1
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Ravindra NG, Alfajaro MM, Gasque V, Huston NC, Wan H, Szigeti-Buck K, Yasumoto Y, Greaney AM, Habet V, Chow RD, Chen JS, Wei J, Filler RB, Wang B, Wang G, Niklason LE, Montgomery RR, Eisenbarth SC, Chen S, Williams A, Iwasaki A, Horvath TL, Foxman EF, Pierce RW, Pyle AM, van Dijk D, Wilen CB. Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium identifies target cells, alterations in gene expression, and cell state changes. PLoS Biol 2021; 19:e3001143. [PMID: 33730024 PMCID: PMC8007021 DOI: 10.1371/journal.pbio.3001143] [Citation(s) in RCA: 143] [Impact Index Per Article: 47.7] [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: 09/14/2020] [Revised: 03/29/2021] [Accepted: 02/08/2021] [Indexed: 01/21/2023] Open
Abstract
There are currently limited Food and Drug Administration (FDA)-approved drugs and vaccines for the treatment or prevention of Coronavirus Disease 2019 (COVID-19). Enhanced understanding of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection and pathogenesis is critical for the development of therapeutics. To provide insight into viral replication, cell tropism, and host-viral interactions of SARS-CoV-2, we performed single-cell (sc) RNA sequencing (RNA-seq) of experimentally infected human bronchial epithelial cells (HBECs) in air-liquid interface (ALI) cultures over a time course. This revealed novel polyadenylated viral transcripts and highlighted ciliated cells as a major target at the onset of infection, which we confirmed by electron and immunofluorescence microscopy. Over the course of infection, the cell tropism of SARS-CoV-2 expands to other epithelial cell types including basal and club cells. Infection induces cell-intrinsic expression of type I and type III interferons (IFNs) and interleukin (IL)-6 but not IL-1. This results in expression of interferon-stimulated genes (ISGs) in both infected and bystander cells. This provides a detailed characterization of genes, cell types, and cell state changes associated with SARS-CoV-2 infection in the human airway.
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Affiliation(s)
- Neal G. Ravindra
- Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School Medicine, New Haven, Connecticut, United States of America
- Department of Computer Science, Yale University, New Haven, Connecticut, United States of America
| | - Mia Madel Alfajaro
- Department of Laboratory Medicine, Yale University, New Haven, Connecticut, United States of America
- Department of Immunobiology, Yale University, New Haven, Connecticut, United States of America
| | - Victor Gasque
- Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School Medicine, New Haven, Connecticut, United States of America
- Department of Computer Science, Yale University, New Haven, Connecticut, United States of America
- Universite Claude Bernard Lyon 1, Faculte de Medecine Lyon Est, Lyon, France
- Department de Bioinformatique, Univ Evry, Universite Paris-Saclay, Paris, France
| | - Nicholas C. Huston
- Department of Molecular Biophysics & Biochemistry, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Han Wan
- Department of Molecular, Cellular, and Developmental Biology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Klara Szigeti-Buck
- Department of Comparative Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Neuroscience, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, Connecticut, United of States of America
| | - Yuki Yasumoto
- Department of Comparative Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Neuroscience, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, Connecticut, United of States of America
| | - Allison M. Greaney
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut, United States of America
| | - Victoria Habet
- Department of Pediatrics, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Ryan D. Chow
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Jennifer S. Chen
- Department of Laboratory Medicine, Yale University, New Haven, Connecticut, United States of America
- Department of Immunobiology, Yale University, New Haven, Connecticut, United States of America
| | - Jin Wei
- Department of Laboratory Medicine, Yale University, New Haven, Connecticut, United States of America
- Department of Immunobiology, Yale University, New Haven, Connecticut, United States of America
| | - Renata B. Filler
- Department of Laboratory Medicine, Yale University, New Haven, Connecticut, United States of America
- Department of Immunobiology, Yale University, New Haven, Connecticut, United States of America
| | - Bao Wang
- Department of Laboratory Medicine, Yale University, New Haven, Connecticut, United States of America
- Department of Immunobiology, Yale University, New Haven, Connecticut, United States of America
| | - Guilin Wang
- Yale Center for Genome Analysis, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Laura E. Niklason
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut, United States of America
- Department of Anesthesiology, Yale University, New Haven, Connecticut, United States of America
| | - Ruth R. Montgomery
- Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Stephanie C. Eisenbarth
- Department of Laboratory Medicine, Yale University, New Haven, Connecticut, United States of America
- Department of Immunobiology, Yale University, New Haven, Connecticut, United States of America
| | - Sidi Chen
- Department of Laboratory Medicine, Yale University, New Haven, Connecticut, United States of America
- Department of Immunobiology, Yale University, New Haven, Connecticut, United States of America
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Adam Williams
- The Jackson Laboratory, Farmington, Connecticut, United States of America
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University, New Haven, Connecticut, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Tamas L. Horvath
- Department of Comparative Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Neuroscience, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, Connecticut, United of States of America
| | - Ellen F. Foxman
- Department of Laboratory Medicine, Yale University, New Haven, Connecticut, United States of America
- Department of Immunobiology, Yale University, New Haven, Connecticut, United States of America
| | - Richard W. Pierce
- Department of Pediatrics, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Anna Marie Pyle
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - David van Dijk
- Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School Medicine, New Haven, Connecticut, United States of America
- Department of Computer Science, Yale University, New Haven, Connecticut, United States of America
| | - Craig B. Wilen
- Department of Laboratory Medicine, Yale University, New Haven, Connecticut, United States of America
- Department of Immunobiology, Yale University, New Haven, Connecticut, United States of America
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2
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Tavares RDCA, Mahadeshwar G, Wan H, Huston NC, Pyle AM. The global and local distribution of RNA structure throughout the SARS-CoV-2 genome. J Virol 2021; 95:JVI.02190-20. [PMID: 33268519 PMCID: PMC8092842 DOI: 10.1128/jvi.02190-20] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 11/30/2020] [Indexed: 02/08/2023] Open
Abstract
SARS-CoV-2 is the causative viral agent of COVID-19, the disease at the center of the current global pandemic. While knowledge of highly structured regions is integral for mechanistic insights into the viral infection cycle, very little is known about the location and folding stability of functional elements within the massive, ∼30kb SARS-CoV-2 RNA genome. In this study, we analyze the folding stability of this RNA genome relative to the structural landscape of other well-known viral RNAs. We present an in-silico pipeline to predict regions of high base pair content across long genomes and to pinpoint hotspots of well-defined RNA structures, a method that allows for direct comparisons of RNA structural complexity within the several domains in SARS-CoV-2 genome. We report that the SARS-CoV-2 genomic propensity for stable RNA folding is exceptional among RNA viruses, superseding even that of HCV, one of the most structured viral RNAs in nature. Furthermore, our analysis suggests varying levels of RNA structure across genomic functional regions, with accessory and structural ORFs containing the highest structural density in the viral genome. Finally, we take a step further to examine how individual RNA structures formed by these ORFs are affected by the differences in genomic and subgenomic contexts, which given the technical difficulty of experimentally separating cellular mixtures of sgRNA from gRNA, is a unique advantage of our in-silico pipeline. The resulting findings provide a useful roadmap for planning focused empirical studies of SARS-CoV-2 RNA biology, and a preliminary guide for exploring potential SARS-CoV-2 RNA drug targets.Importance The RNA genome of SARS-CoV-2 is among the largest and most complex viral genomes, and yet its RNA structural features remain relatively unexplored. Since RNA elements guide function in most RNA viruses, and they represent potential drug targets, it is essential to chart the architectural features of SARS-CoV-2 and pinpoint regions that merit focused study. Here we show that RNA folding stability of SARS-CoV-2 genome is exceptional among viral genomes and we develop a method to directly compare levels of predicted secondary structure across SARS-CoV-2 domains. Remarkably, we find that coding regions display the highest structural propensity in the genome, forming motifs that differ between the genomic and subgenomic contexts. Our approach provides an attractive strategy to rapidly screen for candidate structured regions based on base pairing potential and provides a readily interpretable roadmap to guide functional studies of RNA viruses and other pharmacologically relevant RNA transcripts.
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Affiliation(s)
| | - Gandhar Mahadeshwar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Han Wan
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Nicholas C Huston
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Anna Marie Pyle
- Department of Chemistry, Yale University, New Haven, CT 06511, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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3
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Huston NC, Wan H, Strine MS, de Cesaris Araujo Tavares R, Wilen CB, Pyle AM. Comprehensive in vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs and mechanisms. Mol Cell 2021; 81:584-598.e5. [PMID: 33444546 PMCID: PMC7775661 DOI: 10.1016/j.molcel.2020.12.041] [Citation(s) in RCA: 157] [Impact Index Per Article: 52.3] [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: 07/13/2020] [Revised: 11/06/2020] [Accepted: 12/21/2020] [Indexed: 02/07/2023]
Abstract
Severe-acute-respiratory-syndrome-related coronavirus 2 (SARS-CoV-2) is the positive-sense RNA virus that causes coronavirus disease 2019 (COVID-19). The genome of SARS-CoV-2 is unique among viral RNAs in its vast potential to form RNA structures, yet as much as 97% of its 30 kilobases have not been structurally explored. Here, we apply a novel long amplicon strategy to determine the secondary structure of the SARS-CoV-2 RNA genome at single-nucleotide resolution in infected cells. Our in-depth structural analysis reveals networks of well-folded RNA structures throughout Orf1ab and reveals aspects of SARS-CoV-2 genome architecture that distinguish it from other RNA viruses. Evolutionary analysis shows that several features of the SARS-CoV-2 genomic structure are conserved across β-coronaviruses, and we pinpoint regions of well-folded RNA structure that merit downstream functional analysis. The native, secondary structure of SARS-CoV-2 presented here is a roadmap that will facilitate focused studies on the viral life cycle, facilitate primer design, and guide the identification of RNA drug targets against COVID-19.
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Affiliation(s)
- Nicholas C Huston
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Han Wan
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Madison S Strine
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06510, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06519, USA
| | | | - Craig B Wilen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06510, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06519, USA
| | - Anna Marie Pyle
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA; Department of Chemistry, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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4
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Crispin A, Guo C, Chen C, Campagna DR, Schmidt PJ, Lichtenstein D, Cao C, Sendamarai AK, Hildick-Smith GJ, Huston NC, Boudreaux J, Bottomley SS, Heeney MM, Paw BH, Fleming MD, Ducamp S. Mutations in the iron-sulfur cluster biogenesis protein HSCB cause congenital sideroblastic anemia. J Clin Invest 2020; 130:5245-5256. [PMID: 32634119 PMCID: PMC7524500 DOI: 10.1172/jci135479] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 06/24/2020] [Indexed: 01/15/2023] Open
Abstract
The congenital sideroblastic anemias (CSAs) can be caused by primary defects in mitochondrial iron-sulfur (Fe-S) cluster biogenesis. HSCB (heat shock cognate B), which encodes a mitochondrial cochaperone, also known as HSC20 (heat shock cognate protein 20), is the partner of mitochondrial heat shock protein A9 (HSPA9). Together with glutaredoxin 5 (GLRX5), HSCB and HSPA9 facilitate the transfer of nascent 2-iron, 2-sulfur clusters to recipient mitochondrial proteins. Mutations in both HSPA9 and GLRX5 have previously been associated with CSA. Therefore, we hypothesized that mutations in HSCB could also cause CSA. We screened patients with genetically undefined CSA and identified a frameshift mutation and a rare promoter variant in HSCB in a female patient with non-syndromic CSA. We found that HSCB expression was decreased in patient-derived fibroblasts and K562 erythroleukemia cells engineered to have the patient-specific promoter variant. Furthermore, gene knockdown and deletion experiments performed in K562 cells, zebrafish, and mice demonstrate that loss of HSCB results in impaired Fe-S cluster biogenesis, a defect in RBC hemoglobinization, and the development of siderocytes and more broadly perturbs hematopoiesis in vivo. These results further affirm the involvement of Fe-S cluster biogenesis in erythropoiesis and hematopoiesis and define HSCB as a CSA gene.
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Affiliation(s)
- Andrew Crispin
- Department of Pathology, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Chaoshe Guo
- Department of Pathology, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Caiyong Chen
- Division of Hematology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Dean R. Campagna
- Department of Pathology, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Paul J. Schmidt
- Department of Pathology, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Daniel Lichtenstein
- Department of Pathology, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Chang Cao
- Department of Pathology, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Anoop K. Sendamarai
- Department of Pathology, Boston Children’s Hospital, Boston, Massachusetts, USA
| | | | - Nicholas C. Huston
- Division of Hematology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Jeanne Boudreaux
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta and Department of Pediatrics, Emory University, Atlanta, Georgia, USA
| | - Sylvia S. Bottomley
- Department of Medicine, University of Oklahoma College of Medicine, Oklahoma City, Oklahoma, USA
| | - Matthew M. Heeney
- Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts, USA
| | - Barry H. Paw
- Division of Hematology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Mark D. Fleming
- Department of Pathology, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Sarah Ducamp
- Department of Pathology, Boston Children’s Hospital, Boston, Massachusetts, USA
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5
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Ravindra NG, Alfajaro MM, Gasque V, Habet V, Wei J, Filler RB, Huston NC, Wan H, Szigeti-Buck K, Wang B, Wang G, Montgomery RR, Eisenbarth SC, Williams A, Pyle AM, Iwasaki A, Horvath TL, Foxman EF, Pierce RW, van Dijk D, Wilen CB. Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium. bioRxiv 2020:2020.05.06.081695. [PMID: 32511382 PMCID: PMC7263511 DOI: 10.1101/2020.05.06.081695] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [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: 12/20/2022]
Abstract
SARS-CoV-2, the causative agent of COVID-19, has tragically burdened individuals and institutions around the world. There are currently no approved drugs or vaccines for the treatment or prevention of COVID-19. Enhanced understanding of SARS-CoV-2 infection and pathogenesis is critical for the development of therapeutics. To reveal insight into viral replication, cell tropism, and host-viral interactions of SARS-CoV-2 we performed single-cell RNA sequencing of experimentally infected human bronchial epithelial cells (HBECs) in air-liquid interface cultures over a time-course. This revealed novel polyadenylated viral transcripts and highlighted ciliated cells as a major target of infection, which we confirmed by electron microscopy. Over the course of infection, cell tropism of SARS-CoV-2 expands to other epithelial cell types including basal and club cells. Infection induces cell-intrinsic expression of type I and type III IFNs and IL6 but not IL1. This results in expression of interferon-stimulated genes in both infected and bystander cells. We observe similar gene expression changes from a COVID-19 patient ex vivo. In addition, we developed a new computational method termed CONditional DENSity Embedding (CONDENSE) to characterize and compare temporal gene dynamics in response to infection, which revealed genes relating to endothelin, angio-genesis, interferon, and inflammation-causing signaling pathways. In this study, we conducted an in-depth analysis of SARS-CoV-2 infection in HBECs and a COVID-19 patient and revealed genes, cell types, and cell state changes associated with infection.
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Affiliation(s)
- Neal G. Ravindra
- Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Computer Science, Yale University, New Haven, CT, USA
| | - Mia Madel Alfajaro
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Victor Gasque
- Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Computer Science, Yale University, New Haven, CT, USA
- Université Claude Bernard Lyon 1, Faculté de Médecine Lyon Est, Lyon, France
- Département de Bioinformatique, Univ Evry, Université Paris-Saclay, Paris, France
| | - Victoria Habet
- Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA
| | - Jin Wei
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Renata B. Filler
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Nicholas C. Huston
- Department of Molecular Biophysics & Biochemistry, Yale School of Medicine, New Haven, CT, USA
| | - Han Wan
- Department of Molecular, Cellular, and Developmental Biology, Yale School of Medicine, New Haven, CT, USA
| | - Klara Szigeti-Buck
- Department of Comparative Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Bao Wang
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Guilin Wang
- Yale Center for Genome Analysis, Yale School of Medicine, New Haven, CT, USA
| | - Ruth R. Montgomery
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Stephanie C. Eisenbarth
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | | | - Anna Marie Pyle
- Department of Molecular Biophysics & Biochemistry, Yale School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Department of Molecular, Cellular, and Developmental Biology, Yale School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Tamas L. Horvath
- Department of Molecular Biophysics & Biochemistry, Yale School of Medicine, New Haven, CT, USA
- Department of Molecular, Cellular, and Developmental Biology, Yale School of Medicine, New Haven, CT, USA
- Department of Comparative Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Ellen F. Foxman
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Richard W. Pierce
- Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA
| | - David van Dijk
- Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Computer Science, Yale University, New Haven, CT, USA
| | - Craig B. Wilen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
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6
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Huston NC, Wan H, de Cesaris Araujo Tavares R, Wilen C, Pyle AM. Comprehensive in-vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs and mechanisms. bioRxiv 2020:2020.07.10.197079. [PMID: 32676598 PMCID: PMC7359520 DOI: 10.1101/2020.07.10.197079] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
SARS-CoV-2 is the positive-sense RNA virus that causes COVID-19, a disease that has triggered a major human health and economic crisis. The genome of SARS-CoV-2 is unique among viral RNAs in its vast potential to form stable RNA structures and yet, as much as 97% of its 30 kilobases have not been structurally explored in the context of a viral infection. Our limited knowledge of SARS-CoV-2 genomic architecture is a fundamental limitation to both our mechanistic understanding of coronavirus life cycle and the development of COVID-19 RNA-based therapeutics. Here, we apply a novel long amplicon strategy to determine for the first time the secondary structure of the SARS-CoV-2 RNA genome probed in infected cells. In addition to the conserved structural motifs at the viral termini, we report new structural features like a conformationally flexible programmed ribosomal frameshifting pseudoknot, and a host of novel RNA structures, each of which highlights the importance of studying viral structures in their native genomic context. Our in-depth structural analysis reveals extensive networks of well-folded RNA structures throughout Orf1ab and reveals new aspects of SARS-CoV-2 genome architecture that distinguish it from other single-stranded, positive-sense RNA viruses. Evolutionary analysis of RNA structures in SARS-CoV-2 shows that several features of its genomic structure are conserved across beta coronaviruses and we pinpoint individual regions of well-folded RNA structure that merit downstream functional analysis. The native, complete secondary structure of SAR-CoV-2 presented here is a roadmap that will facilitate focused studies on mechanisms of replication, translation and packaging, and guide the identification of new RNA drug targets against COVID-19.
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Affiliation(s)
- Nicholas C. Huston
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Han Wan
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA
| | | | - Craig Wilen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Anna Marie Pyle
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA
- Department of Chemistry, Yale University, New Haven, CT, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
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7
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Guo LT, Adams RL, Wan H, Huston NC, Potapova O, Olson S, Gallardo CM, Graveley BR, Torbett BE, Pyle AM. Sequencing and Structure Probing of Long RNAs Using MarathonRT: A Next-Generation Reverse Transcriptase. J Mol Biol 2020; 432:3338-3352. [PMID: 32259542 PMCID: PMC7556701 DOI: 10.1016/j.jmb.2020.03.022] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [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: 12/17/2019] [Revised: 03/03/2020] [Accepted: 03/19/2020] [Indexed: 12/31/2022]
Abstract
Reverse transcriptase (RT) enzymes are indispensable tools for interrogating diverse aspects of RNA metabolism and transcriptome composition. Due to the growing interest in sequence and structural complexity of long RNA molecules, processive RT enzymes are now required for preserving linkage and information content in mixed populations of transcripts, and the low-processivity RT enzymes that are commercially available cannot meet this need. MarathonRT is encoded within a eubacterial group II intron, and it has been shown to efficiently copy highly structured long RNA molecules in a single pass. In this work, we systematically characterize MarathonRT as a tool enzyme and optimize its performance in a variety of applications that include single-cycle reverse transcription of long RNAs, dimethyl sulfate mutational profiling (DMS-MaP), selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP), using ultra-long amplicons and the detection of natural RNA base modifications. By diversifying MarathonRT reaction protocols, we provide an upgraded suite of tools for cutting-edge RNA research and clinical application.
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Affiliation(s)
- Li-Tao Guo
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Rebecca L Adams
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Han Wan
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Nicholas C Huston
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Olga Potapova
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Sara Olson
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT 06030-6403, USA
| | | | - Brenton R Graveley
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT 06030-6403, USA
| | | | - Anna Marie Pyle
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Chemistry, Yale University, New Haven, CT 06520, USA.
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8
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Abstract
Considerable effort has been devoted to developing a comprehensive understanding of CRISPR nuclease specificity. In silico predictions and multiple genome-wide cellular and biochemical approaches have revealed a basic understanding of the Cas9 specificity profile. However, none of these approaches has delivered a model that allows accurate prediction of a CRISPR nuclease's ability to cleave a site based entirely on the sequence of the guide RNA (gRNA) and the target. We describe a library-based biochemical assay that directly reports the cleavage efficiency of a particular Cas9-guide complex by measuring both uncleaved and cleaved target molecules over a wide range of mismatched library members. We applied our assay using libraries of targets to evaluate the specificity of Staphylococcus aureus Cas9 under a variety of experimental conditions. Surprisingly, our data show an unexpectedly high variation in the random gRNA:target DNA mismatch tolerance when cleaving with different gRNAs, indicating guide-intrinsic mismatch permissiveness and challenging the assumption of universal specificity models. We use data generated by our assay to create the first off-target, guide-specific cleavage models. The barcoded libraries of targets approach is rapid, highly modular, and capable of generating protein- and guide-specific models, as well as illuminating the biophysics of Cas9 binding versus cutting. These models may be useful in identifying potential off-targets, and the gRNA-intrinsic nature of mismatch tolerance argues for coupling these specificity models with orthogonal methods for a more complete assessment of gRNA specificity.
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Affiliation(s)
| | - Josh Tycko
- Editas Medicine, Cambridge, Massaschusetts
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9
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Abstract
Technical innovations in structural probing have drastically advanced the field of RNA structure analysis. These advances have led to parallel approaches developed in separate labs for analyzing RNA structure and dynamics. With the wealth of methodologies available, it can be difficult to determine which is best suited for a given application. Here, using a long, highly structured viral RNA as an example (the positive strand genome of Hepatitis C Virus), we present a semi-comprehensive analysis and describe the major approaches for analyzing the architecture of RNA that is modified with structure-sensitive probes. Additionally, we present an updated method for generating in vitro transcribed and folded RNA that maintains native secondary structures in long RNA molecules. We anticipate that the methods described here will streamline the use of current approaches and help investigators who are unfamiliar with structure probing, obviating the need for time-consuming and expensive optimization.
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Affiliation(s)
- Rebecca L Adams
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, United States
| | - Nicholas C Huston
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, United States
| | - Rafael C A Tavares
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, United States; Department of Chemistry, Yale University, New Haven, CT, United States
| | - Anna M Pyle
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, United States; Department of Chemistry, Yale University, New Haven, CT, United States; Howard Hughes Medical Institute, Chevy Chase, MD, United States.
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10
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Tycko J, Barrera LA, Huston NC, Friedland AE, Wu X, Gootenberg JS, Abudayyeh OO, Myer VE, Wilson CJ, Hsu PD. Pairwise library screen systematically interrogates Staphylococcus aureus Cas9 specificity in human cells. Nat Commun 2018; 9:2962. [PMID: 30054474 PMCID: PMC6063963 DOI: 10.1038/s41467-018-05391-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [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: 02/09/2018] [Accepted: 07/03/2018] [Indexed: 12/22/2022] Open
Abstract
Therapeutic genome editing with Staphylococcus aureus Cas9 (SaCas9) requires a rigorous understanding of its potential off-target activity in the human genome. Here we report a high-throughput screening approach to measure SaCas9 genome editing variation in human cells across a large repertoire of 88,692 single guide RNAs (sgRNAs) paired with matched or mismatched target sites in a synthetic cassette. We incorporate randomized barcodes that enable whitelisting of correctly synthesized molecules for further downstream analysis, in order to circumvent the limitation of oligonucleotide synthesis errors. We find SaCas9 sgRNAs with 21-mer or 22-mer spacer sequences are generally more active, although high efficiency 20-mer spacers are markedly less tolerant of mismatches. Using this dataset, we developed an SaCas9 specificity model that performs robustly in ranking off-target sites. The barcoded pairwise library screen enabled high-fidelity recovery of guide-target relationships, providing a scalable framework for the investigation of CRISPR enzyme properties and general nucleic acid interactions.
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Affiliation(s)
- Josh Tycko
- Editas Medicine, 11 Hurley St., Cambridge, MA, 02141, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Luis A Barrera
- Editas Medicine, 11 Hurley St., Cambridge, MA, 02141, USA
- Arrakis Therapeutics, 35 Gatehouse Dr., Waltham, MA, 02451, USA
| | - Nicholas C Huston
- Editas Medicine, 11 Hurley St., Cambridge, MA, 02141, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06511, USA
| | | | - Xuebing Wu
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
| | | | - Omar O Abudayyeh
- Department of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Vic E Myer
- Editas Medicine, 11 Hurley St., Cambridge, MA, 02141, USA
| | | | - Patrick D Hsu
- Editas Medicine, 11 Hurley St., Cambridge, MA, 02141, USA.
- Laboratory of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.
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11
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Seguin A, Takahashi-Makise N, Yien YY, Huston NC, Whitman JC, Musso G, Wallace JA, Bradley T, Bergonia HA, Kafina MD, Matsumoto M, Igarashi K, Phillips JD, Paw BH, Kaplan J, Ward DM. Reductions in the mitochondrial ABC transporter Abcb10 affect the transcriptional profile of heme biosynthesis genes. J Biol Chem 2017; 292:16284-16299. [PMID: 28808058 DOI: 10.1074/jbc.m117.797415] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 08/09/2017] [Indexed: 11/06/2022] Open
Abstract
ATP-binding cassette subfamily B member 10 (Abcb10) is a mitochondrial ATP-binding cassette (ABC) transporter that complexes with mitoferrin1 and ferrochelatase to enhance heme biosynthesis in developing red blood cells. Reductions in Abcb10 levels have been shown to reduce mitoferrin1 protein levels and iron import into mitochondria, resulting in reduced heme biosynthesis. As an ABC transporter, Abcb10 binds and hydrolyzes ATP, but its transported substrate is unknown. Here, we determined that decreases in Abcb10 did not result in protoporphyrin IX accumulation in morphant-treated zebrafish embryos or in differentiated Abcb10-specific shRNA murine Friend erythroleukemia (MEL) cells in which Abcb10 was specifically silenced with shRNA. We also found that the ATPase activity of Abcb10 is necessary for hemoglobinization in MEL cells, suggesting that the substrate transported by Abcb10 is important in mediating increased heme biosynthesis during erythroid development. Inhibition of 5-aminolevulinic acid dehydratase (EC 4.2.1.24) with succinylacetone resulted in both 5-aminolevulinic acid (ALA) accumulation in control and Abcb10-specific shRNA MEL cells, demonstrating that reductions in Abcb10 do not affect ALA export from mitochondria and indicating that Abcb10 does not transport ALA. Abcb10 silencing resulted in an alteration in the heme biosynthesis transcriptional profile due to repression by the transcriptional regulator Bach1, which could be partially rescued by overexpression of Alas2 or Gata1, providing a mechanistic explanation for why Abcb10 shRNA MEL cells exhibit reduced hemoglobinization. In conclusion, our findings rule out that Abcb10 transports ALA and indicate that Abcb10's ATP-hydrolysis activity is critical for hemoglobinization and that the substrate transported by Abcb10 provides a signal that optimizes hemoglobinization.
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Affiliation(s)
- Alexandra Seguin
- From the Division of Microbiology and Immunology, Department of Pathology, and
| | | | | | | | | | - Gabriel Musso
- the Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115
| | - Jared A Wallace
- From the Division of Microbiology and Immunology, Department of Pathology, and
| | - Thomas Bradley
- From the Division of Microbiology and Immunology, Department of Pathology, and
| | - Hector A Bergonia
- the Division of Hematology-Oncology, Department of Medicine, University of Utah School of Medicine, Salt Lake City, Utah 84132
| | | | - Mitsuyo Matsumoto
- the Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8576, Japan
| | - Kazuhiko Igarashi
- the Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai 980-8576, Japan
| | - John D Phillips
- the Division of Hematology-Oncology, Department of Medicine, University of Utah School of Medicine, Salt Lake City, Utah 84132
| | - Barry H Paw
- the Division of Hematology and.,the Division of Hematology-Oncology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, and.,the Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115
| | - Jerry Kaplan
- From the Division of Microbiology and Immunology, Department of Pathology, and
| | - Diane M Ward
- From the Division of Microbiology and Immunology, Department of Pathology, and
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12
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Grillo AS, SantaMaria AM, Kafina MD, Cioffi AG, Huston NC, Han M, Seo YA, Yien YY, Nardone C, Menon AV, Fan J, Svoboda DC, Anderson JB, Hong JD, Nicolau BG, Subedi K, Gewirth AA, Wessling-Resnick M, Kim J, Paw BH, Burke MD. Restored iron transport by a small molecule promotes absorption and hemoglobinization in animals. Science 2017; 356:608-616. [PMID: 28495746 PMCID: PMC5470741 DOI: 10.1126/science.aah3862] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 11/30/2016] [Accepted: 03/21/2017] [Indexed: 12/15/2022]
Abstract
Multiple human diseases ensue from a hereditary or acquired deficiency of iron-transporting protein function that diminishes transmembrane iron flux in distinct sites and directions. Because other iron-transport proteins remain active, labile iron gradients build up across the corresponding protein-deficient membranes. Here we report that a small-molecule natural product, hinokitiol, can harness such gradients to restore iron transport into, within, and/or out of cells. The same compound promotes gut iron absorption in DMT1-deficient rats and ferroportin-deficient mice, as well as hemoglobinization in DMT1- and mitoferrin-deficient zebrafish. These findings illuminate a general mechanistic framework for small molecule-mediated site- and direction-selective restoration of iron transport. They also suggest that small molecules that partially mimic the function of missing protein transporters of iron, and possibly other ions, may have potential in treating human diseases.
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Affiliation(s)
- Anthony S Grillo
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Anna M SantaMaria
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Martin D Kafina
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Alexander G Cioffi
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Nicholas C Huston
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Murui Han
- Department of Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA
| | - Young Ah Seo
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Yvette Y Yien
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Christopher Nardone
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Archita V Menon
- Department of Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA
| | - James Fan
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Dillon C Svoboda
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jacob B Anderson
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - John D Hong
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Bruno G Nicolau
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Kiran Subedi
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Andrew A Gewirth
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Marianne Wessling-Resnick
- Department of Genetic and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.
| | - Jonghan Kim
- Department of Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA.
| | - Barry H Paw
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
- Division of Hematology-Oncology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Martin D Burke
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carle-Illinois College of Medicine, University of Illinois at Urbana-Champaign, Champaign, IL 61820, USA
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13
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Kardon JR, Yien YY, Huston NC, Branco DS, Hildick-Smith GJ, Rhee KY, Paw BH, Baker TA. Mitochondrial ClpX Activates a Key Enzyme for Heme Biosynthesis and Erythropoiesis. Cell 2016; 161:858-67. [PMID: 25957689 DOI: 10.1016/j.cell.2015.04.017] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 01/15/2015] [Accepted: 03/13/2015] [Indexed: 12/21/2022]
Abstract
The mitochondrion maintains and regulates its proteome with chaperones primarily inherited from its bacterial endosymbiont ancestor. Among these chaperones is the AAA+ unfoldase ClpX, an important regulator of prokaryotic physiology with poorly defined function in the eukaryotic mitochondrion. We observed phenotypic similarity in S. cerevisiae genetic interaction data between mitochondrial ClpX (mtClpX) and genes contributing to heme biosynthesis, an essential mitochondrial function. Metabolomic analysis revealed that 5-aminolevulinic acid (ALA), the first heme precursor, is 5-fold reduced in yeast lacking mtClpX activity and that total heme is reduced by half. mtClpX directly stimulates ALA synthase in vitro by catalyzing incorporation of its cofactor, pyridoxal phosphate. This activity is conserved in mammalian homologs; additionally, mtClpX depletion impairs vertebrate erythropoiesis, which requires massive upregulation of heme biosynthesis to supply hemoglobin. mtClpX, therefore, is a widely conserved stimulator of an essential biosynthetic pathway and uses a previously unrecognized mechanism for AAA+ unfoldases.
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Affiliation(s)
- Julia R Kardon
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yvette Y Yien
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Nicholas C Huston
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Diana S Branco
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Gordon J Hildick-Smith
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Kyu Y Rhee
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10065, USA; Division of Infectious Diseases, Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Barry H Paw
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Division of Hematology-Oncology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Tania A Baker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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14
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Shmukler BE, Huston NC, Thon JN, Ni CW, Kourkoulis G, Lawson ND, Paw BH, Alper SL. Homozygous knockout of the piezo1 gene in the zebrafish is not associated with anemia. Haematologica 2015; 100:e483-5. [PMID: 26294733 DOI: 10.3324/haematol.2015.132449] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Boris E Shmukler
- Renal Division, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Nicholas C Huston
- Hematology Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jonathan N Thon
- Hematology Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Chih-Wen Ni
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA, USA
| | - George Kourkoulis
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA, USA
| | - Nathan D Lawson
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA, USA
| | - Barry H Paw
- Hematology Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA Hematology-Oncology Division, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Seth L Alper
- Renal Division, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
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15
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Chung J, Bauer DE, Ghamari A, Nizzi CP, Deck KM, Kingsley PD, Yien YY, Huston NC, Chen C, Schultz IJ, Dalton AJ, Wittig JG, Palis J, Orkin SH, Lodish HF, Eisenstein RS, Cantor AB, Paw BH. The mTORC1/4E-BP pathway coordinates hemoglobin production with L-leucine availability. Sci Signal 2015; 8:ra34. [PMID: 25872869 DOI: 10.1126/scisignal.aaa5903] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
In multicellular organisms, the mechanisms by which diverse cell types acquire distinct amino acids and how cellular function adapts to their availability are fundamental questions in biology. We found that increased neutral essential amino acid (NEAA) uptake was a critical component of erythropoiesis. As red blood cells matured, expression of the amino acid transporter gene Lat3 increased, which increased NEAA import. Inadequate NEAA uptake by pharmacologic inhibition or RNAi-mediated knockdown of LAT3 triggered a specific reduction in hemoglobin production in zebrafish embryos and murine erythroid cells through the mTORC1 (mammalian target of rapamycin complex 1)/4E-BP (eukaryotic translation initiation factor 4E-binding protein) pathway. CRISPR-mediated deletion of members of the 4E-BP family in murine erythroid cells rendered them resistant to mTORC1 and LAT3 inhibition and restored hemoglobin production. These results identify a developmental role for LAT3 in red blood cells and demonstrate that mTORC1 serves as a homeostatic sensor that couples hemoglobin production at the translational level to sufficient uptake of NEAAs, particularly L-leucine.
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Affiliation(s)
- Jacky Chung
- Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel E Bauer
- Division of Hematology-Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA. Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Alireza Ghamari
- Division of Hematology-Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA. Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Christopher P Nizzi
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kathryn M Deck
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Paul D Kingsley
- Department of Pediatrics, Center for Pediatric Biomedical Research, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Yvette Y Yien
- Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Nicholas C Huston
- Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Caiyong Chen
- Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Iman J Schultz
- Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Arthur J Dalton
- Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Johannes G Wittig
- Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - James Palis
- Department of Pediatrics, Center for Pediatric Biomedical Research, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Stuart H Orkin
- Division of Hematology-Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA. Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Harvey F Lodish
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Richard S Eisenstein
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Alan B Cantor
- Division of Hematology-Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA. Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Barry H Paw
- Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA. Division of Hematology-Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA. Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.
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16
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Chung J, Anderson SA, Gwynn B, Deck KM, Chen MJ, Langer NB, Shaw GC, Huston NC, Boyer LF, Datta S, Paradkar PN, Li L, Wei Z, Lambert AJ, Sahr K, Wittig JG, Chen W, Lu W, Galy B, Schlaeger TM, Hentze MW, Ward DM, Kaplan J, Eisenstein RS, Peters LL, Paw BH. Iron regulatory protein-1 protects against mitoferrin-1-deficient porphyria. J Biol Chem 2014. [DOI: 10.1074/jbc.a114.547778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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17
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Chung J, Anderson SA, Gwynn B, Deck KM, Chen MJ, Langer NB, Shaw GC, Huston NC, Boyer LF, Datta S, Paradkar PN, Li L, Wei Z, Lambert AJ, Sahr K, Wittig JG, Chen W, Lu W, Galy B, Schlaeger TM, Hentze MW, Ward DM, Kaplan J, Eisenstein RS, Peters LL, Paw BH. Iron regulatory protein-1 protects against mitoferrin-1-deficient porphyria. J Biol Chem 2014; 289:7835-43. [PMID: 24509859 DOI: 10.1074/jbc.m114.547778] [Citation(s) in RCA: 33] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Mitochondrial iron is essential for the biosynthesis of heme and iron-sulfur ([Fe-S]) clusters in mammalian cells. In developing erythrocytes, iron is imported into the mitochondria by MFRN1 (mitoferrin-1, SLC25A37). Although loss of MFRN1 in zebrafish and mice leads to profound anemia, mutant animals showed no overt signs of porphyria, suggesting that mitochondrial iron deficiency does not result in an accumulation of protoporphyrins. Here, we developed a gene trap model to provide in vitro and in vivo evidence that iron regulatory protein-1 (IRP1) inhibits protoporphyrin accumulation. Mfrn1(+/gt);Irp1(-/-) erythroid cells exhibit a significant increase in protoporphyrin levels. IRP1 attenuates protoporphyrin biosynthesis by binding to the 5'-iron response element (IRE) of alas2 mRNA, inhibiting its translation. Ectopic expression of alas2 harboring a mutant IRE, preventing IRP1 binding, in Mfrn1(gt/gt) cells mimics Irp1 deficiency. Together, our data support a model whereby impaired mitochondrial [Fe-S] cluster biogenesis in Mfrn1(gt/gt) cells results in elevated IRP1 RNA-binding that attenuates ALAS2 mRNA translation and protoporphyrin accumulation.
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Affiliation(s)
- Jacky Chung
- From the Division of Hematology, Brigham and Women's Hospital; Division of Hematology-Oncology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts 02115
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18
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Hildick-Smith GJ, Cooney JD, Garone C, Kremer LS, Haack TB, Thon JN, Miyata N, Lieber DS, Calvo SE, Akman HO, Yien YY, Huston NC, Branco DS, Shah DI, Freedman ML, Koehler CM, Italiano JE, Merkenschlager A, Beblo S, Strom TM, Meitinger T, Freisinger P, Donati MA, Prokisch H, Mootha VK, DiMauro S, Paw BH. Macrocytic anemia and mitochondriopathy resulting from a defect in sideroflexin 4. Am J Hum Genet 2013; 93:906-14. [PMID: 24119684 DOI: 10.1016/j.ajhg.2013.09.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Revised: 09/11/2013] [Accepted: 09/18/2013] [Indexed: 01/19/2023] Open
Abstract
We used exome sequencing to identify mutations in sideroflexin 4 (SFXN4) in two children with mitochondrial disease (the more severe case also presented with macrocytic anemia). SFXN4 is an uncharacterized mitochondrial protein that localizes to the mitochondrial inner membrane. sfxn4 knockdown in zebrafish recapitulated the mitochondrial respiratory defect observed in both individuals and the macrocytic anemia with megaloblastic features of the more severe case. In vitro and in vivo complementation studies with fibroblasts from the affected individuals and zebrafish demonstrated the requirement of SFXN4 for mitochondrial respiratory homeostasis and erythropoiesis. Our findings establish mutations in SFXN4 as a cause of mitochondriopathy and macrocytic anemia.
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Affiliation(s)
- Gordon J Hildick-Smith
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
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