201
|
Bartolucci G, Adame-Arana O, Zhao X, Weber CA. Controlling composition of coexisting phases via molecular transitions. Biophys J 2021; 120:4682-4697. [PMID: 34600899 DOI: 10.1016/j.bpj.2021.09.036] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 08/10/2021] [Accepted: 09/27/2021] [Indexed: 12/24/2022] Open
Abstract
Phase separation and transitions among different molecular states are ubiquitous in living cells. Such transitions can be governed by local equilibrium thermodynamics or by active processes controlled by biological fuel. It remains largely unexplored how the behavior of phase-separating systems with molecular transitions differs between thermodynamic equilibrium and cases in which the detailed balance of the molecular transition rates is broken because of the presence of fuel. Here, we present a model of a phase-separating ternary mixture in which two components can convert into each other. At thermodynamic equilibrium, we find that molecular transitions can give rise to a lower dissolution temperature and thus reentrant phase behavior. Moreover, we find a discontinuous thermodynamic phase transition in the composition of the droplet phase if both converting molecules attract themselves with similar interaction strength. Breaking the detailed balance of the molecular transition leads to quasi-discontinuous changes in droplet composition by varying the fuel amount for a larger range of intermolecular interactions. Our findings showcase that phase separation with molecular transitions provides a versatile mechanism to control properties of intracellular and synthetic condensates via discontinuous switches in droplet composition.
Collapse
Affiliation(s)
- Giacomo Bartolucci
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany; Center for Systems Biology Dresden, Dresden, Germany
| | - Omar Adame-Arana
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Xueping Zhao
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany; Center for Systems Biology Dresden, Dresden, Germany
| | - Christoph A Weber
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany; Center for Systems Biology Dresden, Dresden, Germany.
| |
Collapse
|
202
|
Zhu H, Fu H, Cui T, Ning L, Shao H, Guo Y, Ke Y, Zheng J, Lin H, Wu X, Liu G, He J, Han X, Li W, Zhao X, Lu H, Wang D, Hu K, Shen X. RNAPhaSep: a resource of RNAs undergoing phase separation. Nucleic Acids Res 2021; 50:D340-D346. [PMID: 34718740 PMCID: PMC8728120 DOI: 10.1093/nar/gkab985] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/04/2021] [Accepted: 10/08/2021] [Indexed: 02/04/2023] Open
Abstract
Liquid-liquid phase separation (LLPS) partitions cellular contents, underlies the formation of membraneless organelles and plays essential biological roles. To date, most of the research on LLPS has focused on proteins, especially RNA-binding proteins. However, accumulating evidence has demonstrated that RNAs can also function as ‘scaffolds’ and play essential roles in seeding or nucleating the formation of granules. To better utilize the knowledge dispersed in published literature, we here introduce RNAPhaSep (http://www.rnaphasep.cn), a manually curated database of RNAs undergoing LLPS. It contains 1113 entries with experimentally validated RNA self-assembly or RNA and protein co-involved phase separation events. RNAPhaSep contains various types of information, including RNA information, protein information, phase separation experiment information and integrated annotation from multiple databases. RNAPhaSep provides a valuable resource for exploring the relationship between RNA properties and phase behaviour, and may further enhance our comprehensive understanding of LLPS in cellular functions and human diseases.
Collapse
Affiliation(s)
- Haibo Zhu
- Department of Intelligent Medical Engineering, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou 350122, China.,School of Artificial Intelligence and Information Technology, Nanjing University of Chinese Medicine, Nanjing Jiangsu 210023, China
| | - Hao Fu
- Department of Intelligent Medical Engineering, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou 350122, China.,School of Artificial Intelligence and Information Technology, Nanjing University of Chinese Medicine, Nanjing Jiangsu 210023, China
| | - Tianyu Cui
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Lin Ning
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Huaguo Shao
- Department of Intelligent Medical Engineering, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou 350122, China.,Department of Biochemistry and Molecular Biology, School of Medicine & Holistic Integrative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yehan Guo
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou 350122, China
| | - Yanting Ke
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou 350122, China
| | - Jiayi Zheng
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou 350122, China
| | - Hongyan Lin
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou 350122, China
| | - Xin Wu
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou 350122, China.,Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China
| | - Guanghao Liu
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou 350122, China.,Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China
| | - Jun He
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou 350122, China.,Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China
| | - Xin Han
- Department of Biochemistry and Molecular Biology, School of Medicine & Holistic Integrative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Wenlin Li
- School of Artificial Intelligence and Information Technology, Nanjing University of Chinese Medicine, Nanjing Jiangsu 210023, China.,Jingwen Library, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Xiaoyang Zhao
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Huasong Lu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Dong Wang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Kongfa Hu
- School of Artificial Intelligence and Information Technology, Nanjing University of Chinese Medicine, Nanjing Jiangsu 210023, China
| | - Xiaopei Shen
- Department of Intelligent Medical Engineering, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou 350122, China.,Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou 350122, China.,Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China
| |
Collapse
|
203
|
Bracquemond D, Muriaux D. Betacoronavirus Assembly: Clues and Perspectives for Elucidating SARS-CoV-2 Particle Formation and Egress. mBio 2021; 12:e0237121. [PMID: 34579570 PMCID: PMC8546641 DOI: 10.1128/mbio.02371-21] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
In 2019, a new pandemic virus belonging to the betacoronavirus family emerged, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This new coronavirus appeared in Wuhan, China, and is responsible for severe respiratory pneumonia in humans, namely, coronavirus disease 2019 (COVID-19). Having infected almost 200 million people worldwide and caused more than 4.1 million deaths as of today, this new disease has raised a significant number of questions about its molecular mechanism of replication and, in particular, how infectious viral particles are produced. Although viral entry is well characterized, the full assembly steps of SARS-CoV-2 have still not been fully described. Coronaviruses, including SARS-CoV-2, have four main structural proteins, namely, the spike glycoprotein (S), the membrane glycoprotein (M), the envelope protein (E), and the nucleocapsid protein (N). All these proteins have key roles in the process of coronavirus assembly and budding. In this review, we gathered the current knowledge about betacoronavirus structural proteins involved in viral particle assembly, membrane curvature and scission, and then egress in order to suggest and question a coherent model for SARS-CoV-2 particle production and release.
Collapse
Affiliation(s)
- David Bracquemond
- Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, CNRS UMR9004, Montpellier, France
| | - Delphine Muriaux
- Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, CNRS UMR9004, Montpellier, France
| |
Collapse
|
204
|
The role of dancing duplexes in biology and disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021. [PMID: 34656330 DOI: 10.1016/bs.pmbts.2021.06.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Across species, a common protein assembly arises: proteins containing structured domains separated by long intrinsically disordered regions, and dimerized through a self-association domain or through strong protein interactions. These systems are termed "IDP duplexes." These flexible dimers have roles in diverse pathologies including development of cancer, viral infections, and neurodegenerative disease. Here we discuss the role of disorder in IDP duplexes with similar domain architectures that bind hub protein, LC8. LC8-binding IDP duplexes are categorized into three groups: IDP duplexes that contain a self-association domain that is extended by LC8 binding, IDP duplexes that have no self-association domain and are dimerized through binding several copies of LC8, and multivalent LC8-binders that also have a self-association domain. Additionally, we discuss non-LC8-binding IDP duplexes with similar domain organizations, including the Nucleocapsid protein of SARS-CoV-2. We propose that IDP duplexes have structural features that are essential in many biological processes and that improved understanding of their structure function relationship will provide new therapeutic opportunities.
Collapse
|
205
|
Abstract
Viruses have evolved precise mechanisms for using the cellular physiological pathways for their perpetuation. These virus-driven biochemical events must be separated in space and time from those of the host cell. In recent years, granular structures, known for over a century for rabies virus, were shown to host viral gene function and were named using terms such as viroplasms, replication sites, inclusion bodies, or viral factories (VFs). More recently, these VFs were shown to be liquid-like, sharing properties with membrane-less organelles driven by liquid–liquid phase separation (LLPS) in a process widely referred to as biomolecular condensation. Some of the best described examples of these structures come from negative stranded RNA viruses, where micrometer size VFs are formed toward the end of the infectious cycle. We here discuss some basic principles of LLPS in connection with several examples of VFs and propose a view, which integrates viral replication mechanisms with the biochemistry underlying liquid-like organelles. In this view, viral protein and RNA components gradually accumulate up to a critical point during infection where phase separation is triggered. This yields an increase in transcription that leads in turn to increased translation and a consequent growth of initially formed condensates. According to chemical principles behind phase separation, an increase in the concentration of components increases the size of the condensate. A positive feedback cycle would thus generate in which crucial components, in particular nucleoproteins and viral polymerases, reach their highest levels required for genome replication. Progress in understanding viral biomolecular condensation leads to exploration of novel therapeutics. Furthermore, it provides insights into the fundamentals of phase separation in the regulation of cellular gene function given that virus replication and transcription, in particular those requiring host polymerases, are governed by the same biochemical principles.
Collapse
|
206
|
Spegg V, Altmeyer M. Biomolecular condensates at sites of DNA damage: More than just a phase. DNA Repair (Amst) 2021; 106:103179. [PMID: 34311273 PMCID: PMC7612016 DOI: 10.1016/j.dnarep.2021.103179] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/08/2021] [Accepted: 07/09/2021] [Indexed: 12/12/2022]
Abstract
Protein recruitment to DNA break sites is an integral part of the DNA damage response (DDR). Elucidation of the hierarchy and temporal order with which DNA damage sensors as well as repair and signaling factors assemble around chromosome breaks has painted a complex picture of tightly regulated macromolecular interactions that build specialized compartments to facilitate repair and maintenance of genome integrity. While many of the underlying interactions, e.g. between repair factors and damage-induced histone marks, can be explained by lock-and-key or induced fit binding models assuming fixed stoichiometries, structurally less well defined interactions, such as the highly dynamic multivalent interactions implicated in phase separation, also participate in the formation of multi-protein assemblies in response to genotoxic stress. Although much remains to be learned about these types of cooperative and highly dynamic interactions and their functional roles, the rapidly growing interest in material properties of biomolecular condensates and in concepts from polymer chemistry and soft matter physics to understand biological processes at different scales holds great promises. Here, we discuss nuclear condensates in the context of genome integrity maintenance, highlighting the cooperative potential between clustered stoichiometric binding and phase separation. Rather than viewing them as opposing scenarios, their combined effects can balance structural specificity with favorable physicochemical properties relevant for the regulation and function of multilayered nuclear condensates.
Collapse
Affiliation(s)
- Vincent Spegg
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.
| |
Collapse
|
207
|
de Araujo TS, Barbosa GM, Sanches K, Azevedo JM, Dos Santos Cabral KM, Almeida MS, Almeida FCL. The 1H, 15N, and 13C resonance assignments of the N-terminal domain of the nucleocapsid protein from the Middle East respiratory syndrome coronavirus. BIOMOLECULAR NMR ASSIGNMENTS 2021; 15:341-345. [PMID: 33914244 PMCID: PMC8082218 DOI: 10.1007/s12104-021-10027-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 04/20/2021] [Indexed: 06/12/2023]
Abstract
During the past 17 years, the coronaviruses have become a global public emergency, with the first appearance in 2012 in Saudi Arabia of the Middle East respiratory syndrome. Among the structural proteins encoded in the viral genome, the nucleocapsid protein is the most abundant in infected cells. It is a multifunctional phosphoprotein involved in the capsid formation, in the modulation and regulation of the viral life cycle. The N-terminal domain of N protein specifically interacts with transcriptional regulatory sequence (TRS) and is involved in the discontinuous transcription through the melting activity of double-stranded TRS (dsTRS).
Collapse
Affiliation(s)
- Talita Stelling de Araujo
- Protein Advanced Biochemistry (PAB), Institute of Medical Biochemistry (IBqM)-National Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
- Rio BioNMR Network (RMNRio), Rio de Janeiro, Brazil
| | - Glauce Moreno Barbosa
- National Center of Nuclear Magnetic Resonance (CNRMN), Institute of Medical Biochemistry (IBqM)-Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Rio BioNMR Network (RMNRio), Rio de Janeiro, Brazil
| | - Karoline Sanches
- National Center of Nuclear Magnetic Resonance (CNRMN), Institute of Medical Biochemistry (IBqM)-Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Rio BioNMR Network (RMNRio), Rio de Janeiro, Brazil
| | - Jéssica M Azevedo
- Protein Advanced Biochemistry (PAB), Institute of Medical Biochemistry (IBqM)-National Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
- Rio BioNMR Network (RMNRio), Rio de Janeiro, Brazil
| | - Katia Maria Dos Santos Cabral
- Protein Advanced Biochemistry (PAB), Institute of Medical Biochemistry (IBqM)-National Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
- Rio BioNMR Network (RMNRio), Rio de Janeiro, Brazil
| | - Marcius S Almeida
- Protein Advanced Biochemistry (PAB), Institute of Medical Biochemistry (IBqM)-National Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
- Rio BioNMR Network (RMNRio), Rio de Janeiro, Brazil
| | - Fabio C L Almeida
- National Center of Nuclear Magnetic Resonance (CNRMN), Institute of Medical Biochemistry (IBqM)-Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
- Rio BioNMR Network (RMNRio), Rio de Janeiro, Brazil.
| |
Collapse
|
208
|
Jack A, Ferro LS, Trnka MJ, Wehri E, Nadgir A, Nguyenla X, Fox D, Costa K, Stanley S, Schaletzky J, Yildiz A. SARS-CoV-2 nucleocapsid protein forms condensates with viral genomic RNA. PLoS Biol 2021; 19:e3001425. [PMID: 34634033 PMCID: PMC8553124 DOI: 10.1371/journal.pbio.3001425] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 10/28/2021] [Accepted: 09/28/2021] [Indexed: 12/13/2022] Open
Abstract
The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection causes Coronavirus Disease 2019 (COVID-19), a pandemic that seriously threatens global health. SARS-CoV-2 propagates by packaging its RNA genome into membrane enclosures in host cells. The packaging of the viral genome into the nascent virion is mediated by the nucleocapsid (N) protein, but the underlying mechanism remains unclear. Here, we show that the N protein forms biomolecular condensates with viral genomic RNA both in vitro and in mammalian cells. While the N protein forms spherical assemblies with homopolymeric RNA substrates that do not form base pairing interactions, it forms asymmetric condensates with viral RNA strands. Cross-linking mass spectrometry (CLMS) identified a region that drives interactions between N proteins in condensates, and deletion of this region disrupts phase separation. We also identified small molecules that alter the size and shape of N protein condensates and inhibit the proliferation of SARS-CoV-2 in infected cells. These results suggest that the N protein may utilize biomolecular condensation to package the SARS-CoV-2 RNA genome into a viral particle.
Collapse
Affiliation(s)
- Amanda Jack
- Biophysics Graduate Group, University of California, Berkeley, California, United States of America
| | - Luke S. Ferro
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
| | - Michael J. Trnka
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California, United States of America
| | - Eddie Wehri
- Center for Emerging and Neglected Diseases, University of California, Berkeley, California, United States of America
| | - Amrut Nadgir
- Physics Department, University of California, Berkeley, California, United States of America
| | - Xammy Nguyenla
- School of Public Health, Division of Infectious Diseases and Vaccinology, University of California, Berkeley, California, United States of America
| | - Douglas Fox
- School of Public Health, Division of Infectious Diseases and Vaccinology, University of California, Berkeley, California, United States of America
| | - Katelyn Costa
- Press West Illustrations, Boston, Massachusetts, United States of America
| | - Sarah Stanley
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
- School of Public Health, Division of Infectious Diseases and Vaccinology, University of California, Berkeley, California, United States of America
| | - Julia Schaletzky
- Center for Emerging and Neglected Diseases, University of California, Berkeley, California, United States of America
| | - Ahmet Yildiz
- Biophysics Graduate Group, University of California, Berkeley, California, United States of America
- Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America
- Physics Department, University of California, Berkeley, California, United States of America
| |
Collapse
|
209
|
Ma J, Zhu F, Zhao M, Shao F, Yu D, Ma J, Zhang X, Li W, Qian Y, Zhang Y, Jiang D, Wang S, Xia P. SARS-CoV-2 nucleocapsid suppresses host pyroptosis by blocking Gasdermin D cleavage. EMBO J 2021; 40:e108249. [PMID: 34296442 PMCID: PMC8420271 DOI: 10.15252/embj.2021108249] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 07/07/2021] [Accepted: 07/13/2021] [Indexed: 12/03/2022] Open
Abstract
SARS-CoV-2 is an emerging coronavirus that causes dysfunctions in multiple human cells and tissues. Studies have looked at the entry of SARS-CoV-2 into host cells mediated by the viral spike protein and human receptor ACE2. However, less is known about the cellular immune responses triggered by SARS-CoV-2 viral proteins. Here, we show that the nucleocapsid of SARS-CoV-2 inhibits host pyroptosis by blocking Gasdermin D (GSDMD) cleavage. SARS-CoV-2-infected monocytes show enhanced cellular interleukin-1β (IL-1β) expression, but reduced IL-1β secretion. While SARS-CoV-2 infection promotes activation of the NLRP3 inflammasome and caspase-1, GSDMD cleavage and pyroptosis are inhibited in infected human monocytes. SARS-CoV-2 nucleocapsid protein associates with GSDMD in cells and inhibits GSDMD cleavage in vitro and in vivo. The nucleocapsid binds the GSDMD linker region and hinders GSDMD processing by caspase-1. These insights into how SARS-CoV-2 antagonizes cellular inflammatory responses may open new avenues for treating COVID-19 in the future.
Collapse
Affiliation(s)
- Juan Ma
- Department of ImmunologySchool of Basic Medical SciencesPeking UniversityBeijingChina
- NHC Key Laboratory of Medical ImmunologyPeking UniversityBeijingChina
- Key Laboratory of Molecular ImmunologyChinese Academy of Medical SciencesBeijingChina
| | - Fangrui Zhu
- Department of ImmunologySchool of Basic Medical SciencesPeking UniversityBeijingChina
- NHC Key Laboratory of Medical ImmunologyPeking UniversityBeijingChina
- Key Laboratory of Molecular ImmunologyChinese Academy of Medical SciencesBeijingChina
| | - Min Zhao
- CAS Key Laboratory of Pathogenic Microbiology and ImmunologyInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
- Center for Biosafety Mega‐ScienceChinese Academy of SciencesWuhanChina
| | - Fei Shao
- CAS Key Laboratory of Pathogenic Microbiology and ImmunologyInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
- Center for Biosafety Mega‐ScienceChinese Academy of SciencesWuhanChina
| | - Dou Yu
- CAS Key Laboratory of Pathogenic Microbiology and ImmunologyInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
- Center for Biosafety Mega‐ScienceChinese Academy of SciencesWuhanChina
| | - Jiangwen Ma
- CAS Key Laboratory of Pathogenic Microbiology and ImmunologyInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
- Center for Biosafety Mega‐ScienceChinese Academy of SciencesWuhanChina
| | - Xusheng Zhang
- CAS Key Laboratory of Pathogenic Microbiology and ImmunologyInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
- Center for Biosafety Mega‐ScienceChinese Academy of SciencesWuhanChina
| | - Weitao Li
- Department of ImmunologySchool of Basic Medical SciencesPeking UniversityBeijingChina
- NHC Key Laboratory of Medical ImmunologyPeking UniversityBeijingChina
- Key Laboratory of Molecular ImmunologyChinese Academy of Medical SciencesBeijingChina
| | - Yan Qian
- Department of ImmunologySchool of Basic Medical SciencesPeking UniversityBeijingChina
- NHC Key Laboratory of Medical ImmunologyPeking UniversityBeijingChina
- Key Laboratory of Molecular ImmunologyChinese Academy of Medical SciencesBeijingChina
| | - Yan Zhang
- Department of ImmunologySchool of Basic Medical SciencesPeking UniversityBeijingChina
- NHC Key Laboratory of Medical ImmunologyPeking UniversityBeijingChina
- Key Laboratory of Molecular ImmunologyChinese Academy of Medical SciencesBeijingChina
| | - Dong Jiang
- Department of Sports MedicinePeking University Third HospitalBeijingChina
- Beijing Key Laboratory of Sports InjuriesInstitute of Sports Medicine of Peking UniversityBeijingChina
| | - Shuo Wang
- CAS Key Laboratory of Pathogenic Microbiology and ImmunologyInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
- Center for Biosafety Mega‐ScienceChinese Academy of SciencesWuhanChina
| | - Pengyan Xia
- Department of ImmunologySchool of Basic Medical SciencesPeking UniversityBeijingChina
- NHC Key Laboratory of Medical ImmunologyPeking UniversityBeijingChina
- Key Laboratory of Molecular ImmunologyChinese Academy of Medical SciencesBeijingChina
| |
Collapse
|
210
|
Del Veliz S, Rivera L, Bustos DM, Uhart M. Analysis of SARS-CoV-2 nucleocapsid phosphoprotein N variations in the binding site to human 14-3-3 proteins. Biochem Biophys Res Commun 2021; 569:154-160. [PMID: 34246830 PMCID: PMC8249750 DOI: 10.1016/j.bbrc.2021.06.100] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 06/30/2021] [Indexed: 12/15/2022]
Abstract
The SARS-CoV-2 N protein binds several cell host proteins including 14-3-3γ, a well-characterized regulatory protein. However, the biological function of this interaction is not completely understood. We analyzed the variability of ∼90 000 sequences of the SARS-CoV-2 N protein, particularly, its mutations in disordered regions containing binding motifs for 14-3-3 proteins. We studied how these mutations affect the binding energy to 14-3-3γ and found that changes positively affecting the predicted interaction with 14-3-3γ are the most successfully spread, with the highest prevalence in the phylogenetic tree. Although most residues are highly conserved within the 14-3-3 binding site, compensatory mutations to maintain the interaction energy of N-14-3-3γ were found, including half of the current variants of concern and interest. Our results suggest that binding of N to 14-3-3γ is beneficial for the virus, thus targeting this viral-host protein-protein interaction seems an attractive approach to explore antiviral strategies.
Collapse
Affiliation(s)
- Samanta Del Veliz
- Laboratorio de Integración de Señales Celulares, IHEM, Universidad Nacional de Cuyo, CONICET, Mendoza, Argentina
| | - Lautaro Rivera
- Laboratorio de Integración de Señales Celulares, IHEM, Universidad Nacional de Cuyo, CONICET, Mendoza, Argentina
| | - Diego M. Bustos
- Laboratorio de Integración de Señales Celulares, IHEM, Universidad Nacional de Cuyo, CONICET, Mendoza, Argentina,Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Marina Uhart
- Laboratorio de Integración de Señales Celulares, IHEM, Universidad Nacional de Cuyo, CONICET, Mendoza, Argentina,Corresponding author. IHEM, U.N.Cuyo-CONICET, Av. Libertador 80, 5500, Mendoza, Argentina
| |
Collapse
|
211
|
RNA Structures and Their Role in Selective Genome Packaging. Viruses 2021; 13:v13091788. [PMID: 34578369 PMCID: PMC8472981 DOI: 10.3390/v13091788] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/31/2021] [Accepted: 09/02/2021] [Indexed: 12/13/2022] Open
Abstract
To generate infectious viral particles, viruses must specifically select their genomic RNA from milieu that contains a complex mixture of cellular or non-genomic viral RNAs. In this review, we focus on the role of viral encoded RNA structures in genome packaging. We first discuss how packaging signals are constructed from local and long-range base pairings within viral genomes, as well as inter-molecular interactions between viral and host RNAs. Then, how genome packaging is regulated by the biophysical properties of RNA. Finally, we examine the impact of RNA packaging signals on viral evolution.
Collapse
|
212
|
Lee WS, Yousefi M, Yan B, Yong CL, Ooi YS. Know your enemy and know yourself - the case of SARS-CoV-2 host factors. Curr Opin Virol 2021; 50:159-170. [PMID: 34488003 PMCID: PMC8379091 DOI: 10.1016/j.coviro.2021.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/10/2021] [Accepted: 08/14/2021] [Indexed: 02/06/2023]
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the etiologic agent that causes Coronavirus Disease 2019 (COVID-19) pandemic, is a newly emerging respiratory RNA virus with exceptional transmissibility and pathogenicity. Numerous COVID-19 related studies have been fast-tracked, with the ultimate goal to end the pandemic. Here we review the major stages of SARS-CoV-2 infection cycle in cells, with specific emphasis on essential host factors. Insights into the cell biology of SARS-CoV-2 infection have accelerated the development of host-directed therapeutics, as shown by dozens of clinical trials evaluating COVID-19 treatments using host-targeting compounds.
Collapse
Affiliation(s)
- Wai Suet Lee
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Meisam Yousefi
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Biaoguo Yan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Cythia Lingli Yong
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Yaw Shin Ooi
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore.
| |
Collapse
|
213
|
Selvaraj C, Dinesh DC, Krafcikova P, Boura E, Aarthy M, Pravin MA, Singh SK. Structural Understanding of SARS-CoV-2 Drug Targets, Active Site Contour Map Analysis and COVID-19 Therapeutics. Curr Mol Pharmacol 2021; 15:418-433. [PMID: 34488601 DOI: 10.2174/1874467214666210906125959] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 03/11/2021] [Accepted: 03/17/2021] [Indexed: 11/22/2022]
Abstract
The most iconic word of the year 2020 is 'COVID-19', the shortened name for coronavirus disease 2019. The pandemic, caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), is responsible for multiple worldwide lockdowns, an economic crisis, and a substantial increase in hospitalizations for viral pneumonia along with respiratory failure and multiorgan dysfunctions. Recently, the first few vaccines were approved by World Health Organization (WHO) and can eventually save millions of lives. Even though, few emergency use drugs like Remdesivir and several other repurposed drugs, still there is no approved drug for COVID-19. The coronaviral encoded proteins involved in host-cell entry, replication, and host-cell invading mechanism are potentially therapeutic targets. This perspective review provides the molecular overview of SARS-CoV-2 life cycle for summarizing potential drug targets, structural insights, active site contour map analyses of those selected SARS-CoV-2 protein targets for drug discovery, immunology, and pathogenesis.
Collapse
Affiliation(s)
- Chandrabose Selvaraj
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi-630004, Tamil Nadu. India
| | | | - Petra Krafcikova
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo nam. 2, 166 10 Prague 6. Czech Republic
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo nam. 2, 166 10 Prague 6. Czech Republic
| | - Murali Aarthy
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi-630004, Tamil Nadu. India
| | - Muthuraja Arun Pravin
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi-630004, Tamil Nadu. India
| | - Sanjeev Kumar Singh
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi-630004, Tamil Nadu. India
| |
Collapse
|
214
|
Brown SL, Garrison DJ, May JP. Phase separation of a plant virus movement protein and cellular factors support virus-host interactions. PLoS Pathog 2021; 17:e1009622. [PMID: 34543360 PMCID: PMC8483311 DOI: 10.1371/journal.ppat.1009622] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 09/30/2021] [Accepted: 09/13/2021] [Indexed: 12/27/2022] Open
Abstract
Both cellular and viral proteins can undergo phase separation and form membraneless compartments that concentrate biomolecules. The p26 movement protein from single-stranded, positive-sense Pea enation mosaic virus 2 (PEMV2) separates into a dense phase in nucleoli where p26 and related orthologues must interact with fibrillarin (Fib2) as a pre-requisite for systemic virus movement. Using in vitro assays, viral ribonucleoprotein complexes containing p26, Fib2, and PEMV2 genomic RNAs formed droplets that may provide the basis for self-assembly in planta. Mutating basic p26 residues (R/K-G) blocked droplet formation and partitioning into Fib2 droplets or the nucleolus and prevented systemic movement of a Tobacco mosaic virus (TMV) vector in Nicotiana benthamiana. Mutating acidic residues (D/E-G) reduced droplet formation in vitro, increased nucleolar retention 6.5-fold, and prevented systemic movement of TMV, thus demonstrating that p26 requires electrostatic interactions for droplet formation and charged residues are critical for nucleolar trafficking and virus movement. p26 readily partitioned into stress granules (SGs), which are membraneless compartments that assemble by clustering of the RNA binding protein G3BP following stress. G3BP is upregulated during PEMV2 infection and over-expression of G3BP restricted PEMV2 RNA accumulation >20-fold. Deletion of the NTF2 domain that is required for G3BP condensation restored PEMV2 RNA accumulation >4-fold, demonstrating that phase separation enhances G3BP antiviral activity. These results indicate that p26 partitions into membraneless compartments with either proviral (Fib2) or antiviral (G3BP) factors.
Collapse
Affiliation(s)
- Shelby L. Brown
- Department of Cell and Molecular Biology and Biochemistry, School of Biological and Chemical Sciences, University of Missouri-Kansas City, Kansas City, Missouri, United States of America
| | - Dana J. Garrison
- Department of Cell and Molecular Biology and Biochemistry, School of Biological and Chemical Sciences, University of Missouri-Kansas City, Kansas City, Missouri, United States of America
| | - Jared P. May
- Department of Cell and Molecular Biology and Biochemistry, School of Biological and Chemical Sciences, University of Missouri-Kansas City, Kansas City, Missouri, United States of America
| |
Collapse
|
215
|
Sun Z, Zheng X, Ji F, Zhou M, Su X, Ren K, Li L. Mass Spectrometry Analysis of SARS-CoV-2 Nucleocapsid Protein Reveals Camouflaging Glycans and Unique Post-Translational Modifications. INFECTIOUS MICROBES & DISEASES 2021; 3:149-157. [PMID: 38630108 PMCID: PMC8454284 DOI: 10.1097/im9.0000000000000071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/18/2021] [Accepted: 06/28/2021] [Indexed: 01/08/2023]
Abstract
The devastating coronavirus disease 2019 (COVID-19) pandemic has prompted worldwide efforts to study structural biological traits of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its viral components. Compared to the Spike protein, which is the primary target for currently available vaccines or antibodies, knowledge about other virion structural components is incomplete. Using high-resolution mass spectrometry, we report a comprehensive post-translational modification (PTM) analysis of nucleocapsid phosphoprotein (NCP), the most abundant structural component of the SARS-CoV-2 virion. In addition to phosphoryl groups, we show that the SARS-CoV-2 NCP is decorated with a variety of PTMs, including N-glycans and ubiquitin. Based on newly identified PTMs, refined protein structural models of SARS-CoV-2 NCP were proposed and potential immune recognition epitopes of NCP were aligned with PTMs. These data can facilitate the design of novel vaccines or therapeutics targeting NCP, as valuable alternatives to the current vaccination and treatment paradigm that is under threat of the ever-mutating SARS-CoV-2 Spike protein.
Collapse
Affiliation(s)
- Zeyu Sun
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xiaoqin Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Feiyang Ji
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Menghao Zhou
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xiaoling Su
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Keyi Ren
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| |
Collapse
|
216
|
Almutairy BK, Alshetaili A, Anwer MK, Ali N. In silico identification of MicroRNAs targeting the key nucleator of stress granules, G3BP: Promising therapeutics for SARS-CoV-2 infection. Saudi J Biol Sci 2021; 28:7499-7504. [PMID: 34456603 PMCID: PMC8381622 DOI: 10.1016/j.sjbs.2021.08.056] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 08/03/2021] [Accepted: 08/16/2021] [Indexed: 11/05/2022] Open
Abstract
Stress granules (SGs) are non-membrane ribonucleoprotein condensates formed in response to environmental stress conditions via liquid–liquid phase separation (LLPS). SGs are involved in the pathogenesis of aging and aging-associated diseases, cancers, viral infection, and several other diseases. GTPase-activating protein (SH3 domain)-binding protein 1 and 2 (G3BP1/2) is a key component and commonly used marker of SGs. Recent studies have shown that SARS-CoV-2 nucleocapsid protein via sequestration of G3BPs inhibits SGs formation in the host cells. In this study, we have identified putative miRNAs targeting G3BP in search of modulators of the G3BP expression. These miRNAs could be considered as new therapeutic targets against COVID-19 infection via the regulation of SG assembly and dynamics.
Collapse
Affiliation(s)
- Bjad K Almutairy
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Alkharj, 11942, Saudi Arabia
| | - Abdullah Alshetaili
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Alkharj, 11942, Saudi Arabia
| | - Md Khalid Anwer
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Alkharj, 11942, Saudi Arabia
| | - Nemat Ali
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| |
Collapse
|
217
|
Slavin M, Zamel J, Zohar K, Eliyahu T, Braitbard M, Brielle E, Baraz L, Stolovich-Rain M, Friedman A, Wolf DG, Rouvinski A, Linial M, Schneidman-Duhovny D, Kalisman N. Targeted in situ cross-linking mass spectrometry and integrative modeling reveal the architectures of three proteins from SARS-CoV-2. Proc Natl Acad Sci U S A 2021; 118:e2103554118. [PMID: 34373319 PMCID: PMC8403911 DOI: 10.1073/pnas.2103554118] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Atomic structures of several proteins from the coronavirus family are still partial or unavailable. A possible reason for this gap is the instability of these proteins outside of the cellular context, thereby prompting the use of in-cell approaches. In situ cross-linking and mass spectrometry (in situ CLMS) can provide information on the structures of such proteins as they occur in the intact cell. Here, we applied targeted in situ CLMS to structurally probe Nsp1, Nsp2, and nucleocapsid (N) proteins from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and obtained cross-link sets with an average density of one cross-link per 20 residues. We then employed integrative modeling that computationally combined the cross-linking data with domain structures to determine full-length atomic models. For the Nsp2, the cross-links report on a complex topology with long-range interactions. Integrative modeling with structural prediction of individual domains by the AlphaFold2 system allowed us to generate a single consistent all-atom model of the full-length Nsp2. The model reveals three putative metal binding sites and suggests a role for Nsp2 in zinc regulation within the replication-transcription complex. For the N protein, we identified multiple intra- and interdomain cross-links. Our integrative model of the N dimer demonstrates that it can accommodate three single RNA strands simultaneously, both stereochemically and electrostatically. For the Nsp1, cross-links with the 40S ribosome were highly consistent with recent cryogenic electron microscopy structures. These results highlight the importance of cellular context for the structural probing of recalcitrant proteins and demonstrate the effectiveness of targeted in situ CLMS and integrative modeling.
Collapse
Affiliation(s)
- Moriya Slavin
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Joanna Zamel
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Keren Zohar
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Tsiona Eliyahu
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Merav Braitbard
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Esther Brielle
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Leah Baraz
- Hadassah Academic College Jerusalem, Jerusalem 9101001, Israel
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Kuvin Center for the Study of Infectious and Tropical Diseases, The Hebrew University-Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Miri Stolovich-Rain
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Kuvin Center for the Study of Infectious and Tropical Diseases, The Hebrew University-Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Ahuva Friedman
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Kuvin Center for the Study of Infectious and Tropical Diseases, The Hebrew University-Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Dana G Wolf
- Clinical Virology Unit, Hadassah Hebrew University Medical Center, 9190401 Jerusalem, Israel
| | - Alexander Rouvinski
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Kuvin Center for the Study of Infectious and Tropical Diseases, The Hebrew University-Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Michal Linial
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel;
| | - Dina Schneidman-Duhovny
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel;
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Nir Kalisman
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel;
| |
Collapse
|
218
|
Scoca V, Di Nunzio F. Membraneless organelles restructured and built by pandemic viruses: HIV-1 and SARS-CoV-2. J Mol Cell Biol 2021; 13:259-268. [PMID: 33760045 PMCID: PMC8083626 DOI: 10.1093/jmcb/mjab020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 01/22/2021] [Accepted: 01/25/2021] [Indexed: 12/13/2022] Open
Abstract
Viruses hijack host functions to invade their target cells and spread to new cells. Specifically, viruses learned to usurp liquid‒liquid phase separation (LLPS), a newly exploited mechanism, used by the cell to concentrate enzymes to accelerate and confine a wide variety of cellular processes. LLPS gives rise to actual membraneless organelles (MLOs), which do not only increase reaction rates but also act as a filter to select molecules to be retained or to be excluded from the liquid droplet. This is exactly what seems to happen with the condensation of SARS-CoV-2 nucleocapsid protein to favor the packaging of intact viral genomes, excluding viral subgenomic or host cellular RNAs. Another older pandemic virus, HIV-1, also takes advantage of LLPS in the host cell during the viral cycle. Recent discoveries highlighted that HIV-1 RNA genome condensates in nuclear MLOs accompanied by specific host and viral proteins, breaking the dogma of retroviruses that limited viral synthesis exclusively to the cytoplasmic compartment. Intriguing fundamental properties of viral/host LLPS remain still unclear. Future studies will contribute to deeply understanding the role of pathogen-induced MLOs in the epidemic invasion of pandemic viruses.
Collapse
Affiliation(s)
- Viviana Scoca
- Advanced Molecular Virology and Retroviral Dynamics Group, Department of Virology, Pasteur Institute, Paris, France
- BioSPC Doctoral School, Universitè de Paris, Paris, France
| | - Francesca Di Nunzio
- Advanced Molecular Virology and Retroviral Dynamics Group, Department of Virology, Pasteur Institute, Paris, France
| |
Collapse
|
219
|
Liquid-liquid phase separation in human health and diseases. Signal Transduct Target Ther 2021; 6:290. [PMID: 34334791 PMCID: PMC8326283 DOI: 10.1038/s41392-021-00678-1] [Citation(s) in RCA: 327] [Impact Index Per Article: 81.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/26/2021] [Accepted: 06/10/2021] [Indexed: 02/07/2023] Open
Abstract
Emerging evidence suggests that liquid-liquid phase separation (LLPS) represents a vital and ubiquitous phenomenon underlying the formation of membraneless organelles in eukaryotic cells (also known as biomolecular condensates or droplets). Recent studies have revealed evidences that indicate that LLPS plays a vital role in human health and diseases. In this review, we describe our current understanding of LLPS and summarize its physiological functions. We further describe the role of LLPS in the development of human diseases. Additionally, we review the recently developed methods for studying LLPS. Although LLPS research is in its infancy-but is fast-growing-it is clear that LLPS plays an essential role in the development of pathophysiological conditions. This highlights the need for an overview of the recent advances in the field to translate our current knowledge regarding LLPS into therapeutic discoveries.
Collapse
|
220
|
Saito A, Shofa M, Ode H, Yumiya M, Hirano J, Okamoto T, Yoshimura SH. How Do Flaviviruses Hijack Host Cell Functions by Phase Separation? Viruses 2021; 13:v13081479. [PMID: 34452345 PMCID: PMC8402827 DOI: 10.3390/v13081479] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/21/2021] [Accepted: 07/26/2021] [Indexed: 11/17/2022] Open
Abstract
Viral proteins interact with different sets of host cell components throughout the viral life cycle and are known to localize to the intracellular membraneless organelles (MLOs) of the host cell, where formation/dissolution is regulated by phase separation of intrinsically disordered proteins and regions (IDPs/IDRs). Viral proteins are rich in IDRs, implying that viruses utilize IDRs to regulate phase separation of the host cell organelles and augment replication by commandeering the functions of the organelles and/or sneaking into the organelles to evade the host immune response. This review aims to integrate current knowledge of the structural properties and intracellular localizations of viral IDPs to understand viral strategies in the host cell. First, the properties of viral IDRs are reviewed and similarities and differences with those of eukaryotes are described. The higher IDR content in viruses with smaller genomes suggests that IDRs are essential characteristics of viral proteins. Then, the interactions of the IDRs of flaviviruses with the MLOs of the host cell are investigated with emphasis on the viral proteins localized in the nucleoli and stress granules. Finally, the possible roles of viral IDRs in regulation of the phase separation of organelles and future possibilities for antiviral drug development are discussed.
Collapse
Affiliation(s)
- Akatsuki Saito
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan;
- Center for Animal Disease Control, University of Miyazaki, Miyazaki 889-2192, Japan
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
- Correspondence: (A.S.); (T.O.); (S.H.Y.)
| | - Maya Shofa
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan;
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Hirotaka Ode
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya 460-0001, Japan;
| | - Maho Yumiya
- Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan; (M.Y.); (J.H.)
| | - Junki Hirano
- Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan; (M.Y.); (J.H.)
| | - Toru Okamoto
- Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan; (M.Y.); (J.H.)
- Center for Infectious Diseases Education and Research, Osaka University, Osaka 565-0871, Japan
- Correspondence: (A.S.); (T.O.); (S.H.Y.)
| | - Shige H. Yoshimura
- Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
- Correspondence: (A.S.); (T.O.); (S.H.Y.)
| |
Collapse
|
221
|
Ye Q, Lu S, Corbett KD. Structural Basis for SARS-CoV-2 Nucleocapsid Protein Recognition by Single-Domain Antibodies. Front Immunol 2021; 12:719037. [PMID: 34381460 PMCID: PMC8351461 DOI: 10.3389/fimmu.2021.719037] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 06/29/2021] [Indexed: 12/23/2022] Open
Abstract
The COVID-19 pandemic, caused by the coronavirus SARS-CoV-2, is the most severe public health event of the twenty-first century. While effective vaccines against SARS-CoV-2 have been developed, there remains an urgent need for diagnostics to quickly and accurately detect infections. Antigen tests, particularly those that detect the abundant SARS-CoV-2 Nucleocapsid protein, are a proven method for detecting active SARS-CoV-2 infections. Here we report high-resolution crystal structures of three llama-derived single-domain antibodies that bind the SARS-CoV-2 Nucleocapsid protein with high affinity. Each antibody recognizes a specific folded domain of the protein, with two antibodies recognizing the N-terminal RNA binding domain and one recognizing the C-terminal dimerization domain. The two antibodies that recognize the RNA binding domain affect both RNA binding affinity and RNA-mediated phase separation of the Nucleocapsid protein. All three antibodies recognize highly conserved surfaces on the Nucleocapsid protein, suggesting that they could be used to develop affordable diagnostic tests to detect all circulating SARS-CoV-2 variants.
Collapse
Affiliation(s)
- Qiaozhen Ye
- Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA, United States
| | - Shan Lu
- Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA, United States
| | - Kevin D Corbett
- Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA, United States.,Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, United States
| |
Collapse
|
222
|
Forsythe HM, Rodriguez Galvan J, Yu Z, Pinckney S, Reardon P, Cooley RB, Zhu P, Rolland AD, Prell JS, Barbar E. Multivalent binding of the partially disordered SARS-CoV-2 nucleocapsid phosphoprotein dimer to RNA. Biophys J 2021; 120:2890-2901. [PMID: 33794152 PMCID: PMC8007181 DOI: 10.1016/j.bpj.2021.03.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/16/2021] [Accepted: 03/25/2021] [Indexed: 12/17/2022] Open
Abstract
The nucleocapsid phosphoprotein N plays critical roles in multiple processes of the severe acute respiratory syndrome coronavirus 2 infection cycle: it protects and packages viral RNA in N assembly, interacts with the inner domain of spike protein, binds to structural membrane (M) protein during virion packaging and maturation, and to proteases causing replication of infective virus particle. Even with its importance, very limited biophysical studies are available on the N protein because of its high level of disorder, high propensity for aggregation, and high susceptibility for autoproteolysis. Here, we successfully prepare the N protein and a 1000-nucleotide fragment of viral RNA in large quantities and purity suitable for biophysical studies. A combination of biophysical and biochemical techniques demonstrates that the N protein is partially disordered and consists of an independently folded RNA-binding domain and a dimerization domain, flanked by disordered linkers. The protein assembles as a tight dimer with a dimerization constant of sub-micromolar but can also form transient interactions with other N proteins, facilitating larger oligomers. NMR studies on the ∼100-kDa dimeric protein identify a specific domain that binds 1-1000-nt RNA and show that the N-RNA complex remains highly disordered. Analytical ultracentrifugation, isothermal titration calorimetry, multiangle light scattering, and cross-linking experiments identify a heterogeneous mixture of complexes with a core corresponding to at least 70 dimers of N bound to 1-1000 RNA. In contrast, very weak binding is detected with a smaller construct corresponding to the RNA-binding domain using similar experiments. A model that explains the importance of the bivalent structure of N to its binding on multivalent sites of the viral RNA is presented.
Collapse
Affiliation(s)
| | | | - Zhen Yu
- Department of Biochemistry and Biophysics Corvallis, Oregon
| | - Seth Pinckney
- Department of Biochemistry and Biophysics Corvallis, Oregon
| | | | | | - Phillip Zhu
- Department of Biochemistry and Biophysics Corvallis, Oregon
| | - Amber D Rolland
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon
| | - James S Prell
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon
| | - Elisar Barbar
- Department of Biochemistry and Biophysics Corvallis, Oregon.
| |
Collapse
|
223
|
Song J. Adenosine triphosphate energy-independently controls protein homeostasis with unique structure and diverse mechanisms. Protein Sci 2021; 30:1277-1293. [PMID: 33829608 PMCID: PMC8197423 DOI: 10.1002/pro.4079] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/30/2021] [Accepted: 04/02/2021] [Indexed: 02/06/2023]
Abstract
Proteins function in the crowded cellular environments with high salt concentrations, thus facing tremendous challenges of misfolding/aggregation which represents a pathological hallmark of aging and an increasing spectrum of human diseases. Recently, intrinsically disordered regions (IDRs) were recognized to drive liquid-liquid phase separation (LLPS), a common principle for organizing cellular membraneless organelles (MLOs). ATP, the universal energy currency for all living cells, mysteriously has concentrations of 2-12 mM, much higher than required for its previously-known functions. Only recently, ATP was decoded to behave as a biological hydrotrope to inhibit protein LLPS and aggregation at mM. We further revealed that ATP also acts as a bivalent binder, which not only biphasically modulates LLPS driven by IDRs of human and viral proteins, but also bind to the conserved nucleic-acid-binding surfaces of the folded proteins. Most unexpectedly, ATP appears to act as a hydration mediator to antagonize the crowding-induced destabilization as well as to enhance folding of proteins without significant binding. Here, this review focuses on summarizing the results of these biophysical studies and discussing their implications in an evolutionary context. By linking triphosphate with unique hydration property to adenosine, ATP appears to couple the ability for establishing hydrophobic, π-π, π-cation and electrostatic interactions to the capacity in mediating hydration of proteins, which is at the heart of folding, dynamics, stability, phase separation and aggregation. Consequently, ATP acquired a category of functions at ~mM to energy-independently control protein homeostasis with diverse mechanisms, thus implying a link between cellular ATP concentrations and protein-aggregation diseases.
Collapse
Affiliation(s)
- Jianxing Song
- Department of Biological Sciences, Faculty of ScienceNational University of SingaporeSingaporeSingapore
| |
Collapse
|
224
|
Wang S, Dai T, Qin Z, Pan T, Chu F, Lou L, Zhang L, Yang B, Huang H, Lu H, Zhou F. Targeting liquid-liquid phase separation of SARS-CoV-2 nucleocapsid protein promotes innate antiviral immunity by elevating MAVS activity. Nat Cell Biol 2021; 23:718-732. [PMID: 34239064 DOI: 10.1038/s41556-021-00710-0] [Citation(s) in RCA: 194] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 06/07/2021] [Indexed: 02/06/2023]
Abstract
Patients with Coronavirus disease 2019 exhibit low expression of interferon-stimulated genes, contributing to a limited antiviral response. Uncovering the underlying mechanism of innate immune suppression and rescuing the innate antiviral response remain urgent issues in the current pandemic. Here we identified that the dimerization domain of the SARS-CoV-2 nucleocapsid protein (SARS2-NP) is required for SARS2-NP to undergo liquid-liquid phase separation with RNA, which inhibits Lys63-linked poly-ubiquitination and aggregation of MAVS and thereby suppresses the innate antiviral immune response. Mice infected with an RNA virus carrying SARS2-NP exhibited reduced innate immunity, an increased viral load and high morbidity. Notably, we identified SARS2-NP acetylation at Lys375 by host acetyltransferase and reported frequently occurring acetylation-mimicking mutations of Lys375, all of which impaired SARS2-NP liquid-liquid phase separation with RNA. Importantly, a peptide targeting the dimerization domain was screened out to disrupt the SARS2-NP liquid-liquid phase separation and demonstrated to inhibit SARS-CoV-2 replication and rescue innate antiviral immunity both in vitro and in vivo.
Collapse
Affiliation(s)
- Shuai Wang
- Institutes of Biology and Medical Science, Soochow University, Suzhou, China
| | - Tong Dai
- Institutes of Biology and Medical Science, Soochow University, Suzhou, China
| | - Ziran Qin
- Institutes of Biology and Medical Science, Soochow University, Suzhou, China
| | - Ting Pan
- Center for Infection and Immunity Studies, School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Feng Chu
- Institutes of Biology and Medical Science, Soochow University, Suzhou, China
| | - Lingfeng Lou
- Institutes of Biology and Medical Science, Soochow University, Suzhou, China
| | - Long Zhang
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Bing Yang
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China.,Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Huizhe Huang
- Faculty of Basic Medical Sciences, Chonqing Medical University, Chongqing, China
| | - Huasong Lu
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Fangfang Zhou
- Institutes of Biology and Medical Science, Soochow University, Suzhou, China.
| |
Collapse
|
225
|
Cai T, Yu Z, Wang Z, Liang C, Richard S. Arginine methylation of SARS-Cov-2 nucleocapsid protein regulates RNA binding, its ability to suppress stress granule formation, and viral replication. J Biol Chem 2021; 297:100821. [PMID: 34029587 PMCID: PMC8141346 DOI: 10.1016/j.jbc.2021.100821] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/13/2021] [Accepted: 05/20/2021] [Indexed: 12/18/2022] Open
Abstract
Viral proteins are known to be methylated by host protein arginine methyltransferases (PRMTs) necessary for the viral life cycle, but it remains unknown whether severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteins are methylated. Herein, we show that PRMT1 methylates SARS-CoV-2 nucleocapsid (N) protein at residues R95 and R177 within RGG/RG motifs, preferred PRMT target sequences. We confirmed arginine methylation of N protein by immunoblotting viral proteins extracted from SARS-CoV-2 virions isolated from cell culture. Type I PRMT inhibitor (MS023) or substitution of R95 or R177 with lysine inhibited interaction of N protein with the 5'-UTR of SARS-CoV-2 genomic RNA, a property required for viral packaging. We also defined the N protein interactome in HEK293 cells, which identified PRMT1 and many of its RGG/RG substrates, including the known interacting protein G3BP1 as well as other components of stress granules (SGs), which are part of the host antiviral response. Methylation of R95 regulated the ability of N protein to suppress the formation of SGs, as R95K substitution or MS023 treatment blocked N-mediated suppression of SGs. Also, the coexpression of methylarginine reader Tudor domain-containing protein 3 quenched N protein-mediated suppression of SGs in a dose-dependent manner. Finally, pretreatment of VeroE6 cells with MS023 significantly reduced SARS-CoV-2 replication. Because type I PRMT inhibitors are already undergoing clinical trials for cancer treatment, inhibiting arginine methylation to target the later stages of the viral life cycle such as viral genome packaging and assembly of virions may represent an additional therapeutic application of these drugs.
Collapse
Affiliation(s)
- Ting Cai
- Segal Cancer Center, Lady Davis Institute for Medical Research and Gerald Bronfman Department of Oncology and Departments of Biochemistry, Human Genetics and Medicine, McGill University, Montréal, Québec, Canada
| | - Zhenbao Yu
- Segal Cancer Center, Lady Davis Institute for Medical Research and Gerald Bronfman Department of Oncology and Departments of Biochemistry, Human Genetics and Medicine, McGill University, Montréal, Québec, Canada
| | - Zhen Wang
- McGill Centre for Viral Diseases, Lady Davis Institute for Medical Research and Department of Medicine, Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
| | - Chen Liang
- McGill Centre for Viral Diseases, Lady Davis Institute for Medical Research and Department of Medicine, Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
| | - Stéphane Richard
- Segal Cancer Center, Lady Davis Institute for Medical Research and Gerald Bronfman Department of Oncology and Departments of Biochemistry, Human Genetics and Medicine, McGill University, Montréal, Québec, Canada.
| |
Collapse
|
226
|
Sasson JM, Campo JJ, Carpenter RM, Young MK, Randall AZ, Trappl-Kimmons K, Oberai A, Hung C, Edgar J, Teng AA, Pablo JV, Liang X, Yee A, Petri WA, Camerini D. Diverse Humoral Immune Responses in Younger and Older Adult COVID-19 Patients. mBio 2021; 12:e0122921. [PMID: 34182775 PMCID: PMC8262923 DOI: 10.1128/mbio.01229-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
We sought to discover links between antibody responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and patient clinical variables, cytokine profiles, and antibodies to endemic coronaviruses. Serum samples from 30 patients of younger (26 to 39 years) and older (69 to 83 years) age groups and with varying clinical severities ranging from outpatient to mechanically ventilated were collected and used to probe a novel multi-coronavirus protein microarray. This microarray contained variable-length overlapping fragments of SARS-CoV-2 spike (S), envelope (E), membrane (M), nucleocapsid (N), and open reading frame (ORF) proteins created through in vitro transcription and translation (IVTT). The array also contained SARS-CoV, Middle East respiratory syndrome coronavirus (MERS-CoV), human coronavirus OC43 (HCoV-OC43), and HCoV-NL63 proteins. IgG antibody responses to specific epitopes within the S1 protein region spanning amino acids (aa) 500 to 650 and within the N protein region spanning aa 201 to 300 were found to be significantly higher in older patients and further significantly elevated in those older patients who were ventilated. Additionally, there was a noticeable overlap between antigenic regions and known mutation locations in selected emerging SARS-CoV-2 variants of current clinical consequence (B.1.1.7, B1.351, P.1, CAL20.C, and B.1.526). Moreover, the older age group displayed more consistent correlations of antibody reactivity with systemic cytokine and chemokine responses than the younger adult group. A subset of patients, however, had little or no response to SARS-CoV-2 antigens and disproportionately severe clinical outcomes. Further characterization of these slow-low-responding individuals with cytokine analysis revealed significantly higher interleukin-10 (IL-10), IL-15, and interferon gamma-induced protein 10 (IP-10) levels and lower epidermal growth factor (EGF) and soluble CD40 ligand (sCD40L) levels than those of seroreactive patients in the cohort. IMPORTANCE As numerous viral variants continue to emerge in the coronavirus disease 2019 (COVID-19) pandemic, determining antibody reactivity to SARS-CoV-2 epitopes becomes essential in discerning changes in the immune response to infection over time. This study enabled us to identify specific areas of antigenicity within the SARS-CoV-2 proteome, allowing us to detect correlations of epitopes with clinical metadata and immunological signals to gain holistic insight into SARS-CoV-2 infection. This work also emphasized the risk of mutation accumulation in viral variants and the potential for evasion of the adaptive immune responses in the event of reinfection. We additionally highlighted the correlation of antigenicity between structural proteins of SARS-CoV-2 and endemic HCoVs, raising the possibility of cross-protection between homologous lineages. Finally, we identified a subset of patients with minimal antibody reactivity to SARS-CoV-2 infection, prompting discussion of the potential consequences of this alternative immune response.
Collapse
Affiliation(s)
- Jennifer M. Sasson
- Department of Medicine, University of Virginia Health System, Charlottesville, Virginia, USA
| | | | - Rebecca M. Carpenter
- Department of Medicine, University of Virginia Health System, Charlottesville, Virginia, USA
| | - Mary K. Young
- Department of Medicine, University of Virginia Health System, Charlottesville, Virginia, USA
| | | | | | - Amit Oberai
- Antigen Discovery, Incorporated, Irvine, California, USA
| | | | - Joshua Edgar
- Antigen Discovery, Incorporated, Irvine, California, USA
| | - Andy A. Teng
- Antigen Discovery, Incorporated, Irvine, California, USA
| | | | - Xiaowu Liang
- Antigen Discovery, Incorporated, Irvine, California, USA
| | - Angela Yee
- Antigen Discovery, Incorporated, Irvine, California, USA
| | - William A. Petri
- Department of Medicine, University of Virginia Health System, Charlottesville, Virginia, USA
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia Health System, Charlottesville, Virginia, USA
- Department of Pathology, University of Virginia Health System, Charlottesville, Virginia, USA
| | - David Camerini
- Antigen Discovery, Incorporated, Irvine, California, USA
- Center for Virus Research, University of California, Irvine, Irvine, California, USA
| |
Collapse
|
227
|
Zhao H, Wu D, Nguyen A, Li Y, Adão RC, Valkov E, Patterson GH, Piszczek G, Schuck P. Energetic and structural features of SARS-CoV-2 N-protein co-assemblies with nucleic acids. iScience 2021; 24:102523. [PMID: 33997662 PMCID: PMC8103780 DOI: 10.1016/j.isci.2021.102523] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/26/2021] [Accepted: 05/04/2021] [Indexed: 02/06/2023] Open
Abstract
Nucleocapsid (N) protein of the SARS-CoV-2 virus packages the viral genome into well-defined ribonucleoprotein particles, but the molecular pathway is still unclear. N-protein is dimeric and consists of two folded domains with nucleic acid (NA) binding sites, surrounded by intrinsically disordered regions that promote liquid-liquid phase separation. Here, we use biophysical tools to study N-protein interactions with oligonucleotides of different lengths, examining the size, composition, secondary structure, and energetics of the resulting states. We observe the formation of supramolecular clusters or nuclei preceding growth into phase-separated droplets. Short hexanucleotide NA forms compact 2:2 N-protein/NA complexes with reduced disorder. Longer oligonucleotides expose additional N-protein interactions and multi-valent protein-NA interactions, which generate higher-order mixed oligomers and simultaneously promote growth of droplets. Phase separation is accompanied by a significant change in protein secondary structure, different from that caused by initial NA binding, which may contribute to the assembly of ribonucleoprotein particles within macromolecular condensates.
Collapse
Affiliation(s)
- Huaying Zhao
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, 13 South Drive, Bethesda, MD 20892, USA
| | - Di Wu
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, 50 South Drive, Bethesda, MD 20892, USA
| | - Ai Nguyen
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, 13 South Drive, Bethesda, MD 20892, USA
| | - Yan Li
- Protein/Peptide Sequencing Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Regina C. Adão
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, 13 South Drive, Bethesda, MD 20892, USA
| | - Eugene Valkov
- Messenger RNA Regulation and Decay Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Building 560, Room 21-105A, Frederick, MD 21702, USA
| | - George H. Patterson
- Section on Biophotonics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Grzegorz Piszczek
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, 50 South Drive, Bethesda, MD 20892, USA
| | - Peter Schuck
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, 13 South Drive, Bethesda, MD 20892, USA
| |
Collapse
|
228
|
Wu C, Qavi AJ, Hachim A, Kavian N, Cole AR, Moyle AB, Wagner ND, Sweeney-Gibbons J, Rohrs HW, Gross ML, Peiris JSM, Basler CF, Farnsworth CW, Valkenburg SA, Amarasinghe GK, Leung DW. Characterization of SARS-CoV-2 nucleocapsid protein reveals multiple functional consequences of the C-terminal domain. iScience 2021; 24:102681. [PMID: 34095780 PMCID: PMC8168301 DOI: 10.1016/j.isci.2021.102681] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 05/13/2021] [Accepted: 05/28/2021] [Indexed: 12/13/2022] Open
Abstract
Nucleocapsid (N) encoded by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays key roles in the replication cycle and is a critical serological marker. Here, we characterize essential biochemical properties of N and describe the utility of these insights in serological studies. We define N domains important for oligomerization and RNA binding and show that N oligomerization provides a high-affinity RNA-binding platform. We also map the RNA-binding interface, showing protection in the N-terminal domain and linker region. In addition, phosphorylation causes reduction of RNA binding and redistribution of N from liquid droplets to loose coils, showing how N-RNA accessibility and assembly may be regulated by phosphorylation. Finally, we find that the C-terminal domain of N is the most immunogenic, based on antibody binding to patient samples. Together, we provide a biochemical description of SARS-CoV-2 N and highlight the value of using N domains as highly specific and sensitive diagnostic markers.
Collapse
Affiliation(s)
- Chao Wu
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Abraham J. Qavi
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Asmaa Hachim
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Niloufar Kavian
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong, China
- Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, Assistance Publique–Hôpitaux de Paris, Hôpital Universitaire Paris Centre, Centre Hospitalier Universitaire Cochin, Service d’Immunologie Biologique, Paris, France
- Institut Cochin, INSERM U1016, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Aidan R. Cole
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Austin B. Moyle
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | - Nicole D. Wagner
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | - Joyce Sweeney-Gibbons
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Henry W. Rohrs
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | - J. S. Malik Peiris
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong, China
- Division of Public Health Laboratory Sciences, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Christopher F. Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Christopher W. Farnsworth
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Sophie A. Valkenburg
- HKU-Pasteur Research Pole, School of Public Health, The University of Hong Kong, Hong Kong, China
| | - Gaya K. Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Daisy W. Leung
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
- Department of Internal Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| |
Collapse
|
229
|
Shapiro DM, Ney M, Eghtesadi SA, Chilkoti A. Protein Phase Separation Arising from Intrinsic Disorder: First-Principles to Bespoke Applications. J Phys Chem B 2021; 125:6740-6759. [PMID: 34143622 DOI: 10.1021/acs.jpcb.1c01146] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The phase separation of biomolecules has become the focus of intense research in the past decade, with a growing body of research implicating this phenomenon in essentially all biological functions, including but not limited to homeostasis, stress responses, gene regulation, cell differentiation, and disease. Excellent reviews have been published previously on the underlying physical basis of liquid-liquid phase separation (LLPS) of biological molecules (Nat. Phys. 2015, 11, 899-904) and LLPS as it occurs natively in physiology and disease (Science 2017, 357, eaaf4382; Biochemistry 2018, 57, 2479-2487; Chem. Rev. 2014, 114, 6844-6879). Here, we review how the theoretical physical basis of LLPS has been used to better understand the behavior of biomolecules that undergo LLPS in natural systems and how this understanding has also led to the development of novel synthetic systems that exhibit biomolecular phase separation, and technologies that exploit these phenomena. In part 1 of this Review, we explore the theory behind the phase separation of biomolecules and synthetic macromolecules and introduce a few notable phase-separating biomolecules. In part 2, we cover experimental and computational methods used to study phase-separating proteins and how these techniques have uncovered the mechanisms underlying phase separation in physiology and disease. Finally, in part 3, we cover the development and applications of engineered phase-separating polypeptides, ranging from control of their self-assembly to create defined supramolecular architectures to reprogramming biological processes using engineered IDPs that exhibit LLPS.
Collapse
Affiliation(s)
- Daniel Mark Shapiro
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Max Ney
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Seyed Ali Eghtesadi
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| |
Collapse
|
230
|
Chen SC, Olsthoorn RCL, Yu CH. Structural phylogenetic analysis reveals lineage-specific RNA repetitive structural motifs in all coronaviruses and associated variations in SARS-CoV-2. Virus Evol 2021; 7:veab021. [PMID: 34141447 PMCID: PMC8206606 DOI: 10.1093/ve/veab021] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
In many single-stranded (ss) RNA viruses, the cis-acting packaging signal that confers selectivity genome packaging usually encompasses short structured RNA repeats. These structural units, termed repetitive structural motifs (RSMs), potentially mediate capsid assembly by specific RNA–protein interactions. However, general knowledge of the conservation and/or the diversity of RSMs in the positive-sense ssRNA coronaviruses (CoVs) is limited. By performing structural phylogenetic analysis, we identified a variety of RSMs in nearly all CoV genomic RNAs, which are exclusively located in the 5′-untranslated regions (UTRs) and/or in the inter-domain regions of poly-protein 1ab coding sequences in a lineage-specific manner. In all alpha- and beta-CoVs, except for Embecovirus spp, two to four copies of 5′-gUUYCGUc-3′ RSMs displaying conserved hexa-loop sequences were generally identified in Stem-loop 5 (SL5) located in the 5′-UTRs of genomic RNAs. In Embecovirus spp., however, two to eight copies of 5′-agc-3′/guAAu RSMs were found in the coding regions of non-structural protein (NSP) 3 and/or NSP15 in open reading frame (ORF) 1ab. In gamma- and delta-CoVs, other types of RSMs were found in several clustered structural elements in 5′-UTRs and/or ORF1ab. The identification of RSM-encompassing structural elements in all CoVs suggests that these RNA elements play fundamental roles in the life cycle of CoVs. In the recently emerged SARS-CoV-2, beta-CoV-specific RSMs are also found in its SL5, displaying two copies of 5′-gUUUCGUc-3′ motifs. However, multiple sequence alignment reveals that the majority of SARS-CoV-2 possesses a variant RSM harboring SL5b C241U, and intriguingly, several variations in the coding sequences of viral proteins, such as Nsp12 P323L, S protein D614G, and N protein R203K-G204R, are concurrently found with such variant RSM. In conclusion, the comprehensive exploration for RSMs reveals phylogenetic insights into the RNA structural elements in CoVs as a whole and provides a new perspective on variations currently found in SARS-CoV-2.
Collapse
Affiliation(s)
- Shih-Cheng Chen
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng-Kung University, No.1, University Road, Tainan City 701, Taiwan
| | - René C L Olsthoorn
- Department of Supramolecular Biomaterials Chemistry, Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333 CC, Leiden,The Netherlands
| | - Chien-Hung Yu
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng-Kung University, No.1, University Road, Tainan City 701, Taiwan
| |
Collapse
|
231
|
Roden CA, Dai Y, Seim I, Lee M, Sealfon R, McLaughlin GA, Boerneke MA, Iserman C, Wey SA, Ekena JL, Troyanskaya OG, Weeks KM, You L, Chilkoti A, Gladfelter AS. Double-stranded RNA drives SARS-CoV-2 nucleocapsid protein to undergo phase separation at specific temperatures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 34159327 DOI: 10.1101/2021.06.14.448452] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Betacoronavirus SARS-CoV-2 infections caused the global Covid-19 pandemic. The nucleocapsid protein (N-protein) is required for multiple steps in the betacoronavirus replication cycle. SARS-CoV-2-N-protein is known to undergo liquid-liquid phase separation (LLPS) with specific RNAs at particular temperatures to form condensates. We show that N-protein recognizes at least two separate and distinct RNA motifs, both of which require double-stranded RNA (dsRNA) for LLPS. These motifs are separately recognized by N-protein's two RNA binding domains (RBDs). Addition of dsRNA accelerates and modifies N-protein LLPS in vitro and in cells and controls the temperature condensates form. The abundance of dsRNA tunes N-protein-mediated translational repression and may confer a switch from translation to genome packaging. Thus, N-protein's two RBDs interact with separate dsRNA motifs, and these interactions impart distinct droplet properties that can support multiple viral functions. These experiments demonstrate a paradigm of how RNA structure can control the properties of biomolecular condensates.
Collapse
|
232
|
Bai Z, Cao Y, Liu W, Li J. The SARS-CoV-2 Nucleocapsid Protein and Its Role in Viral Structure, Biological Functions, and a Potential Target for Drug or Vaccine Mitigation. Viruses 2021; 13:v13061115. [PMID: 34200602 PMCID: PMC8227405 DOI: 10.3390/v13061115] [Citation(s) in RCA: 214] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 05/24/2021] [Accepted: 06/04/2021] [Indexed: 12/14/2022] Open
Abstract
The impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on the world is still expanding. Thus, there is an urgent need to better understand this novel virus and find a way to control its spread. Like other coronaviruses, the nucleocapsid (N) protein is one of the most crucial structural components of SARS-CoV-2. This protein shares 90% homology with the severe acute respiratory syndrome coronavirus N protein, implying functional significance. Based on the evolutionary conservation of the N protein in coronavirus, we reviewed the currently available knowledge regarding the SARS-CoV-2 N protein in terms of structure, biological functions, and clinical application as a drug target or vaccine candidate.
Collapse
Affiliation(s)
- Zhihua Bai
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (Z.B.); (Y.C.); (W.L.)
- Savaid Medical School, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Cao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (Z.B.); (Y.C.); (W.L.)
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Wenjun Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (Z.B.); (Y.C.); (W.L.)
- Savaid Medical School, University of the Chinese Academy of Sciences, Beijing 100049, China
- Center for Biosafety Mega-Science, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jing Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (Z.B.); (Y.C.); (W.L.)
- Savaid Medical School, University of the Chinese Academy of Sciences, Beijing 100049, China
- Correspondence:
| |
Collapse
|
233
|
Bottaro S, Bussi G, Lindorff-Larsen K. Conformational Ensembles of Noncoding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations. J Am Chem Soc 2021; 143:8333-8343. [PMID: 34039006 PMCID: PMC8188756 DOI: 10.1021/jacs.1c01094] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Indexed: 12/17/2022]
Abstract
The 5' untranslated region (UTR) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome is a conserved, functional and structured genomic region consisting of several RNA stem-loop elements. While the secondary structure of such elements has been determined experimentally, their three-dimensional structures are not known yet. Here, we predict structure and dynamics of five RNA stem loops in the 5'-UTR of SARS-CoV-2 by extensive atomistic molecular dynamics simulations, more than 0.5 ms of aggregate simulation time, in combination with enhanced sampling techniques. We compare simulations with available experimental data, describe the resulting conformational ensembles, and identify the presence of specific structural rearrangements in apical and internal loops that may be functionally relevant. Our atomic-detailed structural predictions reveal a rich dynamics in these RNA molecules, could help the experimental characterization of these systems, and provide putative three-dimensional models for structure-based drug design studies.
Collapse
Affiliation(s)
- Sandro Bottaro
- Structural
Biology and NMR Laboratory & Linderstrøm-Lang Centre for
Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Giovanni Bussi
- Scuola
Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136, Trieste, Italy
| | - Kresten Lindorff-Larsen
- Structural
Biology and NMR Laboratory & Linderstrøm-Lang Centre for
Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| |
Collapse
|
234
|
Praissman JL, Wells L. Proteomics-Based Insights Into the SARS-CoV-2-Mediated COVID-19 Pandemic: A Review of the First Year of Research. Mol Cell Proteomics 2021; 20:100103. [PMID: 34089862 PMCID: PMC8176883 DOI: 10.1016/j.mcpro.2021.100103] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 05/24/2021] [Indexed: 02/08/2023] Open
Abstract
In late 2019, a virus subsequently named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in China and led to a worldwide pandemic of the disease termed coronavirus disease 2019. The global health threat posed by this pandemic led to an extremely rapid and robust mobilization of the scientific and medical communities as evidenced by the publication of more than 10,000 peer-reviewed articles and thousands of preprints in the first year of the pandemic alone. With the publication of the initial genome sequence of SARS-CoV-2, the proteomics community immediately joined this effort publishing, to date, more than 100 peer-reviewed proteomics studies and submitting many more preprints to preprint servers. In this review, we focus on peer-reviewed articles published on the proteome, glycoproteome, and glycome of SARS-CoV-2. At a basic level, proteomic studies provide valuable information on quantitative aspects of viral infection course; information on the identities, sites, and microheterogeneity of post-translational modifications; and, information on protein-protein interactions. At a biological systems level, these studies elucidate host cell and tissue responses, characterize antibodies and other immune system factors in infection, suggest biomarkers that may be useful for diagnosis and disease-course monitoring, and help in the development or repurposing of potential therapeutics. Here, we summarize results from selected early studies to provide a perspective on the current rapidly evolving literature.
Collapse
Affiliation(s)
- Jeremy L Praissman
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Lance Wells
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA.
| |
Collapse
|
235
|
Cao Y, Yang R, Lee I, Zhang W, Sun J, Wang W, Meng X. Characterization of the SARS-CoV-2 E Protein: Sequence, Structure, Viroporin, and Inhibitors. Protein Sci 2021; 30:1114-1130. [PMID: 33813796 PMCID: PMC8138525 DOI: 10.1002/pro.4075] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 12/19/2022]
Abstract
The COVID-19 epidemic is one of the most influential epidemics in history. Understanding the impact of coronaviruses (CoVs) on host cells is very important for disease treatment. The SARS-CoV-2 envelope (E) protein is a small structural protein involved in many aspects of the viral life cycle. The E protein promotes the packaging and reproduction of the virus, and deletion of this protein weakens or even abolishes the virulence. This review aims to establish new knowledge by combining recent advances in the study of the SARS-CoV-2 E protein and by comparing it with the SARS-CoV E protein. The E protein amino acid sequence, structure, self-assembly characteristics, viroporin mechanisms and inhibitors are summarized and analyzed herein. Although the mechanisms of the SARS-CoV-2 and SARS-CoV E proteins are similar in many respects, specific studies on the SARS-CoV-2 E protein, for both monomers and oligomers, are still lacking. A comprehensive understanding of this protein should prompt further studies on the design and characterization of effective targeted therapeutic measures.
Collapse
Affiliation(s)
- Yipeng Cao
- Tianjin Medical University Cancer Institute and HospitalKey Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for CancerTianjinPeople's Republic of China
- National Supercomputer Center in TianjinTEDA‐Tianjin Economic‐Technological Development AreaTianjinPeople's Republic of China
| | - Rui Yang
- Department of Infection and ImmunityTianjin Union Medical Center, Nankai University Affiliated HospitalTianjinPeople's Republic of China
| | - Imshik Lee
- College of PhysicsNankai UniversityTianjinPeople's Republic of China
| | - Wenwen Zhang
- Tianjin Medical University Cancer Institute and HospitalKey Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for CancerTianjinPeople's Republic of China
| | - Jiana Sun
- Tianjin Medical University Cancer Institute and HospitalKey Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for CancerTianjinPeople's Republic of China
| | - Wei Wang
- Tianjin Medical University Cancer Institute and HospitalKey Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, National Clinical Research Center for CancerTianjinPeople's Republic of China
| | - Xiangfei Meng
- National Supercomputer Center in TianjinTEDA‐Tianjin Economic‐Technological Development AreaTianjinPeople's Republic of China
| |
Collapse
|
236
|
Ye Q, Lu S, Corbett KD. Structural basis for SARS-CoV-2 Nucleocapsid protein recognition by single-domain antibodies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.06.01.446591. [PMID: 34100017 PMCID: PMC8183014 DOI: 10.1101/2021.06.01.446591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The COVID-19 pandemic, caused by the coronavirus SARS-CoV-2, is the most severe public health event of the twenty-first century. While effective vaccines against SARS-CoV-2 have been developed, there remains an urgent need for diagnostics to quickly and accurately detect infections. Antigen tests, particularly those that detect the abundant SARS-CoV-2 Nucleocapsid protein, are a proven method for detecting active SARS-CoV-2 infections. Here we report high-resolution crystal structures of three llama-derived single-domain antibodies that bind the SARS-CoV-2 Nucleocapsid protein with high affinity. Each antibody recognizes a specific folded domain of the protein, with two antibodies recognizing the N-terminal RNA binding domain and one recognizing the C-terminal dimerization domain. The two antibodies that recognize the RNA binding domain affect both RNA binding affinity and RNA-mediated phase separation of the Nucleocapsid protein. All three antibodies recognize highly-conserved surfaces on the Nucleocapsid protein, suggesting that they could be used to develop affordable diagnostic tests to detect all circulating SARS-CoV-2 variants.
Collapse
Affiliation(s)
- Qiaozhen Ye
- Department of Cellular & Molecular Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA
| | - Shan Lu
- Department of Cellular & Molecular Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA
| | - Kevin D. Corbett
- Department of Cellular & Molecular Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA
| |
Collapse
|
237
|
Matsuo T. Viewing SARS-CoV-2 Nucleocapsid Protein in Terms of Molecular Flexibility. BIOLOGY 2021; 10:454. [PMID: 34064163 PMCID: PMC8224284 DOI: 10.3390/biology10060454] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/18/2021] [Accepted: 05/18/2021] [Indexed: 12/23/2022]
Abstract
The latest coronavirus SARS-CoV-2, which causes coronavirus disease 2019 (COVID-19) pneumonia leading to the pandemic, contains 29 proteins. Among them, nucleocapsid protein (NCoV2) is one of the abundant proteins and shows multiple functions including packaging the RNA genome during the infection cycle. It has also emerged as a potential drug target. In this review, the current status of the research of NCoV2 is described in terms of molecular structure and dynamics. NCoV2 consists of two domains, i.e., the N-terminal domain (NTD) and the C-terminal domain (CTD) with a disordered region between them. Recent simulation studies have identified several potential drugs that can bind to NTD or CTD with high affinity. Moreover, it was shown that the degree of flexibility in the disordered region has a large effect on drug binding rate, suggesting the importance of molecular flexibility for the NCoV2 function. Molecular flexibility has also been shown to be integral to the formation of droplets, where NCoV2, RNA and/or other viral proteins gather through liquid-liquid phase separation and considered important for viral replication. Finally, as one of the future research directions, a strategy for obtaining the structural and dynamical information on the proteins contained in droplets is presented.
Collapse
Affiliation(s)
- Tatsuhito Matsuo
- Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai-mura, Naka-gun, Ibaraki 319-1106, Japan;
- Laboratoire Interdisciplinaire de Physique (LiPhy), Grenoble-Alpes University, 140 Rue de la Physique, 38402 Saint Martin d’Hères, France
- Institut Laue-Langevin, 71 Avenue des Martyrs, CS 20156, CEDEX 9, 38042 Grenoble, France
| |
Collapse
|
238
|
Campos-Melo D, Hawley ZCE, Droppelmann CA, Strong MJ. The Integral Role of RNA in Stress Granule Formation and Function. Front Cell Dev Biol 2021; 9:621779. [PMID: 34095105 PMCID: PMC8173143 DOI: 10.3389/fcell.2021.621779] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 03/16/2021] [Indexed: 12/12/2022] Open
Abstract
Stress granules (SGs) are phase-separated, membraneless, cytoplasmic ribonucleoprotein (RNP) assemblies whose primary function is to promote cell survival by condensing translationally stalled mRNAs, ribosomal components, translation initiation factors, and RNA-binding proteins (RBPs). While the protein composition and the function of proteins in the compartmentalization and the dynamics of assembly and disassembly of SGs has been a matter of study for several years, the role of RNA in these structures had remained largely unknown. RNA species are, however, not passive members of RNA granules in that RNA by itself can form homo and heterotypic interactions with other RNA molecules leading to phase separation and nucleation of RNA granules. RNA can also function as molecular scaffolds recruiting multivalent RBPs and their interactors to form higher-order structures. With the development of SG purification techniques coupled to RNA-seq, the transcriptomic landscape of SGs is becoming increasingly understood, revealing the enormous potential of RNA to guide the assembly and disassembly of these transient organelles. SGs are not only formed under acute stress conditions but also in response to different diseases such as viral infections, cancer, and neurodegeneration. Importantly, these granules are increasingly being recognized as potential precursors of pathological aggregates in neurodegenerative diseases. In this review, we examine the current evidence in support of RNA playing a significant role in the formation of SGs and explore the concept of SGs as therapeutic targets.
Collapse
Affiliation(s)
- Danae Campos-Melo
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Zachary C E Hawley
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Cristian A Droppelmann
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Michael J Strong
- Molecular Medicine Group, Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.,Department of Pathology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.,Department of Clinical Neurological Sciences, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| |
Collapse
|
239
|
Ahsan N, Rao RSP, Wilson RS, Punyamurtula U, Salvato F, Petersen M, Ahmed MK, Abid MR, Verburgt JC, Kihara D, Yang Z, Fornelli L, Foster SB, Ramratnam B. Mass spectrometry-based proteomic platforms for better understanding of SARS-CoV-2 induced pathogenesis and potential diagnostic approaches. Proteomics 2021; 21:e2000279. [PMID: 33860983 PMCID: PMC8250252 DOI: 10.1002/pmic.202000279] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 04/09/2021] [Accepted: 04/12/2021] [Indexed: 12/12/2022]
Abstract
While protein–protein interaction is the first step of the SARS‐CoV‐2 infection, recent comparative proteomic profiling enabled the identification of over 11,000 protein dynamics, thus providing a comprehensive reflection of the molecular mechanisms underlying the cellular system in response to viral infection. Here we summarize and rationalize the results obtained by various mass spectrometry (MS)‐based proteomic approaches applied to the functional characterization of proteins and pathways associated with SARS‐CoV‐2‐mediated infections in humans. Comparative analysis of cell‐lines versus tissue samples indicates that our knowledge in proteome profile alternation in response to SARS‐CoV‐2 infection is still incomplete and the tissue‐specific response to SARS‐CoV‐2 infection can probably not be recapitulated efficiently by in vitro experiments. However, regardless of the viral infection period, sample types, and experimental strategies, a thorough cross‐comparison of the recently published proteome, phosphoproteome, and interactome datasets led to the identification of a common set of proteins and kinases associated with PI3K‐Akt, EGFR, MAPK, Rap1, and AMPK signaling pathways. Ephrin receptor A2 (EPHA2) was identified by 11 studies including all proteomic platforms, suggesting it as a potential future target for SARS‐CoV‐2 infection mechanisms and the development of new therapeutic strategies. We further discuss the potentials of future proteomics strategies for identifying prognostic SARS‐CoV‐2 responsive age‐, gender‐dependent, tissue‐specific protein targets.
Collapse
Affiliation(s)
- Nagib Ahsan
- Department of Chemistry and BiochemistryUniversity of OklahomaNormanOklahomaUSA
| | - R. Shyama Prasad Rao
- Biostatistics and Bioinformatics DivisionYenepoya Research CenterYenepoya UniversityMangaluruIndia
| | - Rashaun S. Wilson
- Keck Mass Spectrometry and Proteomics ResourceYale UniversityNew HavenConnecticutUSA
| | - Ujwal Punyamurtula
- COBRE Center for Cancer Research DevelopmentProteomics Core FacilityRhode Island HospitalProvidenceRhode IslandUSA
| | - Fernanda Salvato
- Department of Plant and Microbial BiologyCollege of Agriculture and Life SciencesNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Max Petersen
- Signal Transduction Lab, Division of Hematology/OncologyRhode Island Hospital, Warren Alpert Medical School, Brown UniversityProvidenceRhode IslandUSA
| | - Mohammad Kabir Ahmed
- Department of BiochemistryFaculty of MedicineUniversiti Kuala Lumpur Royal College of Medicine PerakIpohPerakMalaysia
| | - M. Ruhul Abid
- Department of SurgeryCardiovascular Research CenterRhode Island HospitalWarren Alpert Medical SchoolBrown UniversityProvidenceRhode IslandUSA
| | - Jacob C. Verburgt
- Department of Biological SciencesPurdue UniversityWest LafayetteIndianaUSA
| | - Daisuke Kihara
- Department of Biological SciencesPurdue UniversityWest LafayetteIndianaUSA
- Department of Computer SciencePurdue UniversityWest LafayetteIndianaUSA
| | - Zhibo Yang
- Department of Chemistry and BiochemistryUniversity of OklahomaNormanOklahomaUSA
| | - Luca Fornelli
- Department of Chemistry and BiochemistryUniversity of OklahomaNormanOklahomaUSA
- Department of BiologyUniversity of OklahomaNormanOklahomaUSA
| | - Steven B. Foster
- Department of Chemistry and BiochemistryUniversity of OklahomaNormanOklahomaUSA
| | - Bharat Ramratnam
- COBRE Center for Cancer Research DevelopmentProteomics Core FacilityRhode Island HospitalProvidenceRhode IslandUSA
- Division of Infectious DiseasesDepartment of MedicineWarren Alpert Medical SchoolBrown UniversityProvidenceRhode IslandUSA
| |
Collapse
|
240
|
Wu Y, Ma L, Cai S, Zhuang Z, Zhao Z, Jin S, Xie W, Zhou L, Zhang L, Zhao J, Cui J. RNA-induced liquid phase separation of SARS-CoV-2 nucleocapsid protein facilitates NF-κB hyper-activation and inflammation. Signal Transduct Target Ther 2021; 6:167. [PMID: 33895773 PMCID: PMC8065320 DOI: 10.1038/s41392-021-00575-7] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 03/06/2021] [Accepted: 03/18/2021] [Indexed: 02/02/2023] Open
Abstract
The ongoing 2019 novel coronavirus disease (COVID-19) caused by SARS-CoV-2 has posed a worldwide pandemic and a major global public health threat. The severity and mortality of COVID-19 are associated with virus-induced dysfunctional inflammatory responses and cytokine storms. However, the interplay between host inflammatory responses and SARS-CoV-2 infection remains largely unknown. Here, we demonstrate that SARS-CoV-2 nucleocapsid (N) protein, the major structural protein of the virion, promotes the virus-triggered activation of NF-κB signaling. After binding to viral RNA, N protein robustly undergoes liquid-liquid phase separation (LLPS), which recruits TAK1 and IKK complex, the key kinases of NF-κB signaling, to enhance NF-κB activation. Moreover, 1,6-hexanediol, the inhibitor of LLPS, can attenuate the phase separation of N protein and restrict its regulatory functions in NF-κB activation. These results suggest that LLPS of N protein provides a platform to induce NF-κB hyper-activation, which could be a potential therapeutic target against COVID-19 severe pneumonia.
Collapse
Affiliation(s)
- Yaoxing Wu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Ling Ma
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Sihui Cai
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zhen Zhuang
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zhiyao Zhao
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Shouheng Jin
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Weihong Xie
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Lingli Zhou
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Lei Zhang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China.
| | - Jun Cui
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China.
| |
Collapse
|
241
|
Mishra T, Sreepadmanabh M, Ramdas P, Sahu AK, Kumar A, Chande A. SARS CoV-2 Nucleoprotein Enhances the Infectivity of Lentiviral Spike Particles. Front Cell Infect Microbiol 2021; 11:663688. [PMID: 33968806 PMCID: PMC8102828 DOI: 10.3389/fcimb.2021.663688] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/08/2021] [Indexed: 12/11/2022] Open
Abstract
The establishment of SARS CoV-2 spike-pseudotyped lentiviral (LV) systems has enabled the rapid identification of entry inhibitors and neutralizing agents, alongside allowing for the study of this emerging pathogen in BSL-2 level facilities. While such frameworks recapitulate the cellular entry process in ACE2+ cells, they are largely unable to factor in supplemental contributions by other SARS CoV-2 genes. To address this, we performed an unbiased ORF screen and identified the nucleoprotein (N) as a potent enhancer of spike-pseudotyped LV particle infectivity. We further demonstrate that the spike protein is better enriched in virions when the particles are produced in the presence of N protein. This enrichment of spike renders LV particles more infectious as well as less vulnerable to the neutralizing effects of a human IgG-Fc fused ACE2 microbody. Importantly, this improvement in infectivity is observed with both wild-type spike protein as well as the D614G mutant. Our results hold important implications for the design and interpretation of similar LV pseudotyping-based studies.
Collapse
Affiliation(s)
- Tarun Mishra
- Molecular Virology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
| | - M Sreepadmanabh
- Molecular Virology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
| | - Pavitra Ramdas
- Molecular Virology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
| | - Amit Kumar Sahu
- Molecular Virology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
| | - Atul Kumar
- Structural Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
| | - Ajit Chande
- Molecular Virology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
| |
Collapse
|
242
|
Elbaum-Garfinkle S, Kriwacki RW. Phase Separation in Biology & Disease: The next chapter. J Mol Biol 2021; 433:166990. [PMID: 33857471 DOI: 10.1016/j.jmb.2021.166990] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Shana Elbaum-Garfinkle
- Structural Biology Initiative, CUNY Advanced Science Research Center, Biochemistry, The Graduate Center CUNY, 85 St. Nicholas Terrace, New York, NY 10031, United States.
| | - Richard W Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105-3678, United States.
| |
Collapse
|
243
|
Tugaeva KV, Hawkins DEDP, Smith JLR, Bayfield OW, Ker DS, Sysoev AA, Klychnikov OI, Antson AA, Sluchanko NN. The Mechanism of SARS-CoV-2 Nucleocapsid Protein Recognition by the Human 14-3-3 Proteins. J Mol Biol 2021; 433:166875. [PMID: 33556408 PMCID: PMC7863765 DOI: 10.1016/j.jmb.2021.166875] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 01/27/2021] [Accepted: 01/29/2021] [Indexed: 12/24/2022]
Abstract
The coronavirus nucleocapsid protein (N) controls viral genome packaging and contains numerous phosphorylation sites located within unstructured regions. Binding of phosphorylated SARS-CoV N to the host 14-3-3 protein in the cytoplasm was reported to regulate nucleocytoplasmic N shuttling. All seven isoforms of the human 14-3-3 are abundantly present in tissues vulnerable to SARS-CoV-2, where N can constitute up to ~1% of expressed proteins during infection. Although the association between 14-3-3 and SARS-CoV-2 N proteins can represent one of the key host-pathogen interactions, its molecular mechanism and the specific critical phosphosites are unknown. Here, we show that phosphorylated SARS-CoV-2 N protein (pN) dimers, reconstituted via bacterial co-expression with protein kinase A, directly associate, in a phosphorylation-dependent manner, with the dimeric 14-3-3 protein, but not with its monomeric mutant. We demonstrate that pN is recognized by all seven human 14-3-3 isoforms with various efficiencies and deduce the apparent KD to selected isoforms, showing that these are in a low micromolar range. Serial truncations pinpointed a critical phosphorylation site to Ser197, which is conserved among related zoonotic coronaviruses and located within the functionally important, SR-rich region of N. The relatively tight 14-3-3/pN association could regulate nucleocytoplasmic shuttling and other functions of N via occlusion of the SR-rich region, and could also hijack cellular pathways by 14-3-3 sequestration. As such, the assembly may represent a valuable target for therapeutic intervention.
Collapse
Affiliation(s)
- Kristina V Tugaeva
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Dorothy E D P Hawkins
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Jake L R Smith
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Oliver W Bayfield
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - De-Sheng Ker
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Andrey A Sysoev
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Oleg I Klychnikov
- Department of Biochemistry, School of Biology, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom.
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia.
| |
Collapse
|
244
|
Zhao M, Yu Y, Sun LM, Xing JQ, Li T, Zhu Y, Wang M, Yu Y, Xue W, Xia T, Cai H, Han QY, Yin X, Li WH, Li AL, Cui J, Yuan Z, Zhang R, Zhou T, Zhang XM, Li T. GCG inhibits SARS-CoV-2 replication by disrupting the liquid phase condensation of its nucleocapsid protein. Nat Commun 2021; 12:2114. [PMID: 33837182 PMCID: PMC8035206 DOI: 10.1038/s41467-021-22297-8] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/09/2021] [Indexed: 12/12/2022] Open
Abstract
Lack of detailed knowledge of SARS-CoV-2 infection has been hampering the development of treatments for coronavirus disease 2019 (COVID-19). Here, we report that RNA triggers the liquid-liquid phase separation (LLPS) of the SARS-CoV-2 nucleocapsid protein, N. By analyzing all 29 proteins of SARS-CoV-2, we find that only N is predicted as an LLPS protein. We further confirm the LLPS of N during SARS-CoV-2 infection. Among the 100,849 genome variants of SARS-CoV-2 in the GISAID database, we identify that ~37% (36,941) of the genomes contain a specific trio-nucleotide polymorphism (GGG-to-AAC) in the coding sequence of N, which leads to the amino acid substitutions, R203K/G204R. Interestingly, NR203K/G204R exhibits a higher propensity to undergo LLPS and a greater effect on IFN inhibition. By screening the chemicals known to interfere with N-RNA binding in other viruses, we find that (-)-gallocatechin gallate (GCG), a polyphenol from green tea, disrupts the LLPS of N and inhibits SARS-CoV-2 replication. Thus, our study reveals that targeting N-RNA condensation with GCG could be a potential treatment for COVID-19.
Collapse
Affiliation(s)
- Ming Zhao
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing, 100850, China.,Nanhu Laboratory, Jiaxing, Zhejiang Province, 314002, China
| | - Yu Yu
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing, 100850, China.,Cancer Research Institute of Jilin University, The First Hospital of Jilin University, Changchun, Jilin Province, 130021, China
| | - Li-Ming Sun
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing, 100850, China
| | - Jia-Qing Xing
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing, 100850, China
| | - Tingting Li
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing, 100850, China
| | - Yunkai Zhu
- School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Miao Wang
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing, 100850, China
| | - Yin Yu
- School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Wen Xue
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing, 100850, China
| | - Tian Xia
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing, 100850, China
| | - Hong Cai
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing, 100850, China
| | - Qiu-Ying Han
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing, 100850, China
| | - Xiaoyao Yin
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing, 100850, China
| | - Wei-Hua Li
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing, 100850, China
| | - Ai-Ling Li
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing, 100850, China
| | - Jiuwei Cui
- Cancer Research Institute of Jilin University, The First Hospital of Jilin University, Changchun, Jilin Province, 130021, China
| | - Zhenghong Yuan
- School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Rong Zhang
- School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Tao Zhou
- Nanhu Laboratory, Jiaxing, Zhejiang Province, 314002, China.
| | - Xue-Min Zhang
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing, 100850, China. .,School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
| | - Tao Li
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, 27 Tai-Ping Road, Beijing, 100850, China. .,School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
| |
Collapse
|
245
|
Hagan MF, Grason GM. Equilibrium mechanisms of self-limiting assembly. REVIEWS OF MODERN PHYSICS 2021; 93:025008. [PMID: 35221384 PMCID: PMC8880259 DOI: 10.1103/revmodphys.93.025008] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Self-assembly is a ubiquitous process in synthetic and biological systems, broadly defined as the spontaneous organization of multiple subunits (e.g. macromolecules, particles) into ordered multi-unit structures. The vast majority of equilibrium assembly processes give rise to two states: one consisting of dispersed disassociated subunits, and the other, a bulk-condensed state of unlimited size. This review focuses on the more specialized class of self-limiting assembly, which describes equilibrium assembly processes resulting in finite-size structures. These systems pose a generic and basic question, how do thermodynamic processes involving non-covalent interactions between identical subunits "measure" and select the size of assembled structures? In this review, we begin with an introduction to the basic statistical mechanical framework for assembly thermodynamics, and use this to highlight the key physical ingredients that ensure equilibrium assembly will terminate at finite dimensions. Then, we introduce examples of self-limiting assembly systems, and classify them within this framework based on two broad categories: self-closing assemblies and open-boundary assemblies. These include well-known cases in biology and synthetic soft matter - micellization of amphiphiles and shell/tubule formation of tapered subunits - as well as less widely known classes of assemblies, such as short-range attractive/long-range repulsive systems and geometrically-frustrated assemblies. For each of these self-limiting mechanisms, we describe the physical mechanisms that select equilibrium assembly size, as well as potential limitations of finite-size selection. Finally, we discuss alternative mechanisms for finite-size assemblies, and draw contrasts with the size-control that these can achieve relative to self-limitation in equilibrium, single-species assemblies.
Collapse
Affiliation(s)
- Michael F Hagan
- Martin Fisher School of Physics, Brandeis University, Waltham, MA 02454, USA
| | - Gregory M Grason
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA 01003, USA
| |
Collapse
|
246
|
Jack A, Ferro LS, Trnka MJ, Wehri E, Nadgir A, Nguyenla X, Costa K, Stanley S, Schaletzky J, Yildiz A. SARS-CoV-2 nucleocapsid protein forms condensates with viral genomic RNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2020.09.14.295824. [PMID: 32995779 PMCID: PMC7523105 DOI: 10.1101/2020.09.14.295824] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection causes COVID-19, a pandemic that seriously threatens global health. SARS-CoV-2 propagates by packaging its RNA genome into membrane enclosures in host cells. The packaging of the viral genome into the nascent virion is mediated by the nucleocapsid (N) protein, but the underlying mechanism remains unclear. Here, we show that the N protein forms biomolecular condensates with viral genomic RNA both in vitro and in mammalian cells. Phase separation is driven, in part, by hydrophobic and electrostatic interactions. While the N protein forms spherical assemblies with unstructured RNA, it forms asymmetric condensates with viral RNA strands that contain secondary structure elements. Cross-linking mass spectrometry identified a region that forms interactions between N proteins in condensates, and truncation of this region disrupts phase separation. We also identified small molecules that alter the formation of N protein condensates. These results suggest that the N protein may utilize biomolecular condensation to package the SARS-CoV-2 RNA genome into a viral particle.
Collapse
Affiliation(s)
- Amanda Jack
- Biophysics Graduate Group, University of California, Berkeley CA
| | - Luke S. Ferro
- Department of Molecular and Cellular Biology, University of California, Berkeley CA
| | - Michael J. Trnka
- Department of Pharmaceutical Chemistry, University of California, San Francisco CA
| | - Eddie Wehri
- Center for Emerging and Neglected Diseases, University of California, Berkeley CA
| | - Amrut Nadgir
- Physics Department, University of California, Berkeley CA
| | - Xammy Nguyenla
- School of Public Health, Division of Infectious Diseases and Vaccinology, University of California, Berkeley, CA
| | | | - Sarah Stanley
- Department of Molecular and Cellular Biology, University of California, Berkeley CA
- School of Public Health, Division of Infectious Diseases and Vaccinology, University of California, Berkeley, CA
| | - Julia Schaletzky
- Center for Emerging and Neglected Diseases, University of California, Berkeley CA
| | - Ahmet Yildiz
- Biophysics Graduate Group, University of California, Berkeley CA
- Department of Molecular and Cellular Biology, University of California, Berkeley CA
- Physics Department, University of California, Berkeley CA
| |
Collapse
|
247
|
Cubuk J, Alston JJ, Incicco JJ, Singh S, Stuchell-Brereton MD, Ward MD, Zimmerman MI, Vithani N, Griffith D, Wagoner JA, Bowman GR, Hall KB, Soranno A, Holehouse AS. The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA. Nat Commun 2021; 12:1936. [PMID: 33782395 PMCID: PMC8007728 DOI: 10.1038/s41467-021-21953-3] [Citation(s) in RCA: 359] [Impact Index Per Article: 89.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 02/18/2021] [Indexed: 12/15/2022] Open
Abstract
The SARS-CoV-2 nucleocapsid (N) protein is an abundant RNA-binding protein critical for viral genome packaging, yet the molecular details that underlie this process are poorly understood. Here we combine single-molecule spectroscopy with all-atom simulations to uncover the molecular details that contribute to N protein function. N protein contains three dynamic disordered regions that house putative transiently-helical binding motifs. The two folded domains interact minimally such that full-length N protein is a flexible and multivalent RNA-binding protein. N protein also undergoes liquid-liquid phase separation when mixed with RNA, and polymer theory predicts that the same multivalent interactions that drive phase separation also engender RNA compaction. We offer a simple symmetry-breaking model that provides a plausible route through which single-genome condensation preferentially occurs over phase separation, suggesting that phase separation offers a convenient macroscopic readout of a key nanoscopic interaction.
Collapse
Affiliation(s)
- Jasmine Cubuk
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Jhullian J Alston
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - J Jeremías Incicco
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Sukrit Singh
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Melissa D Stuchell-Brereton
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Michael D Ward
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Maxwell I Zimmerman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Neha Vithani
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Daniel Griffith
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Jason A Wagoner
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
| | - Gregory R Bowman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Kathleen B Hall
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA.
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA.
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA.
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA.
| |
Collapse
|
248
|
Tayeb-Fligelman E, Cheng X, Tai C, Bowler JT, Griner S, Sawaya MR, Seidler PM, Jiang YX, Lu J, Rosenberg GM, Salwinski L, Abskharon R, Zee CT, Hou K, Li Y, Boyer DR, Murray KA, Falcon G, Anderson DH, Cascio D, Saelices L, Damoiseaux R, Guo F, Eisenberg DS. Inhibition of amyloid formation of the Nucleoprotein of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.03.05.434000. [PMID: 33688654 PMCID: PMC7941625 DOI: 10.1101/2021.03.05.434000] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The SARS-CoV-2 Nucleoprotein (NCAP) functions in RNA packaging during viral replication and assembly. Computational analysis of its amino acid sequence reveals a central low-complexity domain (LCD) having sequence features akin to LCDs in other proteins known to function in liquid-liquid phase separation. Here we show that in the presence of viral RNA, NCAP, and also its LCD segment alone, form amyloid-like fibrils when undergoing liquid-liquid phase separation. Within the LCD we identified three 6-residue segments that drive amyloid fibril formation. We determined atomic structures for fibrils formed by each of the three identified segments. These structures informed our design of peptide inhibitors of NCAP fibril formation and liquid-liquid phase separation, suggesting a therapeutic route for Covid-19. ONE SENTENCE SUMMARY Atomic structures of amyloid-driving peptide segments from SARS-CoV-2 Nucleoprotein inform the development of Covid-19 therapeutics.
Collapse
|
249
|
Etibor TA, Yamauchi Y, Amorim MJ. Liquid Biomolecular Condensates and Viral Lifecycles: Review and Perspectives. Viruses 2021; 13:366. [PMID: 33669141 PMCID: PMC7996568 DOI: 10.3390/v13030366] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 02/16/2021] [Accepted: 02/20/2021] [Indexed: 02/06/2023] Open
Abstract
Viruses are highly dependent on the host they infect. Their dependence triggers processes of virus-host co-adaptation, enabling viruses to explore host resources whilst escaping immunity. Scientists have tackled viral-host interplay at differing levels of complexity-in individual hosts, organs, tissues and cells-and seminal studies advanced our understanding about viral lifecycles, intra- or inter-species transmission, and means to control infections. Recently, it emerged as important to address the physical properties of the materials in biological systems; membrane-bound organelles are only one of many ways to separate molecules from the cellular milieu. By achieving a type of compartmentalization lacking membranes known as biomolecular condensates, biological systems developed alternative mechanisms of controlling reactions. The identification that many biological condensates display liquid properties led to the proposal that liquid-liquid phase separation (LLPS) drives their formation. The concept of LLPS is a paradigm shift in cellular structure and organization. There is an unprecedented momentum to revisit long-standing questions in virology and to explore novel antiviral strategies. In the first part of this review, we focus on the state-of-the-art about biomolecular condensates. In the second part, we capture what is known about RNA virus-phase biology and discuss future perspectives of this emerging field in virology.
Collapse
Affiliation(s)
- Temitope Akhigbe Etibor
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal;
| | - Yohei Yamauchi
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TL, UK;
| | - Maria João Amorim
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal;
| |
Collapse
|
250
|
Zhao H, Wu D, Nguyen A, Li Y, Adão RC, Valkov E, Patterson GH, Piszczek G, Schuck P. Energetic and structural features of SARS-CoV-2 N-protein co-assemblies with nucleic acids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.02.08.430344. [PMID: 33594360 PMCID: PMC7885910 DOI: 10.1101/2021.02.08.430344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Nucleocapsid (N) protein of the SARS-CoV-2 virus packages the viral genome into well-defined ribonucleoprotein particles, but the molecular pathway is still unclear. N-protein is dimeric and consists of two folded domains with nucleic acid (NA) binding sites, surrounded by intrinsically disordered regions that promote liquid-liquid phase separation. Here we use biophysical tools to study N-protein interactions with oligonucleotides of different length, examining the size, composition, secondary structure, and energetics of the resulting states. We observe formation of supramolecular clusters or nuclei preceding growth into phase-separated droplets. Short hexanucleotide NA forms compact 2:2 N-protein/NA complexes with reduced disorder. Longer oligonucleotides expose additional N-protein interactions and multi-valent protein-NA interactions, which generate higher-order mixed oligomers and simultaneously promote growth of droplets. Phase separation is accompanied by a significant increase in protein secondary structure, different from that caused by initial NA binding, which may contribute to the assembly of ribonucleoprotein particles within molecular condensates.
Collapse
Affiliation(s)
- Huaying Zhao
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, 13 South Drive, Bethesda, MD 20892, USA
| | - Di Wu
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, 50 South Drive, Bethesda, MD 20892, USA
| | - Ai Nguyen
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, 13 South Drive, Bethesda, MD 20892, USA
| | - Yan Li
- Protein/Peptide Sequencing Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Regina C. Adão
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, 13 South Drive, Bethesda, MD 20892, USA
| | - Eugene Valkov
- Messenger RNA Regulation and Decay Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Building 560, Room 21–105A, Frederick, MD 21702
| | - George H. Patterson
- Section on Biophotonics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Grzegorz Piszczek
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, 50 South Drive, Bethesda, MD 20892, USA
| | - Peter Schuck
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, 13 South Drive, Bethesda, MD 20892, USA
| |
Collapse
|