1
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Schmit JD, Michaels TCT. Physical limits to acceleration of enzymatic reactions inside phase-separated compartments. Phys Rev E 2024; 109:064401. [PMID: 39020956 DOI: 10.1103/physreve.109.064401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 04/26/2024] [Indexed: 07/20/2024]
Abstract
We present a theoretical analysis of phase-separated compartments to facilitate enzymatic chemical reactions. While phase separation can facilitate reactions by increasing local concentration, it can also hinder the mobility of reactants. In particular, we find that the attractive interactions that concentrate reactants within the dense phase can inhibit reactions by lowering the mobility of the reactants. This mobility loss severely limits the potential to enhance reaction rates. Phase separation provides greater benefit in situations where multiple sequential reactions occur and/or high order reactions, provided the enzymes are unsaturated, transport to the condensate is not limiting, and the reactants are mobile. We show that mobility can be maintained if recruitment to the condensed phase is driven by multiple attractive moieties that can bind and release independently. However, the spacers necessary to ensure independence between stickers are prone to entangle with the dense phase scaffold. We find an optimal sticker affinity that balances the need for rapid binding/unbinding kinetics and minimal entanglement. Reaction rates can be accelerated by shrinking the size of the dense phase with a corresponding increase in the number of stickers. Our results showcase the potential capabilities of phase-separated compartments to act as biochemical reaction crucibles within living cells.
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2
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Cubuk J, Alston J, Incicco JJ, Holehouse A, Hall K, Stuchell-Brereton M, Soranno A. The disordered N-terminal tail of SARS-CoV-2 Nucleocapsid protein forms a dynamic complex with RNA. Nucleic Acids Res 2024; 52:2609-2624. [PMID: 38153183 PMCID: PMC10954482 DOI: 10.1093/nar/gkad1215] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 11/17/2023] [Accepted: 12/11/2023] [Indexed: 12/29/2023] Open
Abstract
The SARS-CoV-2 Nucleocapsid (N) protein is responsible for condensation of the viral genome. Characterizing the mechanisms controlling nucleic acid binding is a key step in understanding how condensation is realized. Here, we focus on the role of the RNA binding domain (RBD) and its flanking disordered N-terminal domain (NTD) tail, using single-molecule Förster Resonance Energy Transfer and coarse-grained simulations. We quantified contact site size and binding affinity for nucleic acids and concomitant conformational changes occurring in the disordered region. We found that the disordered NTD increases the affinity of the RBD for RNA by about 50-fold. Binding of both nonspecific and specific RNA results in a modulation of the tail configurations, which respond in an RNA length-dependent manner. Not only does the disordered NTD increase affinity for RNA, but mutations that occur in the Omicron variant modulate the interactions, indicating a functional role of the disordered tail. Finally, we found that the NTD-RBD preferentially interacts with single-stranded RNA and that the resulting protein:RNA complexes are flexible and dynamic. We speculate that this mechanism of interaction enables the Nucleocapsid protein to search the viral genome for and bind to high-affinity motifs.
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Affiliation(s)
- Jasmine Cubuk
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 St Euclid Ave, 63110 Saint Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St Louis, 1 Brookings Drive, 63130 Saint Louis, MO, USA
| | - Jhullian J Alston
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 St Euclid Ave, 63110 Saint Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St Louis, 1 Brookings Drive, 63130 Saint Louis, MO, USA
| | - J Jeremías Incicco
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 St Euclid Ave, 63110 Saint Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St Louis, 1 Brookings Drive, 63130 Saint Louis, MO, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 St Euclid Ave, 63110 Saint Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St Louis, 1 Brookings Drive, 63130 Saint Louis, MO, USA
| | - Kathleen B Hall
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 St Euclid Ave, 63110 Saint Louis, MO, USA
| | - Melissa D Stuchell-Brereton
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 St Euclid Ave, 63110 Saint Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St Louis, 1 Brookings Drive, 63130 Saint Louis, MO, USA
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 St Euclid Ave, 63110 Saint Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St Louis, 1 Brookings Drive, 63130 Saint Louis, MO, USA
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3
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Martin EW, Iserman C, Olety B, Mitrea DM, Klein IA. Biomolecular Condensates as Novel Antiviral Targets. J Mol Biol 2024; 436:168380. [PMID: 38061626 DOI: 10.1016/j.jmb.2023.168380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 11/23/2023] [Accepted: 11/30/2023] [Indexed: 12/24/2023]
Abstract
Viral infections pose a significant health risk worldwide. There is a pressing need for more effective antiviral drugs to combat emerging novel viruses and the reemergence of previously controlled viruses. Biomolecular condensates are crucial for viral replication and are promising targets for novel antiviral therapies. Herein, we review the role of biomolecular condensates in the viral replication cycle and discuss novel strategies to leverage condensate biology for antiviral drug discovery. Biomolecular condensates may also provide an opportunity to develop antivirals that are broad-spectrum or less prone to acquired drug resistance.
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4
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Estelle AB, Forsythe HM, Yu Z, Hughes K, Lasher B, Allen P, Reardon PN, Hendrix DA, Barbar EJ. RNA structure and multiple weak interactions balance the interplay between RNA binding and phase separation of SARS-CoV-2 nucleocapsid. PNAS NEXUS 2023; 2:pgad333. [PMID: 37901441 PMCID: PMC10605006 DOI: 10.1093/pnasnexus/pgad333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 10/02/2023] [Indexed: 10/31/2023]
Abstract
The nucleocapsid (N) protein of SARS-CoV-2 binds viral RNA, condensing it inside the virion, and phase separating with RNA to form liquid-liquid condensates. There is little consensus on what differentiates sequence-independent N-RNA interactions in the virion or in liquid droplets from those with specific genomic RNA (gRNA) motifs necessary for viral function inside infected cells. To identify the RNA structures and the N domains responsible for specific interactions and phase separation, we use the first 1,000 nt of viral RNA and short RNA segments designed as models for single-stranded and paired RNA. Binding affinities estimated from fluorescence anisotropy of these RNAs to the two-folded domains of N (the NTD and CTD) and comparison to full-length N demonstrate that the NTD binds preferentially to single-stranded RNA, and while it is the primary RNA-binding site, it is not essential to phase separation. Nuclear magnetic resonance spectroscopy identifies two RNA-binding sites on the NTD: a previously characterized site and an additional although weaker RNA-binding face that becomes prominent when binding to the primary site is weak, such as with dsRNA or a binding-impaired mutant. Phase separation assays of nucleocapsid domains with double-stranded and single-stranded RNA structures support a model where multiple weak interactions, such as with the CTD or the NTD's secondary face promote phase separation, while strong, specific interactions do not. These studies indicate that both strong and multivalent weak N-RNA interactions underlie the multifunctional abilities of N.
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Affiliation(s)
- Aidan B Estelle
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Heather M Forsythe
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Zhen Yu
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Kaitlyn Hughes
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Brittany Lasher
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Patrick Allen
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Patrick N Reardon
- Oregon State University NMR Facility, Oregon State University, Corvallis, OR 97331, USA
| | - David A Hendrix
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR 97331, USA
| | - Elisar J Barbar
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
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5
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Abstract
Multivalent proteins and nucleic acids, collectively referred to as multivalent associative biomacromolecules, provide the driving forces for the formation and compositional regulation of biomolecular condensates. Here, we review the key concepts of phase transitions of aqueous solutions of associative biomacromolecules, specifically proteins that include folded domains and intrinsically disordered regions. The phase transitions of these systems come under the rubric of coupled associative and segregative transitions. The concepts underlying these processes are presented, and their relevance to biomolecular condensates is discussed.
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Affiliation(s)
- Rohit V Pappu
- Department of Biomedical Engineering, Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Samuel R Cohen
- Department of Biomedical Engineering, Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, Missouri 63130, United States
- Center of Regenerative Medicine, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Furqan Dar
- Department of Biomedical Engineering, Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Mina Farag
- Department of Biomedical Engineering, Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Mrityunjoy Kar
- Max Planck Institute of Cell Biology and Genetics, 01307 Dresden, Germany
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6
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Korn SM, Dhamotharan K, Jeffries CM, Schlundt A. The preference signature of the SARS-CoV-2 Nucleocapsid NTD for its 5'-genomic RNA elements. Nat Commun 2023; 14:3331. [PMID: 37286558 DOI: 10.1038/s41467-023-38882-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 05/17/2023] [Indexed: 06/09/2023] Open
Abstract
The nucleocapsid protein (N) of SARS-CoV-2 plays a pivotal role during the viral life cycle. It is involved in RNA transcription and accounts for packaging of the large genome into virus particles. N manages the enigmatic balance of bulk RNA-coating versus precise RNA-binding to designated cis-regulatory elements. Numerous studies report the involvement of its disordered segments in non-selective RNA-recognition, but how N organizes the inevitable recognition of specific motifs remains unanswered. We here use NMR spectroscopy to systematically analyze the interactions of N's N-terminal RNA-binding domain (NTD) with individual cis RNA elements clustering in the SARS-CoV-2 regulatory 5'-genomic end. Supported by broad solution-based biophysical data, we unravel the NTD RNA-binding preferences in the natural genome context. We show that the domain's flexible regions read the intrinsic signature of preferred RNA elements for selective and stable complex formation within the large pool of available motifs.
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Affiliation(s)
- Sophie Marianne Korn
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Karthikeyan Dhamotharan
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany
| | - Cy M Jeffries
- European Molecular Biology Laboratory (EMBL) Hamburg Site, c/o Deutsches Elektronen-Synchrotron, Notkestr. 85, 22607, Hamburg, Germany
| | - Andreas Schlundt
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt/M., Germany.
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt/M., Germany.
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7
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Morse M, Sefcikova J, Rouzina I, Beuning PJ, Williams M. Structural domains of SARS-CoV-2 nucleocapsid protein coordinate to compact long nucleic acid substrates. Nucleic Acids Res 2022; 51:290-303. [PMID: 36533523 PMCID: PMC9841419 DOI: 10.1093/nar/gkac1179] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/28/2022] [Accepted: 11/25/2022] [Indexed: 12/23/2022] Open
Abstract
The SARS-CoV-2 nucleocapsid (N) protein performs several functions including binding, compacting, and packaging the ∼30 kb viral genome into the viral particle. N protein consists of two ordered domains, with the N terminal domain (NTD) primarily associated with RNA binding and the C terminal domain (CTD) primarily associated with dimerization/oligomerization, and three intrinsically disordered regions, an N-arm, a C-tail, and a linker that connects the NTD and CTD. We utilize an optical tweezers system to isolate a long single-stranded nucleic acid substrate to measure directly the binding and packaging function of N protein at a single molecule level in real time. We find that N protein binds the nucleic acid substrate with high affinity before oligomerizing and forming a highly compact structure. By comparing the activities of truncated protein variants missing the NTD, CTD, and/or linker, we attribute specific steps in this process to the structural domains of N protein, with the NTD driving initial binding to the substrate and ensuring high localized protein density that triggers interprotein interactions mediated by the CTD, which forms a compact and stable protein-nucleic acid complex suitable for packaging into the virion.
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Affiliation(s)
- Michael Morse
- Department of Physics, Northeastern University, Boston, MA, USA
| | - Jana Sefcikova
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA
| | - Penny J Beuning
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Mark C Williams
- To whom correspondence should be addressed. Tel: +1 617 373 5705;
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8
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Shillcock JC, Lagisquet C, Alexandre J, Vuillon L, Ipsen JH. Model biomolecular condensates have heterogeneous structure quantitatively dependent on the interaction profile of their constituent macromolecules. SOFT MATTER 2022; 18:6674-6693. [PMID: 36004748 DOI: 10.1039/d2sm00387b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Biomolecular condensates play numerous roles in cells by selectively concentrating client proteins while excluding others. These functions are likely to be sensitive to the spatial organization of the scaffold proteins forming the condensate. We use coarse-grained molecular simulations to show that model intrinsically-disordered proteins phase separate into a heterogeneous, structured fluid characterized by a well-defined length scale. The proteins are modelled as semi-flexible polymers with punctate, multifunctional binding sites in good solvent conditions. Their dense phase is highly solvated with a spatial structure that is more sensitive to the separation of the binding sites than their affinity. We introduce graph theoretic measures to quantify their heterogeneity, and find that it increases with increasing binding site number, and exhibits multi-timescale dynamics. The model proteins also swell on passing from the dilute solution to the dense phase. The simulations predict that the structure of the dense phase is modulated by the location and affinity of binding sites distant from the termini of the proteins, while sites near the termini more strongly affect its phase behaviour. The relations uncovered between the arrangement of weak interaction sites on disordered proteins and the material properties of their dense phase can be experimentally tested to give insight into the biophysical properties, pathological effects, and rational design of biomolecular condensates.
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Affiliation(s)
- Julian C Shillcock
- Blue Brain Project and Laboratory of Molecular and Chemical Biology of Neurodegeneration, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
| | - Clément Lagisquet
- LAMA, Univ. Savoie Mont Blanc, CNRS, LAMA, 73376 Le Bourget du Lac, France.
| | - Jérémy Alexandre
- Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Laurent Vuillon
- LAMA, Univ. Savoie Mont Blanc, CNRS, LAMA, 73376 Le Bourget du Lac, France.
| | - John H Ipsen
- Dept. of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
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9
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Fan S, Sun W, Fan L, Wu N, Sun W, Ma H, Chen S, Li Z, Li Y, Zhang J, Yan J. The highly conserved RNA-binding specificity of nucleocapsid protein facilitates the identification of drugs with broad anti-coronavirus activity. Comput Struct Biotechnol J 2022; 20:5040-5044. [PMID: 36097552 PMCID: PMC9454191 DOI: 10.1016/j.csbj.2022.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/05/2022] [Accepted: 09/05/2022] [Indexed: 11/06/2022] Open
Abstract
The binding of SARS-CoV-2 nucleocapsid (N) protein to both the 5'- and 3'-ends of genomic RNA has different implications arising from its binding to the central region during virion assembly. However, the mechanism underlying selective binding remains unknown. Herein, we performed the high-throughput RNA-SELEX (HTR-SELEX) to determine the RNA-binding specificity of the N proteins of various SARS-CoV-2 variants as well as other β-coronaviruses and showed that N proteins could bind two unrelated sequences, both of which were highly conserved across all variants and species. Interestingly, both sequences are virtually absent from the human transcriptome; however, they exhibit a highly enriched, mutually complementary distribution in the coronavirus genome, highlighting their varied functions in genome packaging. Our results provide mechanistic insights into viral genome packaging, thereby increasing the feasibility of developing drugs with broad-spectrum anti-coronavirus activity by targeting RNA binding by N proteins.
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Affiliation(s)
- Shaorong Fan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education and Provincial Key Laboratory of Biotechnology, School of Medicine, Northwest University, Xi’an, China
- Department of Biomedical Sciences, The Tung Biomedical Sciences Centre, City University of Hong Kong, Kowloon Tong, Hong Kong Special Administrative Region
| | - Wenju Sun
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education and Provincial Key Laboratory of Biotechnology, School of Medicine, Northwest University, Xi’an, China
| | - Ligang Fan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education and Provincial Key Laboratory of Biotechnology, School of Medicine, Northwest University, Xi’an, China
- Department of Biomedical Sciences, The Tung Biomedical Sciences Centre, City University of Hong Kong, Kowloon Tong, Hong Kong Special Administrative Region
- Department of Precision Diagnostic and Therapeutic Technology, The City University of Hong Kong Shenzhen Futian Research Institute, Shenzhen, China
| | - Nan Wu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education and Provincial Key Laboratory of Biotechnology, School of Medicine, Northwest University, Xi’an, China
- Department of Biomedical Sciences, The Tung Biomedical Sciences Centre, City University of Hong Kong, Kowloon Tong, Hong Kong Special Administrative Region
| | - Wei Sun
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education and Provincial Key Laboratory of Biotechnology, School of Medicine, Northwest University, Xi’an, China
| | - Haiqian Ma
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education and Provincial Key Laboratory of Biotechnology, School of Medicine, Northwest University, Xi’an, China
| | - Siyuan Chen
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Sha Tin, Hong Kong Special Administrative Region
| | - Zitong Li
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Sha Tin, Hong Kong Special Administrative Region
| | - Yu Li
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Sha Tin, Hong Kong Special Administrative Region
| | - Jilin Zhang
- Department of Biomedical Sciences, The Tung Biomedical Sciences Centre, City University of Hong Kong, Kowloon Tong, Hong Kong Special Administrative Region
| | - Jian Yan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education and Provincial Key Laboratory of Biotechnology, School of Medicine, Northwest University, Xi’an, China
- Department of Biomedical Sciences, The Tung Biomedical Sciences Centre, City University of Hong Kong, Kowloon Tong, Hong Kong Special Administrative Region
- Department of Precision Diagnostic and Therapeutic Technology, The City University of Hong Kong Shenzhen Futian Research Institute, Shenzhen, China
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10
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Roden C, Dai Y, Giannetti C, Seim I, Lee M, Sealfon R, McLaughlin G, Boerneke M, Iserman C, Wey S, Ekena J, Troyanskaya O, Weeks K, You L, Chilkoti A, Gladfelter A. Double-stranded RNA drives SARS-CoV-2 nucleocapsid protein to undergo phase separation at specific temperatures. Nucleic Acids Res 2022; 50:8168-8192. [PMID: 35871289 PMCID: PMC9371935 DOI: 10.1093/nar/gkac596] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 06/13/2022] [Accepted: 07/19/2022] [Indexed: 12/11/2022] Open
Abstract
Nucleocapsid protein (N-protein) is required for multiple steps in betacoronaviruses replication. SARS-CoV-2-N-protein condenses with specific viral RNAs at particular temperatures making it a powerful model for deciphering RNA sequence specificity in condensates. We identify two separate and distinct double-stranded, RNA motifs (dsRNA stickers) that promote N-protein condensation. These dsRNA stickers are separately recognized by N-protein's two RNA binding domains (RBDs). RBD1 prefers structured RNA with sequences like the transcription-regulatory sequence (TRS). RBD2 prefers long stretches of dsRNA, independent of sequence. Thus, the two N-protein RBDs interact with distinct dsRNA stickers, and these interactions impart specific droplet physical properties that could support varied viral functions. Specifically, we find that addition of dsRNA lowers the condensation temperature dependent on RBD2 interactions and tunes translational repression. In contrast RBD1 sites are sequences critical for sub-genomic (sg) RNA generation and promote gRNA compression. The density of RBD1 binding motifs in proximity to TRS-L/B sequences is associated with levels of sub-genomic RNA generation. The switch to packaging is likely mediated by RBD1 interactions which generate particles that recapitulate the packaging unit of the virion. Thus, SARS-CoV-2 can achieve biochemical complexity, performing multiple functions in the same cytoplasm, with minimal protein components based on utilizing multiple distinct RNA motifs that control N-protein interactions.
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Affiliation(s)
- Christine A Roden
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Yifan Dai
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Catherine A Giannetti
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Ian Seim
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Myungwoon Lee
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Rachel Sealfon
- Flatiron Institute, Simons Foundation, New York, NY 10010, USA
| | - Grace A McLaughlin
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mark A Boerneke
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Christiane Iserman
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Samuel A Wey
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Joanne L Ekena
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Olga G Troyanskaya
- Flatiron Institute, Simons Foundation, New York, NY 10010, USA
- Department of Computer Science, Princeton University, Princeton, NJ 08540, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27708, USA
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Amy S Gladfelter
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
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11
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Cascarina SM, Ross ED. Phase separation by the SARS-CoV-2 nucleocapsid protein: Consensus and open questions. J Biol Chem 2022; 298:101677. [PMID: 35131265 PMCID: PMC8813722 DOI: 10.1016/j.jbc.2022.101677] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 01/26/2022] [Accepted: 01/28/2022] [Indexed: 01/09/2023] Open
Abstract
In response to the recent SARS-CoV-2 pandemic, a number of labs across the world have reallocated their time and resources to better our understanding of the virus. For some viruses, including SARS-CoV-2, viral proteins can undergo phase separation: a biophysical process often related to the partitioning of protein and RNA into membraneless organelles in vivo. In this review, we discuss emerging observations of phase separation by the SARS-CoV-2 nucleocapsid (N) protein-an essential viral protein required for viral replication-and the possible in vivo functions that have been proposed for N-protein phase separation, including viral replication, viral genomic RNA packaging, and modulation of host-cell response to infection. Additionally, since a relatively large number of studies examining SARS-CoV-2 N-protein phase separation have been published in a short span of time, we take advantage of this situation to compare results from similar experiments across studies. Our evaluation highlights potential strengths and pitfalls of drawing conclusions from a single set of experiments, as well as the value of publishing overlapping scientific observations performed simultaneously by multiple labs.
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Affiliation(s)
- Sean M Cascarina
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Eric D Ross
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA.
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