadenylation in response to abiotic stresses in Sorghum. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:916-930. [PMID: 31909843 DOI: 10.1111/tpj.14671] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 12/14/2019] [Accepted: 01/02/2020] [Indexed: 05/28/2023]
Abstract
Alternative polyadenylation (APA) regulates diverse developmental and physiological processes through its effects on gene expression, mRNA stability, translatability, and transport. Sorghum is a major cereal crop in the world and, despite its importance, not much is known about the role of post-transcriptional regulation in mediating responses to abiotic stresses in Sorghum. A genome-wide APA analysis unveiled widespread occurrence of APA in Sorghum in response to drought, heat, and salt stress. Abiotic stress treatments incited changes in poly(A) site choice in a large number of genes. Interestingly, abiotic stresses led to the re-directing of transcriptional output into non-productive pathways defined by the class of poly(A) site utilized. This result revealed APA to be part of a larger global response of Sorghum to abiotic stresses that involves the re-direction of transcriptional output into non-productive transcriptional and translational pathways. Large numbers of stress-inducible poly(A) sites could not be linked with known, annotated genes, suggestive of the existence of numerous unidentified genes whose expression is strongly regulated by abiotic stresses. Furthermore, we uncovered a novel stress-specific cis-element in intronic poly(A) sites used in drought- and heat-stressed plants that might play an important role in non-canonical poly(A) site choice in response to abiotic stresses.
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Affiliation(s)
- Manohar Chakrabarti
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546, USA
| | - Laura de Lorenzo
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546, USA
| | - Salah E Abdel-Ghany
- Department of Biology, and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Anireddy S N Reddy
- Department of Biology, and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Arthur G Hunt
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546, USA
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68
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Ma Z, Chen J. Premature Termination Codon-Bearing mRNA Mediates Genetic Compensation Response. Zebrafish 2020; 17:157-162. [PMID: 32434440 DOI: 10.1089/zeb.2019.1824] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The genetic compensation response (GCR), triggered by deleterious mutations but not by gene knockdown, has been proposed to explain many phenotypic discrepancies between gene-knockout and gene-knockdown models. GCRs have been observed in many model organisms from mice to Arabidopsis. Although the GCR is beneficial for organism survival, it impedes the exploration of gene function as many knockout mutants do not display discernible phenotypes due to the GCR. Uncovering how the mechanism of GCR operates is not only a fundamental goal in biology but also may provide a key solution in the unmasking of phenotypes in mutants displaying GCRs. Using zebrafish as the model, two recent studies have provided a molecular basis to explain this genetic paradox by demonstrating that the nonsense-mediated mRNA decay pathway is essential for nonsense mRNA to upregulate the expression of its homologous genes through an enhancement of histone H3 Lys4 trimethylation (H3K4me3) at the transcription start site regions of the compensatory genes. Here, we summarize the progress on the molecular mechanism of the GCR and make suggestions on how to overcome GCRs in the generation of genetic mutants.
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Affiliation(s)
- Zhipeng Ma
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jun Chen
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
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69
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Inada T. Quality controls induced by aberrant translation. Nucleic Acids Res 2020; 48:1084-1096. [PMID: 31950154 PMCID: PMC7026593 DOI: 10.1093/nar/gkz1201] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 12/01/2019] [Accepted: 12/18/2019] [Indexed: 12/31/2022] Open
Abstract
During protein synthesis, translating ribosomes encounter many challenges imposed by various types of defective mRNAs that can lead to reduced cellular fitness and, in some cases, even threaten cell viability. Aberrant translation leads to activation of one of several quality control pathways depending on the nature of the problem. These pathways promote the degradation of the problematic mRNA as well as the incomplete translation product, the nascent polypeptide chain. Many of these quality control systems feature critical roles for specialized regulatory factors that work in concert with conventional factors. This review focuses on the mechanisms used by these quality control pathways to recognize aberrant ribosome stalling and discusses the conservation of these systems.
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Affiliation(s)
- Toshifumi Inada
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
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70
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Role for ribosome-associated quality control in sampling proteins for MHC class I-mediated antigen presentation. Proc Natl Acad Sci U S A 2020; 117:4099-4108. [PMID: 32047030 PMCID: PMC7049129 DOI: 10.1073/pnas.1914401117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Pathogens and tumors are detected by the immune system through the display of intracellular peptides on MHC-I complexes. These peptides are generated by the ubiquitin−proteasome system preferentially from newly synthesized polypeptides. Here we show that the ribosome-associated quality control (RQC) pathway, responsible for proteasomal degradation of polypeptide chains that stall during translation, mediates efficient antigen presentation of model proteins independent of their intrinsic folding properties. Immunopeptidome characterization of RQC-deficient cells shows that RQC contributes to the presentation of a wide variety of proteins, including proteins that may otherwise evade presentation due to efficient folding. By identifying endogenous substrates of the RQC pathway in human cells, our results also enable the analysis of common principles causing ribosome stalling under physiological conditions. Mammalian cells present a fingerprint of their proteome to the adaptive immune system through the display of endogenous peptides on MHC-I complexes. MHC-I−bound peptides originate from protein degradation by the proteasome, suggesting that stably folded, long-lived proteins could evade monitoring. Here, we investigate the role in antigen presentation of the ribosome-associated quality control (RQC) pathway for the degradation of nascent polypeptides that are encoded by defective messenger RNAs and undergo stalling at the ribosome during translation. We find that degradation of model proteins by RQC results in efficient MHC-I presentation, independent of their intrinsic folding properties. Quantitative profiling of MHC-I peptides in wild-type and RQC-deficient cells by mass spectrometry showed that RQC substantially contributes to the composition of the immunopeptidome. Our results also identify endogenous substrates of the RQC pathway in human cells and provide insight into common principles causing ribosome stalling under physiological conditions.
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71
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Tesina P, Lessen LN, Buschauer R, Cheng J, Wu CC, Berninghausen O, Buskirk AR, Becker T, Beckmann R, Green R. Molecular mechanism of translational stalling by inhibitory codon combinations and poly(A) tracts. EMBO J 2020; 39:e103365. [PMID: 31858614 PMCID: PMC6996574 DOI: 10.15252/embj.2019103365] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 11/08/2019] [Accepted: 12/06/2019] [Indexed: 12/24/2022] Open
Abstract
Inhibitory codon pairs and poly(A) tracts within the translated mRNA cause ribosome stalling and reduce protein output. The molecular mechanisms that drive these stalling events, however, are still unknown. Here, we use a combination of in vitro biochemistry, ribosome profiling, and cryo-EM to define molecular mechanisms that lead to these ribosome stalls. First, we use an in vitro reconstituted yeast translation system to demonstrate that inhibitory codon pairs slow elongation rates which are partially rescued by increased tRNA concentration or by an artificial tRNA not dependent on wobble base-pairing. Ribosome profiling data extend these observations by revealing that paused ribosomes with empty A sites are enriched on these sequences. Cryo-EM structures of stalled ribosomes provide a structural explanation for the observed effects by showing decoding-incompatible conformations of mRNA in the A sites of all studied stall- and collision-inducing sequences. Interestingly, in the case of poly(A) tracts, the inhibitory conformation of the mRNA in the A site involves a nucleotide stacking array. Together, these data demonstrate a novel mRNA-induced mechanisms of translational stalling in eukaryotic ribosomes.
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Affiliation(s)
- Petr Tesina
- Gene Center and Center for Integrated Protein Science MunichDepartment of BiochemistryUniversity of MunichMunichGermany
| | - Laura N Lessen
- Program in Molecular BiophysicsJohns Hopkins University School of MedicineBaltimoreMDUSA
- Department of Molecular Biology and GeneticsJohns Hopkins University School of MedicineBaltimoreMDUSA
| | - Robert Buschauer
- Gene Center and Center for Integrated Protein Science MunichDepartment of BiochemistryUniversity of MunichMunichGermany
| | - Jingdong Cheng
- Gene Center and Center for Integrated Protein Science MunichDepartment of BiochemistryUniversity of MunichMunichGermany
| | - Colin Chih‐Chien Wu
- Department of Molecular Biology and GeneticsJohns Hopkins University School of MedicineBaltimoreMDUSA
- Howard Hughes Medical InstituteJohns Hopkins University School of MedicineBaltimoreMDUSA
| | - Otto Berninghausen
- Gene Center and Center for Integrated Protein Science MunichDepartment of BiochemistryUniversity of MunichMunichGermany
| | - Allen R Buskirk
- Department of Molecular Biology and GeneticsJohns Hopkins University School of MedicineBaltimoreMDUSA
| | - Thomas Becker
- Gene Center and Center for Integrated Protein Science MunichDepartment of BiochemistryUniversity of MunichMunichGermany
| | - Roland Beckmann
- Gene Center and Center for Integrated Protein Science MunichDepartment of BiochemistryUniversity of MunichMunichGermany
| | - Rachel Green
- Department of Molecular Biology and GeneticsJohns Hopkins University School of MedicineBaltimoreMDUSA
- Howard Hughes Medical InstituteJohns Hopkins University School of MedicineBaltimoreMDUSA
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72
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Navickas A, Chamois S, Saint-Fort R, Henri J, Torchet C, Benard L. No-Go Decay mRNA cleavage in the ribosome exit tunnel produces 5'-OH ends phosphorylated by Trl1. Nat Commun 2020; 11:122. [PMID: 31913314 PMCID: PMC6949252 DOI: 10.1038/s41467-019-13991-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 12/11/2019] [Indexed: 11/24/2022] Open
Abstract
The No-Go Decay (NGD) mRNA surveillance pathway degrades mRNAs containing stacks of stalled ribosomes. Although an endoribonuclease has been proposed to initiate cleavages upstream of the stall sequence, the production of two RNA fragments resulting from a unique cleavage has never been demonstrated. Here we use mRNAs expressing a 3'-ribozyme to produce truncated transcripts in vivo to mimic naturally occurring truncated mRNAs known to trigger NGD. This technique allows us to analyse endonucleolytic cleavage events at single-nucleotide resolution starting at the third collided ribosome, which we show to be Hel2-dependent. These cleavages map precisely in the mRNA exit tunnel of the ribosome, 8 nucleotides upstream of the first P-site residue and release 5'-hydroxylated RNA fragments requiring 5'-phosphorylation prior to digestion by the exoribonuclease Xrn1, or alternatively by Dxo1. Finally, we identify the RNA kinase Trl1, alias Rlg1, as an essential player in the degradation of NGD RNAs.
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Affiliation(s)
- Albertas Navickas
- Institut de Biologie Physico-Chimique, UMR8226, CNRS, Sorbonne Université, Laboratoire de Biologie moléculaire et Cellulaire des Eucaryotes, Paris, France
| | - Sébastien Chamois
- Institut de Biologie Physico-Chimique, UMR8226, CNRS, Sorbonne Université, Laboratoire de Biologie moléculaire et Cellulaire des Eucaryotes, Paris, France
| | - Rénette Saint-Fort
- Institut de Biologie Physico-Chimique, UMR8226, CNRS, Sorbonne Université, Laboratoire de Biologie moléculaire et Cellulaire des Eucaryotes, Paris, France
| | - Julien Henri
- Institut de Biologie Physico-Chimique, UMR8226, CNRS, Sorbonne Université, Laboratoire de Biologie moléculaire et Cellulaire des Eucaryotes, Paris, France
| | - Claire Torchet
- Institut de Biologie Physico-Chimique, UMR8226, CNRS, Sorbonne Université, Laboratoire de Biologie moléculaire et Cellulaire des Eucaryotes, Paris, France
| | - Lionel Benard
- Institut de Biologie Physico-Chimique, UMR8226, CNRS, Sorbonne Université, Laboratoire de Biologie moléculaire et Cellulaire des Eucaryotes, Paris, France.
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73
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Ayyub SA, Gao F, Lightowlers RN, Chrzanowska-Lightowlers ZM. Rescuing stalled mammalian mitoribosomes - what can we learn from bacteria? J Cell Sci 2020; 133:133/1/jcs231811. [PMID: 31896602 DOI: 10.1242/jcs.231811] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
In the canonical process of translation, newly completed proteins escape from the ribosome following cleavage of the ester bond that anchors the polypeptide to the P-site tRNA, after which the ribosome can be recycled to initiate a new round of translation. Not all protein synthesis runs to completion as various factors can impede the progression of ribosomes. Rescuing of stalled ribosomes in mammalian mitochondria, however, does not share the same mechanisms that many bacteria use. The classic method for rescuing bacterial ribosomes is trans-translation. The key components of this system are absent from mammalian mitochondria; however, four members of a translation termination factor family are present, with some evidence of homology to members of a bacterial back-up rescue system. To date, there is no definitive demonstration of any other member of this family functioning in mitoribosome rescue. Here, we provide an overview of the processes and key players of canonical translation termination in both bacteria and mammalian mitochondria, followed by a perspective of the bacterial systems used to rescue stalled ribosomes. We highlight any similarities or differences with the mitochondrial translation release factors, and suggest potential roles for these proteins in ribosome rescue in mammalian mitochondria.
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Affiliation(s)
- Shreya Ahana Ayyub
- The Wellcome Centre for Mitochondrial Research, Newcastle University, The Medical School, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Fei Gao
- The Wellcome Centre for Mitochondrial Research, Newcastle University, The Medical School, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Robert N Lightowlers
- The Wellcome Centre for Mitochondrial Research, Newcastle University, The Medical School, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Zofia M Chrzanowska-Lightowlers
- The Wellcome Centre for Mitochondrial Research, Newcastle University, The Medical School, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
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74
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Zinoviev A, Hellen CUT, Pestova TV. In Vitro Characterization of the Activity of the Mammalian RNA Exosome on mRNAs in Ribosomal Translation Complexes. Methods Mol Biol 2020; 2062:327-354. [PMID: 31768984 DOI: 10.1007/978-1-4939-9822-7_16] [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] [Indexed: 10/18/2023]
Abstract
The RNA exosome is a multisubunit protein complex that exhibits a 3' to 5' exoribonuclease activity, endoribonuclease activity, and participates in a variety of RNA processing and degradation pathways in both the nucleus and the cytoplasm. Exosomes interact with various cofactors which target them to specific RNA substrates and processes. Investigation of the mechanisms by which mammalian RNA exosomes are targeted to specific RNA substrates requires the development of in vitro approaches for purification of exosomes and their co-factors, assembly of substrates and monitoring of the exosomal activity. Here, we describe protocols for in vitro reconstitution of ribosomal 80S elongation complexes on cap-labeled mRNAs and for assaying exosomal degradation of mRNAs in such complexes depending on the presence of GTPBP1, which has previously been implicated in directing the exosome to mRNA targets.
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Affiliation(s)
- Alexandra Zinoviev
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Christopher U T Hellen
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Tatyana V Pestova
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, NY, USA.
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75
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Bernardes WS, Menossi M. Plant 3' Regulatory Regions From mRNA-Encoding Genes and Their Uses to Modulate Expression. FRONTIERS IN PLANT SCIENCE 2020; 11:1252. [PMID: 32922424 PMCID: PMC7457121 DOI: 10.3389/fpls.2020.01252] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/29/2020] [Indexed: 05/08/2023]
Abstract
Molecular biotechnology has made it possible to explore the potential of plants for different purposes. The 3' regulatory regions have a great diversity of cis-regulatory elements directly involved in polyadenylation, stability, transport and mRNA translation, essential to achieve the desired levels of gene expression. A complex interaction between the cleavage and polyadenylation molecular complex and cis-elements determine the polyadenylation site, which may result in the choice of non-canonical sites, resulting in alternative polyadenylation events, involved in the regulation of more than 80% of the genes expressed in plants. In addition, after transcription, a wide array of RNA-binding proteins interacts with cis-acting elements located mainly in the 3' untranslated region, determining the fate of mRNAs in eukaryotic cells. Although a small number of 3' regulatory regions have been identified and validated so far, many studies have shown that plant 3' regulatory regions have a higher potential to regulate gene expression in plants compared to widely used 3' regulatory regions, such as NOS and OCS from Agrobacterium tumefaciens and 35S from cauliflower mosaic virus. In this review, we discuss the role of 3' regulatory regions in gene expression, and the superior potential that plant 3' regulatory regions have compared to NOS, OCS and 35S 3' regulatory regions.
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76
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Mechanism of ribosome stalling during translation of a poly(A) tail. Nat Struct Mol Biol 2019; 26:1132-1140. [PMID: 31768042 PMCID: PMC6900289 DOI: 10.1038/s41594-019-0331-x] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 10/10/2019] [Indexed: 12/23/2022]
Abstract
Faulty or damaged mRNAs are detected by the cell when translating ribosomes stall during elongation and trigger pathways of mRNA decay, nascent protein degradation, and ribosome recycling. The most common mRNA defect in eukaryotes is probably inappropriate poly-adenylation at near-cognate sites within the coding region. How ribosomes stall selectively when they encounter poly(A) is unclear. Here, we use biochemical and structural approaches in mammalian systems to show that poly-lysine, encoded by poly(A), favors a peptidyl-tRNA conformation sub-optimal for peptide bond formation. This conformation partially slows elongation, permitting poly(A) mRNA in the ribosome’s decoding center to adopt an rRNA-stabilized single-stranded helix. The reconfigured decoding center clashes with incoming aminoacyl-tRNA, thereby precluding elongation. Thus, coincidence detection of poly-lysine in the exit tunnel and poly(A) in the decoding center allows ribosomes to detect aberrant mRNAs selectively, stall elongation, and trigger downstream quality control pathways essential for cellular homeostasis.
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77
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Olthof AM, Hyatt KC, Kanadia RN. Minor intron splicing revisited: identification of new minor intron-containing genes and tissue-dependent retention and alternative splicing of minor introns. BMC Genomics 2019; 20:686. [PMID: 31470809 PMCID: PMC6717393 DOI: 10.1186/s12864-019-6046-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 08/19/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Mutations in minor spliceosome components such as U12 snRNA (cerebellar ataxia) and U4atac snRNA (microcephalic osteodysplastic primordial dwarfism type 1 (MOPD1)) result in tissue-specific symptoms. Given that the minor spliceosome is ubiquitously expressed, we hypothesized that these restricted phenotypes might be caused by the tissue-specific regulation of the minor spliceosome targets, i.e. minor intron-containing genes (MIGs). The current model of inefficient splicing is thought to apply to the regulation of the ~ 500 MIGs identified in the U12DB. However this database was created more than 10 years ago. Therefore, we first wanted to revisit the classification of minor introns in light of the most recent reference genome. We then sought to address specificity of MIG expression, minor intron retention, and alternative splicing (AS) across mouse and human tissues. RESULTS We employed position-weight matrices to obtain a comprehensive updated list of minor introns, consisting of 722 mouse and 770 human minor introns. These can be found in the Minor Intron DataBase (MIDB). Besides identification of 99% of the minor introns found in the U12DB, we also discovered ~ 150 new MIGs. We then analyzed the RNAseq data from eleven different mouse tissues, which revealed tissue-specific MIG expression and minor intron retention. Additionally, many minor introns were efficiently spliced compared to their flanking major introns. Finally, we identified several novel AS events across minor introns in both mouse and human, which were also tissue-dependent. Bioinformatics analysis revealed that several of the AS events could result in the production of novel tissue-specific proteins. Moreover, like the major introns, we found that these AS events were more prevalent in long minor introns, while retention was favoured in shorter introns. CONCLUSION Here we show that minor intron splicing and AS across minor introns is a highly organised process that might be regulated in coordination with the major spliceosome in a tissue-specific manner. We have provided a framework to further study the impact of the minor spliceosome and the regulation of MIG expression. These findings may shed light on the mechanism underlying tissue-specific phenotypes in diseases associated with minor spliceosome inactivation. MIDB can be accessed at https://midb.pnb.uconn.edu .
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Affiliation(s)
- Anouk M. Olthof
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269 USA
| | - Katery C. Hyatt
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269 USA
| | - Rahul N. Kanadia
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269 USA
- Institute of Systems Genomics, University of Connecticut, Storrs, CT 06269 USA
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Nogimori T, Nishiura K, Kawashima S, Nagai T, Oishi Y, Hosoda N, Imataka H, Kitamura Y, Kitade Y, Hoshino SI. Dom34 mediates targeting of exogenous RNA in the antiviral OAS/RNase L pathway. Nucleic Acids Res 2019; 47:432-449. [PMID: 30395302 PMCID: PMC6326797 DOI: 10.1093/nar/gky1087] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/19/2018] [Indexed: 11/21/2022] Open
Abstract
The 2′-5′-oligoadenylate synthetase (OAS)/RNase L pathway is an innate immune system that protects hosts against pathogenic viruses and bacteria through cleavage of exogenous single-stranded RNA; however, this system's selective targeting mechanism remains unclear. Here, we identified an mRNA quality control factor Dom34 as a novel restriction factor for a positive-sense single-stranded RNA virus. Downregulation of Dom34 and RNase L increases viral replication, as well as half-life of the viral RNA. Dom34 directly binds RNase L to form a surveillance complex to recognize and eliminate the exogenous RNA in a manner dependent on translation. Interestingly, the feature detected by the surveillance complex is not the specific sequence of the viral RNA but the ‘exogenous nature’ of the RNA. We propose the following model for the selective targeting of exogenous RNA; OAS3 activated by the exogenous RNA releases 2′-5′-oligoadenylates (2–5A), which in turn converts latent RNase L to an active dimer. This accelerates formation of the Dom34-RNase L surveillance complex, and its selective localization to the ribosome on the exogenous RNA, thereby promoting degradation of the RNA. Our findings reveal that the selective targeting of exogenous RNA in antiviral defense occurs via a mechanism similar to that in the degradation of aberrant transcripts in RNA quality control.
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Affiliation(s)
- Takuto Nogimori
- Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
| | - Kyutatsu Nishiura
- Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
| | - Sho Kawashima
- Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
| | - Takahiro Nagai
- Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
| | - Yuka Oishi
- Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
| | - Nao Hosoda
- Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
| | - Hiroaki Imataka
- Department of Materials Science and Chemistry and Molecular Nanotechnology Research Center, Graduate School of Engineering, University of Hyogo, Himeji 671-2201, Japan
| | - Yoshiaki Kitamura
- Department of Biomolecular Science, Graduate School of Engineering, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Yukio Kitade
- Department of Biomolecular Science, Graduate School of Engineering, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Shin-Ichi Hoshino
- Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603, Japan
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Increasing targeting scope of adenosine base editors in mouse and rat embryos through fusion of TadA deaminase with Cas9 variants. Protein Cell 2019; 9:814-819. [PMID: 30066232 PMCID: PMC6107483 DOI: 10.1007/s13238-018-0568-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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80
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Zhang E, Khanna V, Dacheux E, Namane A, Doyen A, Gomard M, Turcotte B, Jacquier A, Fromont‐Racine M. A specialised SKI complex assists the cytoplasmic RNA exosome in the absence of direct association with ribosomes. EMBO J 2019; 38:e100640. [PMID: 31304628 PMCID: PMC6627227 DOI: 10.15252/embj.2018100640] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 04/25/2019] [Accepted: 05/13/2019] [Indexed: 11/09/2022] Open
Abstract
The Ski2-Ski3-Ski8 (SKI) complex assists the RNA exosome during the 3' to 5' degradation of cytoplasmic transcripts. Previous reports showed that the SKI complex is involved in the 3' to 5' degradation of mRNAs, including 3' untranslated regions (UTRs) and devoid of ribosomes. Paradoxically, we recently showed that the SKI complex directly interacts with ribosomes during the co-translational mRNA decay and that this interaction is necessary for its RNA degradation promoting activity. Here, we characterised a new SKI-associated factor, Ska1, that associates with a subpopulation of the SKI complex. We showed that Ska1 is specifically involved in the degradation of long 3'UTR-containing mRNAs, poorly translated mRNAs as well as other RNA regions not associated with ribosomes, such as cytoplasmic lncRNAs. We further show that the overexpression of SKA1 antagonises the SKI-ribosome association. We propose that the Ska1-SKI complex assists the cytoplasmic exosome in the absence of direct association of the SKI complex with ribosomes.
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Affiliation(s)
- Elodie Zhang
- Génétique des Interactions MacromoléculairesInstitut PasteurUMR3525 CNRSParisFrance
- Sorbonne UniversitéCollège DoctoralParisFrance
| | - Varun Khanna
- Génétique des Interactions MacromoléculairesInstitut PasteurUMR3525 CNRSParisFrance
- Hub Bioinformatique et BiostatistiqueInstitut Pasteur ‐ C3BIUSR 3756 IP CNRSParisFrance
| | - Estelle Dacheux
- Génétique des Interactions MacromoléculairesInstitut PasteurUMR3525 CNRSParisFrance
| | - Abdelkader Namane
- Génétique des Interactions MacromoléculairesInstitut PasteurUMR3525 CNRSParisFrance
| | - Antonia Doyen
- Génétique des Interactions MacromoléculairesInstitut PasteurUMR3525 CNRSParisFrance
| | - Maïté Gomard
- Génétique des Interactions MacromoléculairesInstitut PasteurUMR3525 CNRSParisFrance
| | - Bernard Turcotte
- Department of MedicineMcGill University Health CentreMontréalQCCanada
| | - Alain Jacquier
- Génétique des Interactions MacromoléculairesInstitut PasteurUMR3525 CNRSParisFrance
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81
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D'Orazio KN, Wu CCC, Sinha N, Loll-Krippleber R, Brown GW, Green R. The endonuclease Cue2 cleaves mRNAs at stalled ribosomes during No Go Decay. eLife 2019; 8:e49117. [PMID: 31219035 PMCID: PMC6598757 DOI: 10.7554/elife.49117] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 06/19/2019] [Indexed: 01/04/2023] Open
Abstract
Translation of problematic sequences in mRNAs leads to ribosome collisions that trigger a series of quality control events including ribosome rescue, degradation of the stalled nascent polypeptide, and targeting of the mRNA for decay (No Go Decay or NGD). Using a reverse genetic screen in yeast, we identify Cue2 as the conserved endonuclease that is recruited to stalled ribosomes to promote NGD. Ribosome profiling and biochemistry provide strong evidence that Cue2 cleaves mRNA within the A site of the colliding ribosome. We demonstrate that NGD primarily proceeds via Xrn1-mediated exonucleolytic decay and Cue2-mediated endonucleolytic decay normally constitutes a secondary decay pathway. Finally, we show that the Cue2-dependent pathway becomes a major contributor to NGD in cells depleted of factors required for the resolution of stalled ribosome complexes. Together these results provide insights into how multiple decay processes converge to process problematic mRNAs in eukaryotic cells..
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Affiliation(s)
- Karole N D'Orazio
- Department of Molecular Biology and GeneticsHoward Hughes Medical Institute, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Colin Chih-Chien Wu
- Department of Molecular Biology and GeneticsHoward Hughes Medical Institute, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Niladri Sinha
- Department of Molecular Biology and GeneticsHoward Hughes Medical Institute, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Raphael Loll-Krippleber
- Donnelly Centre for Cellular and Biomolecular Research, Department of BiochemistryUniversity of TorontoTorontoCanada
| | - Grant W Brown
- Donnelly Centre for Cellular and Biomolecular Research, Department of BiochemistryUniversity of TorontoTorontoCanada
| | - Rachel Green
- Department of Molecular Biology and GeneticsHoward Hughes Medical Institute, Johns Hopkins University School of MedicineBaltimoreUnited States
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82
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The role of DEFB126 variation in male infertility and medically assisted reproduction technique outcome. Reprod Biomed Online 2019; 39:649-657. [PMID: 31474436 DOI: 10.1016/j.rbmo.2019.05.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 04/24/2019] [Accepted: 05/17/2019] [Indexed: 11/23/2022]
Abstract
RESEARCH QUESTION Human DEFB126 is an important component of the glycocalyx of human spermatozoa. Beta-defensins play a primary role in male infertility due to their involvement in maturation and capacitation of spermatozoa. A 2-nt deletion of DEFB126 affects sperm function and so this study investigated the possible association between DEFB126 variants and its protein expression on medically assisted reproduction (MAR) technique outcome in Iranian infertile males. DESIGN The presence of a 2-nt deletion of DEFB126, and its protein expression in spermatozoa, were investigated by standard polymerase chain reaction (PCR) sequencing and immunocytochemistry, respectively. MAR technique outcome according to clinical pregnancy rates was assessed in 277 Iranian males with unexplained infertility, including 139 patients who underwent intrauterine insemination (IUI) and 103 patients who underwent IVF/intracytoplasmic sperm injection (ICSI), as well as 35 infertile males who declined to use any MAR treatment. As the control group, 100 fertile males with a normal spermiogram were enrolled. RESULTS The 2-nt deletion of DEFB126 was significantly higher in infertile patients than controls (P ≤ 0.05). The presence of this deletion resulted in significantly lower clinical pregnancy rates following IUI (P ≤ 0.05); however, there were no differences in IVF/ICSI outcomes according to genotype. The protein expression in del/del males was also remarkably lower than that of the other genotypes. CONCLUSIONS This sequence variation of DEFB126 may impair male reproductive function and can be related to male infertility. Interestingly, males with the del/del genotype have a normal spermiogram; however, their spermatozoa are evidently functionally impaired, which can affect IUI treatment outcome, but not treatment by IVF/ICSI.
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83
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Poidevin L, Unal D, Belda-Palazón B, Ferrando A. Polyamines as Quality Control Metabolites Operating at the Post-Transcriptional Level. PLANTS 2019; 8:plants8040109. [PMID: 31022874 PMCID: PMC6524035 DOI: 10.3390/plants8040109] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 04/17/2019] [Accepted: 04/19/2019] [Indexed: 01/04/2023]
Abstract
Plant polyamines (PAs) have been assigned a large number of physiological functions with unknown molecular mechanisms in many cases. Among the most abundant and studied polyamines, two of them, namely spermidine (Spd) and thermospermine (Tspm), share some molecular functions related to quality control pathways for tightly regulated mRNAs at the level of translation. In this review, we focus on the roles of Tspm and Spd to facilitate the translation of mRNAs containing upstream ORFs (uORFs), premature stop codons, and ribosome stalling sequences that may block translation, thus preventing their degradation by quality control mechanisms such as the nonsense-mediated decay pathway and possible interactions with other mRNA quality surveillance pathways.
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Affiliation(s)
- Laetitia Poidevin
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, 46022 Valencia, Spain.
| | - Dilek Unal
- Biotechnology Application and Research Center, and Department of Molecular Biology, Faculty of Science and Letter, Bilecik Seyh Edebali University, 11230 Bilecik, Turkey.
| | - Borja Belda-Palazón
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, 46022 Valencia, Spain.
| | - Alejandro Ferrando
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, 46022 Valencia, Spain.
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84
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Mechanism for recycling tRNAs on stalled ribosomes. Nat Struct Mol Biol 2019; 26:343-349. [PMID: 31011209 DOI: 10.1038/s41594-019-0211-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 03/06/2019] [Indexed: 11/08/2022]
Abstract
Aberrantly stalled ribosomes initiate the ribosome-associated quality control (RQC) and mRNA surveillance pathways for the degradation of potentially toxic peptides and faulty mRNAs. During RQC, ANKZF1 (yeast Vms1p) releases ubiquitinated nascent proteins from 60S ribosomal subunits for proteasomal degradation. Here, we use a cell-free system to show that ANKZF1 and Vms1p sever polypeptidyl-tRNAs on RQC complexes by precisely cleaving off the terminal 3'CCA nucleotides universal to all tRNAs. This produces a tRNA fragment that cannot be aminoacylated until its 3'CCA end is restored. The recycling of ANKZF1-cleaved tRNAs is intact in the mammalian cytosol via a two-step process that requires the removal of a 2',3'-cyclic phosphate and TRNT1, the sole CCA-adding enzyme that mediates tRNA biogenesis in eukaryotes. TRNT1 also discriminates between properly folded tRNA substrates and aberrant tRNA substrates, selectively tagging the latter for degradation. Thus, ANKZF1 liberates peptidyl-tRNAs from stalled ribosomes such that the tRNA is checked in an obligate way for integrity before reentry into the translation cycle.
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85
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Ibrahim F, Mourelatos Z. Capturing 5' and 3' native ends of mRNAs concurrently with Akron sequencing. Nat Protoc 2019; 14:1578-1602. [PMID: 30971782 DOI: 10.1038/s41596-019-0151-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 02/19/2019] [Indexed: 11/09/2022]
Abstract
Advances in RNA-sequencing methods have uncovered many aspects of RNA metabolism but are limited to surveying either the 3' or 5' terminus of RNAs, thus missing mechanistic aspects that could be revealed if both ends were captured. We developed Akron sequencing (Akron-seq), a method that captures in parallel the native 5' ends of uncapped, polyadenylated mRNAs and 3' ends of capped mRNAs from the same input RNA. Thus, Akron-seq uniquely enables assessment of full-length and truncated mRNAs at single-nucleotide resolution. Akron-seq involves RNA isolation, depletion of ribosomal and abundant small capped RNAs, and selection of capped and polyadenylated mRNAs. The endogenous ends of mRNAs are marked by adaptor ligation, followed by fragmentation, cDNA generation, PCR amplification, and deep sequencing. The step-by-step protocol we describe here is optimized for cultured human cells but can be adapted to primary cells and tissues. Akron-seq can be completed within 6 d, and sequencing and analysis can be completed within 6 d.
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Affiliation(s)
- Fadia Ibrahim
- Division of Neuropathology, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, USA. .,Penn Medicine Translational Neuroscience Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Zissimos Mourelatos
- Division of Neuropathology, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, USA.,Penn Medicine Translational Neuroscience Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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86
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Hashimoto S, Nobuta R, Izawa T, Inada T. Translation arrest as a protein quality control system for aberrant translation of the 3'-UTR in mammalian cells. FEBS Lett 2019; 593:777-787. [PMID: 30883710 DOI: 10.1002/1873-3468.13362] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/23/2019] [Accepted: 03/11/2019] [Indexed: 01/05/2023]
Abstract
Read-through or mutations of a stop codon resulting in translation of the 3'-UTR produce potentially toxic C-terminally extended proteins. However, quality control mechanisms for such proteins are poorly understood in mammalian cells. Here, a comprehensive analysis of the 3'-UTRs of genes associated with hereditary diseases identified novel arrest-inducing sequences in the 3'-UTRs of 23 genes that can repress the levels of their protein products. In silico analysis revealed that the hydrophobicity of the polypeptides encoded in the 3'-UTRs is correlated with arrest efficiency. These results provide new insight into quality control mechanisms mediated by 3'-UTRs to prevent the production of C-terminally extended cytotoxic proteins.
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Affiliation(s)
- Satoshi Hashimoto
- Graduate School of Pharmaceutical Science, Tohoku University, Sendai, Japan
| | - Risa Nobuta
- Graduate School of Pharmaceutical Science, Tohoku University, Sendai, Japan
| | - Toshiaki Izawa
- Graduate School of Pharmaceutical Science, Tohoku University, Sendai, Japan
| | - Toshifumi Inada
- Graduate School of Pharmaceutical Science, Tohoku University, Sendai, Japan
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87
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Winz ML, Peil L, Turowski TW, Rappsilber J, Tollervey D. Molecular interactions between Hel2 and RNA supporting ribosome-associated quality control. Nat Commun 2019; 10:563. [PMID: 30718516 PMCID: PMC6362110 DOI: 10.1038/s41467-019-08382-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 12/21/2018] [Indexed: 01/28/2023] Open
Abstract
Ribosome-associated quality control (RQC) pathways monitor and respond to ribosome stalling. Using in vivo UV-crosslinking and mass spectrometry, we identified a C-terminal region in Hel2/Rqt1 as an RNA binding domain. Complementary crosslinking and sequencing data for Hel2 revealed binding to 18S rRNA and translated mRNAs. Hel2 preferentially bound mRNAs upstream and downstream of the stop codon. C-terminal truncation of Hel2 abolished the major 18S crosslink and polysome association, and altered mRNA binding. HEL2 deletion caused loss of RQC and, we report here, no-go decay (NGD), with comparable effects for Hel2 truncation including the RNA-binding site. Asc1 acts upstream of Hel2 in RQC and asc1∆ impaired Hel2 binding to 18S and mRNA. In conclusion: Hel2 is recruited or stabilized on translating 40S ribosomal subunits by interactions with 18S rRNA and Asc1. This 18S interaction is required for Hel2 function in RQC and NGD. Hel2 probably interacts with mRNA during translation termination. Ribosome-associated quality control (RQC) pathways monitor and respond to stalling of the translating ribosome. Here the authors show that the ribosome associated RQC factor Hel2/ZNF598, an E3 ubiquitin ligase, generally interacts with mRNAs in the vicinity of stop codons.
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Affiliation(s)
- Marie-Luise Winz
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh, EH9 3BF, Scotland
| | - Lauri Peil
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh, EH9 3BF, Scotland.,Institute of Technology, University of Tartu, Nooruse 150411, Tartu, Estonia
| | - Tomasz W Turowski
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh, EH9 3BF, Scotland
| | - Juri Rappsilber
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh, EH9 3BF, Scotland.,Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355, Berlin, Germany
| | - David Tollervey
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh, EH9 3BF, Scotland.
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88
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O’Connell AE, Gerashchenko MV, O’Donohue MF, Rosen SM, Huntzinger E, Gleeson D, Galli A, Ryder E, Cao S, Murphy Q, Kazerounian S, Morton SU, Schmitz-Abe K, Gladyshev VN, Gleizes PE, Séraphin B, Agrawal PB. Mammalian Hbs1L deficiency causes congenital anomalies and developmental delay associated with Pelota depletion and 80S monosome accumulation. PLoS Genet 2019; 15:e1007917. [PMID: 30707697 PMCID: PMC6373978 DOI: 10.1371/journal.pgen.1007917] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 02/13/2019] [Accepted: 12/25/2018] [Indexed: 12/18/2022] Open
Abstract
Hbs1 has been established as a central component of the cell's translational quality control pathways in both yeast and prokaryotic models; however, the functional characteristics of its human ortholog (Hbs1L) have not been well-defined. We recently reported a novel human phenotype resulting from a mutation in the critical coding region of the HBS1L gene characterized by facial dysmorphism, severe growth restriction, axial hypotonia, global developmental delay and retinal pigmentary deposits. Here we further characterize downstream effects of the human HBS1L mutation. HBS1L has three transcripts in humans, and RT-PCR demonstrated reduced mRNA levels corresponding with transcripts V1 and V2 whereas V3 expression was unchanged. Western blot analyses revealed Hbs1L protein was absent in the patient cells. Additionally, polysome profiling revealed an abnormal aggregation of 80S monosomes in patient cells under baseline conditions. RNA and ribosomal sequencing demonstrated an increased translation efficiency of ribosomal RNA in Hbs1L-deficient fibroblasts, suggesting that there may be a compensatory increase in ribosome translation to accommodate the increased 80S monosome levels. This enhanced translation was accompanied by upregulation of mTOR and 4-EBP protein expression, suggesting an mTOR-dependent phenomenon. Furthermore, lack of Hbs1L caused depletion of Pelota protein in both patient cells and mouse tissues, while PELO mRNA levels were unaffected. Inhibition of proteasomal function partially restored Pelota expression in human Hbs1L-deficient cells. We also describe a mouse model harboring a knockdown mutation in the murine Hbs1l gene that shared several of the phenotypic elements observed in the Hbs1L-deficient human including facial dysmorphism, growth restriction and retinal deposits. The Hbs1lKO mice similarly demonstrate diminished Pelota levels that were rescued by proteasome inhibition.
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Affiliation(s)
- Amy E. O’Connell
- Division of Newborn Medicine, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Maxim V. Gerashchenko
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Marie-Francoise O’Donohue
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Samantha M. Rosen
- Division of Newborn Medicine, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts, United States of America
| | - Eric Huntzinger
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Université de Strasbourg, Centre National de La Recherche Scientifique UMR 7104, INSERM U964, Strasbourg, France
| | - Diane Gleeson
- Wellcome Sanger Institute, Cambridge, United Kingdom
| | | | - Edward Ryder
- Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Siqi Cao
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts, United States of America
| | - Quinn Murphy
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts, United States of America
| | - Shideh Kazerounian
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts, United States of America
| | - Sarah U. Morton
- Division of Newborn Medicine, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Klaus Schmitz-Abe
- Division of Newborn Medicine, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Vadim N. Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Pierre-Emmanuel Gleizes
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Bertrand Séraphin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Université de Strasbourg, Centre National de La Recherche Scientifique UMR 7104, INSERM U964, Strasbourg, France
| | - Pankaj B. Agrawal
- Division of Newborn Medicine, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
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89
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Delorme-Axford E, Klionsky DJ. On the edge of degradation: Autophagy regulation by RNA decay. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 10:e1522. [PMID: 30560575 DOI: 10.1002/wrna.1522] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 11/21/2018] [Accepted: 11/27/2018] [Indexed: 12/21/2022]
Abstract
Cells must dynamically adapt to altered environmental conditions, particularly during times of stress, to ensure their ability to function effectively and survive. The macroautophagy/autophagy pathway is highly conserved across eukaryotic cells and promotes cell survival during stressful conditions. In general, basal autophagy occurs at a low level to sustain cellular homeostasis and metabolism. However, autophagy is robustly upregulated in response to nutrient deprivation, pathogen infection and increased accumulation of potentially toxic protein aggregates and superfluous organelles. Within the cell, RNA decay maintains quality control to remove aberrant transcripts and regulate appropriate levels of gene expression. Recent evidence has identified components of the cellular mRNA decay machinery as novel regulators of autophagy. Here, we review current findings that demonstrate how autophagy is modulated through RNA decay. This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Turnover and Surveillance > Regulation of RNA Stability.
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Affiliation(s)
| | - Daniel J Klionsky
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan
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90
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Wang YG, Zheng DH, Shi M, Xu XM. T cell dysfunction in chronic hepatitis B infection and liver cancer: evidence from transcriptome analysis. J Med Genet 2018; 56:22-28. [PMID: 30518547 DOI: 10.1136/jmedgenet-2018-105570] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 08/26/2018] [Accepted: 09/22/2018] [Indexed: 12/14/2022]
Abstract
BACKGROUND T cell dysfunction occurs in many diseases, especially in chronic virus infection and cancers. However, up to now, little is known on the distinctions in T cell exhaustion between cancer and chronic virus infection. The objective of this study is to explore the transcriptional similarities and differences in exhausted CD8 +T cell between chronic hepatitis B virus (HBV) infection and hepatocellular carcinoma (HCC). METHODS RNA sequencing was performed to compare the transcriptome of CD8 +T cells isolated from healthy donors' blood, tumour tissues of patients with HCC and chronic HBV infected HCC patients' paracancerous tissues. DESeq2 algorithm was used to determine differentially expressed genes. Gene ontology and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment analysis was conducted for in-depth analysis of these differentially expressed genes. RESULTS A total number of 2109 and 2203 genes were differentially expressed in patients with chronic HBV infection and HCC, respectively. Comparing these two groups of differentially deregulated genes, we found that nearly half of them were shared, and these shared genes were further classified into several functional categories, such as metabolic process, binding and intracellular organelle. KEGG analysis revealed that these shared deregulated genes were involved in many important pathways such as Parkinson's disease, oxidative phosphorylation and messenger RNA surveillance. Interestingly, we reported that chronic HBV infection specific deregulated genes were mainly enriched in graft versus host disease, allograft rejection, phenylalanine, tyrosine and tryptophan biosynthesis pathways. Whereas, HCC-specific deregulated genes were highly enriched in oxidative phosphorylation, thyroid cancer and endometrial cancer pathways. CONCLUSION Our study demonstrated that T cell dysfunction associated with HCC and chronic HBV infection shares high similarities, however, each possesses its own features in terms of specific genes and signalling pathways. Uncovering the differences of T cells dysfunction would facilitate our understanding the diseases pathogenesis and developing innovative therapies in the future.
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Affiliation(s)
- Yu-Gang Wang
- Department of Gastroenterology, Shanghai Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dong-Hui Zheng
- Department of Nephrology, Huai'an Second People's Hospital and The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, China
| | - Min Shi
- Department of Gastroenterology, Shanghai Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xi-Ming Xu
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, China
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91
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Simms CL, Kim KQ, Yan LL, Qiu J, Zaher HS. Interactions between the mRNA and Rps3/uS3 at the entry tunnel of the ribosomal small subunit are important for no-go decay. PLoS Genet 2018; 14:e1007818. [PMID: 30475795 PMCID: PMC6283612 DOI: 10.1371/journal.pgen.1007818] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 12/06/2018] [Accepted: 11/07/2018] [Indexed: 11/25/2022] Open
Abstract
No-go Decay (NGD) is a process that has evolved to deal with stalled ribosomes resulting from structural blocks or aberrant mRNAs. The process is distinguished by an endonucleolytic cleavage prior to degradation of the transcript. While many of the details of the pathway have been described, the identity of the endonuclease remains unknown. Here we identify residues of the small subunit ribosomal protein Rps3 that are important for NGD by affecting the cleavage reaction. Mutation of residues within the ribosomal entry tunnel that contact the incoming mRNA leads to significantly reduced accumulation of cleavage products, independent of the type of stall sequence, and renders cells sensitive to damaging agents thought to trigger NGD. These phenotypes are distinct from those seen in combination with other NGD factors, suggesting a separate role for Rps3 in NGD. Conversely, ribosomal proteins ubiquitination is not affected by rps3 mutations, indicating that upstream ribosome quality control (RQC) events are not dependent on these residues. Together, these results suggest that Rps3 is important for quality control on the ribosome and strongly supports the notion that the ribosome itself plays a central role in the endonucleolytic cleavage reaction during NGD. In all organisms, optimum cellular fitness depends on the ability of cells to recognize and degrade aberrant molecules. Messenger RNA is subject to alterations and, as a result, often presents roadblocks for the translating ribosomes. It is not surprising, then, that organisms evolved pathways to resolve these valuable stuck ribosomes. In eukaryotes, this process is called no-go decay (NGD) because it is coupled with decay of mRNAs that are associated with ribosomes that do not ‘go’. This decay process initiates with cleavage of the mRNA near the stall site, but some important details about this reaction are lacking. Here, we show that the ribosome itself is very central to the cleavage reaction. In particular, we identified a pair of residues of a ribosomal protein to be important for cleavage efficiency. These observations are consistent with prior structural studies showing that the residues make intimate contacts with the incoming mRNA in the entry tunnel. Altogether our data provide important clues about this quality-control pathway and suggest that the endonuclease not only recognizes stalled ribosomes but may have coevolved with the translation machinery to take advantage of certain residues of the ribosome to fulfill its function.
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MESH Headings
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/metabolism
- Amino Acid Sequence
- Amino Acid Substitution
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Endoribonucleases/genetics
- Endoribonucleases/metabolism
- GTP-Binding Proteins/genetics
- GTP-Binding Proteins/metabolism
- Genes, Fungal
- Models, Molecular
- Mutagenesis, Site-Directed
- Mutation
- Peptide Chain Elongation, Translational
- Protein Conformation
- RNA Stability
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Ribosomal Proteins/chemistry
- Ribosomal Proteins/genetics
- Ribosomal Proteins/metabolism
- Ribosome Subunits, Small/genetics
- Ribosome Subunits, Small/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/chemistry
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Sequence Homology, Amino Acid
- Ubiquitination
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Affiliation(s)
- Carrie L. Simms
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Kyusik Q. Kim
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Liewei L. Yan
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Jessica Qiu
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Hani S. Zaher
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
- * E-mail:
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92
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Juszkiewicz S, Chandrasekaran V, Lin Z, Kraatz S, Ramakrishnan V, Hegde RS. ZNF598 Is a Quality Control Sensor of Collided Ribosomes. Mol Cell 2018; 72:469-481.e7. [PMID: 30293783 PMCID: PMC6224477 DOI: 10.1016/j.molcel.2018.08.037] [Citation(s) in RCA: 234] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 08/07/2018] [Accepted: 08/22/2018] [Indexed: 01/30/2023]
Abstract
Aberrantly slow translation elicits quality control pathways initiated by the ubiquitin ligase ZNF598. How ZNF598 discriminates physiologic from pathologic translation complexes and ubiquitinates stalled ribosomes selectively is unclear. Here, we find that the minimal unit engaged by ZNF598 is the collided di-ribosome, a molecular species that arises when a trailing ribosome encounters a slower leading ribosome. The collided di-ribosome structure reveals an extensive 40S-40S interface in which the ubiquitination targets of ZNF598 reside. The paucity of 60S interactions allows for different ribosome rotation states, explaining why ZNF598 recognition is indifferent to how the leading ribosome has stalled. The use of ribosome collisions as a proxy for stalling allows the degree of tolerable slowdown to be tuned by the initiation rate on that mRNA; hence, the threshold for triggering quality control is substrate specific. These findings illustrate how higher-order ribosome architecture can be exploited by cellular factors to monitor translation status. ZNF598 is a direct sensor of ribosome collisions incurred by many unrelated causes The minimal target recognized and ubiquitinated by ZNF598 is a collided di-ribosome Collided di-ribosome structure shows that ZNF598 ubiquitin sites are near the interface Collisions are required to terminally arrest translation in ZNF598-dependent manner
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Affiliation(s)
| | | | - Zhewang Lin
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | - V Ramakrishnan
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
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93
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Karamyshev AL, Karamysheva ZN. Lost in Translation: Ribosome-Associated mRNA and Protein Quality Controls. Front Genet 2018; 9:431. [PMID: 30337940 PMCID: PMC6180196 DOI: 10.3389/fgene.2018.00431] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 09/11/2018] [Indexed: 12/15/2022] Open
Abstract
Aberrant, misfolded, and mislocalized proteins are often toxic to cells and result in many human diseases. All proteins and their mRNA templates are subject to quality control. There are several distinct mechanisms that control the quality of mRNAs and proteins during translation at the ribosome. mRNA quality control systems, nonsense-mediated decay, non-stop decay, and no-go decay detect premature stop codons, the absence of a natural stop codon, and stalled ribosomes in translation, respectively, and degrade their mRNAs. Defective truncated polypeptide nascent chains generated from faulty mRNAs are degraded by ribosome-associated protein quality control pathways. Regulation of aberrant protein production, a novel pathway, senses aberrant proteins by monitoring the status of nascent chain interactions during translation and triggers degradation of their mRNA. Here, we review the current progress in understanding of the molecular mechanisms of mRNA and protein quality controls at the ribosome during translation.
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Affiliation(s)
- Andrey L Karamyshev
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | - Zemfira N Karamysheva
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
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94
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Ghiasi SM, Krogh N, Tyrberg B, Mandrup-Poulsen T. The No-Go and Nonsense-Mediated RNA Decay Pathways Are Regulated by Inflammatory Cytokines in Insulin-Producing Cells and Human Islets and Determine β-Cell Insulin Biosynthesis and Survival. Diabetes 2018; 67:2019-2037. [PMID: 30065031 DOI: 10.2337/db18-0073] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 07/23/2018] [Indexed: 11/13/2022]
Abstract
Stress-related changes in β-cell mRNA levels result from a balance between gene transcription and mRNA decay. The regulation of RNA decay pathways has not been investigated in pancreatic β-cells. We found that no-go and nonsense-mediated RNA decay pathway components (RDPCs) and exoribonuclease complexes were expressed in INS-1 cells and human islets. Pelo, Dcp2, Dis3L2, Upf2, and Smg1/5/6/7 were upregulated by inflammatory cytokines in INS-1 cells under conditions where central β-cell mRNAs were downregulated. These changes in RDPC mRNA or corresponding protein levels were largely confirmed in INS-1 cells and rat/human islets. Cytokine-induced upregulation of Pelo, Xrn1, Dis3L2, Upf2, and Smg1/6 was reduced by inducible nitric oxide synthase inhibition, as were endoplasmic reticulum (ER) stress, inhibition of Ins1/2 mRNA, and accumulated insulin secretion. Reactive oxygen species inhibition or iron chelation did not affect RDPC expression. Pelo or Xrn1 knockdown (KD) aggravated, whereas Smg6 KD ameliorated, cytokine-induced INS-1 cell death without affecting ER stress; both increased insulin biosynthesis and medium accumulation but not glucose-stimulated insulin secretion in cytokine-exposed INS-1 cells. In conclusion, RDPCs are regulated by inflammatory stress in β-cells. RDPC KD improved insulin biosynthesis, likely by preventing Ins1/2 mRNA clearance. Pelo/Xrn1 KD aggravated, but Smg6 KD ameliorated, cytokine-mediated β-cell death, possibly through prevention of proapoptotic and antiapoptotic mRNA degradation, respectively.
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Affiliation(s)
- Seyed Mojtaba Ghiasi
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nicolai Krogh
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Björn Tyrberg
- Translational Science; Cardiovascular, Renal and Metabolism; and IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
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95
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Kalisiak K, Kuliński TM, Tomecki R, Cysewski D, Pietras Z, Chlebowski A, Kowalska K, Dziembowski A. A short splicing isoform of HBS1L links the cytoplasmic exosome and SKI complexes in humans. Nucleic Acids Res 2018; 45:2068-2080. [PMID: 28204585 PMCID: PMC5389692 DOI: 10.1093/nar/gkw862] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 08/25/2016] [Accepted: 09/20/2016] [Indexed: 12/18/2022] Open
Abstract
The exosome complex is a major eukaryotic exoribonuclease that requires the SKI complex for its activity in the cytoplasm. In yeast, the Ski7 protein links both complexes, whereas a functional equivalent of the Ski7 has remained unknown in the human genome. Proteomic analysis revealed that a previously uncharacterized short splicing isoform of HBS1L (HBS1LV3) is the long-sought factor linking the exosome and SKI complexes in humans. In contrast, the canonical HBS1L variant, HBS1LV1, which acts as a ribosome dissociation factor, does not associate with the exosome and instead interacts with the mRNA surveillance factor PELOTA. Interestingly, both HBS1LV1 and HBS1LV3 interact with the SKI complex and HBS1LV1 seems to antagonize SKI/exosome supercomplex formation. HBS1LV3 contains a unique C-terminal region of unknown structure, with a conserved RxxxFxxxL motif responsible for exosome binding and may interact with the exosome core subunit RRP43 in a way that resembles the association between Rrp6 RNase and Rrp43 in yeast. HBS1LV3 or the SKI complex helicase (SKI2W) depletion similarly affected the transcriptome, deregulating multiple genes. Furthermore, half-lives of representative upregulated mRNAs were increased, supporting the involvement of HBS1LV3 and SKI2W in the same mRNA degradation pathway, essential for transcriptome homeostasis in the cytoplasm.
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Affiliation(s)
- Katarzyna Kalisiak
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Tomasz M. Kuliński
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Rafał Tomecki
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Dominik Cysewski
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Zbigniew Pietras
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
- International Institute of Molecular and Cell Biology in Warsaw, Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Aleksander Chlebowski
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Katarzyna Kowalska
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Andrzej Dziembowski
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
- To whom correspondence should be addressed. Tel: +48 22 5922033; Fax: +48 22 6584176;
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96
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Arthur LL, Djuranovic S. PolyA tracks, polybasic peptides, poly-translational hurdles. WILEY INTERDISCIPLINARY REVIEWS. RNA 2018; 9:e1486. [PMID: 29869837 PMCID: PMC6281860 DOI: 10.1002/wrna.1486] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 04/25/2018] [Accepted: 04/26/2018] [Indexed: 12/26/2022]
Abstract
The abundance of messenger RNA (mRNA) is one of the major determinants of protein synthesis. As such, factors that influence mRNA stability often contribute to gene regulation. Polyadenylation of the 3' end of mRNA transcripts, the poly(A) tail, has long been recognized as one of these regulatory elements given its influence on translation efficiency and mRNA stability. Unwanted translation of the poly(A) tail signals to the cell an aberrant polyadenylation event or the lack of stop codons, which makes this sequence an important element in translation fidelity and mRNA surveillance response. Consequently, investigations into the effects of the poly(A) tail lead to the discoveries that poly-lysine as well as other polybasic peptide sequences and, to a much greater extent, polyA mRNA sequences within the open reading frame influence mRNA stability and translational efficiency. Conservation and evolutionary selection of codon usage in polyA track sequences across multiple organisms suggests a biological significance for coding polyA tracks in the regulation of gene expression. Here, we discuss the cellular responses and consequences of coding polyA track translation and synthesis of polybasic peptides. This article is categorized under: Translation > Translation Mechanisms Translation > Translation Regulation RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms.
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Affiliation(s)
- Laura L Arthur
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri
| | - Sergej Djuranovic
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri
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97
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Genome-wide atlas of alternative polyadenylation in the forage legume red clover. Sci Rep 2018; 8:11379. [PMID: 30054540 PMCID: PMC6063945 DOI: 10.1038/s41598-018-29699-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 07/05/2018] [Indexed: 12/13/2022] Open
Abstract
Studies on prevalence and significance of alternative polyadenylation (APA) in plants have been so far limited mostly to the model plants. Here, a genome-wide analysis of APA was carried out in different tissue types in the non-model forage legume red clover (Trifolium pratense L). A profile of poly(A) sites in different tissue types was generated using so-called 'poly(A)-tag sequencing' (PATseq) approach. Our analysis revealed tissue-wise dynamics of usage of poly(A) sites located at different genomic locations. We also identified poly(A) sites and underlying genes displaying APA in different tissues. Functional categories enriched in groups of genes manifesting APA between tissue types were determined. Analysis of spatial expression of genes encoding different poly(A) factors showed significant differential expression of genes encoding orthologs of FIP1(V) and PCFS4, suggesting that these two factors may play a role in regulating spatial APA in red clover. Our analysis also revealed a high degree of conservation in diverse plant species of APA events in mRNAs encoding two key polyadenylation factors, CPSF30 and FIP1(V). Together with our previously reported study of spatial gene expression in red clover, this study will provide a comprehensive account of transcriptome dynamics in this non-model forage legume.
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98
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Conservation of mRNA quality control factor Ski7 and its diversification through changes in alternative splicing and gene duplication. Proc Natl Acad Sci U S A 2018; 115:E6808-E6816. [PMID: 29967155 DOI: 10.1073/pnas.1801997115] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Eukaryotes maintain fidelity of gene expression by preferential degradation of aberrant mRNAs that arise by errors in RNA processing reactions. In Saccharomyces cerevisiae, Ski7 plays an important role in this mRNA quality control by mediating mRNA degradation by the RNA exosome. Ski7 was initially thought to be restricted to Saccharomyces cerevisiae and close relatives because the SKI7 gene and its paralog HBS1 arose by whole genome duplication (WGD) in a recent ancestor. We have recently shown that the preduplication gene was alternatively spliced and that Ski7 function predates WGD. Here, we use transcriptome analysis of diverse eukaryotes to show that diverse eukaryotes use alternative splicing of SKI7/HBS1 to encode two proteins. Although alternative splicing affects the same intrinsically disordered region of the protein, the pattern of splice site usage varies. This alternative splicing event arose in an early eukaryote that is a common ancestor of plants, animals, and fungi. Remarkably, through changes in alternative splicing and gene duplication, the Ski7 protein has diversified such that different species express one of four distinct Ski7-like proteins. We also show experimentally that the Saccharomyces cerevisiae SKI7 gene has undergone multiple changes that are incompatible with the Hbs1 function and may also have undergone additional changes to optimize mRNA quality control. The combination of transcriptome analysis in diverse eukaryotes and genetic analysis in yeast clarifies the mechanism by which a Ski7-like protein is expressed across eukaryotes and provides a unique view of changes in alternative splicing patterns of one gene over long evolutionary time.
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99
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Szádeczky-Kardoss I, Csorba T, Auber A, Schamberger A, Nyikó T, Taller J, Orbán TI, Burgyán J, Silhavy D. The nonstop decay and the RNA silencing systems operate cooperatively in plants. Nucleic Acids Res 2018; 46:4632-4648. [PMID: 29672715 PMCID: PMC5961432 DOI: 10.1093/nar/gky279] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 03/28/2018] [Accepted: 04/11/2018] [Indexed: 12/27/2022] Open
Abstract
Translation-dependent mRNA quality control systems protect the protein homeostasis of eukaryotic cells by eliminating aberrant transcripts and stimulating the decay of their protein products. Although these systems are intensively studied in animals, little is known about the translation-dependent quality control systems in plants. Here, we characterize the mechanism of nonstop decay (NSD) system in Nicotiana benthamiana model plant. We show that plant NSD efficiently degrades nonstop mRNAs, which can be generated by premature polyadenylation, and stop codon-less transcripts, which are produced by endonucleolytic cleavage. We demonstrate that in plants, like in animals, Pelota, Hbs1 and SKI2 proteins are required for NSD, supporting that NSD is an ancient and conserved eukaryotic quality control system. Relevantly, we found that NSD and RNA silencing systems cooperate in plants. Plant silencing predominantly represses target mRNAs through endonucleolytic cleavage in the coding region. Here we show that NSD is required for the elimination of 5' cleavage product of mi- or siRNA-guided silencing complex when the cleavage occurs in the coding region. We also show that NSD and nonsense-mediated decay (NMD) quality control systems operate independently in plants.
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Affiliation(s)
| | - Tibor Csorba
- Agricultural Biotechnology Institute, Szent-Györgyi 4, H-2100 Gödöllő, Hungary
| | - Andor Auber
- Agricultural Biotechnology Institute, Szent-Györgyi 4, H-2100 Gödöllő, Hungary
| | - Anita Schamberger
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, 1117 Budapest, Hungary
| | - Tünde Nyikó
- Agricultural Biotechnology Institute, Szent-Györgyi 4, H-2100 Gödöllő, Hungary
| | - János Taller
- University Pannonia Georgikon, Festetics 7, 8360 Keszthely, Hungary
| | - Tamás I Orbán
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, 1117 Budapest, Hungary
| | - József Burgyán
- Agricultural Biotechnology Institute, Szent-Györgyi 4, H-2100 Gödöllő, Hungary
| | - Dániel Silhavy
- Agricultural Biotechnology Institute, Szent-Györgyi 4, H-2100 Gödöllő, Hungary
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100
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Bak RO, Porteus MH. CRISPR-Mediated Integration of Large Gene Cassettes Using AAV Donor Vectors. Cell Rep 2018; 20:750-756. [PMID: 28723575 DOI: 10.1016/j.celrep.2017.06.064] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 04/17/2017] [Accepted: 06/22/2017] [Indexed: 12/31/2022] Open
Abstract
The CRISPR/Cas9 system has recently been shown to facilitate high levels of precise genome editing using adeno-associated viral (AAV) vectors to serve as donor template DNA during homologous recombination (HR). However, the maximum AAV packaging capacity of ∼4.5 kb limits the donor size. Here, we overcome this constraint by showing that two co-transduced AAV vectors can serve as donors during consecutive HR events for the integration of large transgenes. Importantly, the method involves a single-step procedure applicable to primary cells with relevance to therapeutic genome editing. We use the methodology in primary human T cells and CD34+ hematopoietic stem and progenitor cells to site-specifically integrate an expression cassette that, as a single donor vector, would otherwise amount to a total of 6.5 kb. This approach now provides an efficient way to integrate large transgene cassettes into the genomes of primary human cells using HR-mediated genome editing with AAV vectors.
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Affiliation(s)
- Rasmus O Bak
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA.
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA.
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