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Grove DJ, Russell PJ, Kearse MG. To initiate or not to initiate: A critical assessment of eIF2A, eIF2D, and MCT-1·DENR to deliver initiator tRNA to ribosomes. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1833. [PMID: 38433101 DOI: 10.1002/wrna.1833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 03/05/2024]
Abstract
Selection of the correct start codon is critical for high-fidelity protein synthesis. In eukaryotes, this is typically governed by a multitude of initiation factors (eIFs), including eIF2·GTP that directly delivers the initiator tRNA (Met-tRNAi Met ) to the P site of the ribosome. However, numerous reports, some dating back to the early 1970s, have described other initiation factors having high affinity for the initiator tRNA and the ability of delivering it to the ribosome, which has provided a foundation for further work demonstrating non-canonical initiation mechanisms using alternative initiation factors. Here we provide a critical analysis of current understanding of eIF2A, eIF2D, and the MCT-1·DENR dimer, the evidence surrounding their ability to initiate translation, their implications in human disease, and lay out important key questions for the field. This article is categorized under: RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes Translation > Mechanisms Translation > Regulation.
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Affiliation(s)
- Daisy J Grove
- The Ohio State Biochemistry Program, Department of Biological Chemistry, Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Paul J Russell
- The Ohio State Biochemistry Program, Department of Biological Chemistry, Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
- The Cellular, Molecular, Biochemical Sciences Program, Department of Biological Chemistry, Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
| | - Michael G Kearse
- The Ohio State Biochemistry Program, Department of Biological Chemistry, Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
- The Cellular, Molecular, Biochemical Sciences Program, Department of Biological Chemistry, Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
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2
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Wu J, Wu W, Jiang P, Xu Y, Yu M. Identification of SV2C and DENR as Key Biomarkers for Parkinson's Disease Based on Bioinformatics, Machine Learning, and Experimental Verification. J Mol Neurosci 2024; 74:6. [PMID: 38189881 DOI: 10.1007/s12031-023-02182-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/15/2023] [Indexed: 01/09/2024]
Abstract
The objective of this study is to investigate the potential biomarkers and therapeutic target genes for Parkinson's disease (PD). We analyzed four datasets (GSE8397, GSE20292, GSE20163, GSE20164) from the Gene Expression Omnibus database. We employed weighted gene co-expression network analysis and differential expression analysis to select genes and perform functional analysis. We applied three algorithms, namely, random forest, support vector machine recursive feature elimination, and least absolute shrinkage and selection operator, to identify hub genes, perform functional analysis, and assess their clinical diagnostic potential using receiver operating characteristic (ROC) curve analysis. We employed the xCell website to evaluate differences in the composition patterns of immune cells in the GEO datasets. We also collected serum samples from PD patients and established PD cell model to validate the expression of hub genes using enzyme-linked immunosorbent assay and quantitative real-time polymerase chain reaction. Our findings identified SV2C and DENR as two hub genes for PD and decreased in PD brain tissue compared with controls. ROC analysis showed effectively value of SV2C and DENR to diagnose PD, and they were downregulated in the serum of PD patients and cell model. Functional analysis revealed that dopamine vesicle transport and synaptic vesicle recycling are crucial pathways in PD. Besides, the differences in the composition of immune cells, especially basophils and T cells, were discovered between PD and controls. In summary, our study identifies SV2C and DENR as potential biomarkers for diagnosing PD and provides a new perspective for exploring the molecular mechanisms of PD.
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Affiliation(s)
- Jiecong Wu
- Department of Neurology, The Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, 212001, China
| | - Wenqi Wu
- Department of Neurology, The Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, 212001, China
| | - Ping Jiang
- Department of Neurology, The Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, 212001, China.
| | - Yuhao Xu
- Department of Neurology, The Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, 212001, China.
| | - Ming Yu
- Department of Neurology, The Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, 212001, China.
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3
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Sherlock ME, Baquero Galvis L, Vicens Q, Kieft JS, Jagannathan S. Principles, mechanisms, and biological implications of translation termination-reinitiation. RNA (NEW YORK, N.Y.) 2023; 29:865-884. [PMID: 37024263 PMCID: PMC10275272 DOI: 10.1261/rna.079375.122] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 03/28/2023] [Indexed: 06/11/2023]
Abstract
The gene expression pathway from DNA sequence to functional protein is not as straightforward as simple depictions of the central dogma might suggest. Each step is highly regulated, with complex and only partially understood molecular mechanisms at play. Translation is one step where the "one gene-one protein" paradigm breaks down, as often a single mature eukaryotic mRNA leads to more than one protein product. One way this occurs is through translation reinitiation, in which a ribosome starts making protein from one initiation site, translates until it terminates at a stop codon, but then escapes normal recycling steps and subsequently reinitiates at a different downstream site. This process is now recognized as both important and widespread, but we are only beginning to understand the interplay of factors involved in termination, recycling, and initiation that cause reinitiation events. There appear to be several ways to subvert recycling to achieve productive reinitiation, different types of stresses or signals that trigger this process, and the mechanism may depend in part on where the event occurs in the body of an mRNA. This perspective reviews the unique characteristics and mechanisms of reinitiation events, highlights the similarities and differences between three major scenarios of reinitiation, and raises outstanding questions that are promising avenues for future research.
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Affiliation(s)
- Madeline E Sherlock
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Laura Baquero Galvis
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Quentin Vicens
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Jeffrey S Kieft
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Sujatha Jagannathan
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
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4
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Makeeva DS, Riggs CL, Burakov AV, Ivanov PA, Kushchenko AS, Bykov DA, Popenko VI, Prassolov VS, Ivanov PV, Dmitriev SE. Relocalization of Translation Termination and Ribosome Recycling Factors to Stress Granules Coincides with Elevated Stop-Codon Readthrough and Reinitiation Rates upon Oxidative Stress. Cells 2023; 12:259. [PMID: 36672194 PMCID: PMC9856671 DOI: 10.3390/cells12020259] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/27/2022] [Accepted: 01/03/2023] [Indexed: 01/11/2023] Open
Abstract
Upon oxidative stress, mammalian cells rapidly reprogram their translation. This is accompanied by the formation of stress granules (SGs), cytoplasmic ribonucleoprotein condensates containing untranslated mRNA molecules, RNA-binding proteins, 40S ribosomal subunits, and a set of translation initiation factors. Here we show that arsenite-induced stress causes a dramatic increase in the stop-codon readthrough rate and significantly elevates translation reinitiation levels on uORF-containing and bicistronic mRNAs. We also report the recruitment of translation termination factors eRF1 and eRF3, as well as ribosome recycling and translation reinitiation factors ABCE1, eIF2D, MCT-1, and DENR to SGs upon arsenite treatment. Localization of these factors to SGs may contribute to a rapid resumption of mRNA translation after stress relief and SG disassembly. It may also suggest the presence of post-termination, recycling, or reinitiation complexes in SGs. This new layer of translational control under stress conditions, relying on the altered spatial distribution of translation factors between cellular compartments, is discussed.
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Affiliation(s)
- Desislava S. Makeeva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Claire L. Riggs
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Anton V. Burakov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Pavel A. Ivanov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Artem S. Kushchenko
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Dmitri A. Bykov
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Vladimir I. Popenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Vladimir S. Prassolov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Pavel V. Ivanov
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sergey E. Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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5
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Young DJ, Guydosh NR. Rebirth of the translational machinery: The importance of recycling ribosomes. Bioessays 2022; 44:e2100269. [PMID: 35147231 PMCID: PMC9270684 DOI: 10.1002/bies.202100269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 11/10/2022]
Abstract
Translation of the genetic code occurs in a cycle where ribosomes engage mRNAs, synthesize protein, and then disengage in order to repeat the process again. The final part of this process-ribosome recycling, where ribosomes dissociate from mRNAs-involves a complex molecular choreography of specific protein factors to remove the large and small subunits of the ribosome in a coordinated fashion. Errors in this process can lead to the accumulation of ribosomes at stop codons or translation of downstream open reading frames (ORFs). Ribosome recycling is also critical when a ribosome stalls during the elongation phase of translation and must be rescued to allow continued translation of the mRNA. Here we discuss the molecular interactions that drive ribosome recycling, and their regulation in the cell. We also examine the consequences of inefficient recycling with regards to disease, and its functional roles in synthesis of novel peptides, regulation of gene expression, and control of mRNA-associated proteins. Alterations in ribosome recycling efficiency have the potential to impact many cellular functions but additional work is needed to understand how this regulatory power is utilized.
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Affiliation(s)
- David J Young
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Nicholas R Guydosh
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
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6
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Clemm von Hohenberg K, Müller S, Schleich S, Meister M, Bohlen J, Hofmann TG, Teleman AA. Cyclin B/CDK1 and Cyclin A/CDK2 phosphorylate DENR to promote mitotic protein translation and faithful cell division. Nat Commun 2022; 13:668. [PMID: 35115540 PMCID: PMC8813921 DOI: 10.1038/s41467-022-28265-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 01/12/2022] [Indexed: 12/11/2022] Open
Abstract
DENR and MCTS1 have been identified as oncogenes in several different tumor entities. The heterodimeric DENR·MCTS1 protein complex promotes translation of mRNAs containing upstream Open Reading Frames (uORFs). We show here that DENR is phosphorylated on Serine 73 by Cyclin B/CDK1 and Cyclin A/CDK2 at the onset of mitosis, and then dephosphorylated as cells exit mitosis. Phosphorylation of Ser73 promotes mitotic stability of DENR protein and prevents its cleavage at Asp26. This leads to enhanced translation of mRNAs involved in mitosis. Indeed, we find that roughly 40% of all mRNAs with elevated translation in mitosis are DENR targets. In the absence of DENR or of Ser73 phosphorylation, cells display elevated levels of aberrant mitoses and cell death. This provides a mechanism how the cell cycle regulates translation of a subset of mitotically relevant mRNAs during mitosis. The cell cycle regulates translation during mitosis by controlling DENR stability. Here, the authors show the non-canonical translation initiation complex DENR·MCTS1 is phosphorylated during mitosis by CDK1 and 2, enabling the translation of genes needed for proper mitotic progression.
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Affiliation(s)
- Katharina Clemm von Hohenberg
- German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Heidelberg University, 69120, Heidelberg, Germany.,CellNetworks-Cluster of Excellence, Heidelberg University, Heidelberg, Germany.,Department of Medicine III, Universitätsmedizin Mannheim, 68167, Mannheim, Germany
| | - Sandra Müller
- German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Heidelberg University, 69120, Heidelberg, Germany
| | - Sibylle Schleich
- German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Heidelberg University, 69120, Heidelberg, Germany
| | - Matthias Meister
- Division of Viral Transformation Mechanisms, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jonathan Bohlen
- German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Heidelberg University, 69120, Heidelberg, Germany.,CellNetworks-Cluster of Excellence, Heidelberg University, Heidelberg, Germany.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,University of Paris, Imagine Institute, Paris, France
| | - Thomas G Hofmann
- Institute of Toxicology, University Medical Center Mainz at the Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Aurelio A Teleman
- German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany. .,Heidelberg University, 69120, Heidelberg, Germany. .,CellNetworks-Cluster of Excellence, Heidelberg University, Heidelberg, Germany.
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7
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Does Platelet-Rich Fibrin Prevent Hemorrhagic Complications After Dental Extractions in Patients Using Oral Anticoagulant Therapy? J Oral Maxillofac Surg 2021; 79:2215-2226. [PMID: 34343502 DOI: 10.1016/j.joms.2021.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 01/05/2023]
Abstract
PURPOSE The number of anticoagulated patients requiring dental extractions and other minor dentoalveolar surgical procedures has increased significantly. The purpose of this study was to determine whether the use of platelet-rich fibrin (PRF) prevents hemorrhagic complications after dental extractions in patients being treated with oral anticoagulants. METHODS A 2-phase PROSPERO-registered systematic review of published within-subject controlled trials (CRD42020186678) was conducted in accordance with the PRISMA statement. Searches were conducted through Medline via PubMed, Web of Science, LILACS, Central Cochrane, Scopus, DOSS, and Google Scholar, until May 2020. The predictor variable was the study group (PRF vs use/non-use of other hemostatic agents). The main outcome of interest was the risk of bleeding after tooth extraction and the covariates were postoperative complications. Data analysis included synthesis of results, risk of bias (RoB) evaluation, meta-analysis (random effects; I²-based heterogeneity; 95% confidence), and certainty of evidence assessment. RESULTS From a total of 216 articles, 3 articles (low-moderate RoB) were included for evaluation in this systematic review and meta-analysis. A total of 130 patients were involved. The outcomes of the meta-analysis showed that the use of PRF in extraction wounds did not reduce the risk of bleeding after extraction in anticoagulated patients (P= .330; I² = 99%). Furthermore, the use of PRF did not improve pain scores (P = .470; I² = 96%) or the risk of postoperative alveolitis (P = .4300; I² = 38%) in anticoagulated patients. The certainty of the evidence ranged from moderate to low. CONCLUSIONS The findings of this systematic review and meta-analysis suggest that PRF does not prevent hemorrhagic complications after tooth extraction in patients using oral anticoagulant therapy.
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8
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Park Y, Page N, Salamon I, Li D, Rasin MR. Making sense of mRNA landscapes: Translation control in neurodevelopment. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1674. [PMID: 34137510 DOI: 10.1002/wrna.1674] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/10/2021] [Accepted: 05/11/2021] [Indexed: 12/27/2022]
Abstract
Like all other parts of the central nervous system, the mammalian neocortex undergoes temporally ordered set of developmental events, including proliferation, differentiation, migration, cellular identity, synaptogenesis, connectivity formation, and plasticity changes. These neurodevelopmental mechanisms have been characterized by studies focused on transcriptional control. Recent findings, however, have shown that the spatiotemporal regulation of post-transcriptional steps like alternative splicing, mRNA traffic/localization, mRNA stability/decay, and finally repression/derepression of protein synthesis (mRNA translation) have become just as central to the neurodevelopment as transcriptional control. A number of dynamic players act post-transcriptionally in the neocortex to regulate these steps, as RNA binding proteins (RBPs), ribosomal proteins (RPs), long non-coding RNAs, and/or microRNA. Remarkably, mutations in these post-transcriptional regulators have been associated with neurodevelopmental, neurodegenerative, inherited, or often co-morbid disorders, such as microcephaly, autism, epilepsy, intellectual disability, white matter diseases, Rett-syndrome like phenotype, spinocerebellar ataxia, and amyotrophic lateral sclerosis. Here, we focus on the current state, advanced methodologies and pitfalls of this exciting and upcoming field of RNA metabolism with vast potential in understanding fundamental neurodevelopmental processes and pathologies. This article is categorized under: Translation > Translation Regulation RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Yongkyu Park
- RWJ Medical School, Rutgers University, New Brunswick, New Jersey, USA
| | - Nicholas Page
- RWJ Medical School, Rutgers University, New Brunswick, New Jersey, USA
| | - Iva Salamon
- RWJ Medical School, Rutgers University, New Brunswick, New Jersey, USA
| | | | - Mladen-Roko Rasin
- RWJ Medical School, Rutgers University, New Brunswick, New Jersey, USA
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9
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Young DJ, Meydan S, Guydosh NR. 40S ribosome profiling reveals distinct roles for Tma20/Tma22 (MCT-1/DENR) and Tma64 (eIF2D) in 40S subunit recycling. Nat Commun 2021; 12:2976. [PMID: 34016977 PMCID: PMC8137927 DOI: 10.1038/s41467-021-23223-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 04/14/2021] [Indexed: 12/21/2022] Open
Abstract
The recycling of ribosomes at stop codons for use in further rounds of translation is critical for efficient protein synthesis. Removal of the 60S subunit is catalyzed by the ATPase Rli1 (ABCE1) while removal of the 40S is thought to require Tma64 (eIF2D), Tma20 (MCT-1), and Tma22 (DENR). However, it remains unclear how these Tma proteins cause 40S removal and control reinitiation of downstream translation. Here we used a 40S ribosome footprinting strategy to directly observe intermediate steps of ribosome recycling in cells. Deletion of the genes encoding these Tma proteins resulted in broad accumulation of unrecycled 40S subunits at stop codons, directly establishing their role in 40S recycling. Furthermore, the Tma20/Tma22 heterodimer was responsible for a majority of 40S recycling events while Tma64 played a minor role. Introduction of an autism-associated mutation into TMA22 resulted in a loss of 40S recycling activity, linking ribosome recycling and neurological disease.
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Affiliation(s)
- David J Young
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sezen Meydan
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
- Postdoctoral Research Associate Training Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Nicholas R Guydosh
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
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10
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Shyrokova EY, Prassolov VS, Spirin PV. The Role of the MCTS1 and DENR Proteins in Regulating the Mechanisms Associated with Malignant Cell Transformation. Acta Naturae 2021; 13:98-105. [PMID: 34377560 PMCID: PMC8327141 DOI: 10.32607/actanaturae.11181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 09/28/2020] [Indexed: 02/05/2023] Open
Abstract
The mutations associated with malignant cell transformation are believed to disrupt the expression of a significant number of normal, non-mutant genes. The proteins encoded by these genes are involved in the regulation of many signaling pathways that are responsible for differentiation and proliferation, as well as sensitivity to apoptotic signals, growth factors, and cytokines. Abnormalities in the balance of signaling pathways can lead to the transformation of a normal cell, which results in tumor formation. Detection of the target genes and the proteins they encode and that are involved in the malignant transformation is one of the major evolutions in anti-cancer biomedicine. Currently, there is an accumulation of data that shed light on the role of the MCTS1 and DENR proteins in oncogenesis.
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Affiliation(s)
- E. Y. Shyrokova
- Engelhardt Institute of Molecular Biology, Russian Academy of Science, Moscow, 119991 Russia
- Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Moscow Region, 141701 Russia
| | - V. S. Prassolov
- Engelhardt Institute of Molecular Biology, Russian Academy of Science, Moscow, 119991 Russia
| | - P. V. Spirin
- Engelhardt Institute of Molecular Biology, Russian Academy of Science, Moscow, 119991 Russia
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11
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DENR promotes translation reinitiation via ribosome recycling to drive expression of oncogenes including ATF4. Nat Commun 2020; 11:4676. [PMID: 32938922 PMCID: PMC7494916 DOI: 10.1038/s41467-020-18452-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 08/14/2020] [Indexed: 12/19/2022] Open
Abstract
Translation efficiency varies considerably between different mRNAs, thereby impacting protein expression. Translation of the stress response master-regulator ATF4 increases upon stress, but the molecular mechanisms are not well understood. We discover here that translation factors DENR, MCTS1 and eIF2D are required to induce ATF4 translation upon stress by promoting translation reinitiation in the ATF4 5'UTR. We find DENR and MCTS1 are only needed for reinitiation after upstream Open Reading Frames (uORFs) containing certain penultimate codons, perhaps because DENR•MCTS1 are needed to evict only certain tRNAs from post-termination 40S ribosomes. This provides a model for how DENR and MCTS1 promote translation reinitiation. Cancer cells, which are exposed to many stresses, require ATF4 for survival and proliferation. We find a strong correlation between DENR•MCTS1 expression and ATF4 activity across cancers. Furthermore, additional oncogenes including a-Raf, c-Raf and Cdk4 have long uORFs and are translated in a DENR•MCTS1 dependent manner.
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12
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Lomakin IB, De S, Wang J, Borkar AN, Steitz TA. Crystal structure of the C-terminal domain of DENR. Comput Struct Biotechnol J 2020; 18:696-704. [PMID: 32257053 PMCID: PMC7114459 DOI: 10.1016/j.csbj.2020.03.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/09/2020] [Accepted: 03/11/2020] [Indexed: 02/04/2023] Open
Abstract
The density regulated protein (DENR) forms a stable heterodimer with malignant T-cell-amplified sequence 1 (MCT-1). DENR-MCT-1 heterodimer then participates in regulation of non-canonical translation initiation and ribosomal recycling. The N-terminal domain of DENR interacts with MCT-1 and carries a classical tetrahedral zinc ion-binding site, which is crucial for the dimerization. DENR-MCT-1 binds the small (40S) ribosomal subunit through interactions between MCT-1 and helix h24 of the 18S rRNA, and through interactions between the C-terminal domain of DENR and helix h44 of the 18S rRNA. This later interaction occurs in the vicinity of the P site that is also the binding site for canonical translation initiation factor eIF1, which plays the key role in initiation codon selection and scanning. Sequence homology modeling and a low-resolution crystal structure of the DENR-MCT-1 complex with the human 40S subunit suggests that the C-terminal domain of DENR and eIF1 adopt a similar fold. Here we present the crystal structure of the C-terminal domain of DENR determined at 1.74 Å resolution, which confirms its resemblance to eIF1 and advances our understanding of the mechanism by which DENR-MCT-1 regulates non-canonical translation initiation and ribosomal recycling.
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Affiliation(s)
- Ivan B. Lomakin
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
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13
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Gilabert-Juan J, López-Campos G, Sebastiá-Ortega N, Guara-Ciurana S, Ruso-Julve F, Prieto C, Crespo-Facorro B, Sanjuán J, Moltó MD. Time dependent expression of the blood biomarkers EIF2D and TOX in patients with schizophrenia. Brain Behav Immun 2019; 80:909-915. [PMID: 31078689 DOI: 10.1016/j.bbi.2019.05.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 05/05/2019] [Accepted: 05/08/2019] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND During last years, there has been an intensive search for blood biomarkers in schizophrenia to assist in diagnosis, prognosis and clinical management of the disease. METHODS In this study, we first conducted a weighted gene coexpression network analysis to address differentially expressed genes in peripheral blood from patients with chronic schizophrenia (n = 30) and healthy controls (n = 15). The discriminating performance of the candidate genes was further tested in an independent cohort of patients with first-episode schizophrenia (n = 124) and healthy controls (n = 54), and in postmortem brain samples (cingulate and prefrontal cortices) from patients with schizophrenia (n = 34) and healthy controls (n = 35). RESULTS The expression of the Eukaryotic Translation Initiation Factor 2D (EIF2D) gene, which is involved in protein synthesis regulation, was increased in the chronic patients of schizophrenia. On the contrary, the expression of the Thymocyte Selection-Associated High Mobility Group Box (TOX) gene, involved in immune function, was reduced. EIF2D expression was also altered in first-episode schizophrenia patients, but showing reduced levels. Any of the postmortem brain areas studied did not show differences of expression of both genes. CONCLUSIONS EIF2D and TOX are putative blood markers of chronic patients of schizophrenia, which expression change from the onset to the chronic disease, unraveling new biological pathways that can be used for the development of new intervention strategies in the diagnosis and prognosis of schizophrenia disease.
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Affiliation(s)
- Javier Gilabert-Juan
- Department of Genetics, Universitat de València, Valencia, Spain; Neurobiology Unit, Cell Biology Department, Interdisciplinary Research Structure for Biotechnology and Biomedicine (BIOTECMED), Universitat de València, Valencia, Spain; Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Spain; INCLIVA, Valencia, Spain.
| | | | - Noelia Sebastiá-Ortega
- Department of Genetics, Universitat de València, Valencia, Spain; Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Spain; INCLIVA, Valencia, Spain
| | | | - Fulgencio Ruso-Julve
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Spain; University Hospital Marqués de Valdecilla, IDIVAL, Department of Psychiatry, School of Medicine, University of Cantabria, Santander, Spain
| | - Carlos Prieto
- Servicio de Bioinformática, Nucleus, Universidad de Salamanca, Salamanca, Spain
| | - Benedicto Crespo-Facorro
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Spain; University Hospital Marqués de Valdecilla, IDIVAL, Department of Psychiatry, School of Medicine, University of Cantabria, Santander, Spain
| | - Julio Sanjuán
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Spain; INCLIVA, Valencia, Spain; Unit of Psychiatry, Universitat de València, Valencia, Spain
| | - María Dolores Moltó
- Department of Genetics, Universitat de València, Valencia, Spain; Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Spain; INCLIVA, Valencia, Spain
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14
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Hemming IA, Clément O, Gladwyn-Ng IE, Cullen HD, Ng HL, See HB, Ngo L, Ulgiati D, Pfleger KDG, Agostino M, Heng JIT. Disease-associated missense variants in ZBTB18 disrupt DNA binding and impair the development of neurons within the embryonic cerebral cortex. Hum Mutat 2019; 40:1841-1855. [PMID: 31112317 DOI: 10.1002/humu.23803] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 05/08/2019] [Accepted: 05/19/2019] [Indexed: 12/12/2022]
Abstract
The activities of DNA-binding transcription factors, such as the multi-zinc-finger protein ZBTB18 (also known as RP58, or ZNF238), are essential to coordinate mammalian neurodevelopment, including the birth and radial migration of newborn neurons within the fetal brain. In humans, the majority of disease-associated missense mutations in ZBTB18 lie within the DNA-binding zinc-finger domain and are associated with brain developmental disorder, yet the molecular mechanisms explaining their role in disease remain unclear. To address this, we developed in silico models of ZBTB18, bound to DNA, and discovered that half of the missense variants map to residues (Asn461, Arg464, Glu486) predicted to be essential to sequence-specific DNA contact, whereas others map to residues (Leu434, Tyr447, Arg495) with limited contributions to DNA binding. We studied pathogenic variants to residues with close (N461S) and limited (R495G) DNA contact and found that each bound DNA promiscuously, displayed altered transcriptional regulatory activity in vitro, and influenced the radial migration of newborn neurons in vivo in different ways. Taken together, our results suggest that altered transcriptional regulation could represent an important pathological mechanism for ZBTB18 missense variants in brain developmental disease.
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Affiliation(s)
- Isabel A Hemming
- Molecular Medicine Division, QEII Medical Centre, The Harry Perkins Institute of Medical Research, Nedlands, Australia.,Centre for Medical Research, The University of Western Australia, Crawley, Australia.,Faculty of Health and Medical Sciences, Medical School, The University of Western Australia, Crawley, Australia
| | - Olivier Clément
- Molecular Medicine Division, QEII Medical Centre, The Harry Perkins Institute of Medical Research, Nedlands, Australia.,Centre for Medical Research, The University of Western Australia, Crawley, Australia.,Faculty of Health and Medical Sciences, Medical School, The University of Western Australia, Crawley, Australia.,School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Crawley, Australia
| | - Ivan E Gladwyn-Ng
- Molecular Medicine Division, QEII Medical Centre, The Harry Perkins Institute of Medical Research, Nedlands, Australia.,Centre for Medical Research, The University of Western Australia, Crawley, Australia
| | - Hayley D Cullen
- Molecular Medicine Division, QEII Medical Centre, The Harry Perkins Institute of Medical Research, Nedlands, Australia.,Centre for Medical Research, The University of Western Australia, Crawley, Australia.,Faculty of Health and Medical Sciences, Medical School, The University of Western Australia, Crawley, Australia.,Curtin Health Innovation Research Institute, Curtin University, Bentley, Australia
| | - Han Leng Ng
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Crawley, Australia
| | - Heng B See
- Molecular Medicine Division, QEII Medical Centre, The Harry Perkins Institute of Medical Research, Nedlands, Australia.,Centre for Medical Research, The University of Western Australia, Crawley, Australia
| | - Linh Ngo
- Molecular Medicine Division, QEII Medical Centre, The Harry Perkins Institute of Medical Research, Nedlands, Australia.,Centre for Medical Research, The University of Western Australia, Crawley, Australia
| | - Daniela Ulgiati
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Crawley, Australia
| | - Kevin D G Pfleger
- Molecular Medicine Division, QEII Medical Centre, The Harry Perkins Institute of Medical Research, Nedlands, Australia.,Centre for Medical Research, The University of Western Australia, Crawley, Australia.,ARC Centre for Personalised Therapeutics Technologies, Melbourne, Australia
| | - Mark Agostino
- Curtin Health Innovation Research Institute, Curtin University, Bentley, Australia.,School of Pharmacy and Biomedical Sciences, Curtin University, Bentley, Australia.,Curtin Institute for Computation, Curtin University, Bentley, Australia
| | - Julian I-T Heng
- Curtin Health Innovation Research Institute, Curtin University, Bentley, Australia.,ARC Centre for Personalised Therapeutics Technologies, Melbourne, Australia.,School of Pharmacy and Biomedical Sciences, Curtin University, Bentley, Australia
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15
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Castelo-Szekely V, De Matos M, Tusup M, Pascolo S, Ule J, Gatfield D. Charting DENR-dependent translation reinitiation uncovers predictive uORF features and links to circadian timekeeping via Clock. Nucleic Acids Res 2019; 47:5193-5209. [PMID: 30982898 PMCID: PMC6547434 DOI: 10.1093/nar/gkz261] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 03/25/2019] [Accepted: 04/08/2019] [Indexed: 02/05/2023] Open
Abstract
The non-canonical initiation factor DENR promotes translation reinitiation on mRNAs harbouring upstream open reading frames (uORFs). Moreover, DENR depletion shortens circadian period in mouse fibroblasts, suggesting involvement of uORF usage and reinitiation in clock regulation. To identify DENR-regulated translation events transcriptome-wide and, in particular, specific core clock transcripts affected by this mechanism, we have used ribosome profiling in DENR-deficient NIH3T3 cells. We uncovered 240 transcripts with altered translation rate, and used linear regression analysis to extract 5' UTR features predictive of DENR dependence. Among core clock genes, we identified Clock as a DENR target. Using Clock 5' UTR mutants, we mapped the specific uORF through which DENR acts to regulate CLOCK protein biosynthesis. Notably, these experiments revealed an alternative downstream start codon, likely representing the bona fide CLOCK N-terminus. Our findings provide insights into uORF-mediated translational regulation that can regulate the mammalian circadian clock and gene expression at large.
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Affiliation(s)
- Violeta Castelo-Szekely
- Center for Integrative Genomics, University of Lausanne, Genopode, 1015 Lausanne, Switzerland
| | - Mara De Matos
- Center for Integrative Genomics, University of Lausanne, Genopode, 1015 Lausanne, Switzerland
| | - Marina Tusup
- Department of Dermatology, University Hospital of Zurich, Gloriastrasse 31, 8091 Zurich, Switzerland
- Faculty of Medicine, University of Zurich, 8091 Zurich, Switzerland
| | - Steve Pascolo
- Department of Dermatology, University Hospital of Zurich, Gloriastrasse 31, 8091 Zurich, Switzerland
- Faculty of Medicine, University of Zurich, 8091 Zurich, Switzerland
| | - Jernej Ule
- Department of Neuromuscular Diseases, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - David Gatfield
- Center for Integrative Genomics, University of Lausanne, Genopode, 1015 Lausanne, Switzerland
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16
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Kurki MI, Saarentaus E, Pietiläinen O, Gormley P, Lal D, Kerminen S, Torniainen-Holm M, Hämäläinen E, Rahikkala E, Keski-Filppula R, Rauhala M, Korpi-Heikkilä S, Komulainen-Ebrahim J, Helander H, Vieira P, Männikkö M, Peltonen M, Havulinna AS, Salomaa V, Pirinen M, Suvisaari J, Moilanen JS, Körkkö J, Kuismin O, Daly MJ, Palotie A. Contribution of rare and common variants to intellectual disability in a sub-isolate of Northern Finland. Nat Commun 2019; 10:410. [PMID: 30679432 PMCID: PMC6345990 DOI: 10.1038/s41467-018-08262-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 12/20/2018] [Indexed: 01/19/2023] Open
Abstract
The contribution of de novo variants in severe intellectual disability (ID) has been extensively studied whereas the genetics of mild ID has been less characterized. To elucidate the genetics of milder ID we studied 442 ID patients enriched for mild ID (>50%) from a population isolate of Finland. Using exome sequencing, we show that rare damaging variants in known ID genes are observed significantly more often in severe (27%) than in mild ID (13%) patients. We further observe a significant enrichment of functional variants in genes not yet associated with ID (OR: 2.1). We show that a common variant polygenic risk significantly contributes to ID. The heritability explained by polygenic risk score is the highest for educational attainment (EDU) in mild ID (2.2%) but lower for more severe ID (0.6%). Finally, we identify a Finland enriched homozygote variant in the CRADD ID associated gene.
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Affiliation(s)
- Mitja I Kurki
- Psychiatric & Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, 02114, USA
- The Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00014, Helsinki, Finland
| | - Elmo Saarentaus
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00014, Helsinki, Finland
| | - Olli Pietiläinen
- The Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Stem Cell and Regenerative Biology, University of Harvard, Cambridge, MA, 02138, USA
| | - Padhraig Gormley
- Psychiatric & Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, 02114, USA
- The Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Dennis Lal
- Psychiatric & Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, 02114, USA
- The Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Sini Kerminen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00014, Helsinki, Finland
| | - Minna Torniainen-Holm
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00014, Helsinki, Finland
- National Institute for Health and Welfare, 00271, Helsinki, Finland
| | - Eija Hämäläinen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00014, Helsinki, Finland
| | - Elisa Rahikkala
- PEDEGO Research Unit, University of Oulu, FI-90014, Oulu, Finland
- Medical Research Center, Oulu University Hospital,, University of Oulu, FI-90014, Oulu, Finland
- Department of Clinical Genetics, Oulu University Hospital, 90220, Oulu, Finland
| | - Riikka Keski-Filppula
- PEDEGO Research Unit, University of Oulu, FI-90014, Oulu, Finland
- Medical Research Center, Oulu University Hospital,, University of Oulu, FI-90014, Oulu, Finland
- Department of Clinical Genetics, Oulu University Hospital, 90220, Oulu, Finland
| | - Merja Rauhala
- Northern Ostrobothnia Hospital District, Center for Intellectual Disability Care, 90220, Oulu, Finland
| | - Satu Korpi-Heikkilä
- Northern Ostrobothnia Hospital District, Center for Intellectual Disability Care, 90220, Oulu, Finland
| | - Jonna Komulainen-Ebrahim
- Department of Children and Adolescents, Oulu University Hospital, Medical Research Center Oulu, University of Oulu, FI-90029, Oulu, Finland
| | - Heli Helander
- Department of Children and Adolescents, Oulu University Hospital, Medical Research Center Oulu, University of Oulu, FI-90029, Oulu, Finland
| | - Päivi Vieira
- Department of Children and Adolescents, Oulu University Hospital, Medical Research Center Oulu, University of Oulu, FI-90029, Oulu, Finland
| | - Minna Männikkö
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Infrastructure for population studies, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Markku Peltonen
- National Institute for Health and Welfare, 00271, Helsinki, Finland
| | - Aki S Havulinna
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00014, Helsinki, Finland
- National Institute for Health and Welfare, 00271, Helsinki, Finland
| | - Veikko Salomaa
- National Institute for Health and Welfare, 00271, Helsinki, Finland
| | - Matti Pirinen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00014, Helsinki, Finland
| | - Jaana Suvisaari
- National Institute for Health and Welfare, 00271, Helsinki, Finland
| | - Jukka S Moilanen
- PEDEGO Research Unit, University of Oulu, FI-90014, Oulu, Finland
- Medical Research Center, Oulu University Hospital,, University of Oulu, FI-90014, Oulu, Finland
- Department of Clinical Genetics, Oulu University Hospital, 90220, Oulu, Finland
| | - Jarmo Körkkö
- Northern Ostrobothnia Hospital District, Center for Intellectual Disability Care, 90220, Oulu, Finland
| | - Outi Kuismin
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00014, Helsinki, Finland
- PEDEGO Research Unit, University of Oulu, FI-90014, Oulu, Finland
- Medical Research Center, Oulu University Hospital,, University of Oulu, FI-90014, Oulu, Finland
- Department of Clinical Genetics, Oulu University Hospital, 90220, Oulu, Finland
| | - Mark J Daly
- Psychiatric & Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, 02114, USA
- The Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00014, Helsinki, Finland
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Aarno Palotie
- Psychiatric & Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, 02114, USA.
- The Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00014, Helsinki, Finland.
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA.
- Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA.
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17
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Crystal structure of the DENR-MCT-1 complex revealed zinc-binding site essential for heterodimer formation. Proc Natl Acad Sci U S A 2018; 116:528-533. [PMID: 30584092 DOI: 10.1073/pnas.1809688116] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The density-regulated protein (DENR) and the malignant T cell-amplified sequence 1 (MCT-1/MCTS1) oncoprotein support noncanonical translation initiation, promote translation reinitiation on a specific set of mRNAs with short upstream reading frames, and regulate ribosome recycling. DENR and MCT-1 form a heterodimer, which binds to the ribosome. We determined the crystal structure of the heterodimer formed by human MCT-1 and the N-terminal domain of DENR at 2.0-Å resolution. The structure of the heterodimer reveals atomic details of the mechanism of DENR and MCT-1 interaction. Four conserved cysteine residues of DENR (C34, C37, C44, C53) form a classical tetrahedral zinc ion-binding site, which preserves the structure of the DENR's MCT-1-binding interface that is essential for the dimerization. Substitution of all four cysteines by alanine abolished a heterodimer formation. Our findings elucidate further the mechanism of regulation of DENR-MCT-1 activities in unconventional translation initiation, reinitiation, and recycling.
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18
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Abstract
Proper neuronal wiring is central to all bodily functions, sensory perception, cognition, memory, and learning. Establishment of a functional neuronal circuit is a highly regulated and dynamic process involving axonal and dendritic branching and navigation toward appropriate targets and connection partners. This intricate circuitry includes axo-dendritic synapse formation, synaptic connections formed with effector cells, and extensive dendritic arborization that function to receive and transmit mechanical and chemical sensory inputs. Such complexity is primarily achieved by extensive axonal and dendritic branch formation and pruning. Fundamental to neuronal branching are cytoskeletal dynamics and plasma membrane expansion, both of which are regulated via numerous extracellular and intracellular signaling mechanisms and molecules. This review focuses on recent advances in understanding the biology of neuronal branching.
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Affiliation(s)
- Shalini Menon
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Stephanie Gupton
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, Chapel Hill, NC, 27599, USA.,Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
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19
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Young DJ, Makeeva DS, Zhang F, Anisimova AS, Stolboushkina EA, Ghobakhlou F, Shatsky IN, Dmitriev SE, Hinnebusch AG, Guydosh NR. Tma64/eIF2D, Tma20/MCT-1, and Tma22/DENR Recycle Post-termination 40S Subunits In Vivo. Mol Cell 2018; 71:761-774.e5. [PMID: 30146315 PMCID: PMC6225905 DOI: 10.1016/j.molcel.2018.07.028] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 06/11/2018] [Accepted: 07/21/2018] [Indexed: 02/05/2023]
Abstract
The recycling of ribosomal subunits after translation termination is critical for efficient gene expression. Tma64 (eIF2D), Tma20 (MCT-1), and Tma22 (DENR) function as 40S recycling factors in vitro, but it is unknown whether they perform this function in vivo. Ribosome profiling of tma deletion strains revealed 80S ribosomes queued behind the stop codon, consistent with a block in 40S recycling. We found that unrecycled ribosomes could reinitiate translation at AUG codons in the 3' UTR, as evidenced by peaks in the footprint data and 3' UTR reporter analysis. In vitro translation experiments using reporter mRNAs containing upstream open reading frames (uORFs) further established that reinitiation increased in the absence of these proteins. In some cases, 40S ribosomes appeared to rejoin with 60S subunits and undergo an 80S reinitiation process in 3' UTRs. These results support a crucial role for Tma64, Tma20, and Tma22 in recycling 40S ribosomal subunits at stop codons and translation reinitiation.
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Affiliation(s)
- David J Young
- Laboratory of Gene Regulation & Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA; Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA
| | - Desislava S Makeeva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia; School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Fan Zhang
- Laboratory of Gene Regulation & Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Aleksandra S Anisimova
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Elena A Stolboushkina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russia
| | - Fardin Ghobakhlou
- Laboratory of Gene Regulation & Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Ivan N Shatsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia; Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia; Department of Biochemistry, Biological Faculty, Lomonosov Moscow State University, Moscow 119234, Russia.
| | - Alan G Hinnebusch
- Laboratory of Gene Regulation & Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA.
| | - Nicholas R Guydosh
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA.
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20
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Ahmed YL, Schleich S, Bohlen J, Mandel N, Simon B, Sinning I, Teleman AA. DENR-MCTS1 heterodimerization and tRNA recruitment are required for translation reinitiation. PLoS Biol 2018; 16:e2005160. [PMID: 29889857 PMCID: PMC6013234 DOI: 10.1371/journal.pbio.2005160] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 06/21/2018] [Accepted: 05/23/2018] [Indexed: 02/05/2023] Open
Abstract
The succession of molecular events leading to eukaryotic translation reinitiation—whereby ribosomes terminate translation of a short open reading frame (ORF), resume scanning, and then translate a second ORF on the same mRNA—is not well understood. Density-regulated reinitiation and release factor (DENR) and multiple copies in T-cell lymphoma-1 (MCTS1) are implicated in promoting translation reinitiation both in vitro in translation extracts and in vivo. We present here the crystal structure of MCTS1 bound to a fragment of DENR. Based on this structure, we identify and experimentally validate that DENR residues Glu42, Tyr43, and Tyr46 are important for MCTS1 binding and that MCTS1 residue Phe104 is important for tRNA binding. Mutation of these residues reveals that DENR-MCTS1 dimerization and tRNA binding are both necessary for DENR and MCTS1 to promote translation reinitiation in human cells. These findings thereby link individual residues of DENR and MCTS1 to specific molecular functions of the complex. Since DENR–MCTS1 can bind tRNA in the absence of the ribosome, this suggests the DENR–MCTS1 complex could recruit tRNA to the ribosome during reinitiation analogously to the eukaryotic initiation factor 2 (eIF2) complex in cap-dependent translation. Usually, eukaryotic ribosomes translate only a single open reading frame (ORF) on an mRNA and then dissociate from the mRNA. In some cases, when there is a short upstream open reading frame (uORF) that precedes the main ORF, ribosomes can translate the uORF, terminate translation, and then undergo a poorly understood process called “translation reinitiation” whereby they resume scanning for another AUG initiation codon and then translate the main ORF. The molecular functions required for translation reinitiation are not known. We previously showed that two noncanonical initiation factors, density-regulated reinitiation and release factor (DENR) and multiple copies in T-cell lymphoma-1 (MCTS1), are involved in this process. We show here, based on a structure of MCTS1 bound to a fragment of DENR, that in order to successfully promote translation reinitiation, DENR and MCTS1 need to dimerize, and they need to bind tRNA. We thereby identify two molecular functions needed for translation reinitiation.
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Affiliation(s)
| | - Sibylle Schleich
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Heidelberg, Germany
| | - Jonathan Bohlen
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Heidelberg, Germany
| | - Nicolas Mandel
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Heidelberg, Germany
| | - Bernd Simon
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
- * E-mail: (IS); (AAT)
| | - Aurelio A. Teleman
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
- * E-mail: (IS); (AAT)
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21
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Lomakin IB, Stolboushkina EA, Vaidya AT, Zhao C, Garber MB, Dmitriev SE, Steitz TA. Crystal Structure of the Human Ribosome in Complex with DENR-MCT-1. Cell Rep 2018; 20:521-528. [PMID: 28723557 DOI: 10.1016/j.celrep.2017.06.025] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 05/12/2017] [Accepted: 06/07/2017] [Indexed: 12/24/2022] Open
Abstract
The repertoire of the density-regulated protein (DENR) and the malignant T cell-amplified sequence 1 (MCT-1/MCTS1) oncoprotein was recently expanded to include translational control of a specific set of cancer-related mRNAs. DENR and MCT-1 form the heterodimer, which binds to the ribosome and operates at both translation initiation and reinitiation steps, though by a mechanism that is yet unclear. Here, we determined the crystal structure of the human small ribosomal subunit in complex with DENR-MCT-1. The structure reveals the location of the DENR-MCT-1 dimer bound to the small ribosomal subunit. The binding site of the C-terminal domain of DENR on the ribosome has a striking similarity with those of canonical initiation factor 1 (eIF1), which controls the fidelity of translation initiation and scanning. Our findings elucidate how the DENR-MCT-1 dimer interacts with the ribosome and have functional implications for the mechanism of unconventional translation initiation and reinitiation.
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Affiliation(s)
- Ivan B Lomakin
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA.
| | - Elena A Stolboushkina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia; Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Anand T Vaidya
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Chenguang Zhao
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
| | - Maria B Garber
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Sergey E Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia; Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Thomas A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8114, USA.
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22
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Abstract
This review by Kearse and Wilusz discusses the profound impact of non-AUG start codons in eukaryotic translation. It describes how misregulation of non-AUG initiation events contributes to multiple human diseases, including cancer and neurodegeneration, and how modulation of non-AUG usage may represent a novel therapeutic strategy. Although it was long thought that eukaryotic translation almost always initiates at an AUG start codon, recent advancements in ribosome footprint mapping have revealed that non-AUG start codons are used at an astonishing frequency. These non-AUG initiation events are not simply errors but instead are used to generate or regulate proteins with key cellular functions; for example, during development or stress. Misregulation of non-AUG initiation events contributes to multiple human diseases, including cancer and neurodegeneration, and modulation of non-AUG usage may represent a novel therapeutic strategy. It is thus becoming increasingly clear that start codon selection is regulated by many trans-acting initiation factors as well as sequence/structural elements within messenger RNAs and that non-AUG translation has a profound impact on cellular states.
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Affiliation(s)
- Michael G Kearse
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, 19104 USA
| | - Jeremy E Wilusz
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, 19104 USA
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23
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Weisser M, Schäfer T, Leibundgut M, Böhringer D, Aylett CHS, Ban N. Structural and Functional Insights into Human Re-initiation Complexes. Mol Cell 2017; 67:447-456.e7. [PMID: 28732596 DOI: 10.1016/j.molcel.2017.06.032] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 06/14/2017] [Accepted: 06/27/2017] [Indexed: 02/05/2023]
Abstract
After having translated short upstream open reading frames, ribosomes can re-initiate translation on the same mRNA. This process, referred to as re-initiation, controls the translation of a large fraction of mammalian cellular mRNAs, many of which are important in cancer. Key ribosomal binding proteins involved in re-initiation are the eukaryotic translation initiation factor 2D (eIF2D) or the homologous complex of MCT-1/DENR. We determined the structures of these factors bound to the human 40S ribosomal subunit in complex with initiator tRNA positioned on an mRNA start codon in the P-site using a combination of cryoelectron microscopy and X-ray crystallography. The structures, supported by biochemical experiments, reveal how eIF2D emulates the function of several canonical translation initiation factors by using three independent, flexibly connected RNA binding domains to simultaneously monitor codon-anticodon interactions in the ribosomal P-site and position the initiator tRNA.
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Affiliation(s)
- Melanie Weisser
- Department of Biology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Tanja Schäfer
- Department of Biology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Marc Leibundgut
- Department of Biology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Daniel Böhringer
- Department of Biology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, ETH Zurich, CH-8093 Zurich, Switzerland
| | | | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, Otto-Stern-Weg 5, ETH Zurich, CH-8093 Zurich, Switzerland.
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24
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Abstract
The non-canonical initiation factors DENR and MCTS1 have been linked to cancer and autism. We recently showed in Drosophila that DENR and MCTS1 regulate translation re-initiation on transcripts containing upstream Open Reading Frames (uORFs) with strong Kozak sequences (stuORFs). Due to the medical relevance of DENR and MCTS1, it is worthwhile identifying the transcripts in human cells that depend on DENR and MCTS1 for their translation. We show here that in humans, as in Drosophila, transcripts with short stuORFs require DENR and MCTS1 for their optimal expression. In contrast to Drosophila, however, the dependence on stuORF length in human cells is very strong, so that only transcripts with very short stuORFs coding for 1 amino acid are dependent on DENR and MCTS1. This identifies circa 100 genes as putative DENR and MCTS1 translational targets. These genes are enriched for neuronal genes and G protein-coupled receptors. The identification of DENR and MCTS1 target transcripts will serve as a basis for future studies aimed at understanding the mechanistic involvement of DENR and MCTS1 in cancer and autism.
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25
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Clément O, Hemming IA, Gladwyn-Ng IE, Qu Z, Li SS, Piper M, Heng JIT. Rp58 and p27 kip1 coordinate cell cycle exit and neuronal migration within the embryonic mouse cerebral cortex. Neural Dev 2017; 12:8. [PMID: 28506232 PMCID: PMC5433244 DOI: 10.1186/s13064-017-0084-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 05/01/2017] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND During the development of the mammalian cerebral cortex, newborn postmitotic projection neurons are born from local neural stem cells and must undergo radial migration so as to position themselves appropriately to form functional neural circuits. The zinc finger transcriptional repressor Rp58 (also known as Znf238 or Zbtb18) is critical for coordinating corticogenesis, but its underlying molecular mechanism remains to be better characterised. FINDINGS Here, we demonstrate that the co-expression of Rp58 and the cyclin dependent kinase inhibitor (CDKI) p27kip1 is important for E14.5-born cortical neurons to coordinate cell cycle exit and initiate their radial migration. Notably, we find that the impaired radial positioning of Rp58-deficient cortical neurons within the embryonic (E17.5) mouse cortex, as well as their multipolar to bipolar transition from the intermediate zone to the cortical plate can be restored by forced expression of p27kip1 in concert with suppression of Rnd2, a downstream target gene of Rp58. Furthermore, the restorative effects of p27kip1 and Rnd2 abrogation are reminiscent of suppressing RhoA signalling in Rp58-deficient cells. CONCLUSIONS Our findings demonstrate functional interplay between a transcriptional regulator and a CDKI to mediate neuroprogenitor cell cycle exit, as well as to promote radial migration through a molecular mechanism consistent with suppression of RhoA signalling.
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Affiliation(s)
- Olivier Clément
- The Harry Perkins Institute of Medical Research, Perth, WA 6009 Australia
- The Centre for Medical Research, University of Western Australia, Perth, WA 6009 Australia
| | - Isabel Anne Hemming
- The Harry Perkins Institute of Medical Research, Perth, WA 6009 Australia
- The Centre for Medical Research, University of Western Australia, Perth, WA 6009 Australia
| | - Ivan Enghian Gladwyn-Ng
- The Harry Perkins Institute of Medical Research, Perth, WA 6009 Australia
- The Centre for Medical Research, University of Western Australia, Perth, WA 6009 Australia
| | - Zhengdong Qu
- EMBL Australia, The Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800 Australia
| | - Shan Shan Li
- EMBL Australia, The Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800 Australia
| | - Michael Piper
- The School of Biomedical Sciences, University of Queensland, Brisbane, 4072 Australia
- Queensland Brain Institute, University of Queensland, Brisbane, 4072 Australia
| | - Julian Ik-Tsen Heng
- The Harry Perkins Institute of Medical Research, Perth, WA 6009 Australia
- The Centre for Medical Research, University of Western Australia, Perth, WA 6009 Australia
- EMBL Australia, The Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800 Australia
- Curtin Health Innovation Research Institute, Curtin University, Bentley, 6845 Australia
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