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Peña N, Zhang W, Watkins C, Halucha M, Alshammary H, Hernandez MM, Liu WC, Albrecht RA, Garcia-Sastre A, Simon V, Katanski C, Pan T. Profiling Selective Packaging of Host RNA and Viral RNA Modification in SARS-CoV-2 Viral Preparations. Front Cell Dev Biol 2022; 10:768356. [PMID: 35186917 PMCID: PMC8851031 DOI: 10.3389/fcell.2022.768356] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 01/18/2022] [Indexed: 11/24/2022] Open
Abstract
Viruses package host RNAs in their virions which are associated with a range of functions in the viral life cycle. Previous transcriptomic profiling of host RNA packaging mostly focused on retroviruses. Which host RNAs are packaged in other viruses at the transcriptome level has not been thoroughly examined. Here we perform proof-of-concept studies using both small RNA and large RNA sequencing of six different SARS-CoV-2 viral isolates grown on VeroE6 cells to profile host RNAs present in cell free viral preparations and to explore SARS-CoV-2 genomic RNA modifications. We find selective enrichment of specific host transfer RNAs (tRNAs), tRNA fragments and signal recognition particle (SRP) RNA in SARS-CoV-2 viral preparations. Different viral preparations contain the same set of host RNAs, suggesting a common mechanism of packaging. We estimate that a single SARS-CoV-2 particle likely contains up to one SRP RNA and four tRNA molecules. We identify tRNA modification differences between the tRNAs present in viral preparations and those in the uninfected VeroE6 host cells. Furthermore, we find uncharacterized candidate modifications in the SARS-CoV-2 genomic RNA. Our results reveal an under-studied aspect of viral-host interactions that may be explored for viral therapeutics.
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Affiliation(s)
- Noah Peña
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, United States
| | - Wen Zhang
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, United States
| | - Christopher Watkins
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, United States
| | - Mateusz Halucha
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, United States
| | - Hala Alshammary
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Matthew M. Hernandez
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Wen-Chun Liu
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Global Health and Emerging Pathogen Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Randy A. Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Global Health and Emerging Pathogen Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Adolfo Garcia-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Global Health and Emerging Pathogen Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Global Health and Emerging Pathogen Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Christopher Katanski
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, United States
| | - Tao Pan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, United States
- Committee on Microbiology, University of Chicago, Chicago, IL, United States
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Li J, Shalev-Benami M, Sando R, Jiang X, Kibrom A, Wang J, Leon K, Katanski C, Nazarko O, Lu YC, Südhof TC, Skiniotis G, Araç D. Structural Basis for Teneurin Function in Circuit-Wiring: A Toxin Motif at the Synapse. Cell 2019; 173:735-748.e15. [PMID: 29677516 DOI: 10.1016/j.cell.2018.03.036] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 02/14/2018] [Accepted: 03/15/2018] [Indexed: 11/28/2022]
Abstract
Teneurins (TENs) are cell-surface adhesion proteins with critical roles in tissue development and axon guidance. Here, we report the 3.1-Å cryoelectron microscopy structure of the human TEN2 extracellular region (ECR), revealing a striking similarity to bacterial Tc-toxins. The ECR includes a large β barrel that partially encapsulates a C-terminal domain, which emerges to the solvent through an opening in the mid-barrel region. An immunoglobulin (Ig)-like domain seals the bottom of the barrel while a β propeller is attached in a perpendicular orientation. We further show that an alternatively spliced region within the β propeller acts as a switch to regulate trans-cellular adhesion of TEN2 to latrophilin (LPHN), a transmembrane receptor known to mediate critical functions in the central nervous system. One splice variant activates trans-cellular signaling in a LPHN-dependent manner, whereas the other induces inhibitory postsynaptic differentiation. These results highlight the unusual structural organization of TENs giving rise to their multifarious functions.
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Affiliation(s)
- Jingxian Li
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA; Grossman Institute for Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, Chicago, IL 60637, USA
| | - Moran Shalev-Benami
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
| | - Richard Sando
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Xian Jiang
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Amanuel Kibrom
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA; Grossman Institute for Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, Chicago, IL 60637, USA
| | - Jie Wang
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Katherine Leon
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA; Grossman Institute for Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, Chicago, IL 60637, USA
| | - Christopher Katanski
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA; Grossman Institute for Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, Chicago, IL 60637, USA
| | - Olha Nazarko
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA; Grossman Institute for Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, Chicago, IL 60637, USA
| | - Yue C Lu
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA; Grossman Institute for Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, Chicago, IL 60637, USA
| | - Thomas C Südhof
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
| | - Georgios Skiniotis
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University, Stanford, CA 94305, USA.
| | - Demet Araç
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA; Grossman Institute for Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, Chicago, IL 60637, USA.
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Kahan DN, Chen R, Riback J, Katanski C, Drummond A, Sosnick TR. Molecular Factors Underlying Stress-Triggered Phase-Separation of Pab1. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.1903] [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: 11/30/2022] Open
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Drummond DA, Pilipenko E, Riback J, Scott J, Rojek A, Budnik B, Wallace E, Katanski C. Selective RNA Sequestration Mediated by a Heat‐Sensing Disordered Protein Region. FASEB J 2015. [DOI: 10.1096/fasebj.29.1_supplement.563.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- D Allan Drummond
- Dept. of Biochemistry & Molecular BiologyUniversity of ChicagoChicagoIllinoisUnited States
- Dept. of Human Genetics University of ChicagoChicagoIllinoisUnited States
| | - Evgeny Pilipenko
- Dept. of Biochemistry & Molecular BiologyUniversity of ChicagoChicagoIllinoisUnited States
| | - Joshua Riback
- Dept. of Biochemistry & Molecular BiologyUniversity of ChicagoChicagoIllinoisUnited States
| | - Jamie Scott
- Dept. of Biochemistry & Molecular BiologyUniversity of ChicagoChicagoIllinoisUnited States
| | - Alexandra Rojek
- FAS Center for Systems BiologyHarvard UniversityCambridgeMAUnited States
| | - Bogdan Budnik
- FAS Center for Systems BiologyHarvard UniversityCambridgeMAUnited States
| | - Edward Wallace
- Dept. of Biochemistry & Molecular BiologyUniversity of ChicagoChicagoIllinoisUnited States
| | - Christopher Katanski
- Dept. of Biochemistry & Molecular BiologyUniversity of ChicagoChicagoIllinoisUnited States
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Bass C, Katanski C, Maynard B, Zurro I, Mariane E, Matta M, Loi M, Melis V, Capponi V, Muroni P, Setzu M, Nichols R. Conserved residues in RF-NH₂ receptor models identify predicted contact sites in ligand-receptor binding. Peptides 2014; 53:278-85. [PMID: 23811075 DOI: 10.1016/j.peptides.2013.06.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Revised: 06/04/2013] [Accepted: 06/05/2013] [Indexed: 01/05/2023]
Abstract
Peptides in the RF-NH2 family are grouped together based on an amidated dipeptide C terminus and signal through G-protein coupled receptors (GPCRs) to influence diverse physiological functions. By determining the mechanisms underlying RF-NH2 signaling targets can be identified to modulate physiological activity; yet, how RF-NH2 peptides interact with GPCRs is relatively unexplored. We predicted conserved residues played a role in Drosophila melanogaster RF-NH2 ligand-receptor interactions. In this study D. melanogaster rhodopsin-like family A peptide GPCRs alignments identified eight conserved residues unique to RF-NH2 receptors. Three of these residues were in extra-cellular loops of modeled RF-NH2 receptors and four in transmembrane helices oriented into a ligand binding pocket to allow contact with a peptide. The eighth residue was unavailable for interaction; yet its conservation suggested it played another role. A novel hydrophobic region representative of RF-NH2 receptors was also discovered. The presence of rhodopsin-like family A GPCR structural motifs including a toggle switch indicated RF-NH2s signal classically; however, some features of the DMS receptors were distinct from other RF-NH2 GPCRs. Additionally, differences in RF-NH2 receptor structures which bind the same peptide explained ligand specificity. Our novel results predicted conserved residues as RF-NH2 ligand-receptor contact sites and identified unique and classic structural features. These discoveries will aid antagonist design to modulate RF-NH2 signaling.
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Affiliation(s)
- C Bass
- Biological Chemistry Department, University of Michigan, Ann Arbor, MI 48109-0600, USA
| | - C Katanski
- Biochemistry Undergraduate Program, University of Michigan, Ann Arbor, MI 48109-0600, USA
| | - B Maynard
- Biochemistry Undergraduate Program, University of Michigan, Ann Arbor, MI 48109-0600, USA
| | - I Zurro
- Biological Cellulare e Moleculare, Università di Cagliari-Monserrato, 09042 Monserrato, Cagliari, Italy
| | - E Mariane
- Biological Cellulare e Moleculare, Università di Cagliari-Monserrato, 09042 Monserrato, Cagliari, Italy
| | - M Matta
- Biological Cellulare e Moleculare, Università di Cagliari-Monserrato, 09042 Monserrato, Cagliari, Italy
| | - M Loi
- Biological Cellulare e Moleculare, Università di Cagliari-Monserrato, 09042 Monserrato, Cagliari, Italy
| | - V Melis
- Biological Cellulare e Moleculare, Università di Cagliari-Monserrato, 09042 Monserrato, Cagliari, Italy
| | - V Capponi
- Biological Cellulare e Moleculare, Università di Cagliari-Monserrato, 09042 Monserrato, Cagliari, Italy
| | - P Muroni
- Dipartimento di Biologia Sperimentale, Sezione di Fisiologia Generale, Università di Cagliari-Monserrato, 09042 Monserrato, Cagliari, Italy
| | - M Setzu
- Dipartimento di Biologia Sperimentale, Sezione di Fisiologia Generale, Università di Cagliari-Monserrato, 09042 Monserrato, Cagliari, Italy
| | - R Nichols
- Biological Chemistry Department, University of Michigan, Ann Arbor, MI 48109-0600, USA; Biochemistry Undergraduate Program, University of Michigan, Ann Arbor, MI 48109-0600, USA; Visiting Professor Program, Università di Cagliari-Monserrato, 09042 Monserrato, Cagliari, Italy.
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