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Busarello E, Biancon G, Lauria F, Ibnat Z, Ramirez C, Tomè G, Aass KR, VanOudenhove J, Standal T, Viero G, Halene S, Tebaldi T. Interpreting single-cell messages in normal and aberrant hematopoiesis with the Cell Marker Accordion. bioRxiv 2024:2024.03.08.584053. [PMID: 38559181 PMCID: PMC10979856 DOI: 10.1101/2024.03.08.584053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Single-cell technologies offer a unique opportunity to explore cellular heterogeneity in hematopoiesis, reveal malignant hematopoietic cells with clinically significant features and measure gene signatures linked to pathological pathways. However, reliable identification of cell types is a crucial bottleneck in single-cell analysis. Available databases contain dissimilar nomenclature and non-concurrent marker sets, leading to inconsistent annotations and poor interpretability. Furthermore, current tools focus mostly on physiological cell types, lacking extensive applicability in disease. We developed the Cell Marker Accordion, a user-friendly platform for the automatic annotation and biological interpretation of single-cell populations based on consistency weighted markers. We validated our approach on peripheral blood and bone marrow single-cell datasets, using surface markers and expert-based annotation as the ground truth. In all cases, we significantly improved the accuracy in identifying cell types with respect to any single source database. Moreover, the Cell Marker Accordion can identify disease-critical cells and pathological processes, extracting potential biomarkers in a wide variety of contexts in human and murine single-cell datasets. It characterizes leukemia stem cell subtypes, including therapy-resistant cells in acute myeloid leukemia patients; it identifies malignant plasma cells in multiple myeloma samples; it dissects cell type alterations in splicing factor-mutant cells from myelodysplastic syndrome patients; it discovers activation of innate immunity pathways in bone marrow from mice treated with METTL3 inhibitors. The breadth of these applications elevates the Cell Marker Accordion as a flexible, faithful and standardized tool to annotate and interpret hematopoietic populations in single-cell datasets focused on the study of hematopoietic development and disease.
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Affiliation(s)
- Emma Busarello
- Laboratory of RNA and Disease Data Science, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Giulia Biancon
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Fabio Lauria
- Institute of Biophysics, CNR Unit at Trento, Italy
| | - Zuhairia Ibnat
- Laboratory of RNA and Disease Data Science, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Christian Ramirez
- Laboratory of RNA and Disease Data Science, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Gabriele Tomè
- Laboratory of RNA and Disease Data Science, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
- Institute of Biophysics, CNR Unit at Trento, Italy
| | - Kristin R Aass
- Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Jennifer VanOudenhove
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Therese Standal
- Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | | | - Stephanie Halene
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Toma Tebaldi
- Laboratory of RNA and Disease Data Science, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
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2
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Sharma G, Paganin M, Lauria F, Perenthaler E, Viero G. The SMN-ribosome interplay: a new opportunity for Spinal Muscular Atrophy therapies. Biochem Soc Trans 2024; 52:465-479. [PMID: 38391004 PMCID: PMC10903476 DOI: 10.1042/bst20231116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 02/24/2024]
Abstract
The underlying cause of Spinal Muscular Atrophy (SMA) is in the reduction of survival motor neuron (SMN) protein levels due to mutations in the SMN1 gene. The specific effects of SMN protein loss and the resulting pathological alterations are not fully understood. Given the crucial roles of the SMN protein in snRNP biogenesis and its interactions with ribosomes and translation-related proteins and mRNAs, a decrease in SMN levels below a specific threshold in SMA is expected to affect translational control of gene expression. This review covers both direct and indirect SMN interactions across various translation-related cellular compartments and processes, spanning from ribosome biogenesis to local translation and beyond. Additionally, it aims to outline deficiencies and alterations in translation observed in SMA models and patients, while also discussing the implications of the relationship between SMN protein and the translation machinery within the context of current and future therapies.
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Popper B, Bürkle M, Ciccopiedi G, Marchioretto M, Forné I, Imhof A, Straub T, Viero G, Götz M, Schieweck R. Ribosome inactivation regulates translation elongation in neurons. J Biol Chem 2024; 300:105648. [PMID: 38219816 PMCID: PMC10869266 DOI: 10.1016/j.jbc.2024.105648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 12/10/2023] [Accepted: 01/02/2024] [Indexed: 01/16/2024] Open
Abstract
Cellular plasticity is crucial for adapting to ever-changing stimuli. As a result, cells consistently reshape their translatome, and, consequently, their proteome. The control of translational activity has been thoroughly examined at the stage of translation initiation. However, the regulation of ribosome speed in cells is widely unknown. In this study, we utilized a timed ribosome runoff approach, along with proteomics and transmission electron microscopy, to investigate global translation kinetics in cells. We found that ribosome speeds vary among various cell types, such as astrocytes, induced pluripotent human stem cells, human neural stem cells, and human and rat neurons. Of all cell types studied, mature cortical neurons exhibit the highest rate of translation. This finding is particularly remarkable because mature cortical neurons express the eukaryotic elongation factor 2 (eEF2) at lower levels than other cell types. Neurons solve this conundrum by inactivating a fraction of their ribosomes. As a result, the increase in eEF2 levels leads to a reduction of inactive ribosomes and an enhancement of active ones. Processes that alter the demand for active ribosomes, like neuronal excitation, cause increased inactivation of redundant ribosomes in an eEF2-dependent manner. Our data suggest a novel regulatory mechanism in which neurons dynamically inactivate ribosomes to facilitate translational remodeling. These findings have important implications for developmental brain disorders characterized by, among other things, aberrant translation.
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Affiliation(s)
- Bastian Popper
- Core Facility Animal Models, Biomedical Center (BMC), LMU Munich, Munich, Germany
| | - Martina Bürkle
- Department of Physiological Genomics, Biomedical Center (BMC), LMU Munich, Munich, Germany
| | - Giuliana Ciccopiedi
- Department for Cell Biology & Anatomy, Biomedical Center (BMC), LMU Munich, Munich, Germany; Graduate School of Systemic Neurosciences, LMU Munich, Munich, Germany
| | - Marta Marchioretto
- Institute of Biophysics, National Research Council (CNR) Unit at Trento, Povo, Italy
| | - Ignasi Forné
- Protein Analysis Unit, Department for Molecular Biology, Biomedical Center (BMC), LMU Munich, Munich, Germany
| | - Axel Imhof
- Protein Analysis Unit, Department for Molecular Biology, Biomedical Center (BMC), LMU Munich, Munich, Germany
| | - Tobias Straub
- Bioinformatics Core Facility, Department of Molecular Biology, Biomedical Center (BMC), LMU Munich, Munich, Germany
| | - Gabriella Viero
- Institute of Biophysics, National Research Council (CNR) Unit at Trento, Povo, Italy
| | - Magdalena Götz
- Department of Physiological Genomics, Biomedical Center (BMC), LMU Munich, Munich, Germany; Institute of Stem Cell Research, Helmholtz Center Munich, German Research Center for Environmental Health, Munich, Germany; SYNERGY, Excellence Cluster of Systems Neurology, Biomedical Center (BMC), LMU Munich, Munich, Germany
| | - Rico Schieweck
- Department of Physiological Genomics, Biomedical Center (BMC), LMU Munich, Munich, Germany; Department for Cell Biology & Anatomy, Biomedical Center (BMC), LMU Munich, Munich, Germany; Institute of Biophysics, National Research Council (CNR) Unit at Trento, Povo, Italy.
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4
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Pisciottani A, Croci L, Lauria F, Marullo C, Savino E, Ambrosi A, Podini P, Marchioretto M, Casoni F, Cremona O, Taverna S, Quattrini A, Cioni JM, Viero G, Codazzi F, Consalez GG. Neuronal models of TDP-43 proteinopathy display reduced axonal translation, increased oxidative stress, and defective exocytosis. Front Cell Neurosci 2023; 17:1253543. [PMID: 38026702 PMCID: PMC10679756 DOI: 10.3389/fncel.2023.1253543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/13/2023] [Indexed: 12/01/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive, lethal neurodegenerative disease mostly affecting people around 50-60 years of age. TDP-43, an RNA-binding protein involved in pre-mRNA splicing and controlling mRNA stability and translation, forms neuronal cytoplasmic inclusions in an overwhelming majority of ALS patients, a phenomenon referred to as TDP-43 proteinopathy. These cytoplasmic aggregates disrupt mRNA transport and localization. The axon, like dendrites, is a site of mRNA translation, permitting the local synthesis of selected proteins. This is especially relevant in upper and lower motor neurons, whose axon spans long distances, likely accentuating their susceptibility to ALS-related noxae. In this work we have generated and characterized two cellular models, consisting of virtually pure populations of primary mouse cortical neurons expressing a human TDP-43 fusion protein, wt or carrying an ALS mutation. Both forms facilitate cytoplasmic aggregate formation, unlike the corresponding native proteins, giving rise to bona fide primary culture models of TDP-43 proteinopathy. Neurons expressing TDP-43 fusion proteins exhibit a global impairment in axonal protein synthesis, an increase in oxidative stress, and defects in presynaptic function and electrical activity. These changes correlate with deregulation of axonal levels of polysome-engaged mRNAs playing relevant roles in the same processes. Our data support the emerging notion that deregulation of mRNA metabolism and of axonal mRNA transport may trigger the dying-back neuropathy that initiates motor neuron degeneration in ALS.
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Affiliation(s)
- Alessandra Pisciottani
- Faculty of Medicine and Surgery, Università Vita-Salute San Raffaele, Milan, Italy
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Laura Croci
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Fabio Lauria
- Institute of Biophysics, CNR Unit at Trento, Povo, Italy
| | - Chiara Marullo
- Faculty of Medicine and Surgery, Università Vita-Salute San Raffaele, Milan, Italy
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Elisa Savino
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Alessandro Ambrosi
- Faculty of Medicine and Surgery, Università Vita-Salute San Raffaele, Milan, Italy
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Paola Podini
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Filippo Casoni
- Faculty of Medicine and Surgery, Università Vita-Salute San Raffaele, Milan, Italy
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Ottavio Cremona
- Faculty of Medicine and Surgery, Università Vita-Salute San Raffaele, Milan, Italy
| | - Stefano Taverna
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Angelo Quattrini
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Jean-Michel Cioni
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Franca Codazzi
- Faculty of Medicine and Surgery, Università Vita-Salute San Raffaele, Milan, Italy
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - G. Giacomo Consalez
- Faculty of Medicine and Surgery, Università Vita-Salute San Raffaele, Milan, Italy
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
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Brina D, Ponzoni A, Troiani M, Calì B, Pasquini E, Attanasio G, Mosole S, Mirenda M, D'Ambrosio M, Colucci M, Guccini I, Revandkar A, Alajati A, Tebaldi T, Donzel D, Lauria F, Parhizgari N, Valdata A, Maddalena M, Calcinotto A, Bolis M, Rinaldi A, Barry S, Rüschoff JH, Sabbadin M, Sumanasuriya S, Crespo M, Sharp A, Yuan W, Grinu M, Boyle A, Miller C, Trotman L, Delaleu N, Fassan M, Moch H, Viero G, de Bono J, Alimonti A. The Akt/mTOR and MNK/eIF4E pathways rewire the prostate cancer translatome to secrete HGF, SPP1 and BGN and recruit suppressive myeloid cells. Nat Cancer 2023; 4:1102-1121. [PMID: 37460872 DOI: 10.1038/s43018-023-00594-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/13/2023] [Indexed: 08/25/2023]
Abstract
Cancer is highly infiltrated by myeloid-derived suppressor cells (MDSCs). Currently available immunotherapies do not completely eradicate MDSCs. Through a genome-wide analysis of the translatome of prostate cancers driven by different genetic alterations, we demonstrate that prostate cancer rewires its secretome at the translational level to recruit MDSCs. Among different secreted proteins released by prostate tumor cells, we identified Hgf, Spp1 and Bgn as the key factors that regulate MDSC migration. Mechanistically, we found that the coordinated loss of Pdcd4 and activation of the MNK/eIF4E pathways regulate the mRNAs translation of Hgf, Spp1 and Bgn. MDSC infiltration and tumor growth were dampened in prostate cancer treated with the MNK1/2 inhibitor eFT508 and/or the AKT inhibitor ipatasertib, either alone or in combination with a clinically available MDSC-targeting immunotherapy. This work provides a therapeutic strategy that combines translation inhibition with available immunotherapies to restore immune surveillance in prostate cancer.
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Affiliation(s)
- Daniela Brina
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Adele Ponzoni
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
- Ima Biotech, Lille, France
| | - Martina Troiani
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland
| | - Bianca Calì
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Emiliano Pasquini
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Giuseppe Attanasio
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Simone Mosole
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Michela Mirenda
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
- Evotec, Toulouse, France
| | - Mariantonietta D'Ambrosio
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
- Imperial College London, London, UK
| | - Manuel Colucci
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Ilaria Guccini
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Ajinkya Revandkar
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
- Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Abdullah Alajati
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
- Department of Urology, Universitätklinikum Bonn, Bonn, Germany
| | - Toma Tebaldi
- Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Deborah Donzel
- Institute of Biophysics, CNR Unit at Trento, Povo, Italy
| | - Fabio Lauria
- Institute of Biophysics, CNR Unit at Trento, Povo, Italy
| | - Nahjme Parhizgari
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
- Biosun Pharmed, Kordan, Iran
| | - Aurora Valdata
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Martino Maddalena
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Arianna Calcinotto
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Marco Bolis
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland
- Bioinformatics Core Unit, Swiss Institute of Bioinformatics, Bellinzona, Switzerland
- Computational Oncology Unit, Department of Oncology, Istituto di Richerche Farmacologiche 'Mario Negri' IRCCS, Milano, Italy
| | - Andrea Rinaldi
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Simon Barry
- IMED Oncology AstraZeneca, Li Ka Shing Centre, Cambridge, UK
| | - Jan Hendrik Rüschoff
- Department of Pathology and Molecular Pathology, University Hospital Zurich (USZ), Zurich, Switzerland
| | | | - Semini Sumanasuriya
- Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, UK
| | - Mateus Crespo
- Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, UK
| | - Adam Sharp
- Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, UK
| | - Wei Yuan
- Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, UK
| | - Mathew Grinu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Alexandra Boyle
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Cynthia Miller
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Lloyd Trotman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | | | - Matteo Fassan
- Veneto Institute of Oncology, IOV-IRCCS, Padua, Italy
- Department of Medicine (DIMED), Surgical Pathology Unit, University of Padua, Padua, Italy
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich (USZ), Zurich, Switzerland
| | | | - Johann de Bono
- Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, UK
- The Royal Marsden Hospital, London, UK
| | - Andrea Alimonti
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland.
- Department of Medicine, Venetian Institute of Molecular Medicine, University of Padova, Padova, Italy.
- Department of Health Sciences and Technology, Eidgenössische Technische Hochschule (ETH) Zürich, Zurich, Switzerland.
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Paganin M, Tebaldi T, Lauria F, Viero G. Visualizing gene expression changes in time, space, and single cells with expressyouRcell. iScience 2023; 26:106853. [PMID: 37250782 PMCID: PMC10220493 DOI: 10.1016/j.isci.2023.106853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/05/2023] [Accepted: 05/05/2023] [Indexed: 05/31/2023] Open
Abstract
The last decade has witnessed massive advancements in high-throughput techniques capable of producing increasingly complex gene expression datasets across time and space and at the resolution of single cells. Yet, the large volume of big data available and the complexity of experimental designs hamper an easy understanding and effective communication of the results. We present expressyouRcell, an easy-to-use R package to map the multi-dimensional variations of transcript and protein levels in dynamic cell pictographs. expressyouRcell visualizes gene expression variations as pictographic representations of cell-type thematic maps. expressyouRcell visually reduces the complexity of displaying gene expression and protein level changes across multiple measurements (time points or single-cell trajectories) by generating dynamic representations of cellular pictographs. We applied expressyouRcell to single cell, bulk RNA sequencing (RNA-seq), and proteomics datasets, demonstrating its flexibility and usability in the visualization of complex variations in gene expression. Our approach improves the standard quantitative interpretation and communication of relevant results.
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Affiliation(s)
| | - Toma Tebaldi
- Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
- Department CIBIO, University of Trento, Trento, Italy
| | - Fabio Lauria
- Institute of Biophysics, CNR Unit Trento, Trento, Italy
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7
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Cella F, Perrino G, Tedeschi F, Viero G, Bosia C, Stan GB, Siciliano V. MIRELLA: a mathematical model explains the effect of microRNA-mediated synthetic genes regulation on intracellular resource allocation. Nucleic Acids Res 2023; 51:3452-3464. [PMID: 36912077 PMCID: PMC10123119 DOI: 10.1093/nar/gkad151] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/11/2023] [Accepted: 02/21/2023] [Indexed: 03/14/2023] Open
Abstract
Competition for intracellular resources, also known as gene expression burden, induces coupling between independently co-expressed genes, a detrimental effect on predictability and reliability of gene circuits in mammalian cells. We recently showed that microRNA (miRNA)-mediated target downregulation correlates with the upregulation of a co-expressed gene, and by exploiting miRNAs-based incoherent-feed-forward loops (iFFLs) we stabilise a gene of interest against burden. Considering these findings, we speculate that miRNA-mediated gene downregulation causes cellular resource redistribution. Despite the extensive use of miRNA in synthetic circuits regulation, this indirect effect was never reported before. Here we developed a synthetic genetic system that embeds miRNA regulation, and a mathematical model, MIRELLA, to unravel the miRNA (MI) RolE on intracellular resource aLLocAtion. We report that the link between miRNA-gene downregulation and independent genes upregulation is a result of the concerted action of ribosome redistribution and 'queueing-effect' on the RNA degradation pathway. Taken together, our results provide for the first time insights into the hidden regulatory interaction of miRNA-based synthetic networks, potentially relevant also in endogenous gene regulation. Our observations allow to define rules for complexity- and context-aware design of genetic circuits, in which transgenes co-expression can be modulated by tuning resource availability via number and location of miRNA target sites.
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Affiliation(s)
- Federica Cella
- Istituto Italiano di Tecnologia-IIT, Largo Barsanti e Matteucci, Naples, Italy
| | - Giansimone Perrino
- Department of Bioengineering and Centre of Excellence in Synthetic Biology, Imperial College London, London, UK
| | - Fabiana Tedeschi
- Istituto Italiano di Tecnologia-IIT, Largo Barsanti e Matteucci, Naples, Italy.,University of Naples Federico II, Naples, Italy
| | | | - Carla Bosia
- Department of Applied Science and Technology, Politecnico di Torino, Torino, Italy.,Italian Institute for Genomic Medicine, c/o IRCCS, Candiolo, Italy
| | - Guy-Bart Stan
- Department of Bioengineering and Centre of Excellence in Synthetic Biology, Imperial College London, London, UK
| | - Velia Siciliano
- Istituto Italiano di Tecnologia-IIT, Largo Barsanti e Matteucci, Naples, Italy
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8
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Negro S, Lauria F, Stazi M, Tebaldi T, D’Este G, Pirazzini M, Megighian A, Lessi F, Mazzanti CM, Sales G, Romualdi C, Fillo S, Lista F, Sleigh JN, Tosolini AP, Schiavo G, Viero G, Rigoni M. Hydrogen peroxide induced by nerve injury promotes axon regeneration via connective tissue growth factor. Acta Neuropathol Commun 2022; 10:189. [PMID: 36567321 PMCID: PMC9791753 DOI: 10.1186/s40478-022-01495-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 12/12/2022] [Indexed: 12/26/2022] Open
Abstract
Regeneration of the neuromuscular junction (NMJ) leverages on extensive exchange of factors released from motor axon terminals (MATs), muscle fibers and perisynaptic Schwann cells (PSCs), among which hydrogen peroxide (H2O2) is a major pro-regenerative signal. To identify critical determinants of NMJ remodeling in response to injury, we performed temporal transcriptional profiling of NMJs from 2 month-old mice during MAT degeneration/regeneration, and cross-referenced the differentially expressed genes with those elicited by H2O2 in SCs. We identified an enrichment in extracellular matrix (ECM) transcripts, including Connective Tissue Growth Factor (Ctgf), which is usually expressed during development. We discovered that Ctgf levels are increased in a Yes-associated protein (YAP)-dependent fashion in response to rapid, local H2O2 signaling generated by stressed mitochondria in the injured sciatic nerve, a finding highlighting the importance of signals triggered by mechanical force to motor nerve repair. Through sequestration of Ctgf or inactivation of H2O2, we delayed the recovery of neuromuscular function by impairing SC migration and, in turn, axon-oriented re-growth. These data indicate that H2O2 and its downstream effector Ctgf are pro-regenerative factors that enable axonal growth, and reveal a striking ECM remodeling process during nerve regeneration upon local H2O2 signaling. Our study identifies key transcriptomic changes at the regenerating NMJ, providing a rich source of pro-regenerative factors with potential for alleviating the consequences of peripheral nerve injuries.
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Affiliation(s)
- Samuele Negro
- grid.5608.b0000 0004 1757 3470Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy ,grid.5608.b0000 0004 1757 3470U.O.C. Clinica Neurologica, Azienda Ospedale, University of Padua, 35128 Padua, Italy
| | - Fabio Lauria
- grid.419463.d0000 0004 1756 3731Institute of Biophysics, CNR Unit at Trento, 38123 Povo, Italy
| | - Marco Stazi
- grid.5608.b0000 0004 1757 3470Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy
| | - Toma Tebaldi
- grid.11696.390000 0004 1937 0351Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Povo, Italy ,grid.47100.320000000419368710Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT 06520 USA
| | - Giorgia D’Este
- grid.5608.b0000 0004 1757 3470Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy
| | - Marco Pirazzini
- grid.5608.b0000 0004 1757 3470Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy ,grid.5608.b0000 0004 1757 3470Myology Center (CIR-Myo), University of Padua, 35129 Padua, Italy
| | - Aram Megighian
- grid.5608.b0000 0004 1757 3470Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy ,grid.5608.b0000 0004 1757 3470Padua Neuroscience Center, University of Padua, 35131 Padua, Italy
| | - Francesca Lessi
- Laboratory of Genomics, Pisa Science Foundation, 56017 San Giuliano Terme, Italy
| | - Chiara M. Mazzanti
- Laboratory of Genomics, Pisa Science Foundation, 56017 San Giuliano Terme, Italy
| | - Gabriele Sales
- grid.5608.b0000 0004 1757 3470Department of Biology, University of Padua, 35131 Padua, Italy
| | - Chiara Romualdi
- grid.5608.b0000 0004 1757 3470Department of Biology, University of Padua, 35131 Padua, Italy
| | - Silvia Fillo
- grid.470599.60000 0004 1760 920XCenter of Medical and Veterinary Research of the Ministry of Defence, 00184 Rome, Italy
| | - Florigio Lista
- grid.470599.60000 0004 1760 920XCenter of Medical and Veterinary Research of the Ministry of Defence, 00184 Rome, Italy
| | - James N. Sleigh
- grid.83440.3b0000000121901201Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG UK ,grid.83440.3b0000000121901201UCL Queen Square Motor Neuron Disease Centre, University College London, London, WC1N 3BG UK ,grid.83440.3b0000000121901201UK Dementia Research Institute, University College London, London, WC1E 6BT UK
| | - Andrew P. Tosolini
- grid.83440.3b0000000121901201Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG UK ,grid.83440.3b0000000121901201UCL Queen Square Motor Neuron Disease Centre, University College London, London, WC1N 3BG UK
| | - Giampietro Schiavo
- grid.83440.3b0000000121901201Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG UK ,grid.83440.3b0000000121901201UCL Queen Square Motor Neuron Disease Centre, University College London, London, WC1N 3BG UK ,grid.83440.3b0000000121901201UK Dementia Research Institute, University College London, London, WC1E 6BT UK
| | - Gabriella Viero
- grid.419463.d0000 0004 1756 3731Institute of Biophysics, CNR Unit at Trento, 38123 Povo, Italy
| | - Michela Rigoni
- Department of Biomedical Sciences, University of Padua, 35131, Padua, Italy. .,Myology Center (CIR-Myo), University of Padua, 35129, Padua, Italy.
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9
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Destefanis F, Manara V, Santarelli S, Zola S, Brambilla M, Viola G, Maragno P, Signoria I, Viero G, Pasini ME, Penzo M, Bellosta P. Reduction of nucleolar NOC1 leads to the accumulation of pre-rRNAs and induces Xrp1, affecting growth and resulting in cell competition. J Cell Sci 2022; 135:285861. [PMID: 36314272 PMCID: PMC9789402 DOI: 10.1242/jcs.260110] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 10/25/2022] [Indexed: 12/12/2022] Open
Abstract
NOC1 is a nucleolar protein necessary in yeast for both transport and maturation of ribosomal subunits. Here, we show that Drosophila NOC1 (annotated CG7839) is necessary for rRNAs maturation and for a correct animal development. Its ubiquitous downregulation results in a dramatic decrease in polysome level and of protein synthesis. NOC1 expression in multiple organs, such as the prothoracic gland and the fat body, is necessary for their proper functioning. Reduction of NOC1 in epithelial cells from the imaginal discs results in clones that die by apoptosis, an event that is partially rescued in a Minute/+ background, suggesting that reduction of NOC1 induces the cells to become less fit and to acquire a 'loser' state. NOC1 downregulation activates the pro-apoptotic Eiger-JNK pathway and leads to an increase of Xrp1, which results in the upregulation of DILP8, a member of the insulin/relaxin-like family known to coordinate organ growth with animal development. Our data underline NOC1 as an essential gene in ribosome biogenesis and highlight its novel functions in the control of growth and cell competition.
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Affiliation(s)
- Francesca Destefanis
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Valeria Manara
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Stefania Santarelli
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Sheri Zola
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Marco Brambilla
- Department of Biosciences, University of Milano, Via Celoria 25, 20133 Milano, Italy
| | - Giacomo Viola
- Department of Biosciences, University of Milano, Via Celoria 25, 20133 Milano, Italy
| | - Paola Maragno
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Ilaria Signoria
- Institute of Biophysics, CNR, Via Sommarive 18, 38123 Trento, Italy
| | - Gabriella Viero
- Institute of Biophysics, CNR, Via Sommarive 18, 38123 Trento, Italy
| | - Maria Enrica Pasini
- Department of Biosciences, University of Milano, Via Celoria 25, 20133 Milano, Italy
| | - Marianna Penzo
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Via Massarenti 9, 40138 Bologna, Italy,Center for Applied Biomedical Research, University of Bologna, Via Massarenti 9, 40138 Bologna, Italy
| | - Paola Bellosta
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento, Italy,Department of Medicine, NYU Langone School of Medicine, 550 First Avenue, New York, 10016 NY, USA,Author for correspondence ()
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10
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Biancon G, Joshi P, Zimmer JT, Hunck T, Gao Y, Lessard MD, Courchaine E, Barentine AES, Machyna M, Botti V, Qin A, Gbyli R, Patel A, Song Y, Kiefer L, Viero G, Neuenkirchen N, Lin H, Bewersdorf J, Simon MD, Neugebauer KM, Tebaldi T, Halene S. Precision analysis of mutant U2AF1 activity reveals deployment of stress granules in myeloid malignancies. Mol Cell 2022; 82:1107-1122.e7. [PMID: 35303483 PMCID: PMC8988922 DOI: 10.1016/j.molcel.2022.02.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 12/21/2021] [Accepted: 02/15/2022] [Indexed: 12/13/2022]
Abstract
Splicing factor mutations are common among cancers, recently emerging as drivers of myeloid malignancies. U2AF1 carries hotspot mutations in its RNA-binding motifs; however, how they affect splicing and promote cancer remain unclear. The U2AF1/U2AF2 heterodimer is critical for 3' splice site (3'SS) definition. To specifically unmask changes in U2AF1 function in vivo, we developed a crosslinking and immunoprecipitation procedure that detects contacts between U2AF1 and the 3'SS AG at single-nucleotide resolution. Our data reveal that the U2AF1 S34F and Q157R mutants establish new 3'SS contacts at -3 and +1 nucleotides, respectively. These effects compromise U2AF2-RNA interactions, resulting predominantly in intron retention and exon exclusion. Integrating RNA binding, splicing, and turnover data, we predicted that U2AF1 mutations directly affect stress granule components, which was corroborated by single-cell RNA-seq. Remarkably, U2AF1-mutant cell lines and patient-derived MDS/AML blasts displayed a heightened stress granule response, pointing to a novel role for biomolecular condensates in adaptive oncogenic strategies.
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Affiliation(s)
- Giulia Biancon
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA.
| | - Poorval Joshi
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Joshua T Zimmer
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA; Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT, USA
| | - Torben Hunck
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Yimeng Gao
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Mark D Lessard
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Edward Courchaine
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA
| | - Andrew E S Barentine
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA; Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Martin Machyna
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA
| | - Valentina Botti
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA
| | - Ashley Qin
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Rana Gbyli
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Amisha Patel
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Yuanbin Song
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA; Department of Hematologic Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Lea Kiefer
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | | | - Nils Neuenkirchen
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA
| | - Haifan Lin
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA; Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA; Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA; Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT, USA; Institute for Biomolecular Design and Discovery, Yale University, West Haven, CT, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA; Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Toma Tebaldi
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA; Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy.
| | - Stephanie Halene
- Section of Hematology, Department of Internal Medicine, Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA; Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT, USA; Department of Pathology, Yale University School of Medicine, New Haven, CT, USA.
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11
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Licata NV, Cristofani R, Salomonsson S, Wilson KM, Kempthorne L, Vaizoglu D, D’Agostino VG, Pollini D, Loffredo R, Pancher M, Adami V, Bellosta P, Ratti A, Viero G, Quattrone A, Isaacs AM, Poletti A, Provenzani A. C9orf72 ALS/FTD dipeptide repeat protein levels are reduced by small molecules that inhibit PKA or enhance protein degradation. EMBO J 2022; 41:e105026. [PMID: 34791698 PMCID: PMC8724771 DOI: 10.15252/embj.2020105026] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 09/21/2021] [Accepted: 10/12/2021] [Indexed: 11/09/2022] Open
Abstract
Intronic GGGGCC (G4C2) hexanucleotide repeat expansion within the human C9orf72 gene represents the most common cause of familial forms of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) (C9ALS/FTD). Repeat-associated non-AUG (RAN) translation of repeat-containing C9orf72 RNA results in the production of neurotoxic dipeptide-repeat proteins (DPRs). Here, we developed a high-throughput drug screen for the identification of positive and negative modulators of DPR levels. We found that HSP90 inhibitor geldanamycin and aldosterone antagonist spironolactone reduced DPR levels by promoting protein degradation via the proteasome and autophagy pathways respectively. Surprisingly, cAMP-elevating compounds boosting protein kinase A (PKA) activity increased DPR levels. Inhibition of PKA activity, by both pharmacological and genetic approaches, reduced DPR levels in cells and rescued pathological phenotypes in a Drosophila model of C9ALS/FTD. Moreover, knockdown of PKA-catalytic subunits correlated with reduced translation efficiency of DPRs, while the PKA inhibitor H89 reduced endogenous DPR levels in C9ALS/FTD patient-derived iPSC motor neurons. Together, our results suggest new and druggable pathways modulating DPR levels in C9ALS/FTD.
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Affiliation(s)
- Nausicaa V Licata
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Riccardo Cristofani
- Dipartimento di Scienze Farmacologiche e BiomolecolariUniversità degli Studi di MilanoMilanItaly
| | - Sally Salomonsson
- Department of Neurodegenerative DiseaseUCL Queen Square Institute of NeurologyLondonUK
- UK Dementia Research Institute at UCLUCL Queen Square Institute of NeurologyLondonUK
| | - Katherine M Wilson
- Department of Neurodegenerative DiseaseUCL Queen Square Institute of NeurologyLondonUK
- UK Dementia Research Institute at UCLUCL Queen Square Institute of NeurologyLondonUK
| | - Liam Kempthorne
- Department of Neurodegenerative DiseaseUCL Queen Square Institute of NeurologyLondonUK
- UK Dementia Research Institute at UCLUCL Queen Square Institute of NeurologyLondonUK
| | - Deniz Vaizoglu
- Department of Neurodegenerative DiseaseUCL Queen Square Institute of NeurologyLondonUK
- UK Dementia Research Institute at UCLUCL Queen Square Institute of NeurologyLondonUK
| | - Vito G D’Agostino
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Daniele Pollini
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Rosa Loffredo
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Michael Pancher
- HTS Core Facility, Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Valentina Adami
- HTS Core Facility, Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Paola Bellosta
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
- Department of MedicineNYU at Grossman School of MedicineNYUSA
| | - Antonia Ratti
- Department of NeurologyStroke Unit and Laboratory of NeuroscienceIstituto Auxologico Italiano, IRCCSMilanItaly
- Dipartimento di Biotecnologie Mediche e Medicina TraslazionaleUniversità degli Studi di MilanoMilanItaly
| | | | - Alessandro Quattrone
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Adrian M Isaacs
- Department of Neurodegenerative DiseaseUCL Queen Square Institute of NeurologyLondonUK
- UK Dementia Research Institute at UCLUCL Queen Square Institute of NeurologyLondonUK
| | - Angelo Poletti
- Dipartimento di Scienze Farmacologiche e BiomolecolariUniversità degli Studi di MilanoMilanItaly
| | - Alessandro Provenzani
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
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12
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Del Piano A, Kecman T, Schmid M, Barbieri R, Brocchieri L, Tornaletti S, Firrito C, Minati L, Bernabo P, Signoria I, Lauria F, Gillingwater TH, Viero G, Clamer M. Phospho-RNA sequencing with circAID-p-seq. Nucleic Acids Res 2021; 50:e23. [PMID: 34850942 PMCID: PMC8887461 DOI: 10.1093/nar/gkab1158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 10/27/2021] [Accepted: 11/09/2021] [Indexed: 11/14/2022] Open
Abstract
Most RNA footprinting approaches that require ribonuclease cleavage generate RNA fragments bearing a phosphate or cyclic phosphate group at their 3′ end. Unfortunately, current library preparation protocols rely only on a 3′ hydroxyl group for adaptor ligation or poly-A tailing. Here, we developed circAID-p-seq, a PCR-free library preparation for selective 3′ phospho-RNA sequencing. As a proof of concept, we applied circAID-p-seq to ribosome profiling, which is based on sequencing of RNA fragments protected by ribosomes after endonuclease digestion. CircAID-p-seq, combined with the dedicated computational pipeline circAidMe, facilitates accurate, fast and highly efficient sequencing of phospho-RNA fragments from eukaryotic cells and tissues. We used circAID-p-seq to portray ribosome occupancy in transcripts, providing a versatile and PCR-free strategy to possibly unravel any endogenous 3′-phospho RNA molecules.
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Affiliation(s)
- Alessia Del Piano
- IMMAGINA BioTechnology S.r.l, Via Sommarive 18, Povo, Italy.,Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Tea Kecman
- IMMAGINA BioTechnology S.r.l, Via Sommarive 18, Povo, Italy
| | | | | | - Luciano Brocchieri
- TB-Seq, Inc., 458 Carlton Court, Ste H, South San Francisco, CA 94080, USA
| | - Silvia Tornaletti
- TB-Seq, Inc., 458 Carlton Court, Ste H, South San Francisco, CA 94080, USA
| | | | - Luca Minati
- IMMAGINA BioTechnology S.r.l, Via Sommarive 18, Povo, Italy
| | - Paola Bernabo
- IMMAGINA BioTechnology S.r.l, Via Sommarive 18, Povo, Italy
| | - Ilaria Signoria
- Institute of Biophysics, Unit at Trento, CNR, Via Sommarive, 18 Povo, Italy
| | - Fabio Lauria
- Institute of Biophysics, Unit at Trento, CNR, Via Sommarive, 18 Povo, Italy
| | - Thomas H Gillingwater
- Edinburgh Medical School: Biomedical Sciences & Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh, UK
| | - Gabriella Viero
- Institute of Biophysics, Unit at Trento, CNR, Via Sommarive, 18 Povo, Italy
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13
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Birsa N, Ule AM, Garone MG, Tsang B, Mattedi F, Chong PA, Humphrey J, Jarvis S, Pisiren M, Wilkins OG, Nosella ML, Devoy A, Bodo C, de la Fuente RF, Fisher EMC, Rosa A, Viero G, Forman-Kay JD, Schiavo G, Fratta P. FUS-ALS mutants alter FMRP phase separation equilibrium and impair protein translation. Sci Adv 2021; 7:7/30/eabf8660. [PMID: 34290090 PMCID: PMC8294762 DOI: 10.1126/sciadv.abf8660] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 06/03/2021] [Indexed: 05/16/2023]
Abstract
FUsed in Sarcoma (FUS) is a multifunctional RNA binding protein (RBP). FUS mutations lead to its cytoplasmic mislocalization and cause the neurodegenerative disease amyotrophic lateral sclerosis (ALS). Here, we use mouse and human models with endogenous ALS-associated mutations to study the early consequences of increased cytoplasmic FUS. We show that in axons, mutant FUS condensates sequester and promote the phase separation of fragile X mental retardation protein (FMRP), another RBP associated with neurodegeneration. This leads to repression of translation in mouse and human FUS-ALS motor neurons and is corroborated in vitro, where FUS and FMRP copartition and repress translation. Last, we show that translation of FMRP-bound RNAs is reduced in vivo in FUS-ALS motor neurons. Our results unravel new pathomechanisms of FUS-ALS and identify a novel paradigm by which mutations in one RBP favor the formation of condensates sequestering other RBPs, affecting crucial biological functions, such as protein translation.
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Affiliation(s)
- Nicol Birsa
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK.
- UK Dementia Research Institute, University College London, London WC1E 6BT, UK
| | - Agnieszka M Ule
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Maria Giovanna Garone
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
- Center for Life Nano Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | - Brian Tsang
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Francesca Mattedi
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
- Institute of Biophysics, CNR, Trento, Italy
| | - P Andrew Chong
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Jack Humphrey
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Seth Jarvis
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Melis Pisiren
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Oscar G Wilkins
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
- The Francis Crick Institute, London NW1 1AT, UK
| | - Micheal L Nosella
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Anny Devoy
- Maurice Wohl Clinical Neuroscience Institute, King's College London, London SE5 9RT, UK
| | - Cristian Bodo
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | | | - Elizabeth M C Fisher
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Alessandro Rosa
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
- Center for Life Nano Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | | | - Julie D Forman-Kay
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Giampietro Schiavo
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
- UK Dementia Research Institute, University College London, London WC1E 6BT, UK
| | - Pietro Fratta
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK.
- MRC Centre for Neuromuscular Disease, Queen Square, London WC1N 3BG, UK
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14
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Pollini D, Loffredo R, Maniscalco F, Cardano M, Micaelli M, Bonomo I, Licata NV, Peroni D, Tomaszewska W, Rossi A, Crippa V, Dassi E, Viero G, Quattrone A, Poletti A, Conti L, Provenzani A. Multilayer and MATR3-dependent regulation of mRNAs maintains pluripotency in human induced pluripotent stem cells. iScience 2021; 24:102197. [PMID: 33733063 PMCID: PMC7940987 DOI: 10.1016/j.isci.2021.102197] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 11/22/2020] [Accepted: 02/11/2021] [Indexed: 10/28/2022] Open
Abstract
Matrin3 (MATR3) is a nuclear RNA/DNA-binding protein that plays pleiotropic roles in gene expression regulation by directly stabilizing target RNAs and supporting the activity of transcription factors by modulating chromatin architecture. MATR3 is involved in the differentiation of neural cells, and, here, we elucidate its critical functions in regulating pluripotent circuits in human induced pluripotent stem cells (hiPSCs). MATR3 downregulation affects hiPSCs' differentiation potential by altering key pluripotency regulators' expression levels, including OCT4, NANOG, and LIN28A by pleiotropic mechanisms. MATR3 binds to the OCT4 and YTHDF1 promoters favoring their expression. YTHDF1, in turn, binds the m6A-modified OCT4 mRNA. Furthermore, MATR3 is recruited on ribosomes and controls pluripotency regulating the translation of specific transcripts, including NANOG and LIN28A, by direct binding and favoring their stabilization. These results show that MATR3 orchestrates the pluripotency circuitry by regulating the transcription, translational efficiency, and epitranscriptome of specific transcripts.
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Affiliation(s)
- Daniele Pollini
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Rosa Loffredo
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Federica Maniscalco
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
- Institute of Biophysics, CNR, Trento, Italy
| | - Marina Cardano
- Cell Technology Core Facility, Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Mariachiara Micaelli
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Isabelle Bonomo
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | | | - Daniele Peroni
- Mass Spectrometry Core Facility, Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Weronika Tomaszewska
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Annalisa Rossi
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Valeria Crippa
- Laboratorio di Biologia Applicata, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Erik Dassi
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | | | - Alessandro Quattrone
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Angelo Poletti
- Laboratorio di Biologia Applicata, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Luciano Conti
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Alessandro Provenzani
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
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15
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Minati L, Firrito C, Del Piano A, Peretti A, Sidoli S, Peroni D, Belli R, Gandolfi F, Romanel A, Bernabo P, Zasso J, Quattrone A, Guella G, Lauria F, Viero G, Clamer M. One-shot analysis of translated mammalian lncRNAs with AHARIBO. eLife 2021; 10:59303. [PMID: 33594971 PMCID: PMC7932693 DOI: 10.7554/elife.59303] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 02/16/2021] [Indexed: 12/12/2022] Open
Abstract
A vast portion of the mammalian genome is transcribed as long non-coding RNAs (lncRNAs) acting in the cytoplasm with largely unknown functions. Surprisingly, lncRNAs have been shown to interact with ribosomes, encode peptides, or act as ribosome sponges. These functions still remain mostly undetected and understudied owing to the lack of efficient tools for genome-wide simultaneous identification of ribosome-associated and peptide-producing lncRNAs. Here, we present AHA-mediated RIBOsome isolation (AHARIBO), a method for the detection of lncRNAs either untranslated, but associated with ribosomes, or encoding small peptides. Using AHARIBO in mouse embryonic stem cells during neuronal differentiation, we isolated ribosome-protected RNA fragments, translated RNAs, and corresponding de novo synthesized peptides. Besides identifying mRNAs under active translation and associated ribosomes, we found and distinguished lncRNAs acting as ribosome sponges or encoding micropeptides, laying the ground for a better functional understanding of hundreds of lncRNAs.
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Affiliation(s)
| | | | | | | | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, United States
| | - Daniele Peroni
- Mass Spectrometry Facility, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Romina Belli
- Mass Spectrometry Facility, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Francesco Gandolfi
- Laboratory of Bioinformatics and Computational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Alessandro Romanel
- Laboratory of Bioinformatics and Computational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | | | - Jacopo Zasso
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Alessandro Quattrone
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | | | - Fabio Lauria
- Institute of Biophysics, CNR Unit at Trento, Trento, Italy
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16
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Iosub IA, Marchioretto M, van Nues RW, McKellar S, Viero G, Granneman S. The mRNA derived MalH sRNA contributes to alternative carbon source utilization by tuning maltoporin expression in E. coli. RNA Biol 2020; 18:914-931. [PMID: 33043783 PMCID: PMC8081044 DOI: 10.1080/15476286.2020.1827784] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Previous high-throughput studies in Gram-negative bacteria identified a large number of 3ʹUTR fragments that potentially function as sRNAs. Here we extensively characterize the MalH sRNA. We show that MalH is a stable degradation intermediate derived from the 3ʹ end of malG, which is part of the maltose uptake operon transcript malEFG. Unlike the majority of bacterial sRNAs, MalH is transiently expressed during the transition from the exponential to the stationary growth phase, suggesting that it contributes to adaptation to changes in nutrient availability. Over-expression of MalH reduces expression of general outer membrane porins and MicA, a repressor of the high-affinity maltose/maltodextrin transporter LamB. Disrupting MalH production and function significantly reduces lamB accumulation when maltose is the only available carbon source, presumably due to the accumulation of the MicA repressor. We propose that MalH is part of a regulatory network that, during the transition phase, directly or indirectly promotes accumulation of high-affinity maltose transporters in the outer membrane by dampening competing pathways.
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Affiliation(s)
- Ira A Iosub
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh0, UK
| | | | - Rob W van Nues
- Institute of Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Stuart McKellar
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh0, UK
| | | | - Sander Granneman
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh0, UK
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17
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Lauria F, Bernabò P, Tebaldi T, Groen EJN, Perenthaler E, Maniscalco F, Rossi A, Donzel D, Clamer M, Marchioretto M, Omersa N, Orri J, Dalla Serra M, Anderluh G, Quattrone A, Inga A, Gillingwater TH, Viero G. SMN-primed ribosomes modulate the translation of transcripts related to spinal muscular atrophy. Nat Cell Biol 2020; 22:1239-1251. [PMID: 32958857 PMCID: PMC7610479 DOI: 10.1038/s41556-020-00577-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 08/13/2020] [Indexed: 12/20/2022]
Abstract
The contribution of ribosome heterogeneity and ribosome-associated proteins to the molecular control of proteomes in health and disease remains unclear. Here, we demonstrate that survival motor neuron (SMN) protein-the loss of which causes the neuromuscular disease spinal muscular atrophy (SMA)-binds to ribosomes and that this interaction is tissue-dependent. SMN-primed ribosomes are preferentially positioned within the first five codons of a set of mRNAs that are enriched for translational enhancer sequences in the 5' untranslated region (UTR) and rare codons at the beginning of their coding sequence. These SMN-specific mRNAs are associated with neurogenesis, lipid metabolism, ubiquitination, chromatin regulation and translation. Loss of SMN induces ribosome depletion, especially at the beginning of the coding sequence of SMN-specific mRNAs, leading to impairment of proteins that are involved in motor neuron function and stability, including acetylcholinesterase. Thus, SMN plays a crucial role in the regulation of ribosome fluxes along mRNAs encoding proteins that are relevant to SMA pathogenesis.
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Affiliation(s)
- Fabio Lauria
- Institute of Biophysics, CNR Unit at Trento, Trento, Italy
| | - Paola Bernabò
- Institute of Biophysics, CNR Unit at Trento, Trento, Italy
| | - Toma Tebaldi
- Department CIBIO, University of Trento, Trento, Italy
- Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
| | - Ewout Joan Nicolaas Groen
- Edinburgh Medical School, Biomedical Sciences & Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh, UK
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, Utrecht, the Netherlands
| | - Elena Perenthaler
- Institute of Biophysics, CNR Unit at Trento, Trento, Italy
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Federica Maniscalco
- Institute of Biophysics, CNR Unit at Trento, Trento, Italy
- Department CIBIO, University of Trento, Trento, Italy
| | | | - Deborah Donzel
- Institute of Biophysics, CNR Unit at Trento, Trento, Italy
| | | | | | - Neža Omersa
- National Institute of Chemistry, Ljubljana, Slovenia
| | - Julia Orri
- Institute of Biophysics, CNR Unit at Trento, Trento, Italy
- La Fundació Jesuïtes Educació, Barcelona, Spain
| | | | | | | | - Alberto Inga
- Department CIBIO, University of Trento, Trento, Italy
| | - Thomas Henry Gillingwater
- Edinburgh Medical School, Biomedical Sciences & Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh, UK
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18
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Gao Y, Vasic R, Song Y, Teng R, Liu C, Gbyli R, Biancon G, Nelakanti R, Lobben K, Kudo E, Liu W, Ardasheva A, Fu X, Wang X, Joshi P, Lee V, Dura B, Viero G, Iwasaki A, Fan R, Xiao A, Flavell RA, Li HB, Tebaldi T, Halene S. m 6A Modification Prevents Formation of Endogenous Double-Stranded RNAs and Deleterious Innate Immune Responses during Hematopoietic Development. Immunity 2020; 52:1007-1021.e8. [PMID: 32497523 PMCID: PMC7408742 DOI: 10.1016/j.immuni.2020.05.003] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 02/19/2020] [Accepted: 05/08/2020] [Indexed: 01/02/2023]
Abstract
N6-methyladenosine (m6A) is the most abundant RNA modification, but little is known about its role in mammalian hematopoietic development. Here, we show that conditional deletion of the m6A writer METTL3 in murine fetal liver resulted in hematopoietic failure and perinatal lethality. Loss of METTL3 and m6A activated an aberrant innate immune response, mediated by the formation of endogenous double-stranded RNAs (dsRNAs). The aberrantly formed dsRNAs were long, highly m6A modified in their native state, characterized by low folding energies, and predominantly protein coding. We identified coinciding activation of pattern recognition receptor pathways normally tasked with the detection of foreign dsRNAs. Disruption of the aberrant immune response via abrogation of downstream Mavs or Rnasel signaling partially rescued the observed hematopoietic defects in METTL3-deficient cells in vitro and in vivo. Our results suggest that m6A modification protects against endogenous dsRNA formation and a deleterious innate immune response during mammalian hematopoietic development.
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Affiliation(s)
- Yimeng Gao
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center and Yale RNA Center, Yale University School of Medicine, New Haven, CT 06520, USA.
| | - Radovan Vasic
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center and Yale RNA Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yuanbin Song
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center and Yale RNA Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Rhea Teng
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center and Yale RNA Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Chengyang Liu
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center and Yale RNA Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Rana Gbyli
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center and Yale RNA Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Giulia Biancon
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center and Yale RNA Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Raman Nelakanti
- Department of Genetics and Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Kirsten Lobben
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center and Yale RNA Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Eriko Kudo
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA; Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Wei Liu
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center and Yale RNA Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Anastasia Ardasheva
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center and Yale RNA Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Xiaoying Fu
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center and Yale RNA Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Xiaman Wang
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center and Yale RNA Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Poorval Joshi
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center and Yale RNA Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Veronica Lee
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center and Yale RNA Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Burak Dura
- Yale Stem Cell Center and Yale RNA Center, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Biomedical Engineering and Yale Cancer Center, Yale University, New Haven, CT 06520, USA
| | - Gabriella Viero
- Institute of Biophysics, CNR Unit at Trento, Povo Trento 38123, Italy
| | - Akiko Iwasaki
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA; Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Rong Fan
- Yale Stem Cell Center and Yale RNA Center, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Biomedical Engineering and Yale Cancer Center, Yale University, New Haven, CT 06520, USA
| | - Andrew Xiao
- Department of Genetics and Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Richard A Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
| | - Hua-Bing Li
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Toma Tebaldi
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center and Yale RNA Center, Yale University School of Medicine, New Haven, CT 06520, USA.
| | - Stephanie Halene
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Yale Stem Cell Center and Yale RNA Center, Yale University School of Medicine, New Haven, CT 06520, USA.
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19
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Iosub IA, van Nues RW, McKellar SW, Nieken KJ, Marchioretto M, Sy B, Tree JJ, Viero G, Granneman S. Hfq CLASH uncovers sRNA-target interaction networks linked to nutrient availability adaptation. eLife 2020; 9:54655. [PMID: 32356726 PMCID: PMC7213987 DOI: 10.7554/elife.54655] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 04/30/2020] [Indexed: 01/10/2023] Open
Abstract
By shaping gene expression profiles, small RNAs (sRNAs) enable bacteria to efficiently adapt to changes in their environment. To better understand how Escherichia coli acclimatizes to nutrient availability, we performed UV cross-linking, ligation and sequencing of hybrids (CLASH) to uncover Hfq-associated RNA-RNA interactions at specific growth stages. We demonstrate that Hfq CLASH robustly captures bona fide RNA-RNA interactions. We identified hundreds of novel sRNA base-pairing interactions, including many sRNA-sRNA interactions and involving 3’UTR-derived sRNAs. We rediscovered known and identified novel sRNA seed sequences. The sRNA-mRNA interactions identified by CLASH have strong base-pairing potential and are highly enriched for complementary sequence motifs, even those supported by only a few reads. Yet, steady state levels of most mRNA targets were not significantly affected upon over-expression of the sRNA regulator. Our results reinforce the idea that the reproducibility of the interaction, not base-pairing potential, is a stronger predictor for a regulatory outcome.
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Affiliation(s)
- Ira Alexandra Iosub
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Stuart William McKellar
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Karen Jule Nieken
- Institute of Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Brandon Sy
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Jai Justin Tree
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | | | - Sander Granneman
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, United Kingdom
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20
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Bernabò P, Viero G, Lencioni V. A long noncoding RNA acts as a post-transcriptional regulator of heat shock protein (HSP70) synthesis in the cold hardy Diamesa tonsa under heat shock. PLoS One 2020; 15:e0227172. [PMID: 32240200 PMCID: PMC7117718 DOI: 10.1371/journal.pone.0227172] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 02/28/2020] [Indexed: 12/24/2022] Open
Abstract
Cold stenothermal insects living in glacier-fed streams are stressed by temperature variations resulting from glacial retreat during global warming. The molecular aspects of insect response to environmental stresses remain largely unexplored. The aim of this study was to expand our knowledge of how a cold stenothermal organism controls gene expression at the transcriptional, translational, and protein level under warming conditions. Using the chironomid Diamesa tonsa as target species and a combination of RACE, qPCR, polysomal profiling, western blotting, and bioinformatics techniques, we discovered a new molecular pathway leading to previously overlooked adaptive strategies to stress. We obtained and characterized the complete cDNA sequences of three heat shock inducible 70 (hsp70) and two members of heat-shock cognate 70 (hsc70). Strikingly, we showed that a novel pseudo-hsp70 gene encoding a putative long noncoding RNA (lncRNA) which is transcribed during thermal stress, acting as a ribosome sponge to provide post-transcriptional control of HSP70 protein levels. The expression of the pseudo-hsp70 gene and its function suggest the existence of a new and unexpected mechanism to cope with thermal stress: lowering the pace of protein production to save energy and optimize resources for recovery.
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Affiliation(s)
- Paola Bernabò
- Department of Invertebrate Zoology and Hydrobiology, MUSE-Museo delle Scienze, Trento, Italy
- Institute of Biophysics-CNR Trento Unit, Povo, Trento, Italy
| | - Gabriella Viero
- Institute of Biophysics-CNR Trento Unit, Povo, Trento, Italy
| | - Valeria Lencioni
- Department of Invertebrate Zoology and Hydrobiology, MUSE-Museo delle Scienze, Trento, Italy
- * E-mail:
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21
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Groen EJN, Perenthaler E, Courtney NL, Jordan CY, Shorrock HK, van der Hoorn D, Huang YT, Murray LM, Viero G, Gillingwater TH. Temporal and tissue-specific variability of SMN protein levels in mouse models of spinal muscular atrophy. Hum Mol Genet 2019; 27:2851-2862. [PMID: 29790918 PMCID: PMC6077828 DOI: 10.1093/hmg/ddy195] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 05/14/2018] [Indexed: 02/02/2023] Open
Abstract
Spinal muscular atrophy (SMA) is a progressive motor neuron disease caused by deleterious variants in SMN1 that lead to a marked decrease in survival motor neuron (SMN) protein expression. Humans have a second SMN gene (SMN2) that is almost identical to SMN1. However, due to alternative splicing the majority of SMN2 messenger ribonucleic acid (mRNA) is translated into a truncated, unstable protein that is quickly degraded. Because the presence of SMN2 provides a unique opportunity for therapy development in SMA patients, the mechanisms that regulate SMN2 splicing and mRNA expression have been elucidated in great detail. In contrast, how much SMN protein is produced at different developmental time points and in different tissues remains under-characterized. In this study, we addressed this issue by determining SMN protein expression levels at three developmental time points across six different mouse tissues and in two distinct mouse models of SMA (‘severe’ Taiwanese and ‘intermediate’ Smn2B/− mice). We found that, in healthy control mice, SMN protein expression was significantly influenced by both age and tissue type. When comparing mouse models of SMA, we found that, despite being transcribed from genetically different alleles, control SMN levels were relatively similar. In contrast, the degree of SMN depletion between tissues in SMA varied substantially over time and between the two models. These findings offer an explanation for the differential vulnerability of tissues and organs observed in SMA and further our understanding of the systemic and temporal requirements for SMN with direct relevance for developing effective therapies for SMA.
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Affiliation(s)
- Ewout J N Groen
- Centre for Discovery Brain Sciences, Edinburgh Medical School: Biomedical Sciences.,Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Elena Perenthaler
- Centre for Discovery Brain Sciences, Edinburgh Medical School: Biomedical Sciences.,Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Natalie L Courtney
- Centre for Discovery Brain Sciences, Edinburgh Medical School: Biomedical Sciences.,Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Crispin Y Jordan
- Centre for Discovery Brain Sciences, Edinburgh Medical School: Biomedical Sciences
| | - Hannah K Shorrock
- Centre for Discovery Brain Sciences, Edinburgh Medical School: Biomedical Sciences.,Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Dinja van der Hoorn
- Centre for Discovery Brain Sciences, Edinburgh Medical School: Biomedical Sciences.,Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Yu-Ting Huang
- Centre for Discovery Brain Sciences, Edinburgh Medical School: Biomedical Sciences.,Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Lyndsay M Murray
- Centre for Discovery Brain Sciences, Edinburgh Medical School: Biomedical Sciences.,Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Gabriella Viero
- Institute of Biophysics, CNR Unit at Trento, 38123 Povo, Trento, Italy
| | - Thomas H Gillingwater
- Centre for Discovery Brain Sciences, Edinburgh Medical School: Biomedical Sciences.,Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh EH8 9XD, UK
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22
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Lauria F, Tebaldi T, Bernabò P, Groen EJN, Gillingwater TH, Viero G. riboWaltz: Optimization of ribosome P-site positioning in ribosome profiling data. PLoS Comput Biol 2018; 14:e1006169. [PMID: 30102689 PMCID: PMC6112680 DOI: 10.1371/journal.pcbi.1006169] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 08/28/2018] [Accepted: 04/30/2018] [Indexed: 12/13/2022] Open
Abstract
Ribosome profiling is a powerful technique used to study translation at the genome-wide level, generating unique information concerning ribosome positions along RNAs. Optimal localization of ribosomes requires the proper identification of the ribosome P-site in each ribosome protected fragment, a crucial step to determine the trinucleotide periodicity of translating ribosomes, and draw correct conclusions concerning where ribosomes are located. To determine the P-site within ribosome footprints at nucleotide resolution, the precise estimation of its offset with respect to the protected fragment is necessary. Here we present riboWaltz, an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. Compared to existing tools, riboWaltz shows improved accuracies for P-site estimation and neat ribosome positioning in multiple case studies. riboWaltz was implemented in R and is available as an R package at https://github.com/LabTranslationalArchitectomics/RiboWaltz.
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Affiliation(s)
- Fabio Lauria
- Institute of Biophysics, CNR Unit at Trento, Trento, Italy
- * E-mail: (FL); (GV)
| | - Toma Tebaldi
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Paola Bernabò
- Institute of Biophysics, CNR Unit at Trento, Trento, Italy
| | - Ewout J. N. Groen
- Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Integrative Physiology, University of Edinburgh, Edinburgh, United Kingdom
| | - Thomas H. Gillingwater
- Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Integrative Physiology, University of Edinburgh, Edinburgh, United Kingdom
| | - Gabriella Viero
- Institute of Biophysics, CNR Unit at Trento, Trento, Italy
- * E-mail: (FL); (GV)
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23
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Tebaldi T, Zuccotti P, Peroni D, Köhn M, Gasperini L, Potrich V, Bonazza V, Dudnakova T, Rossi A, Sanguinetti G, Conti L, Macchi P, D'Agostino V, Viero G, Tollervey D, Hüttelmaier S, Quattrone A. HuD Is a Neural Translation Enhancer Acting on mTORC1-Responsive Genes and Counteracted by the Y3 Small Non-coding RNA. Mol Cell 2018; 71:256-270.e10. [PMID: 30029004 PMCID: PMC6060611 DOI: 10.1016/j.molcel.2018.06.032] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 04/24/2018] [Accepted: 06/21/2018] [Indexed: 01/19/2023]
Abstract
The RNA-binding protein HuD promotes neurogenesis and favors recovery from peripheral axon injury. HuD interacts with many mRNAs, altering both stability and translation efficiency. We generated a nucleotide resolution map of the HuD RNA interactome in motor neuron-like cells, identifying HuD target sites in 1,304 mRNAs, almost exclusively in the 3' UTR. HuD binds many mRNAs encoding mTORC1-responsive ribosomal proteins and translation factors. Altered HuD expression correlates with the translation efficiency of these mRNAs and overall protein synthesis, in a mTORC1-independent fashion. The predominant HuD target is the abundant, small non-coding RNA Y3, amounting to 70% of the HuD interaction signal. Y3 functions as a molecular sponge for HuD, dynamically limiting its recruitment to polysomes and its activity as a translation and neuron differentiation enhancer. These findings uncover an alternative route to the mTORC1 pathway for translational control in motor neurons that is tunable by a small non-coding RNA.
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Affiliation(s)
- Toma Tebaldi
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento 38123, Italy
| | - Paola Zuccotti
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento 38123, Italy
| | - Daniele Peroni
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento 38123, Italy
| | - Marcel Köhn
- Institute of Molecular Medicine, Martin-Luther-University Halle-Wittenberg, Halle 06120, Germany; Julius-Bernstein-Institute of Physiology, Martin-Luther-University Halle-Wittenberg, Halle 06097, Germany
| | - Lisa Gasperini
- Laboratory of Molecular and Cellular Neurobiology, Centre for Integrative Biology, University of Trento, Trento 38123, Italy
| | - Valentina Potrich
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento 38123, Italy
| | - Veronica Bonazza
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento 38123, Italy
| | - Tatiana Dudnakova
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Annalisa Rossi
- Laboratory of Molecular and Cellular Neurobiology, Centre for Integrative Biology, University of Trento, Trento 38123, Italy
| | - Guido Sanguinetti
- School of Informatics, University of Edinburgh, Edinburgh EH8 9AB, UK
| | - Luciano Conti
- Laboratory of Stem Cell Biology, Centre for Integrative Biology, University of Trento, Trento 38123, Italy
| | - Paolo Macchi
- Laboratory of Molecular and Cellular Neurobiology, Centre for Integrative Biology, University of Trento, Trento 38123, Italy
| | - Vito D'Agostino
- Centre for Integrative Biology, University of Trento, Trento 38123, Italy
| | - Gabriella Viero
- Institute of Biophysics, CNR Unit at Trento, Trento 38123, Italy
| | - David Tollervey
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Stefan Hüttelmaier
- Institute of Molecular Medicine, Martin-Luther-University Halle-Wittenberg, Halle 06120, Germany
| | - Alessandro Quattrone
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento 38123, Italy.
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Negro S, Stazi M, Marchioretto M, Tebaldi T, Rodella U, Duregotti E, Gerke V, Quattrone A, Montecucco C, Rigoni M, Viero G. Hydrogen peroxide is a neuronal alarmin that triggers specific RNAs, local translation of Annexin A2, and cytoskeletal remodeling in Schwann cells. RNA 2018; 24:915-925. [PMID: 29643068 PMCID: PMC6004060 DOI: 10.1261/rna.064816.117] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 03/26/2018] [Indexed: 06/08/2023]
Abstract
Schwann cells are key players in neuro-regeneration: They sense "alarm" signals released by degenerating nerve terminals and differentiate toward a proregenerative phenotype, with phagocytosis of nerve debris and nerve guidance. At the murine neuromuscular junction, hydrogen peroxide (H2O2) is a key signal of Schwann cells' activation in response to a variety of nerve injuries. Here we report that Schwann cells exposed to low doses of H2O2 rewire the expression of several RNAs at both transcriptional and translational levels. Among the genes positively regulated at both levels, we identified an enriched cluster involved in cytoskeleton remodeling and cell migration, with the Annexin (Anxa) proteins being the most represented family. We show that both Annexin A2 (Anxa2) transcript and protein accumulate at the tips of long pseudopods that Schwann cells extend upon H2O2 exposure. Interestingly, Schwann cells reply to this signal and to nerve injury by locally translating Anxa2 in pseudopods, and undergo an extensive cytoskeleton remodeling. Our results show that, similarly to neurons, Schwann cells take advantage of local protein synthesis to change shape and move toward damaged axonal terminals to facilitate axonal regeneration.
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Affiliation(s)
- Samuele Negro
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy
| | - Marco Stazi
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy
| | | | - Toma Tebaldi
- Centre for Integrative Biology, University of Trento, 38123 Povo, Italy
| | - Umberto Rodella
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy
| | - Elisa Duregotti
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy
| | - Volker Gerke
- Institute of Medical Biochemistry, University of Münster, 48149 Münster, Germany
| | | | - Cesare Montecucco
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy
- CNR Institute of Neuroscience, 35131 Padua, Italy
| | - Michela Rigoni
- Department of Biomedical Sciences, University of Padua, 35131 Padua, Italy
| | - Gabriella Viero
- Institute of Biophysics, CNR Unit at Trento, 38123 Povo, Italy
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25
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Bernabò P, Tebaldi T, Groen EJN, Lane FM, Perenthaler E, Mattedi F, Newbery HJ, Zhou H, Zuccotti P, Potrich V, Shorrock HK, Muntoni F, Quattrone A, Gillingwater TH, Viero G. In Vivo Translatome Profiling in Spinal Muscular Atrophy Reveals a Role for SMN Protein in Ribosome Biology. Cell Rep 2018; 21:953-965. [PMID: 29069603 PMCID: PMC5668566 DOI: 10.1016/j.celrep.2017.10.010] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 07/22/2017] [Accepted: 10/02/2017] [Indexed: 12/13/2022] Open
Abstract
Genetic alterations impacting ubiquitously expressed proteins involved in RNA metabolism often result in neurodegenerative conditions, with increasing evidence suggesting that translation defects can contribute to disease. Spinal muscular atrophy (SMA) is a neuromuscular disease caused by low levels of SMN protein, whose role in pathogenesis remains unclear. Here, we identified in vivo and in vitro translation defects that are cell autonomous and SMN dependent. By determining in parallel the in vivo transcriptome and translatome in SMA mice, we observed a robust decrease in translation efficiency arising during early stages of disease. We provide a catalogue of RNAs with altered translation efficiency, identifying ribosome biology and translation as central processes affected by SMN depletion. This was further supported by a decrease in the number of ribosomes in SMA motor neurons in vivo. Overall, our findings suggest ribosome biology as an important, yet largely overlooked, factor in motor neuron degeneration. Polysomal profiling reveals translation defects in SMA mice Translation defects are SMN dependent and cell autonomous Translation efficiency alterations highlight defects in ribosome biology The number of axonal ribosomes is decreased in SMA in vivo
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Affiliation(s)
- Paola Bernabò
- Institute of Biophysics, CNR Unit at Trento, Via Sommarive 18, 38123 Povo (Trento), Italy
| | - Toma Tebaldi
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123 Povo (Trento), Italy
| | - Ewout J N Groen
- Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Hugh Robson Building, 15 George Square, EH8 9XD Edinburgh, UK; Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Hugh Robson Building, 15 George Square, EH8 9XD Edinburgh, UK
| | - Fiona M Lane
- Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Hugh Robson Building, 15 George Square, EH8 9XD Edinburgh, UK; Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Hugh Robson Building, 15 George Square, EH8 9XD Edinburgh, UK
| | - Elena Perenthaler
- Institute of Biophysics, CNR Unit at Trento, Via Sommarive 18, 38123 Povo (Trento), Italy
| | - Francesca Mattedi
- Institute of Biophysics, CNR Unit at Trento, Via Sommarive 18, 38123 Povo (Trento), Italy
| | - Helen J Newbery
- Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Hugh Robson Building, 15 George Square, EH8 9XD Edinburgh, UK; Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Hugh Robson Building, 15 George Square, EH8 9XD Edinburgh, UK
| | - Haiyan Zhou
- Dubowitz Neuromuscular Centre, Great Ormond Street Institute of Child Health, University College London 30, Guilford Street, WC1N 1EH London, UK
| | - Paola Zuccotti
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123 Povo (Trento), Italy
| | - Valentina Potrich
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123 Povo (Trento), Italy
| | - Hannah K Shorrock
- Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Hugh Robson Building, 15 George Square, EH8 9XD Edinburgh, UK; Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Hugh Robson Building, 15 George Square, EH8 9XD Edinburgh, UK
| | - Francesco Muntoni
- Dubowitz Neuromuscular Centre, Great Ormond Street Institute of Child Health, University College London 30, Guilford Street, WC1N 1EH London, UK
| | - Alessandro Quattrone
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123 Povo (Trento), Italy.
| | - Thomas H Gillingwater
- Euan MacDonald Centre for Motor Neurone Disease Research, University of Edinburgh, Hugh Robson Building, 15 George Square, EH8 9XD Edinburgh, UK; Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Hugh Robson Building, 15 George Square, EH8 9XD Edinburgh, UK.
| | - Gabriella Viero
- Institute of Biophysics, CNR Unit at Trento, Via Sommarive 18, 38123 Povo (Trento), Italy.
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26
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Rossi A, Moro A, Tebaldi T, Cornella N, Gasperini L, Lunelli L, Quattrone A, Viero G, Macchi P. Identification and dynamic changes of RNAs isolated from RALY-containing ribonucleoprotein complexes. Nucleic Acids Res 2017; 45:6775-6792. [PMID: 28379492 PMCID: PMC5499869 DOI: 10.1093/nar/gkx235] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 03/30/2017] [Indexed: 12/13/2022] Open
Abstract
RALY is a member of the heterogeneous nuclear ribonucleoprotein family (hnRNP), a large family of RNA-binding proteins involved in many aspects of RNA metabolism. Although RALY interactome has been recently characterized, a comprehensive global analysis of RALY-associated RNAs is lacking and the biological function of RALY remains elusive. Here, we performed RIP-seq analysis to identify RALY interacting RNAs and assessed the role of RALY in gene expression. We demonstrate that RALY binds specific coding and non-coding RNAs and associates with translating mRNAs of mammalian cells. Among the identified transcripts, we focused on ANXA1 and H1FX mRNAs, encoding for Annexin A1 and for the linker variant of the histone H1X, respectively. Both proteins are differentially expressed by proliferating cells and are considered as markers for tumorigenesis. We demonstrate that cells lacking RALY expression exhibit changes in the levels of H1FX and ANXA1 mRNAs and proteins in an opposite manner. We also provide evidence for a direct binding of RALY to the U-rich elements present within the 3΄UTR of both transcripts. Thus, our results identify RALY as a poly-U binding protein and as a regulator of H1FX and ANXA1 in mammalian cells.
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Affiliation(s)
- Annalisa Rossi
- Laboratory of Molecular and Cellular Neurobiology, Centre for Integrative Biology, University of Trento, via Sommarive 9, 38123 Trento (TN), Italy
| | - Albertomaria Moro
- Laboratory of Molecular and Cellular Neurobiology, Centre for Integrative Biology, University of Trento, via Sommarive 9, 38123 Trento (TN), Italy
| | - Toma Tebaldi
- Laboratory of Translational Genomics, CIBIO - Centre for Integrative Biology, University of Trento, Italy
| | - Nicola Cornella
- Laboratory of Molecular and Cellular Neurobiology, Centre for Integrative Biology, University of Trento, via Sommarive 9, 38123 Trento (TN), Italy
| | - Lisa Gasperini
- Laboratory of Molecular and Cellular Neurobiology, Centre for Integrative Biology, University of Trento, via Sommarive 9, 38123 Trento (TN), Italy
| | - Lorenzo Lunelli
- Laboratory of Biomolecular Sequence and Structure Analysis for Health, Fondazione Bruno Kessler, Via Sommarive 18, 38123 Povo (TN), Italy
| | - Alessandro Quattrone
- Laboratory of Translational Genomics, CIBIO - Centre for Integrative Biology, University of Trento, Italy
| | - Gabriella Viero
- Institute of Biophysics, CNR-Italian National Council for Research, via Sommarive 18, 38123 Trento (TN), Italy
| | - Paolo Macchi
- Laboratory of Molecular and Cellular Neurobiology, Centre for Integrative Biology, University of Trento, via Sommarive 9, 38123 Trento (TN), Italy
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27
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Knap P, Tebaldi T, Di Leva F, Biagioli M, Dalla Serra M, Viero G. The Unexpected Tuners: Are LncRNAs Regulating Host Translation during Infections? Toxins (Basel) 2017; 9:E357. [PMID: 29469820 PMCID: PMC5705972 DOI: 10.3390/toxins9110357] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 10/30/2017] [Accepted: 10/31/2017] [Indexed: 12/27/2022] Open
Abstract
Pathogenic bacteria produce powerful virulent factors, such as pore-forming toxins, that promote their survival and cause serious damage to the host. Host cells reply to membrane stresses and ionic imbalance by modifying gene expression at the epigenetic, transcriptional and translational level, to recover from the toxin attack. The fact that the majority of the human transcriptome encodes for non-coding RNAs (ncRNAs) raises the question: do host cells deploy non-coding transcripts to rapidly control the most energy-consuming process in cells-i.e., host translation-to counteract the infection? Here, we discuss the intriguing possibility that membrane-damaging toxins induce, in the host, the expression of toxin-specific long non-coding RNAs (lncRNAs), which act as sponges for other molecules, encoding small peptides or binding target mRNAs to depress their translation efficiency. Unravelling the function of host-produced lncRNAs upon bacterial infection or membrane damage requires an improved understanding of host lncRNA expression patterns, their association with polysomes and their function during this stress. This field of investigation holds a unique opportunity to reveal unpredicted scenarios and novel approaches to counteract antibiotic-resistant infections.
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Affiliation(s)
- Primoz Knap
- Institute of Biophysics, CNR Unit at Trento, Via Sommarive 18, Povo Trento 38123, Italy.
| | - Toma Tebaldi
- Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06520, USA.
| | - Francesca Di Leva
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, Povo Trento 38123, Italy.
| | - Marta Biagioli
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, Povo Trento 38123, Italy.
| | - Mauro Dalla Serra
- Institute of Biophysics, CNR Unit at Trento, Via Sommarive 18, Povo Trento 38123, Italy.
| | - Gabriella Viero
- Institute of Biophysics, CNR Unit at Trento, Via Sommarive 18, Povo Trento 38123, Italy.
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28
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Bernabò P, Gaglio M, Bellamoli F, Viero G, Lencioni V. DNA damage and translational response during detoxification from copper exposure in a wild population of Chironomus riparius. Chemosphere 2017; 173:235-244. [PMID: 28110013 DOI: 10.1016/j.chemosphere.2017.01.052] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 12/20/2016] [Accepted: 01/10/2017] [Indexed: 06/06/2023]
Abstract
Copper is one of the predominant components of pesticides employed in agriculture and known to be highly toxic once it reaches aquatic organisms. The impact of sublethal concentrations of this metal on wild insects is not yet completely understood. Studies addressing alterations in different levels of gene expression are still lacking. We previously demonstrated that in a wild population of Chironomus riparius, HSP and CYP families of genes were up-regulated at the transcriptional level after copper exposure. Here, we analyse the impact of copper at the genomic, translational and protein functional level, obtaining a comprehensive picture of the molecular reply to this metal. We studied genotoxicity in C. riparius larvae by Comet Assay, the translational response by polysomal profiling and the detoxification capacity by the CYP450 enzymes activity. Fourth-instar larvae from a mountain stream polluted by agricultural land run-off (NE-Italy) were exposed for 3 h copper concentrations ≤ LC50. We report DNA damage induced by copper, even at sublethal levels, as demonstrated by significant increases in all the comet parameters at concentrations ≥1 mg L-1. By estimating the transcript-specific translational efficiency, we observe a specific up-regulation of CYP4G. Furthermore, the enzymatic activity of CYP450 enzymes is increased at all sublethal copper concentrations, confirming the role of this protein family in the detoxification processes. Surprisingly, the HSP transcripts are up-regulated at the transcriptional level, but these changes are buffered at the translational level suggesting the existence of still unknown post-transcriptional controls that may be connected to survival processes.
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Affiliation(s)
- Paola Bernabò
- Centre for Integrative Biology, University of Trento, Via Sommarive n. 9, 38123, Povo (TN), Trento, Italy; Institute of Biophysics - CNR - Trento Unit, Via Sommarive 18, 38123, Povo, Trento, Italy; Section of Invertebrate Zoology and Hydrobiology, MUSE-Museo delle Scienze, Corso del Lavoro e della Scienza 3, 38123 Trento, Italy
| | - Matteo Gaglio
- Institute of Biophysics - CNR - Trento Unit, Via Sommarive 18, 38123, Povo, Trento, Italy
| | - Francesco Bellamoli
- Section of Invertebrate Zoology and Hydrobiology, MUSE-Museo delle Scienze, Corso del Lavoro e della Scienza 3, 38123 Trento, Italy
| | - Gabriella Viero
- Institute of Biophysics - CNR - Trento Unit, Via Sommarive 18, 38123, Povo, Trento, Italy
| | - Valeria Lencioni
- Section of Invertebrate Zoology and Hydrobiology, MUSE-Museo delle Scienze, Corso del Lavoro e della Scienza 3, 38123 Trento, Italy.
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29
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Del Bel Belluz L, Guidi R, Pateras IS, Levi L, Mihaljevic B, Rouf SF, Wrande M, Candela M, Turroni S, Nastasi C, Consolandi C, Peano C, Tebaldi T, Viero G, Gorgoulis VG, Krejsgaard T, Rhen M, Frisan T. The Typhoid Toxin Promotes Host Survival and the Establishment of a Persistent Asymptomatic Infection. PLoS Pathog 2016; 12:e1005528. [PMID: 27055274 PMCID: PMC4824513 DOI: 10.1371/journal.ppat.1005528] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Accepted: 03/04/2016] [Indexed: 02/06/2023] Open
Abstract
Bacterial genotoxins, produced by several Gram-negative bacteria, induce DNA damage in the target cells. While the responses induced in the host cells have been extensively studied in vitro, the role of these effectors during the course of infection remains poorly characterized. To address this issue, we assessed the effects of the Salmonella enterica genotoxin, known as typhoid toxin, in in vivo models of murine infection. Immunocompetent mice were infected with isogenic S. enterica, serovar Typhimurium (S. Typhimurium) strains, encoding either a functional or an inactive typhoid toxin. The presence of the genotoxic subunit was detected 10 days post-infection in the liver of infected mice. Unexpectedly, its expression promoted the survival of the host, and was associated with a significant reduction of severe enteritis in the early phases of infection. Immunohistochemical and transcriptomic analysis confirmed the toxin-mediated suppression of the intestinal inflammatory response. The presence of a functional typhoid toxin further induced an increased frequency of asymptomatic carriers. Our data indicate that the typhoid toxin DNA damaging activity increases host survival and favours long-term colonization, highlighting a complex cross-talk between infection, DNA damage response and host immune response. These findings may contribute to understand why such effectors have been evolutionary conserved and horizontally transferred among Gram-negative bacteria.
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Affiliation(s)
- Lisa Del Bel Belluz
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Riccardo Guidi
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ioannis S. Pateras
- Department of Histology and Embryology, School of Medicine, University of Athens, Athens, Greece
| | - Laura Levi
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Boris Mihaljevic
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Syed Fazle Rouf
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Marie Wrande
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Marco Candela
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Silvia Turroni
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Claudia Nastasi
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Clarissa Consolandi
- Institute of Biomedical Technologies, Italian National Research Council, Segrate, Milan, Italy
| | - Clelia Peano
- Institute of Biomedical Technologies, Italian National Research Council, Segrate, Milan, Italy
| | - Toma Tebaldi
- Centre for Integrative Biology University of Trento, Trento, Italy
| | | | - Vassilis G. Gorgoulis
- Department of Histology and Embryology, School of Medicine, University of Athens, Athens, Greece
- Biomedical Research Foundation, Academy of Athens, Athens, Greece
- Institute for Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
- Manchester Centre for Cellular Metabolism, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Thorbjørn Krejsgaard
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Mikael Rhen
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Teresa Frisan
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
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30
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Abstract
The translational machinery, i.e., the polysome or polyribosome, is one of the biggest and most complex cytoplasmic machineries in cells. Polysomes, formed by ribosomes, mRNAs, several proteins and non-coding RNAs, represent integrated platforms where translational controls take place. However, while the ribosome has been widely studied, the organization of polysomes is still lacking comprehensive understanding. Thus much effort is required in order to elucidate polysome organization and any novel mechanism of translational control that may be embedded. Atomic force microscopy (AFM) is a type of scanning probe microscopy that allows the acquisition of 3D images at nanoscale resolution. Compared to electron microscopy (EM) techniques, one of the main advantages of AFM is that it can acquire thousands of images both in air and in solution, enabling the sample to be maintained under near physiological conditions without any need for staining and fixing procedures. Here, a detailed protocol for the accurate purification of polysomes from mouse brain and their deposition on mica substrates is described. This protocol enables polysome imaging in air and liquid with AFM and their reconstruction as three-dimensional objects. Complementary to cryo-electron microscopy (cryo-EM), the proposed method can be conveniently used for systematically analyzing polysomes and studying their organization.
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Affiliation(s)
- Lorenzo Lunelli
- Laboratory of Biomolecular Sequence and Structure Analysis for Health, Fondazione Bruno Kessler
| | | | | | - Valentina Vaghi
- Laboratory of Biomolecular Sequence and Structure Analysis for Health, Fondazione Bruno Kessler
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31
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Brina D, Miluzio A, Ricciardi S, Clarke K, Davidsen PK, Viero G, Tebaldi T, Offenhäuser N, Rozman J, Rathkolb B, Neschen S, Klingenspor M, Wolf E, Gailus-Durner V, Fuchs H, Hrabe de Angelis M, Quattrone A, Falciani F, Biffo S. eIF6 coordinates insulin sensitivity and lipid metabolism by coupling translation to transcription. Nat Commun 2015; 6:8261. [PMID: 26383020 PMCID: PMC4595657 DOI: 10.1038/ncomms9261] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 08/04/2015] [Indexed: 02/07/2023] Open
Abstract
Insulin regulates glycaemia, lipogenesis and increases mRNA translation. Cells with reduced eukaryotic initiation factor 6 (eIF6) do not increase translation in response to insulin. The role of insulin-regulated translation is unknown. Here we show that reduction of insulin-regulated translation in mice heterozygous for eIF6 results in normal glycaemia, but less blood cholesterol and triglycerides. eIF6 controls fatty acid synthesis and glycolysis in a cell autonomous fashion. eIF6 acts by exerting translational control of adipogenic transcription factors like C/EBPβ, C/EBPδ and ATF4 that have G/C rich or uORF sequences in their 5' UTR. The outcome of the translational activation by eIF6 is a reshaping of gene expression with increased levels of lipogenic and glycolytic enzymes. Finally, eIF6 levels modulate histone acetylation and amounts of rate-limiting fatty acid synthase (Fasn) mRNA. Since obesity, type 2 diabetes, and cancer require a Fasn-driven lipogenic state, we propose that eIF6 could be a therapeutic target for these diseases.
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Affiliation(s)
- Daniela Brina
- INGM, ‘Romeo ed Enrica Invernizzi', 20122 Milano, Italy
| | | | | | - Kim Clarke
- Centre for Computational Biology and Modeling, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Peter K. Davidsen
- Centre for Computational Biology and Modeling, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Gabriella Viero
- Institute of Biophysics, 38123 Trento, Italy
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Toma Tebaldi
- Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
| | | | - Jan Rozman
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Birgit Rathkolb
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Center Munich, 85764 Neuherberg, Germany
- Institute of Molecular Animal Breeding and Biotechnology, Gene Center, Ludwig-Maximilian-University, 81377 Munich, Germany
| | - Susanne Neschen
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Martin Klingenspor
- Else Kröner-Fresenius Center, Technische Universität München, 85354 Freising, Germany
| | - Eckhard Wolf
- Institute of Molecular Animal Breeding and Biotechnology, Gene Center, Ludwig-Maximilian-University, 81377 Munich, Germany
| | - Valerie Gailus-Durner
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Martin Hrabe de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Center Munich, 85764 Neuherberg, Germany
- Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85354 Freising, Germany
- German Center for Diabetes Research, 85764 Neuherberg, Germany
| | | | - Francesco Falciani
- Centre for Computational Biology and Modeling, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Stefano Biffo
- INGM, ‘Romeo ed Enrica Invernizzi', 20122 Milano, Italy
- Department of Biosciences, University of Milan, 20133 Milan, Italy
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32
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Lauria F, Tebaldi T, Lunelli L, Struffi P, Gatto P, Pugliese A, Brigotti M, Montanaro L, Ciribilli Y, Inga A, Quattrone A, Sanguinetti G, Viero G. RiboAbacus: a model trained on polyribosome images predicts ribosome density and translational efficiency from mammalian transcriptomes. Nucleic Acids Res 2015; 43:e153. [PMID: 26240374 PMCID: PMC4678843 DOI: 10.1093/nar/gkv781] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 07/20/2015] [Indexed: 01/14/2023] Open
Abstract
Fluctuations in mRNA levels only partially contribute to determine variations in mRNA availability for translation, producing the well-known poor correlation between transcriptome and proteome data. Recent advances in microscopy now enable researchers to obtain high resolution images of ribosomes on transcripts, providing precious snapshots of translation in vivo. Here we propose RiboAbacus, a mathematical model that for the first time incorporates imaging data in a predictive model of transcript-specific ribosome densities and translational efficiencies. RiboAbacus uses a mechanistic model of ribosome dynamics, enabling the quantification of the relative importance of different features (such as codon usage and the 5′ ramp effect) in determining the accuracy of predictions. The model has been optimized in the human Hek-293 cell line to fit thousands of images of human polysomes obtained by atomic force microscopy, from which we could get a reference distribution of the number of ribosomes per mRNA with unmatched resolution. After validation, we applied RiboAbacus to three case studies of known transcriptome-proteome datasets for estimating the translational efficiencies, resulting in an increased correlation with corresponding proteomes. RiboAbacus is an intuitive tool that allows an immediate estimation of crucial translation properties for entire transcriptomes, based on easily obtainable transcript expression levels.
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Affiliation(s)
- Fabio Lauria
- Institute of Biophysics, CNR Unit at Trento, Via alla Cascata, 56/C-38123 Povo (TN), Italy
| | - Toma Tebaldi
- Laboratory of Translational Genomics, Centre for Integrative Biology, Via delle Regole, 101-38123 Mattarello (TN), Italy
| | - Lorenzo Lunelli
- Laboratory of Biomolecular Sequence and Structure Analysis for Health, Fondazione Bruno Kessler, Via Sommarive, 18-38123 Povo (TN), Italy
| | - Paolo Struffi
- Laboratory of Translational Genomics, Centre for Integrative Biology, Via delle Regole, 101-38123 Mattarello (TN), Italy
| | - Pamela Gatto
- Laboratory of Translational Genomics, Centre for Integrative Biology, Via delle Regole, 101-38123 Mattarello (TN), Italy
| | - Andrea Pugliese
- Mathematics Department, University of Trento, Via Sommarive, 14-38123 Povo (TN), Italy
| | - Maurizio Brigotti
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Via S. Giacomo, 14-40126 Bologna, Italy
| | - Lorenzo Montanaro
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Via S. Giacomo, 14-40126 Bologna, Italy
| | - Yari Ciribilli
- Laboratory of Transcriptional Networks, Centre for Integrative Biology, Via delle Regole, 101-38123 Mattarello (TN), Italy
| | - Alberto Inga
- Laboratory of Transcriptional Networks, Centre for Integrative Biology, Via delle Regole, 101-38123 Mattarello (TN), Italy
| | - Alessandro Quattrone
- Laboratory of Translational Genomics, Centre for Integrative Biology, Via delle Regole, 101-38123 Mattarello (TN), Italy
| | - Guido Sanguinetti
- School of Informatics, University of Edinburgh, 10 Crichton Street, Edinburgh, Midlothian EH8 9AB, UK
| | - Gabriella Viero
- Institute of Biophysics, CNR Unit at Trento, Via alla Cascata, 56/C-38123 Povo (TN), Italy
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Bernabò P, Lunelli L, Quattrone A, Jousson O, Lencioni V, Viero G. Studying translational control in non-model stressed organisms by polysomal profiling. J Insect Physiol 2015; 76:30-35. [PMID: 25796968 DOI: 10.1016/j.jinsphys.2015.03.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 01/30/2015] [Accepted: 03/15/2015] [Indexed: 06/04/2023]
Abstract
In stressed organisms, strategic proteins are selectively translated even if the global process of protein synthesis is compromised. The determination of protein concentrations in tissues of non-model organisms (thus with limited genomic information) is challenging due to the absence of specific antibodies. Moreover, estimating protein levels quantifying transcriptional responses may be misleading, because translational control mechanisms uncouple protein and mRNAs abundances. Translational control is increasingly recognized as a hub where regulation of gene expression converges to shape proteomes, but it is almost completely overlooked in molecular ecology studies. An interesting approach to study translation and its control mechanisms is the analysis of variations of gene-specific translational efficiencies by quantifying mRNAs associated to ribosomes. In this paper, we propose a robust and streamlined pipeline for purifying ribosome-associated mRNAs and calculating global and gene-specific translation efficiencies from non-model insect's species. This method might found applications in molecular ecology to study responses to environmental stressors in non-model organisms.
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Affiliation(s)
- Paola Bernabò
- Institute of Biophysics, CNR Unit at Trento, Italy; Centre for Integrative Biology, Mattarello, Trento, Italy; Section of Invertebrate Zoology and Hydrobiology, MUSE-Museo delle Scienze, Trento, Italy
| | - Lorenzo Lunelli
- Laboratory of Biomolecular Sequence and Structure Analysis for Health, Fondazione Bruno Kessler, Trento, Italy
| | | | | | - Valeria Lencioni
- Section of Invertebrate Zoology and Hydrobiology, MUSE-Museo delle Scienze, Trento, Italy
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Viero G, Lunelli L, Passerini A, Bianchini P, Gilbert RJ, Bernabò P, Tebaldi T, Diaspro A, Pederzolli C, Quattrone A. Three distinct ribosome assemblies modulated by translation are the building blocks of polysomes. ACTA ACUST UNITED AC 2015; 208:581-96. [PMID: 25713412 PMCID: PMC4347638 DOI: 10.1083/jcb.201406040] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Translation is increasingly recognized as a central control layer of gene expression in eukaryotic cells. The overall organization of mRNA and ribosomes within polysomes, as well as the possible role of this organization in translation are poorly understood. Here we show that polysomes are primarily formed by three distinct classes of ribosome assemblies. We observe that these assemblies can be connected by naked RNA regions of the transcript. We show that the relative proportions of the three classes of ribosome assemblies reflect, and probably dictate, the level of translational activity. These results reveal the existence of recurrent supra-ribosomal building blocks forming polysomes and suggest the presence of unexplored translational controls embedded in the polysome structure.
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Affiliation(s)
- Gabriella Viero
- Institute of Biophysics, National Research Council (CNR) Unit at Trento, 38123 Povo, Italy Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, 38123 Mattarello, Italy
| | - Lorenzo Lunelli
- Laboratory of Biomolecular Sequence and Structure Analysis for Health, Fondazione Bruno Kessler, 38123 Povo, Italy
| | - Andrea Passerini
- Department of Information Engineering and Computer Science, University of Trento, 38123 Povo, Italy
| | - Paolo Bianchini
- Nanophysics Department, Italian Institute of Technology, 16163 Genova, Italy
| | - Robert J Gilbert
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, England, UK
| | - Paola Bernabò
- Institute of Biophysics, National Research Council (CNR) Unit at Trento, 38123 Povo, Italy
| | - Toma Tebaldi
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, 38123 Mattarello, Italy
| | - Alberto Diaspro
- Nanophysics Department, Italian Institute of Technology, 16163 Genova, Italy
| | - Cecilia Pederzolli
- Laboratory of Biomolecular Sequence and Structure Analysis for Health, Fondazione Bruno Kessler, 38123 Povo, Italy
| | - Alessandro Quattrone
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, 38123 Mattarello, Italy
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Wang Y, Sun H, Du W, Blanzieri E, Viero G, Xu Y, Liang Y. Identification of essential proteins based on ranking edge-weights in protein-protein interaction networks. PLoS One 2014; 9:e108716. [PMID: 25268881 PMCID: PMC4182551 DOI: 10.1371/journal.pone.0108716] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 09/03/2014] [Indexed: 12/02/2022] Open
Abstract
Essential proteins are those that are indispensable to cellular survival and development. Existing methods for essential protein identification generally rely on knock-out experiments and/or the relative density of their interactions (edges) with other proteins in a Protein-Protein Interaction (PPI) network. Here, we present a computational method, called EW, to first rank protein-protein interactions in terms of their Edge Weights, and then identify sub-PPI-networks consisting of only the highly-ranked edges and predict their proteins as essential proteins. We have applied this method to publicly-available PPI data on Saccharomyces cerevisiae (Yeast) and Escherichia coli (E. coli) for essential protein identification, and demonstrated that EW achieves better performance than the state-of-the-art methods in terms of the precision-recall and Jackknife measures. The highly-ranked protein-protein interactions by our prediction tend to be biologically significant in both the Yeast and E. coli PPI networks. Further analyses on systematically perturbed Yeast and E. coli PPI networks through randomly deleting edges demonstrate that the proposed method is robust and the top-ranked edges tend to be more associated with known essential proteins than the lowly-ranked edges.
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Affiliation(s)
- Yan Wang
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
- Department of Information and Communication Technology, University of Trento, Povo, Italy
- Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
| | - Huiyan Sun
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
| | - Wei Du
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
| | - Enrico Blanzieri
- Department of Information and Communication Technology, University of Trento, Povo, Italy
- * E-mail: (YCL); (EB)
| | - Gabriella Viero
- Institute of Biophysics, National Research Council, University of Trento, Povo, Italy
| | - Ying Xu
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
- Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
| | - Yanchun Liang
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
- * E-mail: (YCL); (EB)
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Corrado G, Tebaldi T, Bertamini G, Costa F, Quattrone A, Viero G, Passerini A. PTRcombiner: mining combinatorial regulation of gene expression from post-transcriptional interaction maps. BMC Genomics 2014; 15:304. [PMID: 24758252 PMCID: PMC4234518 DOI: 10.1186/1471-2164-15-304] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 04/02/2014] [Indexed: 02/07/2023] Open
Abstract
Background The progress in mapping RNA-protein and RNA-RNA interactions at the transcriptome-wide level paves the way to decipher possible combinatorial patterns embedded in post-transcriptional regulation of gene expression. Results Here we propose an innovative computational tool to extract clusters of mRNA trans-acting co-regulators (RNA binding proteins and non-coding RNAs) from pairwise interaction annotations. In addition the tool allows to analyze the binding site similarity of co-regulators belonging to the same cluster, given their positional binding information. The tool has been tested on experimental collections of human and yeast interactions, identifying modules that coordinate functionally related messages. Conclusions This tool is an original attempt to uncover combinatorial patterns using all the post-transcriptional interaction data available so far. PTRcombiner is available at http://disi.unitn.it/~passerini/software/PTRcombiner/.
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Affiliation(s)
| | | | | | | | | | - Gabriella Viero
- Department of Information Engineering and Computer Science (DISI), University of Trento, 38123 Trento, Italy.
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Abstract
Post-transcriptional modifications of the 3'-ends of RNA molecules have a profound impact on their stability and processing in the cell. Uridylation, the addition of uridines to 3'-ends, has recently been found to be an important regulatory signal to stabilize the tagged molecules or to direct them toward degradation. Simple and cost-effective methods for the detection of this post-transcriptional modification are not yet available. Here, we demonstrate the selective and transient binding of 3'-uridylated ssRNAs inside the β barrel of the staphylococcal α-hemolysin (αHL) nanopore and investigate the molecular basis of uridine recognition by the pore. We show the discrimination of 3'-oligouridine tails on the basis of their lengths and propose the αHL nanopore as a useful sensor for this biologically relevant RNA modification.
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Affiliation(s)
- Massimiliano Clamer
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
- Laboratory of Translational Genomics, Center for Integrative Biology, University of Trento, Via delle Regole, 101 38123 Mattarello (TN), Italy
| | - Lajos Höfler
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Ellina Mikhailova
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Gabriella Viero
- Laboratory of Translational Genomics, Center for Integrative Biology, University of Trento, Via delle Regole, 101 38123 Mattarello (TN), Italy
- Institute of Biophysics, CNR, Via alla Cascata 56/C, 38123 (Povo) Trento, Italy
| | - Hagan Bayley
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
- Corresponding Author: Hagan Bayley
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Abstract
Summary: High-throughput technologies have led to an explosion of genomic data available for automated analysis. The consequent possibility to simultaneously sample multiple layers of variation along the gene expression flow requires computational methods integrating raw information from different ‘-omics’. It has been recently demonstrated that translational control is a widespread phenomenon, with profound and still underestimated regulation capabilities. Although detecting changes in the levels of total messenger RNAs (mRNAs; the transcriptome), of polysomally loaded mRNAs (the translatome) and of proteins (the proteome) is experimentally feasible in a high-throughput way, the integration of these levels is still far from being robustly approached. Here we introduce tRanslatome, a new R/Bioconductor package, which is a complete platform for the simultaneous pairwise analysis of transcriptome, translatome and proteome data. The package includes most of the available statistical methods developed for the analysis of high-throughput data, allowing the parallel comparison of differentially expressed genes and the corresponding differentially enriched biological themes. Notably, it also enables the prediction of translational regulatory elements on mRNA sequences. The utility of this tool is demonstrated with two case studies. Availability and implementation: tRanslatome is available in Bioconductor. Contact: t.tebaldi@unitn.it Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Toma Tebaldi
- Laboratory of Translational Genomics - Centre for Integrative Biology, University of Trento, Via delle Regole 101, 38123 Mattarello (TN) and Institute of Biophysics CNR - Via alla Cascata 56/C, 38123 Povo (TN), Italy
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Rojko N, Kristan KČ, Viero G, Žerovnik E, Maček P, Dalla Serra M, Anderluh G. Membrane damage by an α-helical pore-forming protein, Equinatoxin II, proceeds through a succession of ordered steps. J Biol Chem 2013; 288:23704-15. [PMID: 23803608 DOI: 10.1074/jbc.m113.481572] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Actinoporin equinatoxin II (EqtII) is an archetypal example of α-helical pore-forming toxins that porate cellular membranes by the use of α-helices. Previous studies proposed several steps in the pore formation: binding of monomeric protein onto the membrane, followed by oligomerization and insertion of the N-terminal α-helix into the lipid bilayer. We studied these separate steps with an EqtII triple cysteine mutant. The mutant was engineered to monitor the insertion of the N terminus into the lipid bilayer by labeling Cys-18 with a fluorescence probe and at the same time to control the flexibility of the N-terminal region by the disulfide bond formed between cysteines introduced at positions 8 and 69. The insertion of the N terminus into the membrane proceeded shortly after the toxin binding and was followed by oligomerization. The oxidized, non-lytic, form of the mutant was still able to bind to membranes and oligomerize at the same level as the wild-type or the reduced form. However, the kinetics of the N-terminal helix insertion, the release of calcein from erythrocyte ghosts, and hemolysis of erythrocytes was much slower when membrane-bound oxidized mutant was reduced by the addition of the reductant. Results show that the N-terminal region needs to be inserted in the lipid membrane before the oligomerization into the final pore and imply that there is no need for a stable prepore formation. This is different from β-pore-forming toxins that often form β-barrel pores via a stable prepore complex.
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Affiliation(s)
- Nejc Rojko
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000 Ljubljana, Slovenia
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Abstract
The life of an mRNA molecule begins with transcription and ultimately ends in degradation. In the course of its life, however, mRNA is examined, modified in various ways and transported before eventually being translated into proteins. All these processes are performed by proteins and non-coding RNAs whose complex interplay in the cell contributes to determining the proteome changes and the phenotype of cells. On May 23‒26, 2012, over 150 scientists from around the world convened in the sunny shores of Riva del Garda, Italy, for the workshop entitled: "mRNA fate: Life and Death of mRNA in the Cytoplasm." Sessions included mRNA trafficking, mRNA translational control, RNA metabolism and disease, RNA-protein structures and systems biology of RNA. This report highlights some of the prominent and recurring themes at the meeting and emerging arenas of future research.
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Alessandrini A, Viero G, Dalla Serra M, Prévost G, Facci P. γ-Hemolysin oligomeric structure and effect of its formation on supported lipid bilayers: an AFM investigation. Biochim Biophys Acta 2012; 1828:405-11. [PMID: 23036932 DOI: 10.1016/j.bbamem.2012.09.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 09/05/2012] [Accepted: 09/25/2012] [Indexed: 11/28/2022]
Abstract
γ-Hemolysins are bicomponent β-barrel pore forming toxins produced by Staphylococcus aureus as water-soluble monomers, which assemble into oligomeric pores on the surface of lipid bilayers. Here, after investigating the oligomeric structure of γ-hemolysins on supported lipid bilayers (SLBs) by atomic force microscopy (AFM), we studied the effect produced by this toxin on the structure of SLBs. We found that oligomeric structures with different number of monomers can assemble on the lipid bilayer being the octameric form the stablest one. Moreover, in this membrane model we found that γ-hemolysins can form clusters of oligomers inducing a curvature in the lipid bilayer, which could probably enhance the aggressiveness of these toxins at high concentrations.
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Affiliation(s)
- Andrea Alessandrini
- Centro S3, CNR-Istituto di Nanoscienze, Via Campi 213/A, 41125 Modena, Italy.
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Tebaldi T, Re A, Viero G, Pegoretti I, Passerini A, Blanzieri E, Quattrone A. Widespread uncoupling between transcriptome and translatome variations after a stimulus in mammalian cells. BMC Genomics 2012; 13:220. [PMID: 22672192 PMCID: PMC3441405 DOI: 10.1186/1471-2164-13-220] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 06/06/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The classical view on eukaryotic gene expression proposes the scheme of a forward flow for which fluctuations in mRNA levels upon a stimulus contribute to determine variations in mRNA availability for translation. Here we address this issue by simultaneously profiling with microarrays the total mRNAs (the transcriptome) and the polysome-associated mRNAs (the translatome) after EGF treatment of human cells, and extending the analysis to other 19 different transcriptome/translatome comparisons in mammalian cells following different stimuli or undergoing cell programs. RESULTS Triggering of the EGF pathway results in an early induction of transcriptome and translatome changes, but 90% of the significant variation is limited to the translatome and the degree of concordant changes is less than 5%. The survey of other 19 different transcriptome/translatome comparisons shows that extensive uncoupling is a general rule, in terms of both RNA movements and inferred cell activities, with a strong tendency of translation-related genes to be controlled purely at the translational level. By different statistical approaches, we finally provide evidence of the lack of dependence between changes at the transcriptome and translatome levels. CONCLUSIONS We propose a model of diffused independency between variation in transcript abundances and variation in their engagement on polysomes, which implies the existence of specific mechanisms to couple these two ways of regulating gene expression.
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Affiliation(s)
- Toma Tebaldi
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, 38123 Trento, Italy
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Moncini S, Salvi A, Zuccotti P, Viero G, Quattrone A, Barlati S, De Petro G, Venturin M, Riva P. The role of miR-103 and miR-107 in regulation of CDK5R1 expression and in cellular migration. PLoS One 2011; 6:e20038. [PMID: 21625387 PMCID: PMC3100319 DOI: 10.1371/journal.pone.0020038] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Accepted: 04/24/2011] [Indexed: 11/26/2022] Open
Abstract
CDK5R1 encodes p35, a specific activator of the serine/threonine kinase CDK5, which plays crucial roles in CNS development and maintenance. CDK5 activity strongly depends on p35 levels and p35/CDK5 misregulation is deleterious for correct CNS function, suggesting that a tightly controlled regulation of CDK5R1 expression is needed for proper CDK5 activity. Accordingly, CDK5R1 expression was demonstrated to be controlled at both transcriptional and post-transcriptional levels, but a possible regulation through microRNAs (miRNAs) has never been investigated. We predicted, within the large CDK5R1 3′UTR several miRNA target sites. Among them, we selected for functional studies miR-103 and miR-107, whose expression has shown a strong inverse correlation with p35 levels in different cell lines. A significant reduction of CDK5R1 mRNA and p35 levels was observed after transfection of SK-N-BE neuroblastoma cells with the miR-103 or miR-107 precursor (pre-miR-103 or pre-miR-107). Conversely, p35 levels significantly increased following transfection of the corresponding antagonists (anti-miR-103 or anti-miR-107). Moreover, the level of CDK5R1 transcript shifts from the polysomal to the subpolysomal mRNA fraction after transfection with pre-miR-107 and, conversely, from the subpolysomal to the polysolmal mRNA fraction after transfection with anti-miR-107, suggesting a direct action on translation efficiency. We demonstrate, by means of luciferase assays, that miR-103 and miR-107 are able to directly interact with the CDK5R1 3′-UTR, in correspondence of a specific target site. Finally, miR-103 and miR-107 overexpression, as well as CDK5R1 silencing, caused a reduction in SK-N-BE migration ability, indicating that these miRNAs affect neuronal migration by modulating CDK5R1 expression. These findings indicate that miR-103 and miR-107 regulate CDK5R1 expression, allowing us to hypothesize that a miRNA-mediated mechanism may influence CDK5 activity and the associated molecular pathways.
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Affiliation(s)
- Silvia Moncini
- Department of Biology and Genetics for Medical Sciences, University of Milan, Milan, Italy
| | - Alessandro Salvi
- Division of Biology and Genetics, Department of Biomedical Sciences and Biotechnology, University of Brescia, Brescia, Italy
| | - Paola Zuccotti
- Department of Biology and Genetics for Medical Sciences, University of Milan, Milan, Italy
| | - Gabriella Viero
- Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
- Institute of Biophysics, National Research Council, Trento, Italy
| | | | - Sergio Barlati
- Division of Biology and Genetics, Department of Biomedical Sciences and Biotechnology, University of Brescia, Brescia, Italy
| | - Giuseppina De Petro
- Division of Biology and Genetics, Department of Biomedical Sciences and Biotechnology, University of Brescia, Brescia, Italy
| | - Marco Venturin
- Department of Biology and Genetics for Medical Sciences, University of Milan, Milan, Italy
| | - Paola Riva
- Department of Biology and Genetics for Medical Sciences, University of Milan, Milan, Italy
- * E-mail:
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Praper T, Sonnen A, Viero G, Kladnik A, Froelich CJ, Anderluh G, Dalla Serra M, Gilbert RJC. Human perforin employs different avenues to damage membranes. J Biol Chem 2010; 286:2946-55. [PMID: 20889983 PMCID: PMC3024789 DOI: 10.1074/jbc.m110.169417] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Perforin (PFN) is a pore-forming protein produced by cytotoxic lymphocytes that aids in the clearance of tumor or virus-infected cells by a mechanism that involves the formation of transmembrane pores. The properties of PFN pores and the mechanism of their assembly remain unclear. Here, we studied pore characteristics by functional and structural methods to show that perforin forms pores more heterogeneous than anticipated. Planar lipid bilayer experiments indicate that perforin pores exhibit a broad range of conductances, from 0.15 to 21 nanosiemens. In comparison with large pores that possessed low noise and remained stably open, small pores exhibited high noise and were very unstable. Furthermore, the opening step and the pore size were dependent on the lipid composition of the membrane. The heterogeneity in pore sizes was confirmed with cryo-electron microscopy and showed a range of sizes matching that observed in the conductance measurements. Furthermore, two different membrane-bound PFN conformations were observed, interpreted as pre-pore and pore states of the protein. The results collectively indicate that PFN forms heterogeneous pores through a multistep mechanism and provide a new paradigm for understanding the range of different effects of PFN and related membrane attack complex/perforin domain proteins observed in vivo and in vitro.
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Affiliation(s)
- Tilen Praper
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000 Ljubljana, Slovenia
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Abstract
Actinoporins are effective pore-forming toxins produced by sea anemones. These extremely potent, basic 20 kDa proteins readily form pores in membranes that contain sphingomyelin. Much has been learned about the molecular basis of their pore-forming mechanism in recent years. Pore formation is a multi-step process that involves recognition of membrane sphingomyelin, firm binding to the membrane accompanied by the transfer of the N-terminal region to the lipid-water interface and finally pore formation after oligomerisation of three to four monomers. The final conductive pathway is formed by amphipathic alpha-helices, hence actinoporins are an important example of so-called alpha-helical pore-forming toxins. Actinoporins have become useful model proteins to study protein-membrane interactions, specific recognition of lipids in the membrane, and protein oligomerisation in the lipid milieu. Recent sequence and structural data of proteins similar to actinoporins indicate that they are not a unique family restricted to sea anemones as was long believed. An AF domain superfamily (abbreviated from actinoporin-like proteins and fungal fruit-body lectins) was defined and shown to contain members from three animal and two plant phyla. On the basis of functional properties of some members we hypothesise that AF domain proteins are peripheral membrane proteins. Finally, ability of actinoporins to form transmembrane pores has been exploited in some novel biomedical applications.
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Affiliation(s)
- Katarina Crnigoj Kristan
- Department of Biology, Biotechnical faculty, University of Ljubljana, Vecna pot 111, 1000 Ljubljana, Slovenia
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Rabzelj S, Viero G, Gutiérrez-Aguirre I, Turk V, Dalla Serra M, Anderluh G, Žerovnik E. Interaction with model membranes and pore formation by human stefin B - studying the native and prefibrillar states. FEBS J 2008; 275:2455-66. [DOI: 10.1111/j.1742-4658.2008.06390.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Kristan K, Viero G, Macek P, Dalla Serra M, Anderluh G. The equinatoxin N-terminus is transferred across planar lipid membranes and helps to stabilize the transmembrane pore. FEBS J 2006; 274:539-50. [PMID: 17229155 DOI: 10.1111/j.1742-4658.2006.05608.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Equinatoxin II is a cytolytic protein isolated from the sea anemone Actinia equina. It is a member of the actinoporins, a family of eukaryotic pore-forming toxins with a unique mechanism of pore formation. Equinatoxin II is a 20 kDa cysteineless protein, with sphingomyelin-dependent activity. Recent studies showed that the N-terminal region of the molecule requires conformational flexibility during pore formation. An understanding of the N-terminal position in the final pore and its role in membrane insertion and pore stability is essential to define the precise molecular mechanism of pore formation. The formation of pores and their electrophysiologic characteristics were studied with planar lipid membranes. We show that amino acids at positions 1 and 3 of equinatoxin II are exposed to the lumen of the pore. Moreover, sulfhydryl reagents and a hexa-histidine tag attached to the N-terminus revealed that the N-terminus of the toxin extends through the pore to the other (trans) side of the membrane and that negatively charged residues inside the pore are crucial to define the electrophysiologic characteristics of the channel. Finally, we detected a new, less stable, state with a lower conductance by using a deletion mutant in which the first five N-terminal amino acids were removed. We propose that the first five amino acids help to anchor the amphipathic helix on the trans side of the membrane and consequently stabilize the final transmembrane pore.
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Affiliation(s)
- Katarina Kristan
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
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Dalla Serra M, Coraiola M, Viero G, Comai M, Potrich C, Ferreras M, Baba-Moussa L, Colin DA, Menestrina G, Bhakdi S, Prévost G. Staphylococcus aureus bicomponent gamma-hemolysins, HlgA, HlgB, and HlgC, can form mixed pores containing all components. J Chem Inf Model 2006; 45:1539-45. [PMID: 16309251 DOI: 10.1021/ci050175y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Staphylococcal gamma-hemolysins are bicomponent toxins forming a protein family with leucocidins and alpha-toxin. Two active toxins (AB and CB) can be formed combining one of the class-S components, HlgA or HlgC, with the class-F component HlgB. These two gamma-hemolysins form pores with marked similarities to alpha-toxin in terms of conductance, nonlinearity of the current-voltage curve, and channel stability in the open state. AB and CB pores, however, are cation-selective, whereas alpha-toxin is anion-selective. gamma-Hemolysins' pores are hetero-oligomers formed by three or four copies of each component (indicated as 3A3B and 3C3B or 4A4B and 4C4B). Point mutants located on a beta-strand of the class-S component that forms part of the protomer-protomer contact region can prevent oligomer assembly. Interestingly, these mutants inhibit growth of pores formed not only by their natural components but also by nonstandard components. This lead to the hypothesis that mixed ABC pores could also be formed. By studying the conductance of pores, assembled in the presence of all three components (in different ratios), it was observed that the magnitudes expected for mixed pores were, indeed, present. We conclude that the gamma-hemolysin/leucocidin bicomponent toxin family may form a larger than expected number of active toxins by cross-combining various S and F components.
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Affiliation(s)
- Mauro Dalla Serra
- Istituto Trentino di Cultura-Consiglio Nazionale delle Ricerche (ITC-CNR) Istituto di Biofisica, Via Sommarive 18, I-38050 Povo (Trento), Italy.
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Joubert O, Viero G, Keller D, Martinez E, Colin D, Monteil H, Mourey L, Dalla serra M, Prévost G. Engineered covalent leucotoxin heterodimers form functional pores: insights into S-F interactions. Biochem J 2006; 396:381-9. [PMID: 16494579 PMCID: PMC1462717 DOI: 10.1042/bj20051878] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The staphylococcal alpha-toxin and bipartite leucotoxins belong to a single family of pore-forming toxins that are rich in beta-strands, although the stoichiometry and electrophysiological characteristics of their pores are different. The different known structures show a common beta-sandwich domain that plays a key role in subunit-subunit interactions, which could be targeted to inhibit oligomerization of these toxins. We used several cysteine mutants of both HlgA (gamma-haemolysin A) and HlgB (gamma-haemolysin B) to challenge 20 heterodimers linked by disulphide bridges. A new strategy was developed in order to obtain a good yield for S-S bond formation and dimer stabilization. Functions of the pores formed by 14 purified dimers were investigated on model membranes, i.e. planar lipid bilayers and large unilamellar vesicles, and on target cells, i.e. rabbit and human red blood cells and polymorphonuclear neutrophils. We observed that dimers HlgA T28C-HlgB N156C and HlgA T21C-HlgB T157C form pores with similar characteristics as the wild-type toxin, thus suggesting that the mutated residues are facing one another, allowing pore formation. Our results also confirm the octameric stoichiometry of the leucotoxin pores, as well as the parity of the two monomers in the pore. Correctly assembled heterodimers thus constitute the minimal functional unit of leucotoxins. We propose amino acids involved in interactions at one of the two interfaces for an assembled leucotoxin.
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Affiliation(s)
- Olivier Joubert
- *Laboratoire de Physiopathologie et d'Antibiologie Microbiennes, EA 3432, Institut de Bactériologie de la Faculté de Médecine (Université Louis Pasteur), Hôpitaux Universitaires de Strasbourg, 3 rue Koeberlé, F-67000 Strasbourg, France
| | - Gabriella Viero
- †ITC and CNR-IBF Unit at Trento, 18 Via Sommarive, I-38050 Povo (Trento), Italy
| | - Daniel Keller
- *Laboratoire de Physiopathologie et d'Antibiologie Microbiennes, EA 3432, Institut de Bactériologie de la Faculté de Médecine (Université Louis Pasteur), Hôpitaux Universitaires de Strasbourg, 3 rue Koeberlé, F-67000 Strasbourg, France
| | - Eric Martinez
- *Laboratoire de Physiopathologie et d'Antibiologie Microbiennes, EA 3432, Institut de Bactériologie de la Faculté de Médecine (Université Louis Pasteur), Hôpitaux Universitaires de Strasbourg, 3 rue Koeberlé, F-67000 Strasbourg, France
| | - Didier A. Colin
- *Laboratoire de Physiopathologie et d'Antibiologie Microbiennes, EA 3432, Institut de Bactériologie de la Faculté de Médecine (Université Louis Pasteur), Hôpitaux Universitaires de Strasbourg, 3 rue Koeberlé, F-67000 Strasbourg, France
| | - Henri Monteil
- *Laboratoire de Physiopathologie et d'Antibiologie Microbiennes, EA 3432, Institut de Bactériologie de la Faculté de Médecine (Université Louis Pasteur), Hôpitaux Universitaires de Strasbourg, 3 rue Koeberlé, F-67000 Strasbourg, France
| | - Lionel Mourey
- ‡Groupe de Biophysique Structurale, Département Mécanismes Moléculaires des Infections Mycobactériennes, CNRS-IPBS UMR 5089, 205 route de Narbonne, F-31077 Toulouse Cedex, France
| | - Mauro Dalla serra
- †ITC and CNR-IBF Unit at Trento, 18 Via Sommarive, I-38050 Povo (Trento), Italy
| | - Gilles Prévost
- *Laboratoire de Physiopathologie et d'Antibiologie Microbiennes, EA 3432, Institut de Bactériologie de la Faculté de Médecine (Université Louis Pasteur), Hôpitaux Universitaires de Strasbourg, 3 rue Koeberlé, F-67000 Strasbourg, France
- To whom correspondence should be addressed (email )
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Viero G, Cunaccia R, Prévost G, Werner S, Monteil H, Keller D, Joubert O, Menestrina G, Dalla Serra M. Homologous versus heterologous interactions in the bicomponent staphylococcal gamma-haemolysin pore. Biochem J 2006; 394:217-25. [PMID: 16241903 PMCID: PMC1386019 DOI: 10.1042/bj20051210] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Staphylococcal gamma-haemolysin HlgA-HlgB forms a beta-barrel transmembrane pore in cells and in model membranes. The pore is formed by the oligomerization of two different proteins and a still debated number of monomers. To clarify the topology of the pore, we have mutated single residues - placed near the right and left interfaces of each monomer into cysteine. The mutants were labelled with fluorescent probes, forming a donor-acceptor pair for FRET (fluorescence resonance energy transfer). Heterologous couples (labelled on complementary left and right interfaces) displayed a marked FRET, suggesting extensive HlgA-HlgB or HlgB-HlgA contacts. Heterologous control couples (with both components labelled on the same side) showed absent or low FRET. We found the same result for the homologous couple formed by HlgA [i.e. HlgA-HlgA in the presence of wt (wild-type) HlgB]. The homologous HlgB couple (HlgB-HlgB labelled on left and right interfaces and in the presence of wt HlgA) displayed a transient, declining FRET, which may indicate fast formation of an intermediate that is consumed during pore formation. We conclude that bicomponent pores are assembled by alternating heterologous monomers.
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Affiliation(s)
- Gabriella Viero
- *Istituto Trentino di Cultura (ITC) and Consiglio Nazionale delle Ricerche (CNR), Istituto di Biofisica, Sezione di Trento, Via Sommarive 18, I-38050 Povo (TN), Italy
| | - Romina Cunaccia
- *Istituto Trentino di Cultura (ITC) and Consiglio Nazionale delle Ricerche (CNR), Istituto di Biofisica, Sezione di Trento, Via Sommarive 18, I-38050 Povo (TN), Italy
| | - Gilles Prévost
- †Institut de Bactériologie de la Faculté de Médecine, UPRES EA-3432, ULP-HUS, 3 rue Koeberlé, F-67000 Strasbourg, France
| | - Sandra Werner
- †Institut de Bactériologie de la Faculté de Médecine, UPRES EA-3432, ULP-HUS, 3 rue Koeberlé, F-67000 Strasbourg, France
| | - Henri Monteil
- †Institut de Bactériologie de la Faculté de Médecine, UPRES EA-3432, ULP-HUS, 3 rue Koeberlé, F-67000 Strasbourg, France
| | - Daniel Keller
- †Institut de Bactériologie de la Faculté de Médecine, UPRES EA-3432, ULP-HUS, 3 rue Koeberlé, F-67000 Strasbourg, France
| | - Olivier Joubert
- †Institut de Bactériologie de la Faculté de Médecine, UPRES EA-3432, ULP-HUS, 3 rue Koeberlé, F-67000 Strasbourg, France
| | - Gianfranco Menestrina
- *Istituto Trentino di Cultura (ITC) and Consiglio Nazionale delle Ricerche (CNR), Istituto di Biofisica, Sezione di Trento, Via Sommarive 18, I-38050 Povo (TN), Italy
| | - Mauro Dalla Serra
- *Istituto Trentino di Cultura (ITC) and Consiglio Nazionale delle Ricerche (CNR), Istituto di Biofisica, Sezione di Trento, Via Sommarive 18, I-38050 Povo (TN), Italy
- To whom correspondence should be addressed (email )
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